WorldWideScience

Sample records for development mechanistic studies

  1. Organometallic Reactions Development, Mechanistic Studies and Synthetic Applications

    DEFF Research Database (Denmark)

    Dam, Johan Hygum

    a mechanistic study of the Barbier allylation of benzaldehydes with six different metals (Zn, In, Sb, Sn, Bi and Mg) in aqueous media. The mechanism of the allylation was investigated by means of Hammett plots and the secondary deuterium kinetic isotope effect. It was found that all metals except magnesium form...... a discrete allylmetal species and the rate-determining step is the polar addition to the carbonyl. For magnesium data indicates that the selectivity-determining step is generation of the radical anion of the benzaldehyde. The second project discusses a concise and enantiopure total synthesis...

  2. Mechanistic studies of olefin metathesis

    Energy Technology Data Exchange (ETDEWEB)

    Grubbs, R.H.

    1979-03-01

    A review covers studies of the olefin metathesis mechanism which indicated that the reaction proceeds by a non-pairwise mechanism; detailed mechanistic studies on the homogeneously and heterogeneously catalyzed metathesis; and stereochemical investigations.

  3. Enantioselective Decarboxylative Alkylation Reactions: Catalyst Development, Substrate Scope, and Mechanistic Studies

    KAUST Repository

    Behenna, Douglas C.

    2011-11-14

    α-Quaternary ketones are accessed through novel enantioselective alkylations of allyl and propargyl electrophiles by unstabilized prochiral enolate nucleophiles in the presence of palladium complexes with various phosphinooxazoline (PHOX) ligands. Excellent yields and high enantiomeric excesses are obtained from three classes of enolate precursor: enol carbonates, enol silanes, and racemic β-ketoesters. Each of these substrate classes functions with nearly identical efficiency in terms of yield and enantioselectivity. Catalyst discovery and development, the optimization of reaction conditions, the exploration of reaction scope, and applications in target-directed synthesis are reported. Experimental observations suggest that these alkylation reactions occur through an unusual inner-sphere mechanism involving binding of the prochiral enolate nucleophile directly to the palladium center.

  4. Mechanistic studies aimed at the development of single site metal alkoxide catalysts for the production of polyoxygenates from renewable resources.

    Energy Technology Data Exchange (ETDEWEB)

    Chisholm, Malcolm H. [The Ohio State Univ., Columbus, OH (United States)

    2015-12-15

    The work proposed herein follows on directly from the existing 3 year grant and the request for funding is for 12 months to allow completion of this work and graduation of current students supported by DOE. The three primary projects are as follows. 1.) A comparative study of the reactivity of LMg(OR) (solvent), where L= a β-diiminate or pyrromethene ligand, in the ring-opening of cyclic esters. 2.) The homopolymerization of expoxides, particularly propylene oxide and styrene oxide, and their copolymerizations with carbon dioxide or organic anhydrides to yield polycarbonates or polyesters, respectively. 3.) The development of well-defined bismuth (III) complexes for ring-opening polymerizations that are tolerant of both air and water. In each of these topics special emphasis is placed on developing a detailed mechanistic understanding of the ring-opening event and how this is modified by the employment of specific metal and ligand combinations. This document also provides a report on findings of the past grant period that are not yet in the public domain/published and shows how the proposed work will bring the original project to conclusion.

  5. Applying mechanistic models in bioprocess development

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita; Bodla, Vijaya Krishna; Carlquist, Magnus

    2013-01-01

    models should be combined with proper model analysis tools, such as uncertainty and sensitivity analysis. When assuming distributed inputs, the resulting uncertainty in the model outputs can be decomposed using sensitivity analysis to determine which input parameters are responsible for the major part...... of the output uncertainty. Such information can be used as guidance for experimental work; i.e., only parameters with a significant influence on model outputs need to be determined experimentally. The use of mechanistic models and model analysis tools is demonstrated in this chapter. As a practical case study......, experimental data from Saccharomyces cerevisiae fermentations are used. The data are described with the well-known model of Sonnleitner and Käppeli (Biotechnol Bioeng 28:927-937, 1986) and the model is analyzed further. The methods used are generic, and can be transferred easily to other, more complex case...

  6. SELECTIVE REDUCTION OF NOX IN OXYGEN RICH ENVIRONMENTS WITH PLASMA-ASSISTED CATALYSIS: CATALYST DEVELOPMENT AND MECHANISTIC STUDIES

    Energy Technology Data Exchange (ETDEWEB)

    Peden, C; Barlow, S; Hoard, J; Kwak, J; *Balmer-Millar, M; *Panov, A; Schmieg, S; Szanyi, J; Tonkyn, R

    2003-08-24

    The control of NOx (NO and NO2) emissions from so-called ''lean-burn'' vehicle engines remains a challenge. In recent years, there have been a number of reports that show that a plasma device combined with a catalyst can reduce as high as 90% or more of NOx in simulated diesel and other ''lean-burn'' exhaust. In the case of propylene containing simulated diesel exhaust, the beneficial role of a plasma treatment is now thought to be due to oxidation of NO to NO2, and the formation of partially oxidized hydrocarbons that are more active for the catalytic reduction of NO2 than propylene. Thus, the overall system can be most usefully described as hydrocarbon selective catalytic reduction (SCR) enhanced by 'reforming' the exhaust with a non-thermal plasma (NTP) device. For plasma-enhanced catalysis, both zeolite- and alumina-based materials have shown high activity, albeit in somewhat different temperature ranges, when preceded by an NTP reactor. This paper will briefly describe our research efforts aimed at optimizing the catalyst materials for NTP-catalysis devices based, in part, on our continuing studies of the NTP- and catalytic-reaction mechanisms. Various alkali- and alkaline earth-cation-exchanged Y zeolites have been prepared, their material properties characterized, and they have been tested as catalytic materials for NOx reduction in laboratory NTP-catalysis reactors. Interestingly, NO2 formed in the plasma and not subsequently removed over these catalysts, will back-convert to NO, albeit to varying extents depending upon the nature of the cation. Besides this comparative reactivity, we will also discuss selected synthesis strategies for enhancing the performance of these zeolite-based catalyst materials. A particularly important result from our mechanistic studies is the observation that aldehydes, formed during the plasma treatment of simulated diesel exhaust, are the important species for the reduction of

  7. Mechanistic studies of carbon monoxide reduction

    Energy Technology Data Exchange (ETDEWEB)

    Geoffroy, G.L.

    1990-06-12

    The progress made during the current grant period (1 January 1988--1 April 1990) in three different areas of research is summarized. The research areas are: (1) oxidatively-induced double carbonylation reactions to form {alpha}-ketoacyl complexes and studies of the reactivity of the resulting compounds, (2) mechanistic studies of the carbonylation of nitroaromatics to form isocyanates, carbamates, and ureas, and (3) studies of the formation and reactivity of unusual metallacycles and alkylidene ligands supported on binuclear iron carbonyl fragments. 18 refs., 5 figs., 1 tab.

  8. Development of Improved Mechanistic Deterioration Models for Flexible Pavements

    DEFF Research Database (Denmark)

    Ullidtz, Per; Ertman, Hans Larsen

    1998-01-01

    The paper describes a pilot study in Denmark with the main objective of developing improved mechanistic deterioration models for flexible pavements based on an accelerated full scale test on an instrumented pavement in the Danish Road Tessting Machine. The study was the first in "International...... Pavement Subgrade Performance Study" sponsored by the Federal Highway Administration (FHWA), USA. The paper describes in detail the data analysis and the resulting models for rutting, roughness, and a model for the plastic strain in the subgrade.The reader will get an understanding of the work needed...

  9. Advanced reach tool (ART) : Development of the mechanistic model

    NARCIS (Netherlands)

    Fransman, W.; Tongeren, M. van; Cherrie, J.W.; Tischer, M.; Schneider, T.; Schinkel, J.; Kromhout, H.; Warren, N.; Goede, H.; Tielemans, E.

    2011-01-01

    This paper describes the development of the mechanistic model within a collaborative project, referred to as the Advanced REACH Tool (ART) project, to develop a tool to model inhalation exposure for workers sharing similar operational conditions across different industries and locations in Europe. T

  10. Mechanistic considerations in benzene physiological model development

    Energy Technology Data Exchange (ETDEWEB)

    Medinsky, M.A.; Kenyon, E.M.; Seaton, M.J.; Schlosser, P.M. [Chemical Industry Institute of Toxicology, Research Triangle Park, NC (United States)

    1996-12-01

    Benzene, an important industrial solvent, is also present in unleaded gasoline and cigarette smoke. The hematotoxic effects of benzene in humans are well documented and include aplastic anemia, pancytopenia, and acute myelogenous leukemia. However, the risks of leukemia at low exposure concentrations have not been established. A combination of metabolites (hydroquinone and phenol, for example) may be necessary to duplicate the hematotoxic effect of benzene, perhaps due in part to the synergistic effect of phenol on myeloperoxidase-mediated oxidation of hydroquinone to the reactive metabolite benzoquinone. Because benzene and its hydroxylated metabolites (phenol, hydroquinone, and catechol) are substrates for the same cytochrome P450 enzymes, competitive interactions among the metabolites are possible. In vivo data on metabolite formation by mice exposed to various benzene concentrations are consistent with competitive inhibition of phenol oxidation by benzene. In vitro studies of the metabolic oxidation of benzene, phenol, and hydroquinone are consistent with the mechanism of competitive interaction among the metabolites. The dosimetry of benzene and its metabolites in the target tissue, bone marrow, depends on the balance of activation processes such as enzymatic oxidation and deactivation processes such as conjugation and excretion. Phenol, the primary benzene metabolite, can undergo both oxidation and conjugation. Thus the potential exists for competition among various enzymes for phenol. Zonal localization of phase I and phase 11 enzymes in various regions of the liver acinus also impacts this competition. Biologically based dosimetry models that incorporate the important determinants of benzene flux, including interactions with other chemicals, will enable prediction of target tissue doses of benzene and metabolites at low exposure concentrations relevant for humans. 39 refs., 4 figs., 2 tabs.

  11. MECHANISTIC STUDIES OF IMPROVED FOAM EOR PROCESSES

    Energy Technology Data Exchange (ETDEWEB)

    William R. Rossen

    2003-03-31

    . We find that such behavior is consistent with earlier models of foam viscosity in tubes, and a modified model for the low-quality regime can account for this behavior. It is not yet clear why this new regime appears in some cases and not in others. Simple modeling suggests that the answer may have to do with the sensitivity of gas trapping to pressure gradient. Research on Task 3 continued to focus on foam generation at limited pressure gradient in sandpacks. We investigated the effects of permeability, surfactant concentration and liquid injection rates on foam generation. In addition, a careful review of published studies showed that repeated snap-off is not a plausible mechanism of foam generation in homogeneous porous media beyond the stage of initial drainage from a fully liquid-saturated state. Snap-off has been the focus of much research on foam generation and is incorporated into most mechanistic foam simulators. This finding should force a reconsideration of its role in foam generation and properties in porous media.

  12. Advanced Reach Tool (ART): development of the mechanistic model.

    Science.gov (United States)

    Fransman, Wouter; Van Tongeren, Martie; Cherrie, John W; Tischer, Martin; Schneider, Thomas; Schinkel, Jody; Kromhout, Hans; Warren, Nick; Goede, Henk; Tielemans, Erik

    2011-11-01

    This paper describes the development of the mechanistic model within a collaborative project, referred to as the Advanced REACH Tool (ART) project, to develop a tool to model inhalation exposure for workers sharing similar operational conditions across different industries and locations in Europe. The ART mechanistic model is based on a conceptual framework that adopts a source receptor approach, which describes the transport of a contaminant from the source to the receptor and defines seven independent principal modifying factors: substance emission potential, activity emission potential, localized controls, segregation, personal enclosure, surface contamination, and dispersion. ART currently differentiates between three different exposure types: vapours, mists, and dust (fumes, fibres, and gases are presently excluded). Various sources were used to assign numerical values to the multipliers to each modifying factor. The evidence used to underpin this assessment procedure was based on chemical and physical laws. In addition, empirical data obtained from literature were used. Where this was not possible, expert elicitation was applied for the assessment procedure. Multipliers for all modifying factors were peer reviewed by leading experts from industry, research institutes, and public authorities across the globe. In addition, several workshops with experts were organized to discuss the proposed exposure multipliers. The mechanistic model is a central part of the ART tool and with advancing knowledge on exposure, determinants will require updates and refinements on a continuous basis, such as the effect of worker behaviour on personal exposure, 'best practice' values that describe the maximum achievable effectiveness of control measures, the intrinsic emission potential of various solid objects (e.g. metal, glass, plastics, etc.), and extending the applicability domain to certain types of exposures (e.g. gas, fume, and fibre exposure).

  13. Mechanistic approach to stability studies as a tool for the optimization and development of new products based on L. rhamnosus Lcr35® in compliance with current regulations.

    Science.gov (United States)

    Muller, Claudia; Busignies, Virginie; Mazel, Vincent; Forestier, Christiane; Nivoliez, Adrien; Tchoreloff, Pierre

    2013-01-01

    Probiotics are of great current interest in the pharmaceutical industry because of their multiple effects on human health. To beneficially affect the host, an adequate dosage of the probiotic bacteria in the product must be guaranteed from the time of manufacturing to expiration date. Stability test guidelines as laid down by the ICH-Q1A stipulate a minimum testing period of 12 months. The challenge for producers is to reduce this time. In this paper, a mechanistic approach using the Arrhenius model is proposed to predict stability. Applied for the first time to laboratory and industrial probiotic powders, the model was able to provide a reliable mathematical representation of the effects of temperature on bacterial death (R(2)>0.9). The destruction rate (k) was determined according to the manufacturing process, strain and storage conditions. The marketed product demonstrated a better stability (k = 0.08 months(-1)) than the laboratory sample (k = 0.80 months(-1)). With industrial batches, k obtained at 6 months of studies was comparable to that obtained at 12 months, evidence of the model's robustness. In addition, predicted values at 12 months were greatly similar (±30%) to those obtained by real-time assessing the model's reliability. This method could be an interesting approach to predict the probiotic stability and could reduce to 6 months the length of stability studies as against 12 (ICH guideline) or 24 months (expiration date).

  14. Ecotoxicology, ecophysiology, and mechanistic studies with rotifers.

    Science.gov (United States)

    Dahms, Hans-U; Hagiwara, Atsushi; Lee, Jae-Seong

    2011-01-17

    Invertebrates play an increasing role in assessing the impacts of environmental contaminants in aquatic ecosystems. Substantial efforts were made to identify suitable and environmentally relevant models for toxicity testing. Rotifers have a number of promising characteristics which make them candidates worth considering in such efforts. They are small, simple in their organization, genetically homozygous, easy to cultivate. Rotifers are further widely distributed and ecologically important in freshwaters, in estuaries and coast, and also play an important role in the transportation of aquatic pollutants across the food web. In the last decades there has been a substantial increase of contributions on rotifers, particularly in areas of their ecology, geophylogeny, genomics and their behavioral, physiological, biochemical and molecular responses, following exposure to environmental chemicals and other stressors. Gene expression analysis enables ecotoxicologists to study molecular mechanisms of toxicity. Rotifers also appear as useful tools in the risk assessment of pharmaceuticals and their metabolites that find their way into aquatic ecosystems because their sensitivity to some of these substances is higher than that of cladocerans and algae. In respect to endocrine disruptors, rotifers seem to be particularly sensitive to androgenic and anti-androgenic substances, whereas copepods and cladocerans are typically more affected by estrogens and juvenile hormone-like compounds. Generally, a combination of whole-animal bioassays and gene expression studies allow an understanding of toxicological mechanisms. The purpose of this review is to demarcate the potential of using rotifers as important invertebrate aquatic model organisms for ecophysiology, ecotoxicology and environmental genomics. This review does not claim to find reasons for a superior use of rotifers in these fields. But the different phylogenetic allocation of rotifers in the Platyzoa (formerly

  15. Mechanistic Studies of Planetary Haze Formation

    Science.gov (United States)

    Hicks, Raea Kay

    2015-10-01

    Planetary atmospheres can be thought of as global-scale reactors capable of synthesizing large, complex molecules from small gases such as methane (CH4), carbon dioxide (CO2), and nitrogen (N2). The atmosphere of Titan, the largest moon of Saturn covered by a thick organic haze, contains trace amounts (2%) of CH4 in an atmosphere of N2 at a surface pressure of 1.5 bar. This is similar to the Earth's Archaean atmosphere, which possibly contained trace amounts of CH4 and CO2 (˜1,000 ppmv each) in an N2 -dominant atmosphere before the rise of biogenic oxygen. Laboratory simulations of the atmospheric chemistry on Titan and the early Earth have shown that these atmospheres are capable of generating biologically-relevant molecules that condense to form particles which can then settle to the surface of the planetary body, possibly providing the molecules required for the emergence of life. The work presented here examines the mechanisms by which FUV photochemistry initiates incorporation of N atoms into Titan aerosol analogs, and C atoms into early Earth aerosol analogs. Results from the Aerosol Collector and Pyrolyser onboard the Huygens lander reveal the presence of nitrogen in Titan's aerosols. This nitrogen incorporation is thought to occur primarily by extreme-UV photons or energetic electrons. However, recent results from our laboratory indicate a surprising amount of nitrogen incorporation- up to 16% by mass- in Titan aerosol analogs produced by photochemistry initiated by FUV irradiation of CH4/N 2 mixtures. The termolecular reaction CH+N2 +M → HCN2 has been proposed to account for this observation. Here, we test this hypothesis by using a high- resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) to measure the mass loading and chemical composition of aerosol produced at a range of pressures from roughly 0.1 to 1 atm. We report a 10-fold increase in aerosol mass loading across the range of pressures studied, indicating that the mechanism

  16. Mechanistic studies on the Heck-Mizoroki cross-coupling reaction of a hindered vinylboronate ester as a key approach to developing a highly stereoselective synthesis of a C1-C7 Z,Z,E-triene synthon for viridenomycin.

    Science.gov (United States)

    Batsanov, Andrei S; Knowles, Jonathan P; Whiting, Andrew

    2007-03-30

    Mechanistic studies of the Heck-Mizoroki reaction of a vinylboronate ester with electronically different (four-substituted) aryl iodides shows that electron donors accelerate the cross-coupling, demonstrating that the oxidative addition step is not rate determining and that there is development of some degree of positive charge in the rate determining step. These results were used as a basis to allow the development of reaction conditions for the Heck-Mizoroki coupling of a hindered vinylboronate ester with electron deficient methyl cis-2-iodoacrylate. The resulting dienylboronate ester was converted through a series of highly stereoselective iodo-deboronations and Heck-Mizoroki reactions into a trienyl iodide precursor for further application in the total synthesis of viridenomycin.

  17. Novel catalytic and mechanistic studies on wastewater denitrification with hydrogen.

    Science.gov (United States)

    Theologides, C P; Olympiou, G G; Savva, P G; Pantelidou, N A; Constantinou, B K; Chatziiona, V K; Valanidou, L Y; Piskopianou, C T; Costa, C N

    2014-01-01

    The present work reports up-to-date information regarding the reaction mechanism of the catalytic hydrogenation of nitrates in water media. In the present mechanistic study, an attempt is made, for the first time, to elucidate the crucial role of several catalysts and reaction parameters in the mechanism of the NO(3)(-)/H(2) reaction. Steady-state isotopic transient kinetic analysis (SSITKA) experiments coupled with ex situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) were performed on supported Pd-Cu catalysts for the NO(3)(-)/H(2) and NO(3)(-)/H(2)/O(2) reactions. The latter experiments revealed that the formation and surface coverage of various adsorbed active intermediate N-species on the support or Pd/Cu metal surface is significantly favored in the presence of TiO(2) in the support mixture and in the presence of oxygen in the reaction's gaseous feed stream. The differences in the reactivity of these adsorbed N-species, found in the present work, adequately explain the large effect of the chemical composition of the support and the gas feed composition on catalyst behaviour (activity and selectivity). The present study leads to solid mechanistic evidence concerning the presence of a hydrogen spillover process from the metal to the support. Moreover, this study shows that Cu clusters are active sites for the reduction of nitrates to nitrites.

  18. Are Mechanistic and Statistical QSAR Approaches Really Different? MLR Studies on 158 Cycloalkyl-Pyranones.

    Science.gov (United States)

    Bhhatarai, Barun; Garg, Rajni; Gramatica, Paola

    2010-07-12

    Two parallel approaches for quantitative structure-activity relationships (QSAR) are predominant in literature, one guided by mechanistic methods (including read-across) and another by the use of statistical methods. To bridge the gap between these two approaches and to verify their main differences, a comparative study of mechanistically relevant and statistically relevant QSAR models, developed on a case study of 158 cycloalkyl-pyranones, biologically active on inhibition (Ki ) of HIV protease, was performed. Firstly, Multiple Linear Regression (MLR) based models were developed starting from a limited amount of molecular descriptors which were widely proven to have mechanistic interpretation. Then robust and predictive MLR models were developed on the same set using two different statistical approaches unbiased of input descriptors. Development of models based on Statistical I method was guided by stepwise addition of descriptors while Genetic Algorithm based selection of descriptors was used for the Statistical II. Internal validation, the standard error of the estimate, and Fisher's significance test were performed for both the statistical models. In addition, external validation was performed for Statistical II model, and Applicability Domain was verified as normally practiced in this approach. The relationships between the activity and the important descriptors selected in all the models were analyzed and compared. It is concluded that, despite the different type and number of input descriptors, and the applied descriptor selection tools or the algorithms used for developing the final model, the mechanistical and statistical approach are comparable to each other in terms of quality and also for mechanistic interpretability of modelling descriptors. Agreement can be observed between these two approaches and the better result could be a consensus prediction from both the models. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. UTILITY OF MECHANISTIC MODELS FOR DIRECTING ADVANCED SEPARATIONS RESEARCH & DEVELOPMENT ACTIVITIES: Electrochemically Modulated Separation Example

    Energy Technology Data Exchange (ETDEWEB)

    Schwantes, Jon M.

    2009-06-01

    The objective for this work was to demonstrate the utility of mechanistic computer models designed to simulate actinide behavior for use in efficiently and effectively directing advanced laboratory R&D activities associated with developing advanced separations methods.

  20. Mechanistic study of ZnO nanorod array electrodeposition

    Energy Technology Data Exchange (ETDEWEB)

    El Belghiti, H.; Pauporte, T.; Lincot, D. [Laboratoire d' Electrochimie et Chimie Analytique, UMR7575, Ecole Nationale Superieure de Chimie de Paris-Universite Paris 6 (France)

    2008-10-15

    The growth of ZnO nanorods by electrodeposition from oxygenated aqueous mixture of zinc chloride and potassium chloride is studied experimentally as a function of the deposition time, zinc concentration and the substrate. These parameters influence markedly the characteristics of the deposits (rod density, aspect ratio, orientation). A mechanistic model is presented in order to explain the formation of ZnO nanorod arrays by electrodeposition. The model is based on the effect of zinc concentration on the interfacial pH at the electrode surface and then on the charged stable zinc species able to react with the growing film. The charge of the complex seems to be the key parameter which stops the lateral growth and then significantly increases the aspect ratio of the single crystalline nanorods. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  1. Development of a mechanistic model for forced convection subcooled boiling

    Science.gov (United States)

    Shaver, Dillon R.

    The focus of this work is on the formulation, implementation, and testing of a mechanistic model of subcooled boiling. Subcooled boiling is the process of vapor generation on a heated wall when the bulk liquid temperature is still below saturation. This is part of a larger effort by the US DoE's CASL project to apply advanced computational tools to the simulation of light water reactors. To support this effort, the formulation of the dispersed field model is described and a complete model of interfacial forces is formulated. The model has been implemented in the NPHASE-CMFD computer code with a K-epsilon model of turbulence. The interfacial force models are built on extensive work by other authors, and include novel formulations of the turbulent dispersion and lift forces. The complete model of interfacial forces is compared to experiments for adiabatic bubbly flows, including both steady-state and unsteady conditions. The same model is then applied to a transient gas/liquid flow in a complex geometry of fuel channels in a sodium fast reactor. Building on the foundation of the interfacial force model, a mechanistic model of forced-convection subcooled boiling is proposed. This model uses the heat flux partitioning concept and accounts for condensation of bubbles attached to the wall. This allows the model to capture the enhanced heat transfer associated with boiling before the point of net generation of vapor, a phenomenon consistent with existing experimental observations. The model is compared to four different experiments encompassing flows of light water, heavy water, and R12 at different pressures, in cylindrical channels, an internally heated annulus, and a rectangular channel. The experimental data includes axial and radial profiles of both liquid temperature and vapor volume fraction, and the agreement can be considered quite good. The complete model is then applied to simulations of subcooled boiling in nuclear reactor subchannels consistent with the

  2. Synthesis of 3,3-Disubstituted Oxindoles by Palladium-Catalyzed Asymmetric Intramolecular α-Arylation of Amides: Reaction Development and Mechanistic Studies.

    Science.gov (United States)

    Katayev, Dmitry; Jia, Yi-Xia; Sharma, Akhilesh K; Banerjee, Dipshikha; Besnard, Céline; Sunoj, Raghavan B; Kündig, E Peter

    2013-09-02

    Palladium complexes incorporating chiral N-heterocyclic carbene (NHC) ligands catalyze the asymmetric intramolecular α-arylation of amides producing 3,3-disubstituted oxindoles. Comprehensive DFT studies have been performed to gain insight into the mechanism of this transformation. Oxidative addition is shown to be rate-determining and reductive elimination to be enantioselectivity-determining. The synthesis of seven new NHC ligands is detailed and their performance is compared. One of them, L8, containing a tBu and a 1-naphthyl group at the stereogenic centre, proved superior and was very efficient in the asymmetric synthesis of fifteen new spiro-oxindoles and three azaspiro-oxindoles often in high yields (up to 99 %) and enantioselectivities (up to 97 % ee; ee=enantiomeric excess). Three palladacycle intermediates resulting from the oxidative addition of [Pd(NHC)] into the aryl halide bond were isolated and structurally characterized (X-ray). Using these intermediates as catalysts showed alkene additives to play an important role in increasing turnover number and frequency.

  3. Rearrangements of Allylic Sulfinates to Sulfones: A Mechanistic Study

    Science.gov (United States)

    Ball, David B.; Mollard, Paul; Voigtritter, Karl R.; Ball, Jenelle L.

    2010-01-01

    Most current organic chemistry textbooks are organized by functional groups and those of us who teach organic chemistry use functional-group organization in our courses but ask students to learn organic chemistry from a mechanistic approach. To enrich and extend the chemical understanding and knowledge of pericyclic-type reactions for chemistry…

  4. Mechanistic Models for Process Development and Optimization of Fed-batch Fermentation Systems

    DEFF Research Database (Denmark)

    Mears, Lisa; Stocks, Stuart M.; Albæk, Mads O.

    2016-01-01

    into account the oxygen transfer conditions, as well as the evaporation rates of the system. Mechanistic models are valuable tools which are applicable for both process development and optimization. The state estimator described will be a valuable tool for future work as part of control strategy development...... for on-line process control and optimization....

  5. Ferritin Diversity: Mechanistic Studies, Disease Implications, and Materials Chemistry

    Science.gov (United States)

    Hilton, Robert J.

    2011-07-01

    The study of ferritin includes a rich history of discoveries and scientific progress. Initially, the composition of ferritin was determined. Soon, it was shown that ferritin is a spherical, hollow protein. Eventually, over several decades of research, the structure and some function of this interesting protein was elucidated. However, the ferritin field was not completely satisfied. Today, for example, researchers are interested in refining the details of ferritin function, in discovering the role of ferritin in a variety of diseases, and in using ferritin for materials chemistry applications. The work presented in this dissertation highlights the progress that we have made in each of these three areas: (1) Mechanistic studies: The buffer used during horse spleen ferritin iron loading significantly influences the mineralization process and the quantity of iron deposited in ferritin. The ferrihydrite core of ferritin is crystalline and ordered when iron is loaded into ferritin in the presence of imidazole buffer. On the other hand, when iron is loaded into ferritin in the presence of MOPS buffer, the ferrihydrite core is less crystalline and less ordered, and a smaller amount of total iron is loaded in ferritin. We also show that iron can be released from the ferritin core in a non-reductive manner. The rate of Fe3+ release from horse spleen ferritin was measured using the Fe3+-specific chelator desferoxamine. We show that iron release occurs by three kinetic events. (2) Disease studies: In order to better understand iron disruption during disease states, we performed in vitro assays that mimicked chronic kidney disease. We tested the hypothesis that elevated levels of serum phosphate interrupted normal iron binding by transferrin and ferritin. Results show that phosphate competes for iron, forming an iron(III)-phosphate complex that is inaccessible to either transferrin or ferritin. Ferritin samples separated from the iron(III)-phosphate complex shows that as the

  6. Utilizing Mechanistic Cross-Linking Technology to Study Protein-Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab

    Science.gov (United States)

    Finzel, Kara; Beld, Joris; Burkart, Michael D.; Charkoudian, Louise K.

    2017-01-01

    Over the past decade, mechanistic cross-linking probes have been used to study protein-protein interactions in natural product biosynthetic pathways. This approach is highly interdisciplinary, combining elements of protein biochemistry, organic chemistry, and computational docking. Herein, we described the development of an experiment to engage…

  7. Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Casey, Charles P

    2012-11-14

    Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis Charles P. Casey, Principal Investigator Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706 Phone 608-262-0584 FAX: 608-262-7144 Email: casey@chem.wisc.edu http://www.chem.wisc.edu/main/people/faculty/casey.html Executive Summary. Our goal was to learn the intimate mechanistic details of reactions involved in homogeneous catalysis and to use the insight we gain to develop new and improved catalysts. Our work centered on the hydrogenation of polar functional groups such as aldehydes and ketones and on hydroformylation. Specifically, we concentrated on catalysts capable of simultaneously transferring hydride from a metal center and a proton from an acidic oxygen or nitrogen center to an aldehyde or ketone. An economical iron based catalyst was developed and patented. Better understanding of fundamental organometallic reactions and catalytic processes enabled design of energy and material efficient chemical processes. Our work contributed to the development of catalysts for the selective and mild hydrogenation of ketones and aldehydes; this will provide a modern green alternative to reductions by LiAlH4 and NaBH4, which require extensive work-up procedures and produce waste streams. (C5R4OH)Ru(CO)2H Hydrogenation Catalysts. Youval Shvo described a remarkable catalytic system in which the key intermediate (C5R4OH)Ru(CO)2H (1) has an electronically coupled acidic OH unit and a hydridic RuH unit. Our efforts centered on understanding and improving upon this important catalyst for reduction of aldehydes and ketones. Our mechanistic studies established that the reduction of aldehydes by 1 to produce alcohols and a diruthenium bridging hydride species occurs much more rapidly than regeneration of the ruthenium hydride from the diruthenium bridging hydride species. Our mechanistic studies require simultaneous transfer of hydride from ruthenium to

  8. Regulatory Technology Development Plan - Sodium Fast Reactor: Mechanistic Source Term – Trial Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Grabaskas, David [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Bucknor, Matthew [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Jerden, James [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Brunett, Acacia J. [Argonne National Lab. (ANL), Argonne, IL (United States). Nuclear Engineering Division; Denman, Matthew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Nuclear Engineering Division; Clark, Andrew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Nuclear Engineering Division; Denning, Richard S. [Consultant, Columbus, OH (United States)

    2016-10-01

    The potential release of radioactive material during a plant incident, referred to as the source term, is a vital design metric and will be a major focus of advanced reactor licensing. The U.S. Nuclear Regulatory Commission has stated an expectation for advanced reactor vendors to present a mechanistic assessment of the potential source term in their license applications. The mechanistic source term presents an opportunity for vendors to realistically assess the radiological consequences of an incident and may allow reduced emergency planning zones and smaller plant sites. However, the development of a mechanistic source term for advanced reactors is not without challenges, as there are often numerous phenomena impacting the transportation and retention of radionuclides. This project sought to evaluate U.S. capabilities regarding the mechanistic assessment of radionuclide release from core damage incidents at metal fueled, pool-type sodium fast reactors (SFRs). The purpose of the analysis was to identify, and prioritize, any gaps regarding computational tools or data necessary for the modeling of radionuclide transport and retention phenomena. To accomplish this task, a parallel-path analysis approach was utilized, as shown below. One path, led by Argonne and Sandia National Laboratories, sought to perform a mechanistic source term assessment using available codes, data, and models, with the goal to identify gaps in the current knowledge base. The second path, performed by an independent contractor, performed sensitivity analyses to determine the importance of particular radionuclides and transport phenomena in regards to offsite consequences. The results of the two pathways were combined to prioritize gaps in current capabilities.

  9. Mechanistic studies of protein arginine deiminase 2: evidence for a substrate-assisted mechanism.

    Science.gov (United States)

    Dreyton, Christina J; Knuckley, Bryan; Jones, Justin E; Lewallen, Daniel M; Thompson, Paul R

    2014-07-15

    Citrullination, which is catalyzed by protein arginine deiminases (PADs 1-4 and 6), is a post-translational modification (PTM) that effectively neutralizes the positive charge of a guanidinium group by its replacement with a neutral urea. Given the sequence similarity of PAD2 across mammalian species and the genomic organization of the PAD2 gene, PAD2 is predicted to be the ancestral homologue of the PADs. Although PAD2 has long been known to play a role in myelination, it has only recently been linked to other cellular processes, including gene transcription and macrophage extracellular trap formation. For example, PAD2 deiminates histone H3 at R26, and this PTM leads to the increased transcription of more than 200 genes under the control of the estrogen receptor. Given that our understanding of PAD2 biology remains incomplete, we initiated mechanistic studies on this enzyme to aid the development of PAD2-specific inhibitors. Herein, we report that the substrate specificity and calcium dependence of PAD2 are similar to those of PADs 1, 3, and 4. However, unlike those isozymes, PAD2 appears to use a substrate-assisted mechanism of catalysis in which the positively charged substrate guanidinium depresses the pKa of the nucleophilic cysteine. By contrast, PADs 1, 3, and 4 use a reverse-protonation mechanism. These mechanistic differences will aid the development of isozyme-specific inhibitors.

  10. Development of Mechanistic-Empirical Pavement Design for Tropical Climate Using Cement-Treated Base Layer

    OpenAIRE

    Aderinola, O.S

    2016-01-01

    A mechanistic-empirical pavement design method is developed characterising cement-treated base layers for pavement design in Nigeria or other similar tropical and subtropical countries. Asphalt Concrete surface, Subbase and Aggregate base were characterised based on back calculation data from Claros et al (1986) while cement-treated base layer was based on modulus tests that had been conducted by past researchers. Failure criteria for the Asphalt Concrete fatigue failure and the s...

  11. Development and experimental validation of a mechanistic model of in vitro DNA recombination.

    Science.gov (United States)

    Bowyer, Jack; Jia Zhao; Rosser, Susan; Colloms, Sean; Bates, Declan

    2015-08-01

    Engineering cellular memory is a key area of research in which Synthetic Biology has already begun to make significant impacts. Recent work elucidating transcriptional memory devices has paved the way for the creation of bistable genetic switches based on DNA recombination. Attempts to experimentally design and build synthetic systems using recombinases have thus far been hindered by a lack of validated computational models that capture the mechanistic basis of DNA recombination. The predictive capabilities of such models could be exploited by Synthetic Biologists to reduce the number of iterative cycles required to align experimental results with design performance requirements. Here, we develop and validate the first detailed mechanistic model of DNA recombination, with a focus on how efficiently recombination can occur, and the model features required to replicate and predict experimental data.

  12. Pollution and skin: from epidemiological and mechanistic studies to clinical implications.

    Science.gov (United States)

    Krutmann, Jean; Liu, Wei; Li, Li; Pan, Xiaochuan; Crawford, Martha; Sore, Gabrielle; Seite, Sophie

    2014-12-01

    In recent years, the health effects associated with air pollution have been intensively studied. Most studies focus on air pollution effects on the lung and the cardiovascular system. More recently, however, epidemiological and mechanistic studies suggest that air pollution is also affecting skin integrity. This state-of-the-art review focuses on this latter aspect; it was developed with the collaboration of European and Chinese board of experts with specific interests in environmental health, clinical and basic research in dermatology and cosmetic dermatology. A literature review limited to pollution and health effects and (sensitive) skin was performed using PubMed. Review and original articles were chosen. We summarize the existing scientific evidence that air pollution exerts detrimental effects on human skin, discuss potential clinical implications and suggest specific and unspecific cosmetic protective measures.

  13. A mechanistic study of copper electropolishing in phosphoric acid solutions

    Science.gov (United States)

    Mansson, Andrew

    The microelectronics industry is using copper as the interconnect material for microchips. A study of copper electropolishing is important for the process development of a new, low downforce approach, which is being developed to replace chemical mechanical polishing (CMP) of the copper overburden. A promising technology is a combination of electropolishing with conventional CMP. Electropolishing of copper in phosphoric acid has been studied for, more than 70 years. Previous work has shown that the polishing rate, as measured by current density is directly related to the viscosity of the electrolyte. Also, the limiting species is water. In this study, a multidimensional design of experiments was performed to develop an in-depth model of copper electropolishing. Phosphoric acid was mixed with alcohols of different molecular weight and related viscosity to investigate how the solvents' properties affected polishing. The alcohols used were methanol, ethanol, isopropanol, butanol, ethylene glycol, and glycerol. The limiting current densities and electrochemical behavior of each solution was measured by potentiodynamic and potentiostatic experiments. Also, the kinematic viscosity and density were measured to determine the dynamic viscosity to investigate the relationship of current density and viscosity. Water, methanol, ethanol, and isopropanol solutions were also examined at 20°C to 60°C. Next, the relative percentage of dissociated phosphoric acid was measured by Raman spectroscopy for each polishing solution. Raman spectroscopy was also used to measure the relative dissociation of phosphoric acid inside the polishing film. Additionally, wafers were electropolished and electrochemical mechanically polished to investigate the effects of the different solvents, fluid flow, current, and potential. The results of these experiments have shown that the molecular mass and the ability of the solvent to dissociate phosphoric acid are the primary electrolyte properties that

  14. Development of a mechanistically based computer simulation of nitrogen oxide absorption in packed towers

    Energy Technology Data Exchange (ETDEWEB)

    Counce, R.M.

    1981-01-01

    A computer simulation for nitrogen oxide (NO/sub x/) scrubbing in packed towers was developed for use in process design and process control. This simulation implements a mechanistically based mathematical model, which was formulated from (1) an exhaustive literature review; (2) previous NO/sub x/ scrubbing experience with sieve-plate towers; and (3) comparisons of sequential sets of experiments. Nitrogen oxide scrubbing is characterized by simultaneous absorption and desorption phenomena: the model development is based on experiments designed to feature these two phenomena. The model was then successfully tested in experiments designed to put it in jeopardy.

  15. A mechanistic study of impurity segregation at silicon grain boundaries

    Science.gov (United States)

    Käshammer, Peter; Sinno, Talid

    2015-09-01

    The segregation behavior of carbon and oxygen atoms at various silicon grain boundaries was studied using a combination of atomistic simulation and analytical modeling. First, quasi-lattice Grand Canonical Monte Carlo simulations were used to compute segregation isotherms as a function of grain boundary type, impurity atom loading level, and temperature. Next, the atomistic results were employed to regress different analytical segregation models and extract thermodynamic and structural properties. The multilayer Brunauer-Emmett-Teller (BET) isotherm was found to quantitatively capture all the simulation conditions probed in this work, while simpler, single layer models such as the Langmuir-McLean model did not. Some of the BET parameters, namely, the binding free energy of the first adsorption layer and the impurity holding capacity of each layer, were tested for correlation with various measures of grain boundary structure and/or mechanical properties. It was found that certain measures of the atomistic stress distribution correlate strongly with the first-layer binding free energy for substitutional carbon atoms, while common grain boundary identifiers such as sigma value and energy density are not useful in this regard. Preliminary analysis of the more complex case of interstitial oxygen segregation showed that similar measures based on atomistic stress also may be useful here, but more systematic correlative studies are needed to develop a comprehensive picture.

  16. Validation and Evaluation of a Mechanistic Model of Phasic and Phenological Development in Wheat

    Institute of Scientific and Technical Information of China (English)

    YAN Mei-chun; CAO Wei-xing; LI Cun-dong; WANG Zhao-long

    2001-01-01

    Three sets of data from the field experiments with different wheat( Triticum L. ) varieties and sowing dates in China and USA were used to test the performance of the mechanistic model of wheat development. The results showed that the absolute prediction errors for most phasic and phenological stages ranged within 0 - 5 days, and the root mean square errors were generally less than 5 days. The model was of high accuracy and low error especially for emergence, tillering, stamen and pistil initiation, and heading stages, reflecting an enhanced level of mechanism and prediction.

  17. Mechanistic studies on a peptide-based self-replicating system

    NARCIS (Netherlands)

    Colomb-Delsuc, Mathieu

    2015-01-01

    Dit proefschrift beschrijft de werkzaamheden uitgevoerd op een zelfassemblerende en self-replicating systeem. Het werk is opgedeeld in verschillende studies, waarbij een eerste studie gedaan die een demonstratie en een beschrijving van de exponentiële zelfreplicerende aard van het systeem. Mechanist

  18. Boron-Nitrogen Polymers. I. Mechanistic Studies of Borazine Pyrolyses.

    Science.gov (United States)

    1984-09-28

    Inorg. Chem., 2, 29 8) S. 3. Groszos and.S. F. Stafiej, J. Am. Chem. Soc., 80, 1357 (1958). 9) L. F. Hohnsredt and D. T. Haworth , J. Am. Chem. Soc...53201 Dr. E. Fischer , Code 2853 Dr. Martin H. Kaufman Naval Ship Research and Code 38506 Development Center Naval Weapons Center Annapolis, Maryland

  19. Regulatory Technology Development Plan Sodium Fast Reactor. Mechanistic Source Term Development

    Energy Technology Data Exchange (ETDEWEB)

    Grabaskas, David S. [Argonne National Lab. (ANL), Argonne, IL (United States); Brunett, Acacia Joann [Argonne National Lab. (ANL), Argonne, IL (United States); Bucknor, Matthew D. [Argonne National Lab. (ANL), Argonne, IL (United States); Sienicki, James J. [Argonne National Lab. (ANL), Argonne, IL (United States); Sofu, Tanju [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-02-28

    Construction and operation of a nuclear power installation in the U.S. requires licensing by the U.S. Nuclear Regulatory Commission (NRC). A vital part of this licensing process and integrated safety assessment entails the analysis of a source term (or source terms) that represents the release of radionuclides during normal operation and accident sequences. Historically, nuclear plant source term analyses have utilized deterministic, bounding assessments of the radionuclides released to the environment. Significant advancements in technical capabilities and the knowledge state have enabled the development of more realistic analyses such that a mechanistic source term (MST) assessment is now expected to be a requirement of advanced reactor licensing. This report focuses on the state of development of an MST for a sodium fast reactor (SFR), with the intent of aiding in the process of MST definition by qualitatively identifying and characterizing the major sources and transport processes of radionuclides. Due to common design characteristics among current U.S. SFR vendor designs, a metal-fuel, pool-type SFR has been selected as the reference design for this work, with all phenomenological discussions geared toward this specific reactor configuration. This works also aims to identify the key gaps and uncertainties in the current knowledge state that must be addressed for SFR MST development. It is anticipated that this knowledge state assessment can enable the coordination of technology and analysis tool development discussions such that any knowledge gaps may be addressed. Sources of radionuclides considered in this report include releases originating both in-vessel and ex-vessel, including in-core fuel, primary sodium and cover gas cleanup systems, and spent fuel movement and handling. Transport phenomena affecting various release groups are identified and qualitatively discussed, including fuel pin and primary coolant retention, and behavior in the cover gas and

  20. Catalytic intermolecular amination of C-H bonds: method development and mechanistic insights.

    Science.gov (United States)

    Fiori, Kristin Williams; Du Bois, J

    2007-01-24

    Reaction methodology for intermolecular C-H amination of benzylic and 3 degrees C-H bonds is described. This process uses the starting alkane as the limiting reagent, gives optically pure tetrasubstituted amines through stereospecific insertion into enantiomeric 3 degrees centers, displays high chemoselectivity for benzylic oxidation, and enables the facile preparation of isotopically enriched 15N-labeled compounds. Access to substituted amines, amino alcohols, and diamines is thereby made possible in a single transformation. Important information relevant to understanding the initial steps in the catalytic cycle, reaction chemoselectivity, the nature of the active oxidant, and pathways for catalyst inactivation has been gained through mechanistic analysis; these studies are also presented.

  1. Mechanistic study on the ruthenium-catalyzed direct amination of alcohols

    NARCIS (Netherlands)

    Pingen, Dennis; Lutz, Martin; Vogt, Dieter

    2014-01-01

    The Ru-catalyzed direct amination of alcohols with ammonia was investigated for the RuHCl(CO)(PPh3)3/Xantphos system in order to gain mechanistic insight. For several Ru(II) precursor complexes the influence of different additives on catalytic performance was investigated. NMR studies revealed that

  2. Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study.

    Science.gov (United States)

    Maia, Luisa B; Fonseca, Luis; Moura, Isabel; Moura, José J G

    2016-07-20

    Carbon dioxide accumulation is a major concern for the ecosystems, but its abundance and low cost make it an interesting source for the production of chemical feedstocks and fuels. However, the thermodynamic and kinetic stability of the carbon dioxide molecule makes its activation a challenging task. Studying the chemistry used by nature to functionalize carbon dioxide should be helpful for the development of new efficient (bio)catalysts for atmospheric carbon dioxide utilization. In this work, the ability of Desulfovibrio desulfuricans formate dehydrogenase (Dd FDH) to reduce carbon dioxide was kinetically and mechanistically characterized. The Dd FDH is suggested to be purified in an inactive form that has to be activated through a reduction-dependent mechanism. A kinetic model of a hysteretic enzyme is proposed to interpret and predict the progress curves of the Dd FDH-catalyzed reactions (initial lag phase and subsequent faster phase). Once activated, Dd FDH is able to efficiently catalyze, not only the formate oxidation (kcat of 543 s(-1), Km of 57.1 μM), but also the carbon dioxide reduction (kcat of 46.6 s(-1), Km of 15.7 μM), in an overall reaction that is thermodynamically and kinetically reversible. Noteworthy, both Dd FDH-catalyzed formate oxidation and carbon dioxide reduction are completely inactivated by cyanide. Current FDH reaction mechanistic proposals are discussed and a different mechanism is here suggested: formate oxidation and carbon dioxide reduction are proposed to proceed through hydride transfer and the sulfo group of the oxidized and reduced molybdenum center, Mo(6+)═S and Mo(4+)-SH, are suggested to be the direct hydride acceptor and donor, respectively.

  3. Planning a Kinetic and Mechanistic Study with Cerium (IV)

    Science.gov (United States)

    Hanna, Samir B.; And Others

    1976-01-01

    Presents a kinetic study that utilizes a method for varying the concentrations of the possible Ce(IV) species and computing the concentration distribution of the sulfato and hydroxo species of Ce(IV). (MLH)

  4. Obesity and cancer: mechanistic insights from transdisciplinary studies

    OpenAIRE

    Allott, Emma H.; Hursting, Stephen D.

    2015-01-01

    Obesity is associated with a range of health outcomes that are of clinical and public health significance, including cancer. Herein, we summarize epidemiologic and preclinical evidence for an association between obesity and increased risk of breast and prostate cancer incidence and mortality. Moreover, we describe data from observational studies of weight change in humans and from calorie restriction studies in mouse models which support a potential role for weight loss in counteracting tumor...

  5. Experimental Study of Mechanistic Acid Deconstruction of Lignin

    Energy Technology Data Exchange (ETDEWEB)

    Sturgeon, M.; Kim, S.; Chmely, S. C.; Katahira, R.; Foust, T. D.; Beckham, G. T.

    2012-01-01

    Lignin is a major component of biomass, which remains highly underutilized in selective biomass conversion strategies to renewable fuels and chemicals. Here we are interested in studying the mechanisms related to the acid deconstruction of lignin with a combined theoretical and experimental approach. Quantum mechanical calculations were employed to elucidate possible deconstruction mechanisms with transition state theory. Model dimers, imitating H, S, and G lignins, were synthesized with the most abundant {beta} - O - 4 linkage in lignin. These compounds were then depolymerized using various acids and at different operating conditions. The deconstruction products were analyzed to complement the QM studies and investigate proposed mechanisms.

  6. Obesity and cancer: mechanistic insights from transdisciplinary studies.

    Science.gov (United States)

    Allott, Emma H; Hursting, Stephen D

    2015-12-01

    Obesity is associated with a range of health outcomes that are of clinical and public health significance, including cancer. Herein, we summarize epidemiologic and preclinical evidence for an association between obesity and increased risk of breast and prostate cancer incidence and mortality. Moreover, we describe data from observational studies of weight change in humans and from calorie-restriction studies in mouse models that support a potential role for weight loss in counteracting tumor-promoting properties of obesity in breast and prostate cancers. Given that weight loss is challenging to achieve and maintain, we also consider evidence linking treatments for obesity-associated co-morbidities, including metformin, statins and non-steroidal anti-inflammatory drugs, with reduced breast and prostate cancer incidence and mortality. Finally, we highlight several challenges that should be considered when conducting epidemiologic and preclinical research in the area of obesity and cancer, including the measurement of obesity in population-based studies, the timing of obesity and weight change in relation to tumor latency and cancer diagnosis, and the heterogeneous nature of obesity and its associated co-morbidities. Given that obesity is a complex trait, comprised of behavioral, epidemiologic and molecular/metabolic factors, we argue that a transdisciplinary approach is the key to understanding the mechanisms linking obesity and cancer. As such, this review highlights the critical need to integrate evidence from both epidemiologic and preclinical studies to gain insight into both biologic and non-biologic mechanisms contributing to the obesity-cancer link.

  7. Mechanistic studies on transcriptional coactivator protein arginine methyltransferase 1.

    Science.gov (United States)

    Rust, Heather L; Zurita-Lopez, Cecilia I; Clarke, Steven; Thompson, Paul R

    2011-04-26

    Protein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the guanidinium group of arginine residues in a number of important cell signaling proteins. PRMT1 is the founding member of this family, and its activity appears to be dysregulated in heart disease and cancer. To begin to characterize the catalytic mechanism of this isozyme, we assessed the effects of mutating a number of highly conserved active site residues (i.e., Y39, R54, E100, E144, E153, M155, and H293), which are believed to play key roles in SAM recognition, substrate binding, and catalysis. The results of these studies, as well as pH-rate studies, and the determination of solvent isotope effects (SIEs) indicate that M155 plays a critical role in both SAM binding and the processivity of the reaction but is not responsible for the regiospecific formation of asymmetrically dimethylated arginine (ADMA). Additionally, mutagenesis studies on H293, combined with pH studies and the lack of a normal SIE, do not support a role for this residue as a general base. Furthermore, the lack of a normal SIE with either the wild type or catalytically impaired mutants suggests that general acid/base catalysis is not important for promoting methyl transfer. This result, combined with the fact that the E144A/E153A double mutant retains considerably more activity then the single mutants alone, suggests that the PRMT1-catalyzed reaction is primarily driven by bringing the substrate guanidinium into the proximity of the S-methyl group of SAM and that the prior deprotonation of the substrate guanidinium is not required for methyl transfer.

  8. Mechanistic and therapeutic insights gained from studying rare skeletal diseases.

    Science.gov (United States)

    Tosi, Laura L; Warman, Matthew L

    2015-07-01

    Rare bone diseases account for 5% of all birth defects and can cause significant morbidity throughout patients' lives. Significant progress is being made to elucidate the pathophysiological mechanisms underlying these diseases. This paper summarizes presentation highlights of a workshop on Rare Skeletal Diseases convened to explore how the study of rare diseases has influenced the field's understanding of bone anabolism and catabolism and directed the search for new therapies benefiting patients with rare conditions as well as patients with common skeletal disorders.

  9. Structural and mechanistic studies of measles virus illuminate paramyxovirus entry.

    Directory of Open Access Journals (Sweden)

    Richard K Plemper

    2011-06-01

    Full Text Available Measles virus (MeV, a member of the paramyxovirus family of enveloped RNA viruses and one of the most infectious viral pathogens identified, accounts for major pediatric morbidity and mortality worldwide although coordinated efforts to achieve global measles control are in place. Target cell entry is mediated by two viral envelope glycoproteins, the attachment (H and fusion (F proteins, which form a complex that achieves merger of the envelope with target cell membranes. Despite continually expanding knowledge of the entry strategies employed by enveloped viruses, our molecular insight into the organization of functional paramyxovirus fusion complexes and the mechanisms by which the receptor binding by the attachment protein triggers the required conformational rearrangements of the fusion protein remain incomplete. Recently reported crystal structures of the MeV attachment protein in complex with its cellular receptors CD46 or SLAM and newly developed functional assays have now illuminated some of the fundamental principles that govern cell entry by this archetype member of the paramyxovirus family. Here, we review these advances in our molecular understanding of MeV entry in the context of diverse entry strategies employed by other members of the paramyxovirus family.

  10. Testing for mechanistic interactions in long-term follow-up studies.

    Directory of Open Access Journals (Sweden)

    Jui-Hsiang Lin

    Full Text Available In follow-up studies, interactions are often assessed by including a cross-product term in a (multiplicative Cox model. However, epidemiologists/clinicians often misinterpret a significant multiplicative interaction as a genuine mechanistic interaction. Though indices specific to mechanistic interactions have been proposed, including the 'relative excess risk due to interaction' (RERI and the 'peril ratio index of synergy based on multiplicativity' (PRISM, these indices assume no loss to follow up and no competing death in a study. In this paper, the authors propose a novel 'mechanistic interaction test' (MIT for censored data. Monte-Carlo simulation shows that when the hazard curves are proportional to, non-proportional to, or even crossing over one another, the proposed MIT can maintain reasonably accurate type I error rates for censored data. It has far greater powers than the modified RERI and PRISM tests (modified for censored data scenarios. To test mechanistic interactions in censored data, we recommend using MIT in light of its desirable statistical properties.

  11. Kinetic and mechanistic studies of allicin as an antioxidant.

    Science.gov (United States)

    Okada, Youji; Tanaka, Kaoru; Sato, Eisuke; Okajima, Haruo

    2006-11-21

    We have undertaken a detailed study of the antioxidant activity of allicin, one of the main thiosulfinates in garlic, in order to obtain quantitative information on it as a chain-breaking antioxidant. The antioxidant actions of allicin against the oxidation of cumene and methyl linoleate (ML) in chlorobenzene were studied in detail using HPLC. The hydroperoxides formed during the course of the inhibited oxidation of ML were analyzed as their corresponding alcohols by HPLC, and it is apparent that an allylic hydrogen atom of the allicin is responsible for the antioxidant activity. Furthermore, it is clear that the radical-scavenging reactions of allicin proceed via a one-step hydrogen atom transfer based on the results of the reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) in the presence of Mg2+ and calculation of the ionization potential value. In addition, we determined the stoichiometric factor (n), the number of peroxyl radicals trapped by one antioxidant molecule, of allicin by measuring the reactivity toward DPPH in chlorobenzene, and the value of n for allicin was about 1.0. Therefore, we measured the rate constants, k(inh), for the reaction of allicin with peroxyl radicals during the induction period of the cumene and the ML oxidation. As a result, we found that allicin reacts with peroxyl radicals derived from cumene and ML with the rate constants k(inh) = 2.6 x 10(3) M(-1)s(-1) and 1.6 x 10(5) M(-1)s(-1) in chlorobenzene, respectively. Our results demonstrate for the first time reliable quantitative kinetic data and the antioxidative mechanism of allicin as an antioxidant.

  12. Electrochemistry and spectroelectrochemistry of bioactive hydroxyquinolines: a mechanistic study.

    Science.gov (United States)

    Sokolová, Romana; Nycz, Jacek E; Ramešová, Šárka; Fiedler, Jan; Degano, Ilaria; Szala, Marcin; Kolivoška, Viliam; Gál, Miroslav

    2015-05-21

    The oxidation mechanism of selected hydroxyquinoline carboxylic acids such as 8-hydroxyquinoline-7-carboxylic acid (1), the two positional isomers 2-methyl-8-hydroxyquinoline-7-carboxylic acid (3) and 2-methyl-5-hydroxyquinoline-6-carboxylic acid (4), as well as other hydroxyquinolines were studied in aprotic environment using cyclic voltammetry, controlled potential electrolysis, in situ UV-vis and IR spectroelectrochemistry, and HPLC-MS/MS techniques. IR spectroelectrochemistry showed that oxidation unexpectedly proceeds together with protonation of the starting compound. We proved that the nitrogen atom in the heterocycle of hydroxyquinolines is protonated during the apparent 0.7 electron oxidation process. This was rationalized by the autodeprotonation reaction by another two starting molecules of hydroxyquinoline, so that the overall oxidation mechanism involves two electrons and three starting molecules. Both the electrochemical and spectroelectrochemical results showed that the oxidation mechanism is not influenced by the presence of the carboxylic group in the chemical structure of hydroxyquinolines, as results from oxidation of 2,7-dimethyl-5-hydroxyquinoline (6). In the presence of a strong proton acceptor such as pyridine, the oxidation ECEC process involves two electrons and two protons per one molecule of the hydroxyquinoline derivative. The electron transfer efficiency of hydroxyquinolines in biosystems may be related to protonation of biocompounds containing nitrogen bases. Molecular orbital calculations support the experimental findings.

  13. Mechanistic Study of the Acid Degradation of Lignin Model Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Sturgeon, M.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2012-01-01

    Lignin is a major constituent of biomass, which remains underutilized in selective biomass conversion strategies to renewable fuels and chemicals. Here we are interested in understanding the mechanisms related to the acid deconstruction of lignin with a combined theoretical and experimental approach. Two model dimers with a b-O-4 aryl ether linkage (2-phenoxy-1-phenethanol and 2-phenoxy-1-phenyl-1,3 propanediol) and model dimmers with an a-O-4 aryl ether linkage were synthesized and deconstructed in H2SO4. The major products of the acidolysis of the b-O-4 compounds consisted of phenol and two aldehydes, phenylacetaldehyde and benzaldehyde. Quantum mechanical calculations were employed to elucidate possible deconstruction mechanisms with transition state theory. To confirm proposed mechanisms several possible intermediates were studied under similar acidolysis conditions. Although the resonance time for cleavage was on the order several hours, we have shown that the cleavage of the aryl ether linkage affords phenol and aldehydes. We would next like to utilize our mechanism of aryl ether cleavage in actual lignin.

  14. A mechanistic study of ciprofloxacin removal by kaolinite.

    Science.gov (United States)

    Li, Zhaohui; Hong, Hanlie; Liao, Libing; Ackley, Caren J; Schulz, Laura A; MacDonald, Roberta A; Mihelich, Amanda L; Emard, Shannon M

    2011-11-01

    As one of the most important soil components, kaolinite plays a vital role in transport and retention of ionizable contaminants in soils of warm and wet climate. Ciprofloxacin (Cip) is a second generation fluoroquinolone (FQ) antibiotic of high use. It has high aqueous solubility under high and low pH conditions and higher stability in soil system. In this study, the interactions between Cip and kaolinite in aqueous solution were investigated by batch experiments, XRD and FTIR analyses. Quantitative correlation between the exchangeable cations desorbed and Cip adsorbed confirmed experimentally that cation exchange was the dominant mechanism of Cip adsorption on kaolinite. Fitting of experimental data to the cation exchange model resulted in a selectivity coefficient of 27, suggesting a strong affinity of Cip on negatively charged kaolinite surfaces. At the adsorption maximum 190-200 Å(2) was available per Cip molecule, much larger than the Cip molecule area, confirming charge-limited instead of surface-limited Cip adsorption. The invariable d-spacing after uptake of different amounts of Cip suggested that the adsorption of Cip was on the external surfaces of kaolinite. As solution pH increased beyond 8, the amount of Cip adsorption decreased significantly and reached close to zero at pH 11. The high adsorption rate constant due to surface adsorption instead of intercalation and the wide distribution of kaolinite in different soils suggest that the fate and transport of Cip may be governed by the transport of colloidal sized clays. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Mechanistic study of inhibition of levofloxacin absorption by aluminum hydroxide.

    Science.gov (United States)

    Tanaka, M; Kurata, T; Fujisawa, C; Ohshima, Y; Aoki, H; Okazaki, O; Hakusui, H

    1993-10-01

    The mechanisms of reduction in absorption of levofloxacin (LVFX) by coadministration of aluminum hydroxide were studied. The partition coefficient of LVFX (0.1 mM) between chloroform and phosphate buffer (pH 5.0) was reduced by 60 to 70% with the addition of metal ions such as Cu2+, Al3+, and Fe2+ (0.8 mM), which indicated the formation of LVFX-metal ion chelates. However, there was no significant difference in absorption from rat intestine between the synthetic LVFX-Al3+ (1:1) chelate (6.75 mM) and LVFX (6.75 mM) in an in situ recirculation experiment. On the other hand, Al(NO3)3 (1.5 mM) significantly inhibited the absorption of LVFX (1.5 mM) by 20% of the control in the in situ ligated loop experiment, in which partial precipitation of aluminum hydroxide was observed in the dosing solution. Data for adsorption of LVFX and ofloxacin (OFLX) from aqueous solution by aluminum hydroxide were shown to fit Langmuir plots, and the adsorptive capacities (rmax) and the K values were 7.0 mg/g and 1.77 x 10(4) M-1 for LVFX and 7.4 mg/g and 1.42 x 10(4) M-1 for OFLX, respectively. The rate of adsorption of several quinolones (50 microM) onto aluminum hydroxide (2.5 mg/ml) followed the order norfloxacin (NFLX) (72.0%) > enoxacin (ENX) (61.0%) > OFLX (47.2%) approximately LVFX (48.1%). The elution rate of adsorbed quinolones with water followed the rank order LVFX (17.9%) approximately OFLX (20.9%) approximately ENX (18.3%) > NFLX (11.9%). These results strongly suggest that adsorption of quinolones by aluminum hydroxide reprecipitated in the small intestine would play an important role in the reduced bioavailability of quinolones after coadministration with aluminum-containing antacids.

  16. Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology.

    Science.gov (United States)

    Verma, Mukesh

    2017-04-01

    This article reviews the significance of the microbiome in cancer epidemiology, mechanistic and technical challenges in the field, and characterization of the microbiome in different tumor types to identify biomarkers of risk, progression, and prognosis. Publications on the microbiome and cancer epidemiology were reviewed to analyze sample collection and processing, microbiome taxa characterization by 16S ribosomal RNA sequencing, and microbiome metabolite characterization (metabotyping) by nuclear magnetic resonance and mass spectrometry. The analysis identified methodology types, research design, sample types, and issues in integrating data from different platforms. Aerodigestive cancer epidemiology studies conducted by different groups demonstrated the significance of microbiome information in developing approaches to improve health. Challenges exist in sample preparation and processing (eg, standardization of methods for collection and analysis). These challenges relate to technology, data integration from "omics" studies, inherent bias in primer selection during 16S ribosomal RNA sequencing, the need for large consortia with well-characterized biospecimens, cause and effect issues, resilience of microbiota to exposure events (requires longitudinal studies), and expanding studies for fungal and viral diversity (most studies used bacterial 16S ribosomal RNA sequencing for microbiota characterization). Despite these challenges, microbiome and cancer epidemiology studies are significant and may facilitate cancer risk assessment, diagnosis, and prognosis. In the future, clinical trials likely will use microbiota modifications to improve the efficacy of existing treatments.

  17. Reactivity of γ-Terpinene with NO3 radicals: experimental approach for kinetic and mechanistic study.

    Science.gov (United States)

    Fouqueau, Axel; Cirtog, Manuela; Le Quilleuc, Meryll; Cazaunau, Mathieu; Pangui, Edouard; Duncianu, Marius; Doussin, Jean-François; Picquet-Varrault, Bénédicte

    2017-04-01

    Biogenic Volatile Organic Compounds (BVOC) are highly emitted by vegetation and play a key role in atmospheric chemistry. They are very reactive with atmospheric oxidants (OH, NO3, ozone) and significantly contribute to the formation of Secondary Organic Aerosol (SOA) at the global scale [1]. In addition, night-time chemistry initiated by NO3 radicals leads to the formation of organic nitrates which behave as reservoirs for reactive nitrogen. However, the reactivity of NO3 radical with BVOCs other than isoprene and α- and β-pinene, remains poorly understood. Among the BVOCs, γ-Terpinene is one of the most emitted by vegetation[2]. Two kinetic works were previously published on γ-Terpinene [3] [4], but mechanistic has never been studied. Thus, the aim of this work is to study the reactivity of γ-Terpinene with NO3 by performing experiments in simulation chambers. Kinetic, mechanism and SOA yield will be investigated. For this purpose, two different simulation chambers have been used: - First one, consisting of a Pyrex reactor of 1 m3 [5] coupled to a long path in situ FTIR spectrometer and a Proton Transfer Reaction Time of Flight Mass Spectrometer (PTR-ToF-MS) in NO+ mode which was internally developed in LISA, to measure organic nitrates concentration. - Second one, the CESAM chamber (http://cesam.cnrs.fr) [6] is a 4.2 m3 stainless steel chamber which permits to conduct SOA experiments at different temperature and relative humidity. In situ FTIR and PTR-ToF-MS are used to measure gaseous concentrations, and a SMPS was used to characterize particulate phase. Kinetic and mechanistic results will be discussed and compared with the literature values. References [1] Brown S. S., Stutz J., Nighttime radical observations and chemistry. Chem. Soc. Rev. (2012) 41, 6405-6447 [2] Helmig D., Klinger L.F., et al., Biogenic volatile organic compound emissions (BVOCs) I. Identifications from three continental sites in the U.S. Chemosphere. (1999), Vol. 38, No. 9, pp. 2163

  18. Substrate inhibition in the heterogeneous catalyzed aldol condensation: A mechanistic study of supported organocatalysts

    Energy Technology Data Exchange (ETDEWEB)

    Kandel, Kapil; Althaus, Stacey M.; Peeraphatdit, Chorthip; Kobayashi, Takeshi; Trewyn, Brian G.; Pruski, Marek; Slowing, Igor I.

    2012-05-23

    In this study, we demonstrate how materials science can be combined with the established methods of organic chemistry to find mechanistic bottlenecks and redesign heterogeneous catalysts for improved performance. By using solid-state NMR, infrared spectroscopy, surface and kinetic analysis, we prove the existence of a substrate inhibition in the aldol condensation catalyzed by heterogeneous amines. We show that modifying the structure of the supported amines according to the proposed mechanism dramatically enhances the activity of the heterogeneous catalyst. We also provide evidence that the reaction benefits significantly from the surface chemistry of the silica support, which plays the role of a co-catalyst, giving activities up to two orders of magnitude larger than those of homogeneous amines. This study confirms that the optimization of a heterogeneous catalyst depends as much on obtaining organic mechanistic information as it does on controlling the structure of the support.

  19. Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Metal Fuel Radionuclide Release

    Energy Technology Data Exchange (ETDEWEB)

    Grabaskas, David [Argonne National Lab. (ANL), Argonne, IL (United States); Bucknor, Matthew [Argonne National Lab. (ANL), Argonne, IL (United States); Jerden, James [Argonne National Lab. (ANL), Argonne, IL (United States)

    2016-02-01

    The development of an accurate and defensible mechanistic source term will be vital for the future licensing efforts of metal fuel, pool-type sodium fast reactors. To assist in the creation of a comprehensive mechanistic source term, the current effort sought to estimate the release fraction of radionuclides from metal fuel pins to the primary sodium coolant during fuel pin failures at a variety of temperature conditions. These release estimates were based on the findings of an extensive literature search, which reviewed past experimentation and reactor fuel damage accidents. Data sources for each radionuclide of interest were reviewed to establish release fractions, along with possible release dependencies, and the corresponding uncertainty levels. Although the current knowledge base is substantial, and radionuclide release fractions were established for the elements deemed important for the determination of offsite consequences following a reactor accident, gaps were found pertaining to several radionuclides. First, there is uncertainty regarding the transport behavior of several radionuclides (iodine, barium, strontium, tellurium, and europium) during metal fuel irradiation to high burnup levels. The migration of these radionuclides within the fuel matrix and bond sodium region can greatly affect their release during pin failure incidents. Post-irradiation examination of existing high burnup metal fuel can likely resolve this knowledge gap. Second, data regarding the radionuclide release from molten high burnup metal fuel in sodium is sparse, which makes the assessment of radionuclide release from fuel melting accidents at high fuel burnup levels difficult. This gap could be addressed through fuel melting experimentation with samples from the existing high burnup metal fuel inventory.

  20. H2 evolution by a cobalt selenolate electrocatalyst and related mechanistic studies.

    Science.gov (United States)

    Downes, Courtney A; Yoo, Joseph W; Orchanian, Nicholas M; Haiges, Ralf; Marinescu, Smaranda C

    2017-06-29

    [Co(bds)2][nBu4N] (where bds = 1,2-benzenediselenolate) was identified as an electrocatalyst for the hydrogen evolution reaction. Mechanistic studies indicated that a black precipitate, which formed upon treating [Co(bds)2](-) with acid, as well as the one-electron reduced species, [Co(bds)2](2-), were viable catalytic intermediates. We propose two kinetically-competent pathways for H2 evolution: EC and CE (E = electrochemical, C = chemical step).

  1. Studies on the interaction of isocyanides with imines: reaction scope and mechanistic variations

    Directory of Open Access Journals (Sweden)

    Ouldouz Ghashghaei

    2014-01-01

    Full Text Available The interaction of imines with isocyanides has been studied. The main product results from a sequential process involving the attack of two units of isocyanide, under Lewis acid catalysis, upon the carbon–nitrogen double bond of the imine to form the 4-membered ring system. The scope of the reaction regarding the imine and isocyanide ranges has been determined, and also some mechanistic variations and structural features have been described.

  2. Development of Mechanistic-Empirical Pavement Design for Tropical Climate Using Cement-Treated Base Layer

    Directory of Open Access Journals (Sweden)

    O. S. Aderinola

    2016-08-01

    Full Text Available A mechanistic-empirical pavement design method is developed characterising cement-treated base layers for pavement design in Nigeria or other similar tropical and subtropical countries. Asphalt Concrete surface, Subbase and Aggregate base were characterised based on back calculation data from Claros et al (1986 while cement-treated base layer was based on modulus tests that had been conducted by past researchers. Failure criteria for the Asphalt Concrete fatigue failure and the subgrade rutting failure were based on those by Claros and Ijeh (1987 for Nigerian pavements. Cracking criterion used for the cement-treated layer was that developed by Otee et al. (1982. The comparison between the Soil-Cement and Aggregate base showed that at a low Equivalent Single Axle Load (ESAL (0.5 million repetitions was considered, the use of Aggregate base was better than Soil-Cement base. That for Aggregate base and Cement-Treated Gravel Base showed that the Cement-Treated Gravel Base was better than the Aggregate base at high ESAL (2.5 million repetitions was considered

  3. Ruthenium-Catalyzed Transformations of Alcohols: Mechanistic Investigations and Methodology Development

    DEFF Research Database (Denmark)

    Makarov, Ilya; Madsen, Robert; Fristrup, Peter

    The mechanism of the ruthenium-catalyzed dehydrogenative synthesis of amides from alcohols and amines was studied in detail by employing the combination of experimental and theoretical techniques. The Hammett study revealed that a small positive charge is formed at the benzylic position in the tr......The mechanism of the ruthenium-catalyzed dehydrogenative synthesis of amides from alcohols and amines was studied in detail by employing the combination of experimental and theoretical techniques. The Hammett study revealed that a small positive charge is formed at the benzylic position...... obtained from the calculated energies, it was found that only the trans-dihydride pathway was in agreement with the experimentally determined frequencies. The proposed catalytic cycle was used for an in silico search for more effective carbene ligands. The study showed that the ruthenium complexes...... with dimethoxyisopropylidene and pyridilidene ligands could be more active than RuCl2(IiPr)(p-cymene) used in the mechanistic investigation. Two analogs of the calculated complexes were synthesized but were not isolated in a pure form. The amidation reaction catalyzed by a mixture containing the N-ethyl pyridilidene...

  4. Mechanistic Study Of The Atmospheric Photooxidation Of Trimethylbenzene In The Smog Chamber

    Energy Technology Data Exchange (ETDEWEB)

    Dommen, J.; Steinbacher, M.

    2005-03-01

    Mixtures of 1,3,5-trimethylbenzene, propene, NO and NO{sub 2} have been irradiated in our smog chamber. The temporal development of these precursors and many of the formed gaseous oxidation products have been measured and compared with model simulations based on the Master chemical mechanism. The fast reaction progress in the beginning of the experiment lets us assume that there is an additional OH radical source probably due to wall production of HONO. Higher production rates of photo oxidants in the model despite lower reactivity point to some mechanistic deficiencies of the model. (author)

  5. A Mechanistic Treatment of the Dominant Soil Nitrogen Cycling Processes: Model Development, Testing, and Application

    Energy Technology Data Exchange (ETDEWEB)

    Riley, William; Maggi, F.; Gu, C.; Riley, W.J.; Hornberger, G.M.; Venterea, R.T.; Xu, T.; Spycher, N.; Steefel, C.; Miller, N.L.; Oldenburg, C.M.

    2008-05-01

    The development and initial application of a mechanistic model (TOUGHREACT-N) designed to characterize soil nitrogen (N) cycling and losses are described. The model couples advective and diffusive nutrient transport, multiple microbial biomass dynamics, and equilibrium and kinetic chemical reactions. TOUGHREACT-N was calibrated and tested against field measurements to assess pathways of N loss as either gas emission or solute leachate following fertilization and irrigation in a Central Valley, California, agricultural field as functions of fertilizer application rate and depth, and irrigation water volume. Our results, relative to the period before plants emerge, show that an increase in fertilizer rate produced a nonlinear response in terms of N losses. An increase of irrigation volume produced NO{sub 2}{sup -} and NO{sub 3}{sup -} leaching, whereas an increase in fertilization depth mainly increased leaching of all N solutes. In addition, nitrifying bacteria largely increased in mass with increasing fertilizer rate. Increases in water application caused nitrifiers and denitrifiers to decrease and increase their mass, respectively, while nitrifiers and denitrifiers reversed their spatial stratification when fertilizer was applied below 15 cm depth. Coupling aqueous advection and diffusion, and gaseous diffusion with biological processes, closely captured actual conditions and, in the system explored here, significantly clarified interpretation of field measurements.

  6. A mechanistic treatment of the dominant soil nitrogen cycling processes: Model development, testing, and application

    Science.gov (United States)

    Maggi, F.; Gu, C.; Riley, W. J.; Hornberger, G. M.; Venterea, R. T.; Xu, T.; Spycher, N.; Steefel, C.; Miller, N. L.; Oldenburg, C. M.

    2008-06-01

    The development and initial application of a mechanistic model (TOUGHREACT-N) designed to characterize soil nitrogen (N) cycling and losses are described. The model couples advective and diffusive nutrient transport, multiple microbial biomass dynamics, and equilibrium and kinetic chemical reactions. TOUGHREACT-N was calibrated and tested against field measurements to assess pathways of N loss as either gas emission or solute leachate following fertilization and irrigation in a Central Valley, California, agricultural field as functions of fertilizer application rate and depth, and irrigation water volume. Our results, relative to the period before plants emerge, show that an increase in fertilizer rate produced a nonlinear response in terms of N losses. An increase of irrigation volume produced NO2- and NO3- leaching, whereas an increase in fertilization depth mainly increased leaching of all N solutes. In addition, nitrifying bacteria largely increased in mass with increasing fertilizer rate. Increases in water application caused nitrifiers and denitrifiers to decrease and increase their mass, respectively, while nitrifiers and denitrifiers reversed their spatial stratification when fertilizer was applied below 15 cm depth. Coupling aqueous advection and diffusion, and gaseous diffusion with biological processes, closely captured actual conditions and, in the system explored here, significantly clarified interpretation of field measurements.

  7. Cross-Coupling Synthesis of Methylallyl Alkenes: Scope Extension and Mechanistic Study

    Directory of Open Access Journals (Sweden)

    Clémence Tabélé

    2015-12-01

    Full Text Available Cross-coupling reactions between 2-methyl-2-propen-1-ol and various boronic acids are used to obtain aromatic-(2-methylallyl derivatives. However, deboronation or isomerization side reactions may occur for several boronic acids. We describe herein the synthesis of original alkenes with good yields under mild reaction conditions that decrease these side reactions. The scope of this environmentally benign reaction is thereby extended to a wide variety of boronic acids. A mechanistic study was conducted and suggested a plausible catalytic cycle mechanism, pointing to the importance of the Lewis acidity of the boronic acid used.

  8. Safety, Efficacy, and Mechanistic Studies Regarding Citrus aurantium (Bitter Orange) Extract and p-Synephrine.

    Science.gov (United States)

    Stohs, Sidney J

    2017-07-28

    Citrus aurantium L. (bitter orange) extracts that contain p-synephrine as the primary protoalkaloid are widely used for weight loss/weight management, sports performance, appetite control, energy, and mental focus and cognition. Questions have been raised about the safety of p-synephrine because it has some structural similarity to ephedrine. This review focuses on current human, animal, in vitro, and mechanistic studies that address the safety, efficacy, and mechanisms of action of bitter orange extracts and p-synephrine. Numerous studies have been conducted with respect to p-synephrine and bitter orange extract because ephedra and ephedrine were banned from use in dietary supplements in 2004. Approximately 30 human studies indicate that p-synephrine and bitter orange extracts do not result in cardiovascular effects and do not act as stimulants at commonly used doses. Mechanistic studies suggest that p-synephrine exerts its effects through multiple actions, which are discussed. Because p-synephrine exhibits greater adrenergic receptor binding in rodents than humans, data from animals cannot be directly extrapolated to humans. This review, as well as several other assessments published in recent years, has concluded that bitter orange extract and p-synephrine are safe for use in dietary supplements and foods at the commonly used doses. Copyright © 2017 The Authors Phytotherapy Research Published by John Wiley & Sons Ltd. Copyright © 2017 The Authors Phytotherapy Research Published by John Wiley & Sons Ltd.

  9. Planning for climate change: The need for mechanistic systems-based approaches to study climate change impacts on diarrheal diseases.

    Science.gov (United States)

    Mellor, Jonathan E; Levy, Karen; Zimmerman, Julie; Elliott, Mark; Bartram, Jamie; Carlton, Elizabeth; Clasen, Thomas; Dillingham, Rebecca; Eisenberg, Joseph; Guerrant, Richard; Lantagne, Daniele; Mihelcic, James; Nelson, Kara

    2016-04-01

    Increased precipitation and temperature variability as well as extreme events related to climate change are predicted to affect the availability and quality of water globally. Already heavily burdened with diarrheal diseases due to poor access to water, sanitation and hygiene facilities, communities throughout the developing world lack the adaptive capacity to sufficiently respond to the additional adversity caused by climate change. Studies suggest that diarrhea rates are positively correlated with increased temperature, and show a complex relationship with precipitation. Although climate change will likely increase rates of diarrheal diseases on average, there is a poor mechanistic understanding of the underlying disease transmission processes and substantial uncertainty surrounding current estimates. This makes it difficult to recommend appropriate adaptation strategies. We review the relevant climate-related mechanisms behind transmission of diarrheal disease pathogens and argue that systems-based mechanistic approaches incorporating human, engineered and environmental components are urgently needed. We then review successful systems-based approaches used in other environmental health fields and detail one modeling framework to predict climate change impacts on diarrheal diseases and design adaptation strategies.

  10. Study of n-Butyl Acrylate Self-Initiation Reaction Experimentally and via Macroscopic Mechanistic Modeling

    Directory of Open Access Journals (Sweden)

    Ahmad Arabi Shamsabadi

    2016-04-01

    Full Text Available This paper presents an experimental study of the self-initiation reaction of n-butyl acrylate (n-BA in free-radical polymerization. For the first time, the frequency factor and activation energy of the monomer self-initiation reaction are estimated from measurements of n-BA conversion in free-radical homo-polymerization initiated only by the monomer. The estimation was carried out using a macroscopic mechanistic mathematical model of the reactor. In addition to already-known reactions that contribute to the polymerization, the model considers a n-BA self-initiation reaction mechanism that is based on our previous electronic-level first-principles theoretical study of the self-initiation reaction. Reaction rate equations are derived using the method of moments. The reaction-rate parameter estimates obtained from conversion measurements agree well with estimates obtained via our purely-theoretical quantum chemical calculations.

  11. Symmetry Analysis in Mechanistic Studies of Nucleophilic Substitution and β-Elimination Reactions

    Directory of Open Access Journals (Sweden)

    Xiaoping Sun

    2010-02-01

    Full Text Available A mechanistic study of the bimolecular nucleophilic substitution (SN2 reaction for halomethane CH3X (X = Cl, Br, or I is approached by using symmetry principles and molecular orbital theory. The electrophilicity of the functionalized sp3–carbon is attributable to a 2p-orbital-based antibonding MO along the C–X bond. This antibonding MO, upon accepting an electron pair from a nucleophile, gives rise to dissociation of the C–X bond and formation of a new Nuc–C bond. Correlations are made between the molecular orbitals of reactants (Nuc- and CH3X and products (NucCH3 and X-. Similar symmetry analysis has been applied to mechanistic study of the bimolecular b-elimination (E2 reactions of haloalkanes. It well explains the necessity of an anti-coplanar arrangement of the Cα–X and Cβ–H bonds for an E2 reaction (anti-elimination. Having this structural arrangement, the bonding Cα–X (σC-X and antibonding Cβ–H (σC-H* orbitals become symmetry–match. They can partially overlap resulting in increase in electron density in σC-H*, which weakens and polarizes the Cβ–H bond making the β-H acidic. An E2 reaction can readily take place in the presence of a base. The applications of symmetry analysis to the SN2 and E2 reactions represent a new approach to studying organic mechanisms.

  12. Revisiting sesquiterpene biosynthetic pathways leading to santalene and its analogues: a comprehensive mechanistic study.

    Science.gov (United States)

    Jindal, Garima; Sunoj, Raghavan B

    2012-10-21

    Santalene and bergamotene are the major olefinic sesquiterpenes responsible for the fragrance of sandalwood oil. Herein we report the details of density functional theory investigations on the biosynthetic pathway of this important class of terpenes. The mechanistic study has been found to be effective toward gaining significant new insight into different possibilities for the formation of the key intermediates involved in santalene and bergamotene biosynthesis. The stereoelectronic features of the transition states and intermediates for (i) ring closure of the initial bisabolyl cation, and (ii) skeletal rearrangements in the ensuing bicyclic carbocationic intermediates leading to (-)-epi-β-santalene, (-)-β-santalene, (-)-α-santalene, (+)-epi-β-santalene, exo-β-bergamotene, endo-β-bergamotene, exo-α-bergamotene, and endo-α-bergamotene are presented. Interesting structural features pertaining to certain new carbocationic intermediates (such as b) resulting from the ring closure of bisabolyl cation are discussed. Extensive conformational sampling of all key intermediates along the biosynthetic pathway offered new insight into the role of the isoprenyl side chain conformation in the formation of santalene and its analogues. Although the major bicyclic products in Santalum album appear to arise from the right or left handed helical form of farnesyl pyrophosphate (FPP), different alternatives for their formation are found to be energetically feasible. The interconversion of the exo and endo isomers of bisabolyl cation and a likely epimerization, both with interesting mechanistic implications, are presented. The exo to endo conversion is identified to be energetically more favorable than another pathway emanating from the left handed helical FPP. The role of pyrophosphate (OPP(-)) in the penultimate deprotonation step leading to olefinic sesquiterpenes is also examined.

  13. Electrochemistry-mass spectrometry for mechanistic studies and simulation of oxidation processes in the environment.

    Science.gov (United States)

    Hoffmann, Th; Hofmann, D; Klumpp, E; Küppers, S

    2011-02-01

    Electrochemistry (EC) coupled to mass spectrometry (MS) has already been successfully applied to metabolism research for pharmaceutical applications, especially for the oxidation behaviour of drug substances. Xenobiotics (chemicals in the environment) also undergo various conversions; some of which are oxidative reactions. Therefore, EC-MS might be a suitable tool for the investigation of oxidative behaviour of xenobiotics. A further evaluation of this approach to environmental research is presented in the present paper using sulfonamide antibiotics. The results with sulfadiazine showed that EC-MS is a powerful tool for the elucidation of the oxidative degradation mechanism within a short time period. In addition, it was demonstrated that EC-MS can be used as a fast and easy method to model the chemical binding of xenobiotics to soil. The reaction of sulfadiazine with catechol, as a model substance for organic matter in soil, led to the expected chemical structure. Finally, by using EC-MS a first indication was obtained of the persistence of a component under chemical oxidation conditions for the comparison of the oxidative stability of different classes of xenobiotics. Overall, using just a few examples, the study demonstrates that EC-MS can be applied as a versatile tool for mechanistic studies of oxidative degradation pathways of xenobiotics and their possible interaction with soil organic matter as well as their oxidative stability in the environment. Further studies are needed to evaluate the full range of possibilities of the application of EC-MS in environmental research.

  14. Station Blackout: A case study in the interaction of mechanistic and probabilistic safety analysis

    Energy Technology Data Exchange (ETDEWEB)

    Curtis Smith; Diego Mandelli; Cristian Rabiti

    2013-11-01

    The ability to better characterize and quantify safety margins is important to improved decision making about nuclear power plant design, operation, and plant life extension. As research and development (R&D) in the light-water reactor (LWR) Sustainability (LWRS) Program and other collaborative efforts yield new data, sensors, and improved scientific understanding of physical processes that govern the aging and degradation of plant SSCs needs and opportunities to better optimize plant safety and performance will become known. The purpose of the Risk Informed Safety Margin Characterization (RISMC) Pathway R&D is to support plant decisions for risk-informed margin management with the aim to improve economics, reliability, and sustain safety of current NPPs. In this paper, we describe the RISMC analysis process illustrating how mechanistic and probabilistic approaches are combined in order to estimate a safety margin. We use the scenario of a “station blackout” wherein offsite power and onsite power is lost, thereby causing a challenge to plant safety systems. We describe the RISMC approach, illustrate the station blackout modeling, and contrast this with traditional risk analysis modeling for this type of accident scenario.

  15. Reactivities of d~0 transition metal complexes toward oxygen:Synthetic and mechanistic studies

    Institute of Scientific and Technical Information of China (English)

    CHEN ShuJian; ZHANG XinHao; LIN ZhenYang; WU YunDong; XUE ZiLing

    2009-01-01

    Transition metals such as Fe in porphyrin complexes are known to bind or react with O_2,and such reactions are critical to many biological functions and catalytic oxidation using O_2.The transition metals in these reactions often contain valence d electrons,and oxidation of metals is an important step.In recent years,reactions of O_2 with d~0 transition metal complexes such as Hf(NR_2)_4 (R=alkyl) have been used to make metal oxide thin films as insulating gate materials in new microelectronic devices.This feature article discusses our recent studies of such reactions and the formation of TiO_2 thin films.In contrast to the reactions of many d~n complexes where metals are often oxidized,reactions of d~0 complexes such as Hf(Nme_2)_4 and Ta(Nme_2)_4(SiR_3) with O_2 usually lead to the oxidation of ligands,forming,e.g.,-ONMe_2 and-OSiR_3 from-Nme_2 and-SiR_3 ligands,respectively.Mechanistic and theoretical studies of these reactions have revealed pathways in the formation of the metal oxide thin films as microelectronic materials.

  16. Kinetic and mechanistic studies of free-radical reactions in combustion

    Energy Technology Data Exchange (ETDEWEB)

    Tully, F.P. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    Combustion is driven by energy-releasing chemical reactions. Free radicals that participate in chain reactions carry the combustion process from reactants to products. Research in chemical kinetics enables us to understand the microscopic mechanisms involved in individual chemical reactions as well as to determine the rates at which they proceed. Both types of information are required for an understanding of how flames burn, why engines knock, how to minimize the production of pollutants, and many other important questions in combustion. In this program the authors emphasize accurate measurements over wide temperature ranges of the rates at which ubiquitous free radicals react with stable molecules. The authors investigate a variety of OH, CN, and CH + stable molecule reactions important to fuel conversion, emphasizing application of the extraordinarily precise technique of laser photolysis/continuous-wave laser-induced fluorescence (LP/cwLIF). This precision enables kinetic measurements to serve as mechanistic probes. Since considerable effort is required to study each individual reaction, prudent selection is critical. Two factors encourage selection of a specific reaction: (1) the rates and mechanisms of the subject reaction are required input to a combustion model; and (2) the reaction is a chemical prototype which, upon characterization, will provide fundamental insight into chemical reactivity, facilitate estimation of kinetic parameters for similar reactions, and constrain and test the computational limits of reaction-rate theory. Most studies performed in this project satisfy both conditions.

  17. Liquid chromatography tandem mass spectrometry analysis of photodegradation of a diazo compound: a mechanistic study.

    Science.gov (United States)

    Meetani, M A; Hisaindee, S M; Abdullah, F; Ashraf, S S; Rauf, M A

    2010-06-01

    The photolytic degradation of the diazo dye, Amido Black, using UV/H(2)O(2) has been carried out experimentally and parameters for most efficient dye degradation have been determined. The degradation of the dye was followed by UV-Vis spectroscopy, HPLC, and LC-MS and is proposed to be initiated by ()OH radicals formed by the photolysis of H(2)O(2). A detailed study was also carried out using LC-MS and LC-MS/MS to determine the degradation pathway of the dye as well as to identify some of the intermediate products formed. Our results suggest that Amido Black degradation occurs preferentially by ()OH radical attack at the more electron rich diazo functionality of the molecule. Furthermore, evidence is presented that subsequent steps in this diazo dye degradation pathway include radical denitration, radical desulfonation and radical diazotization. This report is one of the very few studies that have proposed possible mechanistic pathways for the degradation pathways of a diazo compound.

  18. Reactivities of d~0 transition metal complexes toward oxygen:Synthetic and mechanistic studies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Transition metals such as Fe in porphyrin complexes are known to bind or react with O2,and such reactions are critical to many biological functions and catalytic oxidation using O2.The transition metals in these reactions often contain valence d electrons,and oxidation of metals is an important step.In recent years,reactions of O2 with d0 transition metal complexes such as Hf(NR2)4(R=alkyl) have been used to make metal oxide thin films as insulating gate materials in new microelectronic devices.This feature article discusses our recent studies of such reactions and the formation of TiO2 thin films.In contrast to the reactions of many dn complexes where metals are often oxidized,reactions of d0 complexes such as Hf(NMe2)4 and Ta(NMe2)4(SiR3) with O2 usually lead to the oxidation of ligands,forming,e.g.,-ONMe2 and -OSiR3 from-NMe2 and-SiR3 ligands,respectively.Mechanistic and theoretical studies of these reactions have revealed pathways in the formation of the metal oxide thin films as microelectronic materials.

  19. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL).

    Science.gov (United States)

    Li, Lei

    2012-11-01

    Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue

  20. Mechanistic Studies on the Photoallergy Mediated by Fenofibric Acid: Photoreactivity with Serum Albumins.

    Science.gov (United States)

    Vayá, Ignacio; Andreu, Inmaculada; Monje, Vicente T; Jiménez, M Consuelo; Miranda, Miguel A

    2016-01-19

    The photoreactivity of fenofibric acid (FA) in the presence of human and bovine serum albumins (HSA and BSA, respectively) has been investigated by steady-state irradiation, fluorescence, and laser flash photolysis (LFP). Spectroscopic measurements allowed for the determination of a 1:1 stoichiometry for the FA/SA complexes and pointed to a moderate binding of FA to the proteins; by contrast, the FA photoproducts were complexed more efficiently with SAs. Covalent photobinding to the protein, which is directly related to the photoallergic properties of the drug, was detected after long irradiation times and was found to be significantly higher in the case of BSA. Intermolecular FA-amino acid and FA-albumin irradiations resulted in the formation of photoproducts arising from coupling between both moieties, as indicated by mass spectrometric analysis. Mechanistic studies using model drug-amino acid linked systems indicated that the key photochemical step involved in photoallergy is formal hydrogen atom transfer from an amino acid residue to the excited benzophenone chromophore of FA or (more likely) its photoproducts. This results in the formation of caged radical pairs followed by C-C coupling to give covalent photoaducts.

  1. Dual Lewis Acid/Lewis Base Catalyzed Acylcyanation of Aldehydes: A Mechanistic Study.

    Science.gov (United States)

    Laurell Nash, Anna; Hertzberg, Robin; Wen, Ye-Qian; Dahlgren, Björn; Brinck, Tore; Moberg, Christina

    2016-03-07

    A mechanistic investigation, which included a Hammett correlation analysis, evaluation of the effect of variation of catalyst composition, and low-temperature NMR spectroscopy studies, of the Lewis acid-Lewis base catalyzed addition of acetyl cyanide to prochiral aldehydes provides support for a reaction route that involves Lewis base activation of the acyl cyanide with formation of a potent acylating agent and cyanide ion. The cyanide ion adds to the carbonyl group of the Lewis acid activated aldehyde. O-Acylation by the acylated Lewis base to form the final cyanohydrin ester occurs prior to decomplexation from titanium. For less reactive aldehydes, the addition of cyanide is the rate-determining step, whereas, for more reactive, electron-deficient aldehydes, cyanide addition is rapid and reversible and is followed by rate-limiting acylation. The resting state of the catalyst lies outside the catalytic cycle and is believed to be a monomeric titanium complex with two alcoholate ligands, which only slowly converts into the product. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Simple boron removal from seawater by using polyols as complexing agents: A computational mechanistic study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Min-Kyung; Eom, Ki Heon; Lim, Jun-Heok; Lee, Jea-Keun; Lee, Ju Dong; Won, Yong Sun [Pukyong National University, Busan (Korea, Republic of)

    2015-11-15

    The complexation of boric acid (B(OH){sub 3}), the primary form of aqueous boron at moderate pH, with polyols is proposed and mechanistically studied as an efficient way to improve membrane processes such as reverse osmosis (RO) for removing boron in seawater by increasing the size of aqueous boron compounds. Computational chemistry based on the density functional theory (DFT) was used to manifest the reaction pathways of the complexation of B(OH){sub 3} with various polyols such as glycerol, xylitol, and mannitol. The reaction energies were calculated as −80.6, −98.1, and −87.2 kcal/mol for glycerol, xylitol, and mannitol, respectively, indicating that xylitol is the most thermodynamically favorable for the complexation with B(OH){sub 3}. Moreover, the 1 : 2 molar ratio of B(OH)3 to polyol was found to be more favorable than the ratio of 1 : 1 for the complexation. Meanwhile, latest lab-scale actual RO experiments successfully supported our computational prediction that 2 moles of xylitol are the most effective as the complexing agent for 1 mole of B(OH){sub 3} in aqueous solution.

  3. Observability analysis of biochemical process models as a valuable tool for the development of mechanistic soft sensors.

    Science.gov (United States)

    Golabgir, Aydin; Hoch, Thomas; Zhariy, Mariya; Herwig, Christoph

    2015-01-01

    By enabling the estimation of difficult-to-measure target variables using available indirect measurements, mechanistic soft sensors have become important tools for various bioprocess monitoring and control scenarios. Despite promising higher process efficiencies and increased process understanding, widespread application of soft sensors has been stalled by uncertainty about the feasibility and reliability of their estimations given present process analytical constraints. Observability analysis can provide an indication of the possibility and reliability of soft sensor estimations by analyzing the structural properties of first-principle (mechanistic) models. In addition, it can provide a criteria for selection of suitable measurement methods with respect to their information content; thereby leading to successful implementation of soft sensors in bioprocess development and manufacturing environments. We demonstrate the utility of observability analysis for two classes of upstream bioprocesses: the processes involving growth and ethanol formation by Saccharomyces cerevisiae and the process of penicillin production by Penicillium chrysogenum. Results obtained from laboratory-scale cultivations in addition to in-silico experiments enable a comparison of theoretical aspects of observability analysis and the real-life performance of soft sensors. By taking the expected error of measurements provided to the soft sensor into account, an innovative scaling approach facilitates a higher degree of comparability of observability results among various measurement configurations and process conditions.

  4. A Mechanistic Study of Arsenic (III) Rejection by Reverse Osmosis and Nanofiltration Membranes

    Science.gov (United States)

    Suzuki, Tasuma

    2009-01-01

    Reverse osmosis/nanofiltration (RO/NF) membranes are capable to provide an effective barrier for a wide range of contaminants (including disinfection by-products precursors) in a single treatment step. However, solute rejection mechanisms by RO/NF membranes are not well understood. The lack of mechanistic information arises from experimental…

  5. A Mechanistic Study of Arsenic (III) Rejection by Reverse Osmosis and Nanofiltration Membranes

    Science.gov (United States)

    Suzuki, Tasuma

    2009-01-01

    Reverse osmosis/nanofiltration (RO/NF) membranes are capable to provide an effective barrier for a wide range of contaminants (including disinfection by-products precursors) in a single treatment step. However, solute rejection mechanisms by RO/NF membranes are not well understood. The lack of mechanistic information arises from experimental…

  6. Cine and direct aminations of 5- and 6-halogenopyrimidines : a mechanistic study

    NARCIS (Netherlands)

    Rasmussen, C.A.H.

    1978-01-01

    This thesis describes investigations into the mechanistic aspects of the cine amination of 4-substituted 5-halogenopyrimidines and the direct amination of 4-substituted 6-halogenopyrimidines by potassium amide in liquid ammonia.

    PMR spectra of some 4-R-5-bromopyrimidines (R=C

  7. Cine and direct aminations of 5- and 6-halogeno-pyrimidines. A mechanistic study

    NARCIS (Netherlands)

    Rasmussen, C.A.H.

    1978-01-01

    This thesis describes investigations into the mechanistic aspects of the cine amination of 4-substituted 5-halogenopyrimidines and the direct amination of 4-substituted 6-halogenopyrimidines by potassium amide in liquid ammonia.PMR spectra of some 4-R-5-bromopyrimidines (R=C 6

  8. Thermal degradation events as health hazards: Particle vs gas phase effects, mechanistic studies with particles

    Science.gov (United States)

    Oberdörster, G.; Ferin, J.; Finkelstein, J.; Soderholm, S.

    the highly acute toxicity of fumes. Future studies will include adsorption of typical gas phase components (HCl, HF) on surrogate particles to differentiate between gas and particle phase effects and to perform mechanistic studies aimed at introducing therapeutic/preventive measures. These studies will be complemented by a comparison with actual thermal degradation products.

  9. Synthesis and mechanistic studies of a mitomycin dimer containing an eight-membered cyclic disulfide.

    Science.gov (United States)

    Park, Hyun Jung; Kim, Jae Jin; Kim, Hyoung Rae; Lee, Eun Kyung; Kim, Eun Sook; Jeong, Choon Sik; Moon, Aree; Lee, Sang Hyup

    2011-07-01

    Dimeric DNA alkylating agents have drawn significant interest because these compounds are expected to provide at least two reactive sites and as a result, generate enhanced levels of DNA interstrand cross-link (DNA ISC) adducts compared to their monomeric agents. We report the synthesis and mechanistic studies of a novel mitomycin dimer, 7-N,7'-N'-(1″,2″-dithiocanyl-3″,8″-dimethylenyl)bismitomycin C (8) connected by an eight-membered cyclic disulfide. Mitomycins require prior activation (i.e., transformation to a good electrophile) for DNA adduction and therefore, 8 was aimed to undergo facile nucleophilic activation and produce enhanced levels of DNA ISC. At the core of this function lies a cyclic disulfide in 8. It was expected that disulfide cleavage by an appropriate nucleophile would successively produce two thiols that may trigger activation of two mitomycin rings in a dimer through intramolecular cyclization to quinine rings. Compound 8 was synthesized from mitomycin A (1) and the key intermediate, cyclic disulfide (11), along with the reference diol mitomycin 7-N,7'-N'-(2″,7″-dihydroxy-1″,8″-octanediyl)bismitomycin C (23) which does not contain the disulfide unit. We found that 8 underwent significantly enhanced nucleophilic activation in the presence of Et(3)P compared with 23, and that the disulfide unit in 8 played a key role for the nucleophilic activation. Based on these findings, we proposed a mechanism for nucleophilic activation of 8. We further demonstrated that 8 generated much higher levels of DNA ISC (94%) compared with 23 (4%) and 2 (3%) in the presence of Et(3)P (and L-DTT) leading to the conclusion that 8 is more efficient for DNA ISC processes than 23 and 2 due to the role of disulfide unit.

  10. Linking accelerated laboratory and outdoor exposure results for PV polymeric materials: a mechanistic study of EVA

    Science.gov (United States)

    Gu, Xiaohong; Pang, Yongyan; Lin, Chiao-Chi; Liu, Kaipeng; Nguyen, Tinh; Chin, Jaonnie W.

    2013-09-01

    Linking accelerated laboratory test to field performance for predicting the service life of polymeric materials are being investigated at NIST using the reliability-based methodology. Based on this methodology, a successful linkage between the laboratory and field exposure data for a model polymeric material has been made. Recently, this methodology, for the first time, was introduced to the lifetime assessment of PV polymeric materials. In this paper, a mechanistic study of the degradation of three unstabilized model ethylene vinyl acetate (EVA) systems---uncured EVA, cured EVA and laminated EVA---was carried out under accelerated laboratory exposure and outdoor exposure. The NIST SPHERE (Simulated Photodegradation via High Energy Radiant Exposure) was used for the accelerated laboratory tests, and the outdoor exposure was conducted in Gaithersburg, Maryland. Simultaneous multiple stresses, including temperature, relative humidity and UV radiation, were applied individually or in combination during SPHERE exposure. The effects of the environmental factors on the main degradation mechanisms of different EVA systems were investigated. The results showed that the UV radiation was the most important factor for the degradation of EVA and a synergistic effect occurred between UV radiation and relative humidity. A slower degradation rate was observed for the laminated system as a result of limited diffusion of O2 and H2O into EVA. It was also found that the substantial chemical changes of the uncured EVA system did not yield yellowing, which was dramatically different from the peroxide cured EVA system. Additionally, the chemical degradation modes of the three EVA systems exposed outdoors appeared to be similar to those exposed to the SPHERE. The implication of this work to the current test standards was discussed.

  11. DNA damage and radical reactions: Mechanistic aspects, formation in cells and repair studies

    Energy Technology Data Exchange (ETDEWEB)

    Cadet, J.; Ravanat, J.L. [CEA Grenoble, Inst Nanosci and Cryogenie, SCIB-UMR-E 3, Lab Les Acides Nucl, UJF, F-38054 Grenoble 9 (France); Carell, T. [Univ Munich, Dept Chem and Biochem, Ctr Integrat Prot Sci, D-81377 Munich (Germany); Cellai, L. [CNR, Ist Cristalog, Monterotondo Stn, I-00016 Rome (Italy); Chatgilialoglu, Ch. [CNR, ISOF, I-40129 Bologna, (Italy); Gimisis, Th. [Univ Athens, Dept Chem, Organ Chem Lab, Athens 15784, (Greece); Miranda, M. [Univ Politecn Valencia, Inst Technol Quim, Dept Quim, Valencia 46022 (Spain); O' Neill, P. [Univ Oxford, Oxford OX3 7DQ (United Kingdom); Robert, M. [Univ Paris 07, CNRS, UMR 7591, Electrochim Mol Lab, F-75251 Paris 05 (France)

    2008-07-01

    Several examples of oxidative and reductive reactions of DNA components that lead to single and tandem modifications are discussed in this review. These include nucleophilic addition reactions of the one-electron oxidation-mediated guanine radical cation and the one-electron reduced intermediate of 8-bromo-purine 2'-de-oxy-ribo-nucleosides that give rise to either an oxidizing guanine radical or related 5',8-cyclo-purine nucleosides. In addition, mechanistic insights into the reductive pathways involved in the photolyase induced reversal of cyclo-buta-cli-pyrimidine and pyrimidine (6-4) pyrimidone photoproducts are provided. Evidence for the occurrence and validation in cellular DNA of (OH){sup {center_dot}} radical degradation pathways of guanine that have been established in model systems has been gained from the accurate measurement of degradation products. Relevant information on biochemical aspects of the repair of single and clustered oxidatively generated damage to DNA has been gained from detailed investigations that rely on the synthesis of suitable modified probes. Thus the preparation of stable carbocyclic derivatives of purine nucleoside containing defined sequence oligonucleotides has allowed detailed crystallographic studies of the recognition step of the base damage by enzymes implicated in the base excision repair (BER) pathway. Detailed insights are provided on the BER processing of non-double strand break bi-stranded clustered damage that may consist of base lesions, a single strand break or abasic sites and represent one of the main deleterious classes of radiation-induced DNA damage. (authors)

  12. Final Report for the DOE-BES Program Mechanistic Studies of Activated Hydrogen Release from Amine-Boranes

    Energy Technology Data Exchange (ETDEWEB)

    Larry G. Sneddon; R. Thomas Baker

    2013-01-13

    Effective storage of hydrogen presents one of the most significant technical gaps to successful implementation of the hydrogen economy, particularly for transportation applications. Amine boranes, such as ammonia borane H3NBH3 and ammonia triborane H3NB3H7, have been identified as promising, high-capacity chemical hydrogen storage media containing potentially readily released protic (N-H) and hydridic (B-H) hydrogens. At the outset of our studies, dehydrogenation of ammonia borane had been studied primarily in the solid state, but our DOE sponsored work clearly demonstrated that ionic liquids, base-initiators and/or metal-catalysts can each significantly increase both the rate and extent of hydrogen release from amine boranes under moderate conditions. Our studies also showed that depending upon the activation method, hydrogen release from amine boranes can occur by very different mechanistic steps and yield different types of spent-fuel materials. The fundamental understanding that was developed during this grant of the pathways and controlling factors for each of these hydrogen-release mechanisms is now enabling continuing discovery and optimization of new chemical-hydride based hydrogen storage systems.

  13. In silico predictions of gastrointestinal drug absorption in pharmaceutical product development: application of the mechanistic absorption model GI-Sim.

    Science.gov (United States)

    Sjögren, Erik; Westergren, Jan; Grant, Iain; Hanisch, Gunilla; Lindfors, Lennart; Lennernäs, Hans; Abrahamsson, Bertil; Tannergren, Christer

    2013-07-16

    Oral drug delivery is the predominant administration route for a major part of the pharmaceutical products used worldwide. Further understanding and improvement of gastrointestinal drug absorption predictions is currently a highly prioritized area of research within the pharmaceutical industry. The fraction absorbed (fabs) of an oral dose after administration of a solid dosage form is a key parameter in the estimation of the in vivo performance of an orally administrated drug formulation. This study discloses an evaluation of the predictive performance of the mechanistic physiologically based absorption model GI-Sim. GI-Sim deploys a compartmental gastrointestinal absorption and transit model as well as algorithms describing permeability, dissolution rate, salt effects, partitioning into micelles, particle and micelle drifting in the aqueous boundary layer, particle growth and amorphous or crystalline precipitation. Twelve APIs with reported or expected absorption limitations in humans, due to permeability, dissolution and/or solubility, were investigated. Predictions of the intestinal absorption for different doses and formulations were performed based on physicochemical and biopharmaceutical properties, such as solubility in buffer and simulated intestinal fluid, molecular weight, pK(a), diffusivity and molecule density, measured or estimated human effective permeability and particle size distribution. The performance of GI-Sim was evaluated by comparing predicted plasma concentration-time profiles along with oral pharmacokinetic parameters originating from clinical studies in healthy individuals. The capability of GI-Sim to correctly predict impact of dose and particle size as well as the in vivo performance of nanoformulations was also investigated. The overall predictive performance of GI-Sim was good as >95% of the predicted pharmacokinetic parameters (C(max) and AUC) were within a 2-fold deviation from the clinical observations and the predicted plasma AUC

  14. Ramipril retards development of aortic valve stenosis in a rabbit model: mechanistic considerations.

    Science.gov (United States)

    Ngo, Doan Tm; Stafford, Irene; Sverdlov, Aaron L; Qi, Weier; Wuttke, Ronald D; Zhang, Yuan; Kelly, Darren J; Weedon, Helen; Smith, Malcolm D; Kennedy, Jennifer A; Horowitz, John D

    2011-02-01

    Aortic valve stenosis (AVS) is associated with significant cardiovascular morbidity and mortality. To date, no therapeutic modality has been shown to be effective in retarding AVS progression. We evaluated the effect of angiotensin-converting enzyme inhibition with ramipril on disease progression in a recently developed rabbit model of AVS. The effects of 8 weeks of treatment with either vitamin D₂ at 25,000 IU for 4 days a week alone or in combination with ramipril (0.5 mg·kg⁻¹) on aortic valve structure and function were examined in New Zealand white rabbits. Echocardiographic aortic valve backscatter (AV(BS)) and aortic valve:outflow tract flow velocity ratio were utilized to quantify changes in valve structure and function. Treatment with ramipril significantly reduced AV(BS) and improved aortic valve :outflow tract flow velocity ratio. The intravalvular content of the pro-oxidant thioredoxin-interacting protein was decreased significantly with ramipril treatment. Endothelial function, as measured by asymmetric dimethylarginine concentrations and vascular responses to ACh, was improved significantly with ramipril treatment. Ramipril retards the development of AVS, reduces valvular thioredoxin-interacting protein accumulation and limits endothelial dysfunction in this animal model. These findings provide important insights into the mechanisms of AVS development and an impetus for future human studies of AVS retardation using an angiotensin-converting enzyme inhibitor. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  15. A quantitative approach to developing more mechanistic gas exchange models for field grown potato

    DEFF Research Database (Denmark)

    Ahmadi, Seyed Hamid; Andersen, Mathias Neumann; Poulsen, Rolf Thostrup

    2009-01-01

    of chemical and hydraulic signalling on stomatal conductance as exp(-β[ABA])exp(-δ|ψ|) in which [ABA] and |ψ| are xylem ABA concentration and absolute value of leaf or stem water potential. In this study we found that stem water potential could be a very reliable indicator of how plant water status affects......In this study we introduce new gas exchange models that are developed under natural conditions of field grown potato. The new models could explain about 85% of the stomatal conductance variations, which was much higher than the well-known gas exchange models such as the Ball-Berry model [Ball......, Woodrow, Berry, 1987. In: Nijhoff, M. (Eds.), Progress in Photosynthesis Research, vol. 4. Dordrecht, The Netherlands, pp. 5.221-5.224]. To overcome the limitations of previous models in simulating stomatal conductance when plants are exposed to drought stress, we proposed a down-regulating factor...

  16. Mechanistic Studies of Combustion and Structure Formation During Synthesis of Advanced Materials

    Science.gov (United States)

    Varma, A.; Lau, C.; Mukasyan, A. S.

    2001-01-01

    reactants occurs within each particle, and mixtures of elemental powders, where interparticle contacts are important for the reaction; and 3) Mechanistic Studies of Phase Separation in Combustion of Thermite Systems. Studies are devoted to experiments on thermite systems (metal oxide-reducing metal) where phase separation processes occur to produce alloys with tailored compositions and properties. The separation may be either gravity-driven or due to surface forces, and systematic studies to elucidate the true mechanism are being conducted. The knowledge obtained will be used to find the most promising ways of controlling the microstructure and properties of combustion-synthesized materials. Low-gravity experiments are essential to create idealized an environment for insights into the physics and chemistry of advanced material synthesis processes.

  17. Mechanistic studies on the OH-initiated atmospheric oxidation of selected aromatic hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Nehr, Sascha

    2012-07-01

    Benzene, toluene, the xylenes, and the trimethylbenzenes are among the most abundant aromatic trace constituents of the atmosphere mainly originating from anthropogenic sources. The OH-initiated atmospheric photo-oxidation of aromatic hydrocarbons is the predominant removal process resulting in the formation of O{sub 3} and secondary organic aerosol. Therefore, aromatics are important trace constituents regarding air pollution in urban environments. Our understanding of aromatic photo-oxidation processes is far from being complete. This work presents novel approaches for the investigation of OH-initiated atmospheric degradation mechanisms of aromatic hydrocarbons. Firstly, pulsed kinetic studies were performed to investigate the prompt HO{sub 2} formation from OH+ aromatic hydrocarbon reactions under ambient conditions. For these studies, the existing OH reactivity instrument, based on the flash photolysis/laser-induced fluorescence (FP/LIF) technique, was extended to the detection of HO{sub 2} radicals. The experimental design allows for the determination of HO{sub 2} formation yields and kinetics. Results of the pulsed kinetic experiments complement previous product studies and help to reduce uncertainties regarding the primary oxidation steps. Secondly, experiments with aromatic hydrocarbons were performed under atmospheric conditions in the outdoor atmosphere simulation chamber SAPHIR (Simulation of Atmospheric PHotochemistry In a large Reaction chamber) located at Forschungszentrum Juelich. The experiments were aimed at the evaluation of up-to-date aromatic degradation schemes of the Master Chemical Mechanism (MCMv3.2). The unique combination of analytical instruments operated at SAPHIR allows for a detailed investigation of HO{sub x} and NO{sub x} budgets and for the determination of primary phenolic oxidation product yields. MCMv3.2 deficiencies were identified and most likely originate from shortcomings in the mechanistic representation of ring

  18. Deposition, characterization, patterning and mechanistic study of inorganic resists for next-generation nanolithography

    Science.gov (United States)

    Luo, Feixiang

    The semiconductor industry has witnessed a continuous decrease in the size of logic, memory and other computer chip components since its birth over half a century ago. The shrinking (scaling) of components has to a large extent been enabled by the development of micro- and now nano-lithographic techniques. This thesis focuses on one central component of lithography, the resist, which is essentially a thin film that when appropriately exposed enables a pattern to be printed onto a surface. Smaller features require an ever more precisely focused photon, electron or ion beam with which to expose the resist. The likely next generation source of radiation that will enable sub-20nm features to be written will employ extreme ultraviolet radiation (EUV), 92eV (13.5nm). The work discussed here involves a novel class of inorganic resists (including a solution processed Hf-based resist called HafSOx), as the organic resists that have dominated the microlithography industry for the past few decades have approached fundamental scaling limits. In order to maintain the high throughput required by high volume semiconductor manufacturing, metal oxide resists have been proposed and developed to meet the resolution and sensitivity in EUV lithography. One can think of our resists as the nano-lithographic analog to the silver halide film that dominated the photographic print industry for a century. In this thesis, we mainly describe our work on HafSOx, a "first generation" metal oxide EUV resist system. HafSOx thin films can be deposited by spin-coating a mixed solution of HfOCl2, H2O 2, and H2SO4. Various materials characterization techniques have been employed to achieve a comprehensive understanding of film composition and structure at both surface and bulk level, as well as a mechanistic understanding of the film radiation chemistry. Taking advantage of the high energy x-rays used in the XPS experiment, we developed an experiment to dynamically monitor the photochemistry within the

  19. Thermochemical and Mechanistic Studies of Electrocatalytic Hydrogen Production by Cobalt Complexes Containing Pendant Amines

    Energy Technology Data Exchange (ETDEWEB)

    Wiedner, Eric S.; Appel, Aaron M.; DuBois, Daniel L.; Bullock, R. Morris

    2013-12-16

    Two cobalt(tetraphosphine) complexes [Co(PnC-PPh22NPh2)(CH3CN)](BF4)2 with a tetradentate phosphine ligand (PnC-PPh22NPh2 = 1,5-diphenyl-3,7-bis((diphenylphosphino)alkyl)-1,5-diaza-3,7-diphosphacyclooctane; alkyl = (CH2)2, n = 2 (L2); (CH2)3, n = 3 (L3)) have been studied for electrocatalytic hydrogen production using 1:1 [(DMF)H]+:DMF. A turnover frequency of 980 s–1 with an overpotential of 1210 mV was measured for [CoII(L2)(CH3CN)]2+, and a turnover frequency of 980 s–1 with an overpotential of 930 mV was measured for [CoII(L3)(CH3CN)]2+. Addition of water increases the turnover frequency of [CoII(L2)(CH3CN)]2+ to 19,000 s–1. The catalytic wave for each of these complexes occurs at the reduction potential of the corresponding HCoIII complex. Comprehensive thermochemical studies of [CoII(L2)(CH3CN)]2+ and [CoII(L3)(CH3CN)]2+ and species derived from them by addition/removal of protons/electrons were carried out using values measured experimentally and calculated using DFT. Notably, HCoI(L2) and HCoI(L2) were found to be remarkably strong hydride donors, with HCoI(L2) being a better hydride donor than BH4-. Mechanistic studies of these catalysts reveal that H2 formation can occur by protonation of a HCoII intermediate, and that the pendant amines of these complexes facilitate proton delivery to the cobalt center. The rate-limiting step for catalysis is a net intramolecular isomerization of the protonated pendant amine from the non-productive exo-isomer to the productive endo isomer. We thank Dr. Shentan Chen for many helpful discussions. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Computational resources were provided at the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the

  20. Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development

    Science.gov (United States)

    Davila-Velderrain, Jose; Martinez-Garcia, Juan C.; Alvarez-Buylla, Elena R.

    2015-01-01

    Robust temporal and spatial patterns of cell types emerge in the course of normal development in multicellular organisms. The onset of degenerative diseases may result from altered cell fate decisions that give rise to pathological phenotypes. Complex networks of genetic and non-genetic components underlie such normal and altered morphogenetic patterns. Here we focus on the networks of regulatory interactions involved in cell-fate decisions. Such networks modeled as dynamical non-linear systems attain particular stable configurations on gene activity that have been interpreted as cell-fate states. The network structure also restricts the most probable transition patterns among such states. The so-called Epigenetic Landscape (EL), originally proposed by C. H. Waddington, was an early attempt to conceptually explain the emergence of developmental choices as the result of intrinsic constraints (regulatory interactions) shaped during evolution. Thanks to the wealth of molecular genetic and genomic studies, we are now able to postulate gene regulatory networks (GRN) grounded on experimental data, and to derive EL models for specific cases. This, in turn, has motivated several mathematical and computational modeling approaches inspired by the EL concept, that may be useful tools to understand and predict cell-fate decisions and emerging patterns. In order to distinguish between the classical metaphorical EL proposal of Waddington, we refer to the Epigenetic Attractors Landscape (EAL), a proposal that is formally framed in the context of GRNs and dynamical systems theory. In this review we discuss recent EAL modeling strategies, their conceptual basis and their application in studying the emergence of both normal and pathological developmental processes. In addition, we discuss how model predictions can shed light into rational strategies for cell fate regulation, and we point to challenges ahead. PMID:25954305

  1. High-throughput identification of off-targets for the mechanistic study of severe adverse drug reactions induced by analgesics

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Jian-Bo [Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005 (China); Ji, Nan; Pan, Wen; Hong, Ru [State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102 (China); Wang, Hao [Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005 (China); Ji, Zhi-Liang, E-mail: appo@xmu.edu.cn [State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102 (China); Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005 (China)

    2014-01-01

    Drugs may induce adverse drug reactions (ADRs) when they unexpectedly bind to proteins other than their therapeutic targets. Identification of these undesired protein binding partners, called off-targets, can facilitate toxicity assessment in the early stages of drug development. In this study, a computational framework was introduced for the exploration of idiosyncratic mechanisms underlying analgesic-induced severe adverse drug reactions (SADRs). The putative analgesic-target interactions were predicted by performing reverse docking of analgesics or their active metabolites against human/mammal protein structures in a high-throughput manner. Subsequently, bioinformatics analyses were undertaken to identify ADR-associated proteins (ADRAPs) and pathways. Using the pathways and ADRAPs that this analysis identified, the mechanisms of SADRs such as cardiac disorders were explored. For instance, 53 putative ADRAPs and 24 pathways were linked with cardiac disorders, of which 10 ADRAPs were confirmed by previous experiments. Moreover, it was inferred that pathways such as base excision repair, glycolysis/glyconeogenesis, ErbB signaling, calcium signaling, and phosphatidyl inositol signaling likely play pivotal roles in drug-induced cardiac disorders. In conclusion, our framework offers an opportunity to globally understand SADRs at the molecular level, which has been difficult to realize through experiments. It also provides some valuable clues for drug repurposing. - Highlights: • A novel computational framework was developed for mechanistic study of SADRs. • Off-targets of drugs were identified in large scale and in a high-throughput manner. • SADRs like cardiac disorders were systematically explored in molecular networks. • A number of ADR-associated proteins were identified.

  2. Development and Implementation of Mechanistic Terry Turbine Models in RELAP-7 to Simulate RCIC Normal Operation Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Haihua [Idaho National Lab. (INL), Idaho Falls, ID (United States); Zou, Ling [Idaho National Lab. (INL), Idaho Falls, ID (United States); Zhang, Hongbin [Idaho National Lab. (INL), Idaho Falls, ID (United States); O' Brien, James Edward [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-09-01

    As part of the efforts to understand the unexpected “self-regulating” mode of the RCIC (Reactor Core Isolation Cooling) systems in Fukushima accidents and extend BWR RCIC and PWR AFW (Auxiliary Feed Water) operational range and flexibility, mechanistic models for the Terry turbine, based on Sandia’s original work [1], have been developed and implemented in the RELAP-7 code to simulate the RCIC system. In 2016, our effort has been focused on normal working conditions of the RCIC system. More complex off-design conditions will be pursued in later years when more data are available. In the Sandia model, the turbine stator inlet velocity is provided according to a reduced-order model which was obtained from a large number of CFD (computational fluid dynamics) simulations. In this work, we propose an alternative method, using an under-expanded jet model to obtain the velocity and thermodynamic conditions for the turbine stator inlet. The models include both an adiabatic expansion process inside the nozzle and a free expansion process outside of the nozzle to ambient pressure. The combined models are able to predict the steam mass flow rate and supersonic velocity to the Terry turbine bucket entrance, which are the necessary input information for the Terry turbine rotor model. The analytical models for the nozzle were validated with experimental data and benchmarked with CFD simulations. The analytical models generally agree well with the experimental data and CFD simulations. The analytical models are suitable for implementation into a reactor system analysis code or severe accident code as part of mechanistic and dynamical models to understand the RCIC behaviors. The newly developed nozzle models and modified turbine rotor model according to the Sandia’s original work have been implemented into RELAP-7, along with the original Sandia Terry turbine model. A new pump model has also been developed and implemented to couple with the Terry turbine model. An input

  3. Alcohol amination with ammonia catalyzed by an acridine-based ruthenium pincer complex: a mechanistic study.

    Science.gov (United States)

    Ye, Xuan; Plessow, Philipp N; Brinks, Marion K; Schelwies, Mathias; Schaub, Thomas; Rominger, Frank; Paciello, Rocco; Limbach, Michael; Hofmann, Peter

    2014-04-23

    The mechanistic course of the amination of alcohols with ammonia catalyzed by a structurally modified congener of Milstein's well-defined acridine-based PNP-pincer Ru complex has been investigated both experimentally and by DFT calculations. Several key Ru intermediates have been isolated and characterized. The detailed analysis of a series of possible catalytic pathways (e.g., with and without metal-ligand cooperation, inner- and outer-sphere mechanisms) leads us to conclude that the most favorable pathway for this catalyst does not require metal-ligand cooperation.

  4. TIMES-SS - A mechanistic evaluation of an external validation study using reaction chemistry principles

    DEFF Research Database (Denmark)

    Roberts, David W.; Patlewicz, Grace; Dimitrov, Sabcho D.

    2007-01-01

    -skin metabolism relationships through a number of transformations, some of which are underpinned by mechanistic three-dimensional quantitative structure-activity relationships. Here, we describe an external validation exercise that was recently carried out. As part of this exercise, data were generated for 40 new...... for sensitization. Additional testing on a further four chemicals was carried out to explore some of the specific reaction chemistry findings in more detail. Improvements for TIMES-SS, where appropriate, were put forward together with proposals for further research work. TIMES-SS is a promising tool to aid...

  5. Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Trial Calculation. Work Plan

    Energy Technology Data Exchange (ETDEWEB)

    Grabaskas, David [Argonne National Lab. (ANL), Argonne, IL (United States); Bucknor, Matthew [Argonne National Lab. (ANL), Argonne, IL (United States); Jerden, James [Argonne National Lab. (ANL), Argonne, IL (United States); Brunett, Acacia J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2016-02-01

    The overall objective of the SFR Regulatory Technology Development Plan (RTDP) effort is to identify and address potential impediments to the SFR regulatory licensing process. In FY14, an analysis by Argonne identified the development of an SFR-specific MST methodology as an existing licensing gap with high regulatory importance and a potentially long lead-time to closure. This work was followed by an initial examination of the current state-of-knowledge regarding SFR source term development (ANLART-3), which reported several potential gaps. Among these were the potential inadequacies of current computational tools to properly model and assess the transport and retention of radionuclides during a metal fuel pool-type SFR core damage incident. The objective of the current work is to determine the adequacy of existing computational tools, and the associated knowledge database, for the calculation of an SFR MST. To accomplish this task, a trial MST calculation will be performed using available computational tools to establish their limitations with regard to relevant radionuclide release/retention/transport phenomena. The application of existing modeling tools will provide a definitive test to assess their suitability for an SFR MST calculation, while also identifying potential gaps in the current knowledge base and providing insight into open issues regarding regulatory criteria/requirements. The findings of this analysis will assist in determining future research and development needs.

  6. Comparative approaches from empirical to mechanistic simulation modelling in Land Evaluation studies

    Science.gov (United States)

    Manna, P.; Basile, A.; Bonfante, A.; Terribile, F.

    2009-04-01

    The Land Evaluation (LE) comprise the evaluation procedures to asses the attitudes of the land to a generic or specific use (e.g. biomass production). From local to regional and national scale the approach to the land use planning should requires a deep knowledge of the processes that drive the functioning of the soil-plant-atmosphere system. According to the classical approaches the assessment of attitudes is the result of a qualitative comparison between the land/soil physical properties and the land use requirements. These approaches have a quick and inexpensive applicability; however, they are based on empirical and qualitative models with a basic knowledge structure specifically built for a specific landscape and for the specific object of the evaluation (e.g. crop). The outcome from this situation is the huge difficulties in the spatial extrapolation of the LE results and the rigidity of the system. Modern techniques instead, rely on the application of mechanistic and quantitative simulation modelling that allow a dynamic characterisation of the interrelated physical and chemical processes taking place in the soil landscape. Moreover, the insertion of physical based rules in the LE procedure may make it less difficult in terms of both extending spatially the results and changing the object (e.g. crop species, nitrate dynamics, etc.) of the evaluation. On the other side these modern approaches require high quality and quantity of input data that cause a significant increase in costs. In this scenario nowadays the LE expert is asked to choose the best LE methodology considering costs, complexity of the procedure and benefits in handling a specific land evaluation. In this work we performed a forage maize land suitability study by comparing 9 different methods having increasing complexity and costs. The study area, of about 2000 ha, is located in North Italy in the Lodi plain (Po valley). The range of the 9 employed methods ranged from standard LE approaches to

  7. A mechanistic model to study the thermal ecology of a southeastern pacific dominant intertidal mussel and implications for climate change.

    Science.gov (United States)

    Finke, G R; Bozinovic, F; Navarrete, S A

    2009-01-01

    Developing mechanistic models to predict an organism's body temperature facilitates the study of physiological stresses caused by extreme climatic conditions the species might have faced in the past or making predictions about changes to come in the near future. Because the models combine empirical observation of different climatic variables with essential morphological attributes of the species, it is possible to examine specific aspects of predicted climatic changes. Here, we develop a model for the competitively dominant intertidal mussel Perumytilus purpuratus that estimates body temperature on the basis of meteorological and tidal data with an average difference (+/-SE) of 0.410 degrees +/- 0.0315 degrees C in comparison with a field-deployed temperature logger. Modeled body temperatures of P. purpuratus in central Chile regularly exceeded 30 degrees C in summer months, and values as high as 38 degrees C were found. These results suggest that the temperatures reached by mussels in the intertidal zone in central Chile are not sufficiently high to induce significant mortality on adults of this species; however, because body temperatures >40 degrees C can be lethal for this species, sublethal effects on physiological performance warrant further investigation. Body temperatures of mussels increased sigmoidally with increasing tidal height. Body temperatures of individuals from approximately 70% of the tidal range leveled off and did not increase any further with increasing tidal height. Finally, body size played an important role in determining body temperature. A hypothetical 5-cm-long mussel (only 1 cm longer than mussels found in nature) did reach potentially lethal body temperatures, suggesting that the biophysical environment may play a role in limiting the size of this small species.

  8. Developmental theory of aging revisited: focus on causal and mechanistic links between development and senescence.

    Science.gov (United States)

    Walker, Richard F

    2011-08-01

    Senescence violates the most basic tenet of natural selection by causing death rather than individual survival. Thus, current theories favor the concept of antagonistic pleiotropy (AP) to explain how aging emerged in metazoans. Presumably, pleiotropic genes reduce vigor and limit longevity in adults. However, they also promote fitness and reproduction in juveniles, causing them to be selected and retained in the gene pool. The general hypothesis presented herein is a special case of AP that identifies the common cause and mechanism of aging in iteroparous (i.e., capable of reproducing multiple times) animals. It ascribes senescence to unremitting, nonprogrammed change or remodeling forced upon the adult soma by postmaturation expression of developmental gene(s) affecting dynamic transformation of the single-celled conceptus into a complex, multicellular organism. Whereas persistent somatic change is necessary for development to proceed normally, it also has the potential to erode homeostasis in adults after maturation is complete. Thus, developmental inertia is the primary cause of senescence, whereas decay of internal order and integrated function among interdependent systems of the body is the general mechanism by which aging progresses over time. Accordingly, this global pathogenic process creates an environment in which the many recognized, age-associated physiologic and metabolic sequelae can arise as consequences of senescence rather than causes of it. Paradoxically, the genes that promote somatic remodeling essential for development and survival also guarantee aging and death by the same action whose outcomes differ only by the time it is expressed relevant to maturation.

  9. The loss of ecosystem services due to land degradation. Integration of mechanistic and probabilistic models in an Ethiopian case study

    Science.gov (United States)

    Cerretelli, Stefania; Poggio, Laura; Gimona, Alessandro; Peressotti, Alessandro; Black, Helaina

    2017-04-01

    Land and soil degradation are widespread especially in dry and developing countries such as Ethiopia. Land degradation leads to ecosystems services (ESS) degradation, because it causes the depletion and loss of several soil functions. Ethiopia's farmland faces intense degradation due to deforestation, agricultural land expansion, land overexploitation and overgrazing. In this study we modelled the impact of physical factors on ESS degradation, in particular soil erodibility, carbon storage and nutrient retention, in the Ethiopian Great Rift Valley, northwestern of Hawassa. We used models of the Sediment retention/loss, the Nutrient Retention/loss (from the software suite InVEST) and Carbon Storage. To run the models we coupled soil local data (such as soil organic carbon, soil texture) with remote sensing data as input in the parametrization phase, e.g. to derive a land use map, to calculate the aboveground and belowground carbon, the evapotraspiration coefficient and the capacity of vegetation to retain nutrient. We then used spatialised Bayesian Belief Networks (sBBNs) predicting ecosystem services degradation on the basis of the results of the three mechanistic models. The results show i) the importance of mapping of ESS degradation taking into consideration the spatial heterogeneity and the cross-correlations between impacts ii) the fundamental role of remote sensing data in monitoring and modelling in remote, data-poor areas and iii) the important role of spatial BBNs in providing spatially explicit measures of risk and uncertainty. This approach could help decision makers to identify priority areas for intervention in order to reduce land and ecosystem services degradation.

  10. Platinum-catalyzed direct amination of allylic alcohols under mild conditions: ligand and microwave effects, substrate scope, and mechanistic study.

    Science.gov (United States)

    Ohshima, Takashi; Miyamoto, Yoshiki; Ipposhi, Junji; Nakahara, Yasuhito; Utsunomiya, Masaru; Mashima, Kazushi

    2009-10-14

    Transition metal-catalyzed amination of allylic compounds via a pi-allylmetal intermediate is a powerful and useful method for synthesizing allylamines. Direct catalytic substitution of allylic alcohols, which forms water as the sole coproduct, has recently attracted attention for its environmental and economical advantages. Here, we describe the development of a versatile direct catalytic amination of both aryl- and alkyl-substituted allylic alcohols with various amines using Pt-Xantphos and Pt-DPEphos catalyst systems, which allows for the selective synthesis of various monoallylamines, such as the biologically active compounds Naftifine and Flunarizine, in good to high yield without need for an activator. The choice of the ligand was crucial toward achieving high catalytic activity, and we demonstrated that not only the large bite-angle but also the linker oxygen atom of the Xantphos and DPEphos ligands was highly important. In addition, microwave heating dramatically affected the catalyst activity and considerably decreased the reaction time compared with conventional heating. Furthermore, several mechanistic investigations, including (1)H and (31)P{(1)H} NMR studies; isolation and characterization of several catalytic intermediates, Pt(xantphos)Cl(2), Pt(eta(2)-C(3)H(5)OH)(xantphos), etc; confirmation of the structure of [Pt(eta(3)-allyl)(xantphos)]OTf by X-ray crystallographic analysis; and crossover experiments, suggested that formation of the pi-allylplatinum complex through the elimination of water is an irreversible rate-determining step and that the other processes in the catalytic cycle are reversible, even at room temperature.

  11. In Situ Generation of Molybdenum-Based Catalyst for Alkyne Metathesis: Further Developments and Mechanistic Insights

    Directory of Open Access Journals (Sweden)

    Geng Lopez Joaquin

    2016-03-01

    Full Text Available Molybdenum-based catalysts are among the best candidates to achieve alkyne metathesis. They can be either well-defined carbynes, previously synthesized before their use, but also prepared in situ upon using stable molybdenum carbonyl complexes, or high oxidation state molybdenum salts that need a previous alkylation, both type of precursors being “activated” by hydroxyl-containing compounds such as phenols and silanols. This paper is presenting studies made on these systems, directed towards the knowledge of the reaction paths leading to the active species, and in particular to define the essential role of hydroxyl-containing co-catalyst in the formation of the active species, still ill-defined. From an analysis of the byproducts formed during the reaction, as well as of the initial products, reaction paths to access catalytic carbyne species is suggested, where the ligand environment consists of phenoxy (or siloxy groups, typically required and identified to lead to alkyne metathesis in the case of well-defined catalysts.

  12. Pd-catalyzed carbonylative α-arylation of aryl bromides: scope and mechanistic studies.

    Science.gov (United States)

    Nielsen, Dennis U; Lescot, Camille; Gøgsig, Thomas M; Lindhardt, Anders T; Skrydstrup, Troels

    2013-12-23

    Reaction conditions for the three-component synthesis of aryl 1,3-diketones are reported applying the palladium-catalyzed carbonylative α-arylation of ketones with aryl bromides. The optimal conditions were found by using a catalytic system derived from [Pd(dba)2] (dba=dibenzylideneacetone) as the palladium source and 1,3-bis(diphenylphosphino)propane (DPPP) as the bidentate ligand. These transformations were run in the two-chamber reactor, COware, applying only 1.5 equivalents of carbon monoxide generated from the CO-releasing compound, 9-methylfluorene-9-carbonyl chloride (COgen). The methodology proved adaptable to a wide variety of aryl and heteroaryl bromides leading to a diverse range of aryl 1,3-diketones. A mechanistic investigation of this transformation relying on 31P and 13C NMR spectroscopy was undertaken to determine the possible catalytic pathway. Our results revealed that the combination of [Pd(dba)2] and DPPP was only reactive towards 4-bromoanisole in the presence of the sodium enolate of propiophenone suggesting that a [Pd(dppp)(enolate)] anion was initially generated before the oxidative-addition step. Subsequent CO insertion into an [Pd(Ar)(dppp)(enolate)] species provided the 1,3-diketone. These results indicate that a catalytic cycle, different from the classical carbonylation mechanism proposed by Heck, is operating. To investigate the effect of the dba ligand, the Pd0 precursor, [Pd(η3-1-PhC3H4)(η5-C5H5)], was examined. In the presence of DPPP, and in contrast to [Pd(dba)2], its oxidative addition with 4-bromoanisole occurred smoothly providing the [PdBr(Ar)(dppp)] complex. After treatment with CO, the acyl complex [Pd(CO)Br(Ar)(dppp)] was generated, however, its treatment with the sodium enolate led exclusively to the acylated enol in high yield. Nevertheless, the carbonylative α-arylation of 4-bromoanisole with either catalytic or stoichiometric [Pd(η3-1-PhC3H4)(η5-C5H5)] over a short reaction time, led to the 1,3-diketone product

  13. From mechanistic to functional behaviorism.

    Science.gov (United States)

    Moxley, R A

    1992-11-01

    A shift from mechanistic behaviorism to functional behaviorism is presented against the background of two historical traditions, one with an emphasis on form, the other with an emphasis on function. Skinner's work, which made more contributions to a functional behaviorism than to a mechanistic behaviorism, exemplifies this shift. The two traditions and an account of Skinner's development of functional relations are presented in order to show Skinner's contributions to aligning modern behavior analysis with the functional tradition.

  14. A comparative kinetic and mechanistic study between tetrahydrozoline and naphazoline toward photogenerated reactive oxygen species.

    Science.gov (United States)

    Criado, Susana; García, Norman A

    2010-01-01

    Kinetic and mechanistic aspects of the vitamin B2 (riboflavin [Rf])-sensitized photo-oxidation of the imidazoline derivates (IDs) naphazoline (NPZ) and tetrahydrozoline (THZ) were investigated in aqueous solution. The process appears as important on biomedical grounds, considering that the vitamin is endogenously present in humans, and IDs are active components of ocular medicaments of topical application. Under aerobic visible light irradiation, a complex picture of competitive interactions between sensitizer, substrates and dissolved oxygen takes place: the singlet and triplet ((3)Rf*) excited states of Rf are quenched by the IDs: with IDs concentrations ca. 5.0 mM and 0.02 mM Rf, (3)Rf* is quenched by IDs, in a competitive fashion with dissolved ground state oxygen. Additionally, the reactive oxygen species: O(2)((1)Delta(g)), O(2)(*-), HO(*) and H(2)O(2), generated from (3)Rf* and Rf(*-), were detected with the employment of time-resolved methods or specific scavengers. Oxygen uptake experiments indicate that, for NPZ, only H(2)O(2) was involved in the photo-oxidation. In the case of THZ, O(2)(*-), HO(*) and H(2)O(2) were detected, whereas only HO(*) was unambiguously identified as THZ oxidative agents. Upon direct UV light irradiation NPZ and THZ generate O(2)((1)Delta(g)), with quantum yields of 0.2 (literature value, employed as a reference) and 0.08, respectively, in acetonitrile.

  15. Thermal tides and studies to tune the mechanistic tidal model using UARS observations

    Directory of Open Access Journals (Sweden)

    V. A. Yudin

    Full Text Available Monthly simulations of the thermal diurnal and semidiurnal tides are compared to High-Resolution Doppler Imager (HRDI and Wind Imaging Interferometer (WINDII wind and temperature measurements on the Upper-Atmosphere Research Satellite (UARS. There is encouraging agreement between the observations and the linear global mechanistic tidal model results both for the diurnal and semidiurnal components in the equatorial and mid-latitude regions. This gives us the confidence to outline the first steps of an assimilative analysis/interpretation for tides, dissipation, and mean flow using a combination of model results and the global measurements from HRDI and WINDII. The sensitivity of the proposed technique to the initial guess employed to obtain a best fit to the data by tuning model parameters is discussed for the January and March 1993 cases, when the WINDII day and night measurements of the meridional winds between 90 and 110 km are used along with the daytime HRDI measurements. Several examples for the derivation of the tidal variables and decomposition of the measured winds into tidal and mean flow components using this approach are compared with previous tidal estimates and modeling results for the migrating tides. The seasonal cycle of the derived diurnal tidal amplitudes are discussed and compared with radar observation between 80 and 100 km and 40°S and 40°N.

  16. HTGR Mechanistic Source Terms White Paper

    Energy Technology Data Exchange (ETDEWEB)

    Wayne Moe

    2010-07-01

    The primary purposes of this white paper are: (1) to describe the proposed approach for developing event specific mechanistic source terms for HTGR design and licensing, (2) to describe the technology development programs required to validate the design methods used to predict these mechanistic source terms and (3) to obtain agreement from the NRC that, subject to appropriate validation through the technology development program, the approach for developing event specific mechanistic source terms is acceptable

  17. Mechanistic studies on reduced exercise performance and cardiac deconditioning with simulated zero gravity

    Science.gov (United States)

    Tipton, Charles M.

    1991-01-01

    The primary purpose of this research is to study the physiological mechanisms associated with the exercise performance of rats subjected to conditions of simulated weightlessness. A secondary purpose is to study related physiological changes associated with other systems. To facilitate these goals, a rodent suspension model was developed (Overton-Tipton) and a VO2 max testing procedure was perfected. Three methodological developments occurred during this past year deserving of mention. The first was the refinement of the tail suspension model so that (1) the heat dissipation functions of the caudal artery can be better utilized, and (2) the blood flow distribution to the tail would have less external constriction. The second was the development on a one-leg weight bearing model for use in simulated weightlessness studies concerned with change in muscle mass, muscle enzyme activity, and hind limb blood flow. The chemical body composition of 30 rats was determined and used to develop a prediction equation for percent fat using underwater weighing procedures to measure carcass specific gravity and to calculate body density, body fat, and fat free mass.

  18. Application of comparative vibrational spectroscopic and mechanistic studies in analysis of fisetin structure

    Science.gov (United States)

    Dimitrić Marković, Jasmina M.; Marković, Zoran S.; Milenković, Dejan; Jeremić, Svetlana

    2011-12-01

    This paper addresses experimental and theoretical research in fisetin (2-(3,4-dihydroxyphenyl)-3,7-dihydroxychromen-4-one) structure by means of experimental IR and Raman spectroscopies and mechanistic calculations. Density Functional Theory calculations, with M05-2X functional and the 6-311+G (2df, p) basis set implemented in the Gaussian 09 package, are performed with the aim to support molecular structure, vibrational bands' positions and their intensities. Potential energy distribution (PED) values and the description of the largest vibrational contributions to the normal modes are calculated. The most intense bands appear in the 1650-1500 cm -1 wavenumber region. This region involves a combination of the C dbnd O, C2 dbnd C3 and C-C stretching vibrational modes. Most of the bands in the 1500-1000 cm -1 range involve C-C stretching, O-C stretching and in-plane C-C-H, C-O-H, C-C-O and C-C-C bending vibrations of the rings. The region below 1000 cm -1 is characteristic to the combination of in plane C-C-C-H, H-C-C-H, C-C-C-C, C-C-O-C and out of plane O-C-C-C, C-C-O-C, C-C-C-C torsional modes. The Raman spectra of baicalein and quercetin were used for qualitative comparison with fisetin spectrum and verification of band assignments. The applied detailed vibrational spectral analysis and the assignments of the bands, proposed on the basis of fundamentals, reproduced the experimental results with high degree of accuracy.

  19. Cross-reactivities of mammalian MAPKs antibodies in rotifer and copepod: Application in mechanistic studies in aquatic ecotoxicology.

    Science.gov (United States)

    Kang, Hye-Min; Jeong, Chang-Bum; Lee, Young Hwan; Cui, Yan-Hong; Kim, Duck-Hyun; Lee, Min-Chul; Kim, Hui-Su; Han, Jeonghoon; Hwang, Dae-Sik; Lee, Su-Jae; Lee, Jae-Seong

    2016-12-21

    The mitogen-activated protein kinases (MAPKs) family is known to mediate various biological processes in response to diverse environmental pollutants. Although MAPKs are well characterized and studied in vertebrates, in invertebrates the cross-reactivities of MAPKs antibodies were not clearly known in response to environmental pollutants due to limited information of antibody epitopes with material resources for invertebrates. In this paper, we performed phylogenetic analysis of MAPKs genes in the marine rotifer Brachionus koreanus and the copepods Paracyclopina nana and Tigriopus japonicus. Also in rotifer and copepods, several studies of Western blot of MAPK signaling pathways were shown in response to environmental pollutants, including multi-walled carbon nanotubes (MWCNTs), water-accommodated fractions (WAFs) of crude oil, and microplastics. This paper will provide a better understanding of the underlying mechanistic scenario in terms of cross-reactivities of mammalian antibodies in rotifer and copepod. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Effect of some non functional surfactants and electrolytes on the hexavalent chromium reduction by glycerol. A mechanistic study

    Energy Technology Data Exchange (ETDEWEB)

    Basu, A.; Ghosh, S.K.; Saha, R.; Nandi, R.; Saha, B. [Burdwan Univ., WB (India). Dept. of Chemistry; Gosh, T. [A.B.N. Seal College, Coochbehar, WB (India). Dept. of Chemistry

    2011-11-15

    Hexavalent chromium is a widespread environmental contaminant and a known human carcinogen. Kinetics of reduction of hexavalent chromium by bio-molecule glycerol in micellar media have been studied spectrophotometrically. The cytoplasmic reduction of hexavalent chromium to trivalent chromium occurs in micro-heterogeneous systems. In vitro, the micelles are considered to mimic the cellular membranes. The electron transfer processes occurring in the micellar systems is considered as model to obtain insight into the electron transport process prevailing in biological systems. Micellar media is also a probe to establish the mechanistic paths of reduction of hexavalent chromium to trivalent chromium. Effects of electrolytes common to biological system are studied to establish the proposed reaction mechanism strongly. (orig.)

  1. Mechanistic studies of metal ion binding to water-soluble polymers using potentiometry.

    Science.gov (United States)

    Jarvis, N V; Wagener, J M

    1995-02-01

    A method for elucidating metal ion binding mechanisms with water-soluble polymers has been developed in which the polymer is treated as a collection of monomeric units. Data obtained from potentiometric titrations are analysed by the ESTA library of programs and apparent formation constants may be calculated. From this information, predictions may be made as to metal ion separation using complexation-ultrafiltration techniques. The polymer used in this study was Polymin Water-Free and its complexation with Hg(II), Cd(II), Pb(II), Co(II) and Ni(II) was successfully modelled.

  2. Metabolic chiral inversion of stiripentol in the rat. I. Mechanistic studies.

    Science.gov (United States)

    Zhang, K; Tang, C; Rashed, M; Cui, D; Tombret, F; Botte, H; Lepage, F; Levy, R H; Baillie, T A

    1994-01-01

    To study enantioselective aspects of the disposition of stiripentol (STP), a chiral allylic alcohol undergoing development as an antiepileptic drug, a stereoselective synthesis was developed and the configuration of the two enantiomers determined to be (R)-(+) and (S)-(-). Following a single oral dose (300 mg kg-1) of the individual enantiomers to adult male Sprague-Dawley rats, it was found that (R)-STP was transformed extensively to its antipode, whereas little inversion was detected when (S)-STP was administered. Studies on the mechanism of this apparently unidirectional chiral inversion revealed that the phenomenon was dependent on the presence of the side-chain C==C double bond, because the enantiomers of the corresponding saturated alcohol (D2602) did not interconvert in vivo. Experiments with analogs of STP labeled with deuterium or oxygen-18 at the chiral center showed that, whereas the deuterium was retained in vivo, partial loss of the 18O occurred from both enantiomers of the drug. Pretreatment of rats with pentachlorophenol (40 mumol kg-1 i.p.), an inhibitor of sulfation (and possibly other conjugation reactions), led to a marked decrease in the rate of conversion of (R)-STP to its antipode, suggesting that the chiral inversion phenomenon may be mediated, at least in part, by an enantioselective conjugation process.

  3. Mechanistic pharmacokinetic-pharmacodynamic modeling of BACE1 inhibition in monkeys: development of a predictive model for amyloid precursor protein processing.

    Science.gov (United States)

    Liu, Xingrong; Wong, Harvey; Scearce-Levie, Kimberly; Watts, Ryan J; Coraggio, Melis; Shin, Young G; Peng, Kun; Wildsmith, Kristin R; Atwal, Jasvinder K; Mango, Jason; Schauer, Stephen P; Regal, Kelly; Hunt, Kevin W; Thomas, Allen A; Siu, Michael; Lyssikatos, Joseph; Deshmukh, Gauri; Hop, Cornelis E C A

    2013-07-01

    This study was conducted to determine the pharmacokinetics (PK) and pharmacodynamics (PD) of two novel inhibitors of β-site amyloid precursor protein (APP)-cleaving enzyme (BACE1), GNE-629 [(4S,4a'S,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1-methyl-3',4',4a',10a'-tetrahydro-1'H-spiro[imidazole-4,10'-pyrano[4,3-b]chromen]-5(1H)-one] and GNE-892 [(R)-2-amino-1,3',3'-trimethyl-7'-(pyrimidin-5-yl)-3',4'-dihydro-2'H-spiro[imidazole-4,1'-naphthalen]-5(1H)-one], and to develop a PK-PD model to predict in vivo effects based solely on in vitro activity and PK. GNE-629 and GNE-892 concentrations and PD biomarkers including amyloid β (Aβ) in the plasma and cerebrospinal fluid (CSF), and secreted APPβ (sAPPβ) and secreted APPα (sAPPα) in the CSF were measured after a single oral administration of GNE-629 (100 mg/kg) or GNE-892 (30 or 100 mg/kg) in cynomolgus monkeys. A mechanistic PK-PD model was developed to simultaneously characterize the plasma Aβ and CSF Aβ, sAPPα, and sAPPβ using GNE-629 in vivo data. This model was used to predict the in vivo effects of GNE-892 after adjustments based on differences in in vitro cellular activity and PK. The PK-PD model estimated GNE-629 CSF and free plasma IC₅₀ of 0.0033 μM and 0.065 μM, respectively. These differences in CSF and free plasma IC₅₀ suggest that different mechanisms are involved in Aβ formation in these two compartments. The predicted in vivo effects for GNE-892 using the PK-PD model were consistent with the observed data. In conclusion, a PK-PD model was developed to mechanistically describe the effects of BACE1 inhibition on Aβ, sAPPβ, and sAPPα in the CSF, and Aβ in the plasma. This model can be used to prospectively predict in vivo effects of new BACE1 inhibitors using just their in vitro activity and PK data.

  4. Coupling machine learning with mechanistic models to study runoff production and river flow at the hillslope scale

    Science.gov (United States)

    Marçais, J.; Gupta, H. V.; De Dreuzy, J. R.; Troch, P. A. A.

    2016-12-01

    Geomorphological structure and geological heterogeneity of hillslopes are major controls on runoff responses. The diversity of hillslopes (morphological shapes and geological structures) on one hand, and the highly non linear runoff mechanism response on the other hand, make it difficult to transpose what has been learnt at one specific hillslope to another. Therefore, making reliable predictions on runoff appearance or river flow for a given hillslope is a challenge. Applying a classic model calibration (based on inverse problems technique) requires doing it for each specific hillslope and having some data available for calibration. When applied to thousands of cases it cannot always be promoted. Here we propose a novel modeling framework based on coupling process based models with data based approach. First we develop a mechanistic model, based on hillslope storage Boussinesq equations (Troch et al. 2003), able to model non linear runoff responses to rainfall at the hillslope scale. Second we set up a model database, representing thousands of non calibrated simulations. These simulations investigate different hillslope shapes (real ones obtained by analyzing 5m digital elevation model of Brittany and synthetic ones), different hillslope geological structures (i.e. different parametrizations) and different hydrologic forcing terms (i.e. different infiltration chronicles). Then, we use this model library to train a machine learning model on this physically based database. Machine learning model performance is then assessed by a classic validating phase (testing it on new hillslopes and comparing machine learning with mechanistic outputs). Finally we use this machine learning model to learn what are the hillslope properties controlling runoffs. This methodology will be further tested combining synthetic datasets with real ones.

  5. Detailed comparative study and a mechanistic model of resuspension of spherical particles from rough and smooth surfaces

    CERN Document Server

    Shnapp, Ron

    2014-01-01

    Resuspension of solid particles by a tornado-like vortex from surfaces of different roughness is studied using a three-dimensional particle tracking velocimetry (3D-PTV) method. By utilizing the three-dimensional information on particle positions, velocities and accelerations before, during and after the resuspension (lift-off) event, we demonstrate that the resuspension efficiency is significantly higher from the rough surface, and propose a mechanistic model of this peculiar effect. The results indicate that for all Reynolds numbers tested, the resuspension rate, as well as particle velocities and accelerations, are higher over the rough surface, as compared to the smooth counterpart. The results and the model can help to improve modeling and analysis of resuspension rates in engineering and environmental applications.

  6. Synthesis of highly reactive polyisobutylene with FeCl3/ether complexes in hexane; kinetic and mechanistic studies

    KAUST Repository

    Kumar, Rajeev Ananda

    2015-01-01

    The kinetics and mechanism of the polymerization of isobutylene catalyzed by FeCl3·ether complexes in hexane at 0°C were investigated. The polymerization rates increased in the diisopropyl ether< 2-chloroethyl ethyl ether < bis(2-chloroethyl) ether order, attributed to electronic effects. The polymerization rates increased with increasing initiator and catalyst concentrations. The first order plots, however, deviated from the linear suggesting that the cation concentration decreases with time. The previously proposed mechanism is inadequate to explain this finding. The decrease in the polymerization rate with time is explained by the low solubility of the H+ROR′FeCl4 - complexes that precipitate during polymerization. Based on mechanistic studies the revised mechanism now also includes the equilibrium H+ROR′FeCl4 - ⇋ HCl + FeCl3·ROR′.

  7. Mechanistic studies on the reactions of platinum(II) complexes with nitrogen- and sulfur-donor biomolecules.

    Science.gov (United States)

    Bugarčić, Živadin D; Bogojeski, Jovana; Petrović, Biljana; Hochreuther, Stephanie; van Eldik, Rudi

    2012-10-28

    A brief overview of mechanistic studies on the reactions of different Pt(II) complexes with nitrogen- and sulfur-donor biomolecules is presented. The first part describes the results obtained for substitution reactions of mono-functional Pt(II) complexes with different biomolecules, under various experimental conditions (temperature, pH and ionic strength). In addition, an overview of the results obtained for the substitution reactions of bi-functional Pt(II) complexes, analogous to cisplatin, with biomolecules is given. The last part of this report deals with different polynuclear Pt(II) complexes and their substitution behaviour with different biomolecules. The purpose of this perspective is to improve the understanding of the mechanism of action of Pt(II) complexes as potential anti-tumour drugs in the human body.

  8. Viscoelastic Emulsion Improved the Bioaccessibility and Oral Bioavailability of Crystalline Compound: A Mechanistic Study Using in Vitro and in Vivo Models.

    Science.gov (United States)

    Ting, Yuwen; Jiang, Yike; Lan, Yaqi; Xia, Chunxin; Lin, Zhenyu; Rogers, Michael A; Huang, Qingrong

    2015-07-01

    The oral bioavailability of hydrophobic compound is usually limited by the poor aqueous solubility in the gastrointestinal (GI) tract. Various oral formulations were developed to enhance the systemic concentration of such molecules. Moreover, compounds with high melting temperature that appear as insoluble crystals imposed a great challenge to the development of oral vehicle. Polymethoxyflavone, an emerging category of bioactive compounds with potent therapeutic efficacies, were characterized as having a hydrophobic and highly crystalline chemical structure. To enhance the oral dosing efficiency of polymethoxyflavone, a viscoelastic emulsion system with a high static viscosity was developed and optimized using tangeretin, one of the most abundant polymethoxyflavones found in natural sources, as a modeling compound. In the present study, different in vitro and in vivo models were used to mechanistically evaluate the effect of emulsification on oral bioavailability of tangeretin. In vitro lipolysis revealed that emulsified tangeretin was digested and became bioaccessible much faster than unprocessed tangeretin oil suspension. By simulating the entire human GI tract, TNO's gastrointestinal model (TIM-1) is a valuable tool to mechanistically study the effect of emulsification on the digestion events that lead to a better oral bioavailability of tangeretin. TIM-1 result indicated that tangeretin was absorbed in the upper GI tract. Thus, a higher oral bioavailability can be expected if the compound becomes bioaccessible in the intestinal lumen soon after dosing. In vivo pharmacokinetics analysis on mice again confirmed that the oral bioavailability of tangeretin increased 2.3 fold when incorporated in the viscoelastic emulsion than unformulated oil suspension. By using the combination of in vitro and in vivo models introduced in this work, the mechanism that underlie the effect of viscoelastic emulsion on the oral bioavailability of tangeretin was well-elucidated.

  9. Mechanistic study of the inhibitory activity of Geum urbanum extract against α-Synuclein fibrillation

    DEFF Research Database (Denmark)

    Lobbens, Eva Stephanie; Breydo, Leonid; Pedersen, Thomas Skamris;

    2016-01-01

    The presence of Lewy bodies and Lewy neurites is a major pathological hallmark of Parkinson's disease and is hypothesized to be linked to disease development, although this is not yet conclusive. Lewy bodies and Lewy neurites primarily consist of fibrillated α-Synuclein; yet, there is no treatment...... available targeting stabilization of α-Synuclein in its native state. The aim of the present study was to investigate the inhibitory activity of an ethanolic extract of Geum urbanum against α-Synuclein fibrillation and examine the structural changes of α-Synuclein in the presence of the extract. The anti......-fibrillation and anti aggregation activities of the plant extract were monitored by thioflavin T fibrillation assays and size exclusion chromatography, while structural changes were followed by circular dichroism, Fourier transform infrared spectroscopy, intrinsic fluorescence, small angle X-ray scattering and electron...

  10. Incorporation of basic side chains into cryptolepine scaffold: structure-antimalarial activity relationships and mechanistic studies.

    Science.gov (United States)

    Lavrado, João; Cabal, Ghislain G; Prudêncio, Miguel; Mota, Maria M; Gut, Jiri; Rosenthal, Philip J; Díaz, Cecília; Guedes, Rita C; dos Santos, Daniel J V A; Bichenkova, Elena; Douglas, Kenneth T; Moreira, Rui; Paulo, Alexandra

    2011-02-10

    The synthesis of cryptolepine derivatives containing basic side-chains at the C-11 position and their evaluations for antiplasmodial and cytotoxicity properties are reported. Propyl, butyl, and cycloalkyl diamine side chains significantly increased activity against chloroquine-resistant Plasmodium falciparum strains while reducing cytotoxicity when compared with the parent compound. Localization studies inside parasite blood stages by fluorescence microscopy showed that these derivatives accumulate inside the nucleus, indicating that the incorporation of a basic side chain is not sufficient enough to promote selective accumulation in the acidic digestive vacuole of the parasite. Most of the compounds within this series showed the ability to bind to a double-stranded DNA duplex as well to monomeric hematin, suggesting that these are possible targets associated with the observed antimalarial activity. Overall, these novel cryptolepine analogues with substantially improved antiplasmodial activity and selectivity index provide a promising starting point for development of potent and highly selective agents against drug-resistant malaria parasites.

  11. Mechanistic studies on the binding of Acid Yellow 99 on coir pith.

    Science.gov (United States)

    Khan, Md Motiar R; Ray, Manju; Guha, Arun K

    2011-02-01

    The interaction of Acid Yellow 99 (AY 99) with coir pith has been investigated in aqueous medium to understand the mechanism of adsorption and explore the potentiality of this biomass towards controlling pollution resulting from textile dyes. The obtained results establish that one gram of coir pith can adsorb 442.13 mg of AY 99. The adsorption process is found to be a function of pH of the solution, the optimum pH value being 2.0. The process follows Langmuir-Freundlich dual isotherm model. Scanning electron microscopic analysis demonstrates that on dye adsorption the biomass develops uneven and irregular surface. X-ray diffraction study indicates incorporation of the dye into the micropores and macropores of the adsorbent and thereby enhancing its degree of crystallinity. The results of Fourier transform infrared (FTIR) spectroscopy and chemical modification of the functional groups establish that binding of AY 99 on coir pith occurs through electrostatic and complexation reaction.

  12. BIOMAP A Daily Time Step, Mechanistic Model for the Study of Ecosystem Dynamics

    Science.gov (United States)

    Wells, J. R.; Neilson, R. P.; Drapek, R. J.; Pitts, B. S.

    2010-12-01

    BIOMAP simulates competition between two Plant Functional Types (PFT) at any given point in the conterminous U.S. using a time series of daily temperature (mean, minimum, maximum), precipitation, humidity, light and nutrients, with PFT-specific rooting within a multi-layer soil. The model employs a 2-layer canopy biophysics, Farquhar photosynthesis, the Beer-Lambert Law for light attenuation and a mechanistic soil hydrology. In essence, BIOMAP is a re-built version of the biogeochemistry model, BIOME-BGC, into the form of the MAPSS biogeography model. Specific enhancements are: 1) the 2-layer canopy biophysics of Dolman (1993); 2) the unique MAPSS-based hydrology, which incorporates canopy evaporation, snow dynamics, infiltration and saturated and unsaturated percolation with ‘fast’ flow and base flow and a ‘tunable aquifer’ capacity, a metaphor of D’Arcy’s Law; and, 3) a unique MAPSS-based stomatal conductance algorithm, which simultaneously incorporates vapor pressure and soil water potential constraints, based on physiological information and many other improvements. Over small domains the PFTs can be parameterized as individual species to investigate fundamental vs. potential niche theory; while, at more coarse scales the PFTs can be rendered as more general functional groups. Since all of the model processes are intrinsically leaf to plot scale (physiology to PFT competition), it essentially has no ‘intrinsic’ scale and can be implemented on a grid of any size, taking on the characteristics defined by the homogeneous climate of each grid cell. Currently, the model is implemented on the VEMAP 1/2 degree, daily grid over the conterminous U.S. Although both the thermal and water-limited ecotones are dynamic, following climate variability, the PFT distributions remain fixed. Thus, the model is currently being fitted with a ‘reproduction niche’ to allow full dynamic operation as a Dynamic General Vegetation Model (DGVM). While global simulations

  13. Mechanistic Studies for Synthesis of Bis(indolylmethanes: Pd-Catalyzed C–H Activation of Indole–Carboxylic Acids with Benzyl Alcohols in Water

    Directory of Open Access Journals (Sweden)

    Yuusaku Yokoyama

    2013-05-01

    Full Text Available A method for synthesis without protecting groups of bis(indolylmethanes by the (η3-benzylpalladium system generated from a palladium catalyst and benzyl alcohol in water is developed. This domino protocol involves C3–H bond activation/benzylation of indole–carboxylic acids and benzylic C–H functionalization. Mechanistic studies indicate that the (η3-benzylpalladium(II complex, which is formed via oxidative addition of benzyl alcohol 2 to a Pd(0 species, activates the C–H bond at the C3-position of indole 1. Notably, water plays an important role in our catalytic system for sp3 C–O bond activation and stabilization of OH− by hydration for the smooth generation of the activated Pd(II cation species, as well as for nucleophilic attack of indoles to hydrated benzyl alcohols.

  14. Synthesis and mechanistic studies of a novel homoisoflavanone inhibitor of endothelial cell growth.

    Directory of Open Access Journals (Sweden)

    Halesha D Basavarajappa

    Full Text Available Preventing pathological ocular angiogenesis is key to treating retinopathy of prematurity, diabetic retinopathy and age-related macular degeneration. At present there is no small molecule drug on the market to target this process and hence there is a pressing need for developing novel small molecules that can replace or complement the present surgical and biologic therapies for these neovascular eye diseases. Previously, an antiangiogenic homoisoflavanone was isolated from the bulb of a medicinal orchid, Cremastra appendiculata. In this study, we present the synthesis of a novel homoisoflavanone isomer of this compound. Our compound, SH-11052, has antiproliferative activity against human umbilical vein endothelial cells, and also against more ocular disease-relevant human retinal microvascular endothelial cells (HRECs. Tube formation and cell cycle progression of HRECs were inhibited by SH-11052, but the compound did not induce apoptosis at effective concentrations. SH-11052 also decreased TNF-α induced p38 MAPK phosphorylation in these cells. Intriguingly, SH-11052 blocked TNF-α induced IκB-α degradation, and therefore decreased NF-κB nuclear translocation. It decreased the expression of NF-κB target genes and the pro-angiogenic or pro-inflammatory markers VCAM-1, CCL2, IL8, and PTGS2. In addition SH-11052 inhibited VEGF induced activation of Akt but not VEGF receptor autophosphorylation. Based on these results we propose that SH-11052 inhibits inflammation induced angiogenesis by blocking both TNF-α and VEGF mediated pathways, two major pathways involved in pathological angiogenesis. Synthesis of this novel homoisoflavanone opens the door to structure-activity relationship studies of this class of compound and further evaluation of its mechanism and potential to complement existing antiangiogenic drugs.

  15. Oxidative degradation of alternative gasoline oxygenates in aqueous solution by ultrasonic irradiation: Mechanistic study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Duk Kyung, E-mail: dkim@aum.edu [Department of Physical Science, Auburn University Montgomery, Montgomery, AL 36117 (United States); O' Shea, Kevin E., E-mail: osheak@fiu.edu [Department of Chemistry and Biochemistry, Florida International University, University Park, Miami, FL 33199 (United States); Cooper, William J. [Department of Civil and Environmental Engineering, Urban Water Research Center, University of California Irvine, Irvine, CA 92697-2175 (United States)

    2012-07-15

    Widespread pollution has been associated with gasoline oxygenates of branched ethers methyl tert-butyl ether (MTBE), di-isopropyl ether (DIPE), ethyl tert-butyl ether (ETBE), and tert-amyl ether (TAME) which enter groundwater. The contaminated plume develops rapidly and treatment for the removal/destruction of these ethers is difficult when using conventional methods. Degradation of MTBE, with biological methods and advanced oxidation processes, are rather well known; however, fewer studies have been reported for degradation of alternative oxygenates. Degradation of alternative gasoline oxygenates (DIPE, ETBE, and TAME) by ultrasonic irradiation in aqueous oxygen saturation was investigated to elucidate degradation pathways. Detailed degradation mechanisms are proposed for each gasoline oxygenate. The common major degradation pathways are proposed to involve abstraction of {alpha}-hydrogen atoms by hydroxyl radicals generated during ultrasound cavitation and low temperature pyrolytic degradation of ETBE and TAME. Even some of the products from {beta}-H abstraction overlap with those from high temperature pyrolysis, the effect of {beta}-H abstraction was not shown clearly from product study because of possible 1,5 H-transfer inside cavitating bubbles. Formation of hydrogen peroxide and organic peroxides was also determined during sonolysis. These data provide a better understanding of the degradation pathways of gasoline oxygenates by sonolysis in aqueous solutions. The approach may also serve as a model for others interested in the details of sonolysis. - Highlights: Black-Right-Pointing-Pointer Gasoline oxygenates (ETBE, TAME, DIPE) were completely degraded after 6 hours under ultrasonic irradiation in O{sub 2} saturation. Black-Right-Pointing-Pointer The major degradation pathways were proposed to involve abstraction of {alpha}-hydrogen atoms by hydroxyl radicals and low temperature pyrolytic degradation. Black-Right-Pointing-Pointer The effect of {beta

  16. Mechanistic study for immobilization of cysteine-labeled oligopeptides on UV-activated surfaces.

    Science.gov (United States)

    Ong, Lian Hao; Ding, Xiaokang; Yang, Kun-Lin

    2014-10-01

    In this study, we report immobilization of cysteine-labeled oligopeptides on UV activated surfaces decorated with N,N-dimethyl-n-octadecyl-3-aminopropyltrimethoxysilyl chloride (DMOAP). Our result shows that cysteine group, regardless of its position in the oligopeptide, is essential for successful immobilization of oligopeptide on the UV-activated surface. A possible reaction mechanism is nucleophilic addition of thiolates to surface aldehyde groups generated during UV activation. By using this technique, we are able to incorporate anchoring points into oligopeptides through cysteine residues. Furthermore, immobilized oligopeptides on the UV-activated surface is very stable even under harsh washing conditions. Finally, we show that an HPQ-containing oligopeptide can be immobilized on the UV-activated surface, but the final surface density and its ability to bind streptavidin are affected by the position of cysteine and HPQ. An oligopeptide with a cysteine at the N-terminus and a HPQ motif at the C-terminus gives the highest binding signal in the streptavidin-binding assay. This result is potentially useful for the development of functional oligopeptide microarrays for detecting target protein molecules.

  17. Mechanistic study of the toxicity of ionizing radiation in Daphnia magna

    Energy Technology Data Exchange (ETDEWEB)

    Parisot, F.; Alonzo, F. [Institut de Radioprotection et de Surete Nucleaire, IRSN/PRP-ENV/SERIS/LECO, Laboratoire d' Ecotoxicologie des Radionucleides, Cadarache (France); Bourdineaud, J.P. [UMR CNRS 5805 EPOC - OASU Station Marine d' Arcachon Universite Bordeaux 1, Arcachon (France); Poggiale, J.C. [Mediterranean Institute of Oceanography - MIO - UMR 7294 Pytheas Institute - OSU, Aix-Marseille University, Marseille (France)

    2014-07-01

    In the last decade, the ecological impact of ionizing radiation has emerged as a growing scientific concern for ecosystems protection. However, the assessment of potential radiological effects on the environment is hampered by both a gap of available scientific data and a lack in proven methods. Understanding how ionizing radiation affects wildlife at biologically and ecologically relevant scales is a major issue in environmental protection. This issue is one of the objectives of the Strategic Research Agenda (SRA) developed in the framework of the European program STAR (Strategy for Allied Radioecology). In this context, the present PhD project aims to evaluate chronic effects of external Cs-137 gamma radiation at low doses on a representative species of aquatic ecosystems, the cladoceran crustacean Daphnia magna. More precisely, the objectives of this study are to evaluate multi-generational effects of irradiation on: (i) genotoxic effects and their potential consequences on survival, somatic growth and fecundity, (ii) the energy budget and (iii) the population dynamics of Daphnia. An experimental design was developed to expose daphnids to low doses of ionizing radiation ranging from 0,008 to 32 mGy.h{sup -1} across 3 successive generations (75 days). DNA damages were assessed using random amplified polymorphic DNA and real time PCR (RAPD - PCR). Effects on survival, somatic growth and fecundity were monitored for 21-25 days in each generation, from hatching to release of brood 5. Our aim is to: examine a potential correlation between molecular (DNA) damage and effects observed at the individual level (survival, somatic growth and fecundity) across generations and test the suitability of DNA damage as an early indice of future trans-generational effects. As a future perspective, individual and molecular effects data will be analysed using a DEBtox model (Dynamic Energy Budget Applied to Toxicology) in order to identify the metabolic modes of action of ionizing

  18. Mechanistic study of the anticancer effect of Gynostemma pentaphyllum saponins in R6 fibroblast cell

    Institute of Scientific and Technical Information of China (English)

    MoZ; HsaiW

    2002-01-01

    The anticancer effect of Gynostemma pentaphyllum (Gp)saponins was tested.The results indicated that the Gp saponins inhibited ras-induced foci in dosage and time-dependent manners.To facilitate the investigation of the mode of inhibition of Gp in living cells,a green fluorescent protein-ras fusion construct was generated and used to substitute ras in the study.Cells acquired GFP-ras gene grew into green fluorescent foci with striking transforming morphology in the absence of Gp,whereas the GFP-ras transfected cell,in most of cases,remained as single green fluorescent cell with Gp saponins present in the medium.Gp saponins exhibited non-cytotoxic effect on either normal or the transformed R6 cells.However.Gp saponins posted a strong inhibition against the growth of the rastransformed cells that were co-cultivated with normal R6 cells.The level of Raf-1 protein was sharply down-regulated after Gp treatment.Gp treatment can also induce instability of Raf-1,instead of transcriptional inactivation of the protein expression.A cDNA microarray analysis displayed four genes,i.e.β2-microglobulin,GST7-7,gelatinase A and cathepsin L were up-regulated,while three genes:Erk-1,γIGFBP-6,and 14-3-3 zeta were down-regulated upon treatment with Gp saponins.The results were verified by Northern blot analysis.The finding that an anti-cancer effect of a non-toxic drug may be mediated through the surrounding normal cells is conceptually novel and should have a broad implication in the future development of drugs or dietary supplements with cancer prevention function.

  19. Mechanistic study of the inhibitory activity of Geum urbanum extract against α-Synuclein fibrillation

    DEFF Research Database (Denmark)

    Lobbens, Eva Stephanie; Breydo, Leonid; Pedersen, Thomas Skamris

    2016-01-01

    The presence of Lewy bodies and Lewy neurites is a major pathological hallmark of Parkinson's disease and is hypothesized to be linked to disease development, although this is not yet conclusive. Lewy bodies and Lewy neurites primarily consist of fibrillated α-Synuclein; yet, there is no treatmen...

  20. IRIS Toxicological Review of Hexavalent Chromium Part 2: Human, Toxicokinetic, and Mechanistic Studies (Preliminary Assessment Materials)

    Science.gov (United States)

    In August 2014, EPA released the second part of draft literature searches and associated search strategies, evidence tables, and exposure response arrays for Cr(VI) to obtain input from stakeholders and the public prior to developing the draft IRIS assessment. Specifically, EPA w...

  1. CF3CH(ONO)CF3: Synthesis, IR spectrum, and use as OH radical source for kinetic and mechanistic studies

    DEFF Research Database (Denmark)

    Andersen, Mads Peter Sulbæk; Hurley, MD; Ball, JC;

    2003-01-01

    The synthesis, IR spectrum, and first-principles characterization of CF3CH(ONO)CF3 as well as its use as an OH radical source in kinetic and mechanistic studies are reported. CF3CH(ONO)CF3 exists in two conformers corresponding to rotation about the RCO-NO bond. The more prevalent trans conformer...

  2. Mechanistic Study of Magnesium Carbonate Semibatch Reactive Crystallization with Magnesium Hydroxide and CO2

    DEFF Research Database (Denmark)

    Han, B.; Qu, H. Y.; Niemi, H.;

    2014-01-01

    This work investigates semibatch precipitation of magnesium carbonate at ambient temperature and pressure using Mg(OH)(2) and CO2 as starting materials. A thermal analysis method was developed that reflects the dissolution rate of Mg(OH)(2) and the formation of magnesium carbonate. The method...... the liquid and solid phases. A stirring rate of 650 rpm was found to be the optimum speed as the flow rate of CO2 was 1 L/min. Precipitation rate increased with gas flow rate, which indicates that mass transfer of CO2 plays a critical role in this precipitation case. Magnesium carbonate trihydrate...

  3. A mechanistic study on the amidation of esters mediated by sodium formamide.

    Science.gov (United States)

    Ramirez, Antonio; Mudryk, Boguslaw; Rossano, Lucius; Tummala, Srinivas

    2012-01-06

    Kinetic and computational studies on the amidation of esters with mixtures of formamide and sodium methoxide are described. Rate studies are consistent with a fast deprotonation of formamide followed by two reversible acyl transfers affected by solvent participation. MP2 calculations suggest that the first acyl transfer between the ester and sodium formamide is rate-determining. The transition structures leading to the formation and collapse of the first tetrahedral intermediate are calculated to be isoenergetic.

  4. Mechanistic study on demulsification of water-in-diluted bitumen emulsions by ethylcellulose.

    Science.gov (United States)

    Feng, Xianhua; Mussone, Paolo; Gao, Song; Wang, Shengqun; Wu, Shiau-Yin; Masliyah, Jacob H; Xu, Zhenghe

    2010-03-02

    In our previous study, ethylcellulose (EC), an effective, nontoxic, and biodegradable natural polymer, was found effective in dewatering water-in-diluted bitumen emulsions. In this study, the demulsification mechanism of water-in-diluted bitumen emulsions by EC is investigated. In situ experiments using a micropipet apparatus provided direct evidence on both flocculation and coalescence of water droplets in diluted bitumen by EC. The addition of EC was found to decrease naphtha-diluted bitumen-water interfacial tension significantly. At the molecular level, AFM imaging revealed disruption of the continuous interfacial films formed from surface-active components of bitumen by EC. Our study clearly indicates that the demulsification by EC is through both flocculation and coalescence of water droplets, attained by competitive adsorption of EC at the oil-water interface and disruption of the original protective interfacial films formed from the surface-active components of bitumen.

  5. Mechanistic Studies of Hafnium-Pyridyl Amido-Catalyzed 1-Octene Polymerization and Chain Transfer Using Quench-Labeling Methods.

    Science.gov (United States)

    Cueny, Eric S; Johnson, Heather C; Anding, Bernie J; Landis, Clark R

    2017-08-30

    Chromophore quench-labeling applied to 1-octene polymerization as catalyzed by hafnium-pyridyl amido precursors enables quantification of the amount of active catalyst and observation of the molecular weight distribution (MWD) of Hf-bound polymers via UV-GPC analysis. Comparison of the UV-detected MWD with the MWD of the "bulk" (all polymers, from RI-GPC analysis) provides important mechanistic information. The time evolution of the dual-detection GPC data, concentration of active catalyst, and monomer consumption suggests optimal activation conditions for the Hf pre-catalyst in the presence of the activator [Ph3C][B(C6F5)4]. The chromophore quench-labeling agents do not react with the chain-transfer agent ZnEt2 under the reaction conditions. Thus, Hf-bound polymeryls are selectively labeled in the presence of zinc-polymeryls. Quench-labeling studies in the presence of ZnEt2 reveal that ZnEt2 does not influence the rate of propagation at the Hf center, and chain transfer of Hf-bound polymers to ZnEt2 is fast and quasi-irreversible. The quench-label techniques represent a means to study commercial polymerization catalysts that operate with high efficiency at low catalyst concentrations without the need for specialized equipment.

  6. A Mechanistic Study of Hydroboration of 1-Octene with 1,3,2 ...

    African Journals Online (AJOL)

    NJD

    different products, depending on the experimental conditions under which the reactions ..... measure the time intervals between data sets in the NMR spectrometer. ... increasing in steps of 5 °C. For each experiment, the concentra- tions of the ... compounds we conducted a follow-up computational study to rationalize our ...

  7. Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction

    Science.gov (United States)

    Albrecht, Birgit

    2014-01-01

    The Wittig reaction is one of the most useful reactions in organic chemistry. Despite its prominence early in the organic chemistry curriculum, the exact mechanism of this reaction is still under debate, and this controversy is often neglected in the classroom. Introducing a simple computational study of the Wittig reaction illustrates the…

  8. Mechanistic Studies of the Transdermal Iontophoretic Delivery of 5-OH-DPAT In Vitro

    NARCIS (Netherlands)

    Ackaert, Oliver W.; Van Smeden, Jeroen; De Graan, Jeroen; Dijkstra, Durk; Danhof, Meindert; Bouwstra, Joke A.

    2010-01-01

    A characterization and optimization of the in vitro transdermal iontophoretic transport of 5-hydroxy-2-(N,N,-di-n-propylamino)tetralin (5-OH-DPAT) is presented. The utility of acetaminophen as a marker of electroosmotic flow was studied as well. The following parameters of iontophoretic transport of

  9. The reaction of nitromethane with hydrogen and deuterium atoms in the gas phase. A mechanistic study

    DEFF Research Database (Denmark)

    Lund Thomsen, E.; Nielsen, O.J.; Egsgaard, H.

    1993-01-01

    The mechanism of the reaction between H and CH3NO2, has been studied in a discharge flow system using electron paramagnetic resonance and modulated molecular beam mass spectrometry for the detection of reactants and products. Deuterium atoms have, in addition to CD3NO2, been used to support...... the proposed reaction mechanism. The reaction was studied with the atomic reactant in slight excess at 298 K and a total pressure of 2 Torr. Two concurrent reaction channels: (1a) H+CH3NO2-->HONO+.CH3 and (1b) H+CH3NO2-->CH3NO+.OH were observed. The branching ratio, k1a/(k1a+k1b), is 0.7+/-0.2....

  10. Kinetic and mechanistic study of microcystin-LR degradation by nitrous acid under ultraviolet irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Qingwei; Ren, Jing [Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China); Huang, Honghui [Key Laboratory of Fisheries Ecology Environment, Ministry of Agriculture, Guangzhou 510300 (China); Wang, Shoubing [Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China); Wang, Xiangrong, E-mail: xrxrwang@vip.sina.com [Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China); Fan, Zhengqiu, E-mail: zhqfan@fudan.edu.cn [Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China)

    2012-05-15

    Highlights: Black-Right-Pointing-Pointer For the first time, degradation of MC-LR by nitrous acid under UV 365 nm was discovered. Black-Right-Pointing-Pointer The effects of factors on MC-LR degradation were analyzed based on kinetic study. Black-Right-Pointing-Pointer Mass spectrometry was applied for identification of intermediates and products. Black-Right-Pointing-Pointer Special intermediates involved in this study were identified. Black-Right-Pointing-Pointer Degradation mechanisms were proposed according to the results of LC-MS analysis. - Abstract: Degradation of microcystin-LR (MC-LR) in the presence of nitrous acid (HNO{sub 2}) under irradiation of 365 nm ultraviolet (UV) was studied for the first time. The influence of initial conditions including pH value, NaNO{sub 2} concentration, MC-LR concentration and UV intensity were studied. MC-LR was degraded in the presence of HNO{sub 2}; enhanced degradation of MC-LR was observed with 365 nm UV irradiation, caused by the generation of hydroxyl radicals through the photolysis of HNO{sub 2}. The degradation processes of MC-LR could well fit the pseudo-first-order kinetics. Mass spectrometry was applied for identification of the byproducts and the analysis of degradation mechanisms. Major degradation pathways were proposed according to the results of LC-MS analysis. The degradation of MC-LR was initiated via three major pathways: attack of hydroxyl radicals on the conjugated carbon double bonds of Adda, attack of hydroxyl radicals on the benzene ring of Adda, and attack of nitrosonium ion on the benzene ring of Adda.

  11. A mechanistic study of gold nanoparticle radiosensitisation using targeted microbeam irradiation

    Science.gov (United States)

    Ghita, Mihaela; McMahon, Stephen J.; Taggart, Laura E.; Butterworth, Karl T.; Schettino, Giuseppe; Prise, Kevin M.

    2017-01-01

    Gold nanoparticles (GNPs) have been demonstrated as effective radiosensitizing agents in a range of preclinical models using broad field sources of various energies. This study aimed to distinguish between these mechanisms by applying subcellular targeting using a soft X-ray microbeam in combination with GNPs. DNA damage and repair kinetics were determined following nuclear and cytoplasmic irradiation using a soft X-ray (carbon K-shell, 278 eV) microbeam in MDA-MB-231 breast cancer and AG01522 fibroblast cells with and without GNPs. To investigate the mechanism of the GNP induced radiosensitization, GNP-induced mitochondrial depolarisation was quantified by TMRE staining, and levels of DNA damage were compared in cells with depolarised and functional mitochondria. Differential effects were observed following radiation exposure between the two cell lines. These findings were validated 24 hours after removal of GNPs by flow cytometry analysis of mitochondrial depolarisation. This study provides further evidence that GNP radiosensitisation is mediated by mitochondrial function and it is the first report applying a soft X-ray microbeam to study the radiobiological effects of GNPs to enable the separation of physical and biological effects. PMID:28300190

  12. Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway.

    Science.gov (United States)

    Valegård, Karin; Iqbal, Aman; Kershaw, Nadia J; Ivison, David; Généreux, Catherine; Dubus, Alain; Blikstad, Cecilia; Demetriades, Marina; Hopkinson, Richard J; Lloyd, Adrian J; Roper, David I; Schofield, Christopher J; Andersson, Inger; McDonough, Michael A

    2013-08-01

    Structural and biochemical studies of the orf12 gene product (ORF12) from the clavulanic acid (CA) biosynthesis gene cluster are described. Sequence and crystallographic analyses reveal two domains: a C-terminal penicillin-binding protein (PBP)/β-lactamase-type fold with highest structural similarity to the class A β-lactamases fused to an N-terminal domain with a fold similar to steroid isomerases and polyketide cyclases. The C-terminal domain of ORF12 did not show β-lactamase or PBP activity for the substrates tested, but did show low-level esterase activity towards 3'-O-acetyl cephalosporins and a thioester substrate. Mutagenesis studies imply that Ser173, which is present in a conserved SXXK motif, acts as a nucleophile in catalysis, consistent with studies of related esterases, β-lactamases and D-Ala carboxypeptidases. Structures of wild-type ORF12 and of catalytic residue variants were obtained in complex with and in the absence of clavulanic acid. The role of ORF12 in clavulanic acid biosynthesis is unknown, but it may be involved in the epimerization of (3S,5S)-clavaminic acid to (3R,5R)-clavulanic acid.

  13. Mechanistic studies of antibody mediated clearance of tau aggregates using an ex vivo brain slice model

    Directory of Open Access Journals (Sweden)

    Pavan eKrishnamurthy

    2011-10-01

    Full Text Available Recent studies have shown that immunotherapy clears amyloid beta (A plaques and reduces A levels in mouse models of Alzheimer’s disease (AD, as well as in AD patients. Tangle pathology is also relevant for the neurodegeneration in AD, and our studies have shown that active immunization with an AD related phospho-tau peptide reduces aggregated tau within the brain and slows the progression of tauopathy-induced behavioural impairments. Thus, clearance of neurofibrillary tangles and/or their precursors may reduce synaptic and neuronal loss associated with AD and other tauopathies. So far the mechanisms involved in antibody-mediated clearance of tau pathology are yet to be elucidated. In this study we have used a mouse brain slice model to examine the uptake and localization of FITC labeled anti-tau antibodies. Confocal microscopy analysis showed that the FITC labelled anti-tau antibody co-stained with phosphorylated tau, had a perinuclear appearance and co-localised with markers of the endosomal/lysosomal pathway. Additionally, tau and FITC IgG were found together in an enriched lysosome fraction. In summary, antibody-mediated clearance of intracellular tau aggregates appears to occur via the lysosomal pathway.

  14. Mechanistic studies of the transport of peimine in the Caco-2 cell model

    Directory of Open Access Journals (Sweden)

    Lihua Chen

    2016-03-01

    Full Text Available Fritillaria thunbergii Miq. has been widely used in traditional Chinese medicine for its expectorant, antitussive, antiinflammatory and analgesic properties. Moreover, modern pharmacological studies have demonstrated that F. thunbergii Miq. has efficacy in the treatment of leukemia and cancers of the liver and cervix. Although the alkaloid, peimine, is largely responsible for these pharmacological effects, it has very low oral bioavailability. The aim of this study was to investigate the intestinal absorption of peimine in Caco-2 cell monolayers. Having demonstrated that peimine is non-toxic to Caco-2 cells at concentrations <200 μmol/L, the effect of peimine concentration, pH, temperature, efflux transport protein inhibitors and EDTA-Na2 on peimine transport were studied. The results show that peimine transport is concentration-dependent; that at pH 6.0 and 7.4, the Papp(AP-BL of peimine is not significantly different but the Papp(BL-AP is; that both Papp(AP-BL and Papp(BL-AP at 4 °C are significantly higher than their corresponding values at 37 °C; that the P-glycoprotein (P-gp inhibitors, verapamil and cyclosporin A, increase absorption of peimine; and that EDTA-Na2 has no discernible effect. In summary, the results demonstrate that the intestinal absorption of peimine across Caco-2 cell monolayers involves active transport and that peimine is a substrate of P-gp.

  15. A pact with the embryo: Viktor Hamburger, holistic and mechanistic philosophy in the development of neuroembryology, 1927-1955.

    Science.gov (United States)

    Allen, Garland E

    2004-01-01

    Viktor Hamburger was a developmental biologist interested in the ontogenesis of hte vertebrate nervous system. A student of Hans Spemann at Freiburg in the 1920s, Hamburger picked up a holistic view of the embryo that precluded him from treating it in a reductionist way; at the same time, he was committed to a materialist and analytical approach that eschewed any form of vitalism or metaphysics. This paper explores how Hamburger walked this thin line between mechanistic reductionism and metaphysical vitalism in light of his work on the factors influencing growth of neurons into limb buds, and the discovery of nerve growth factor, work carried out with Rita Levi-Montalcini and Stanley Cohen.

  16. Mechanistic Study of the Inhibitory Effect of Kaempferol on Uterine Fibroids In Vitro

    OpenAIRE

    Li, Yanxia; Ding, Zhaoxia; Wu, Chuanzhong

    2016-01-01

    Background This study examined the effect of kaempferol on uterine fibroids in vitro and the underlying mechanism, and investigated the potential of kaempferol as a clinical drug for the treatment of uterine fibroids. Material/Methods Uterine fibroid tissue and surrounding smooth muscle tissue were collected for primary culture. Different concentrations of kaempferol (12 μM, 24 μM, and 48 μM) were used to treat the cells for 24, 48, and 72 hours. Ethanol was used in the control group. A CCK-8...

  17. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

    Science.gov (United States)

    Das, A K; Meuwly, M

    2016-01-01

    Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.

  18. A mechanistic study to increase understanding of titanium dioxide nanoparticles-increased plasma glucose in mice.

    Science.gov (United States)

    Hu, Hailong; Li, Li; Guo, Qian; Jin, Sanli; Zhou, Ying; Oh, Yuri; Feng, Yujie; Wu, Qiong; Gu, Ning

    2016-09-01

    Titanium dioxide nanoparticle (TiO2 NP) is an authorized food additive. Previous studies determined oral administration of TiO2 NPs increases plasma glucose in mice via inducing insulin resistance. An increase in reactive oxygen species (ROS) has been considered the possible mechanism of increasing plasma glucose. However, persistently high plasma glucose is also a mechanism of increasing ROS. This study aims to explore whether TiO2 NPs increase plasma glucose via ROS. We found after oral administration of TiO2 NPs, an increase in ROS preceded an increase in plasma glucose. Subsequently, mice were treated with two antioxidants (resveratrol and vitamin E) at the same time as oral administration of TiO2 NPs. Results showed resveratrol and vitamin E reduced TiO2 NPs-increased ROS. An increase in plasma glucose was also inhibited. Further research showed resveratrol and vitamin E inhibited the secretion of TNF-α and IL-6, and the phosphorylation of JNK and p38 MAPK, resulting in improved insulin resistance. These results suggest TiO2 NPs increased ROS levels, and then ROS activated inflammatory cytokines and phosphokinases, and thus induced insulin resistance, resulting in an increase in plasma glucose. Resveratrol and vitamin E can reduce TiO2 NPs-increased ROS and thereby inhibit an increase in plasma glucose in mice.

  19. A mechanistic study on the destabilization of whole inactivated influenza virus vaccine in gastric environment.

    Directory of Open Access Journals (Sweden)

    Hyo-Jick Choi

    Full Text Available Oral immunization using whole inactivated influenza virus vaccine promises an efficient vaccination strategy. While oral vaccination was hampered by harsh gastric environment, a systematic understanding about vaccine destabilization mechanisms was not performed. Here, we investigated the separate and combined effects of temperature, retention time, pH, and osmotic stress on the stability of influenza vaccine by monitoring the time-dependent morphological change using stopped-flow light scattering. When exposed to osmotic stress, clustering of vaccine particles was enhanced in an acidic medium (pH 2.0 at ≥25°C. Fluorescence spectroscopic studies showed that hyper-osmotic stress at pH 2.0 and 37°C caused a considerable increase in conformational change of antigenic proteins compared to that in acidic iso-osmotic medium. A structural integrity of membrane was destroyed upon exposure to hyper-osmotic stress, leading to irreversible morphological change, as observed by undulation in stopped-flow light scattering intensity and transmission electron microscopy. Consistent with these analyses, hemagglutination activity decreased more significantly with an increasing magnitude of hyper-osmotic stress than in the presence of the hypo- and iso-osmotic stresses. This study shows that the magnitude and direction of the osmotic gradient has a substantial impact on the stability of orally administrated influenza vaccine.

  20. Mechanistic Study of Delamination Fracture in Al-Li Alloy C458 (2099)

    Science.gov (United States)

    Tayon, W. A.; Crooks, R. E.; Domack, M. S.; Wagner, J. A.; Beaudoin, A. J.; McDonald, R. J.

    2009-01-01

    Delamination fracture has limited the use of lightweight Al-Li alloys. In the present study, electron backscattered diffraction (EBSD) methods were used to characterize crack paths in Al-Li alloy C458 (2099). Secondary delamination cracks in fracture toughness samples showed a pronounced tendency for fracture between grain variants of the same deformation texture component. These results were analyzed by EBSD mapping methods and simulated with finite element analyses. Simulation procedures include a description of material anisotropy, local grain orientations, and fracture utilizing crystal plasticity and cohesive zone elements. Taylor factors computed for each grain orientation subjected to normal and shear stresses indicated that grain pairs with the largest Taylor factor differences were adjacent to boundaries that failed by delamination. Examination of matching delamination fracture surface pairs revealed pronounced slip bands in only one of the grains bordering the delamination. These results, along with EBSD studies, plasticity simulations, and Auger electron spectroscopy observations support a hypothesis that delamination fracture occurs due to poor slip accommodation along boundaries between grains with greatly differing plastic response.

  1. A mechanistic study on the simultaneous elimination of soot and nitric oxide from engine exhaust

    KAUST Repository

    Raj, Abhijeet

    2011-04-01

    The non-catalytic interaction between soot and nitric oxide (NO) resulting in their simultaneous elimination was studied on different types of reactive site present on soot. The reaction mechanism proposed previously was extended by including seven new reaction pathways for which the reaction energetics and kinetics were studied using density functional theory and transition state theory. This has led to the calculation of a new rate for the removal of carbon monoxide (CO) from soot. The new pathways have been added to our polycyclic aromatic hydrocarbon (PAH) growth model and used to simulate the NO-soot interaction to form CO, N2 and N2O. The simulation results show satisfactory agreement with experiment for the new CO removal rate. The NO-soot reaction was found to depend strongly on the soot site type and temperature. For a set of temperatures, computed PAH structures were analysed to determine the functional groups responsible for the decrease in the reactivity of soot with NO with increasing reaction time. In isothermal conditions, it was found that as temperature is increased, the number of oxygen atoms remaining on the soot surface decreases, while the number of nitrogen atoms increases for a given reaction time. © 2010 Elsevier Ltd. All rights reserved.

  2. Cationic Pd(II)-catalyzed C–H activation/cross-coupling reactions at room temperature: synthetic and mechanistic studies

    Science.gov (United States)

    Nishikata, Takashi; Abela, Alexander R; Huang, Shenlin

    2016-01-01

    Summary Cationic palladium(II) complexes have been found to be highly reactive towards aromatic C–H activation of arylureas at room temperature. A commercially available catalyst [Pd(MeCN)4](BF4)2 or a nitrile-free cationic palladium(II) complex generated in situ from the reaction of Pd(OAc)2 and HBF4, effectively catalyzes C–H activation/cross-coupling reactions between aryl iodides, arylboronic acids and acrylates under milder conditions than those previously reported. The nature of the directing group was found to be critical for achieving room temperature conditions, with the urea moiety the most effective in promoting facile coupling reactions at an ortho C–H position. This methodology has been utilized in a streamlined and efficient synthesis of boscalid, an agent produced on the kiloton scale annually and used to control a range of plant pathogens in broadacre and horticultural crops. Mechanistic investigations led to a proposed catalytic cycle involving three steps: (1) C–H activation to generate a cationic palladacycle; (2) reaction of the cationic palladacycle with an aryl iodide, arylboronic acid or acrylate, and (3) regeneration of the active cationic palladium catalyst. The reaction between a cationic palladium(II) complex and arylurea allowed the formation and isolation of the corresponding palladacycle intermediate, characterized by X-ray analysis. Roles of various additives in the stepwise process have also been studied. PMID:27340491

  3. Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells.

    Science.gov (United States)

    Cattoglio, Claudia; Zhang, Elisa T; Grubisic, Ivan; Chiba, Kunitoshi; Fong, Yick W; Tjian, Robert

    2015-05-01

    The embryonic stem cell (ESC) state is transcriptionally controlled by OCT4, SOX2, and NANOG with cofactors, chromatin regulators, noncoding RNAs, and other effectors of signaling pathways. Uncovering components of these regulatory circuits and their interplay provides the knowledge base to deploy ESCs and induced pluripotent stem cells. We recently identified the DNA-repair complex xeroderma pigmentosum C (XPC)-RAD23B-CETN2 as a stem cell coactivator (SCC) required for OCT4/SOX2 transcriptional activation. Here we investigate the role of SCC genome-wide in murine ESCs by mapping regions bound by RAD23B and analyzing transcriptional profiles of SCC-depleted ESCs. We establish OCT4 and SOX2 as the primary transcription factors recruiting SCC to regulatory regions of pluripotency genes and identify the XPC subunit as essential for interaction with the two proteins. The present study reveals new mechanistic and functional aspects of SCC transcriptional activity, and thus underscores the diversified functions of this regulatory complex.

  4. Ni adsorption and Ni-Al LDH precipitation in a sandy aquifer: an experimental and mechanistic modeling study.

    Science.gov (United States)

    Regelink, Inge C; Temminghoff, Erwin J M

    2011-03-01

    Mining activities and industries have created nickel (Ni) contaminations in many parts of the world. The objective of this study is to increase our understanding of Ni adsorption and Nickel-Aluminium Layered Double Hydroxide (Ni-Al LDH) precipitation to reduce Ni mobility in a sandy soil aquifer. At pH ≥ 7.2 both adsorption and Ni-Al LDH precipitation occurred. In batch experiments with the sandy soil up to 70% of oxalate-extractable Al was taken up in LDH formation during 56 days. In a long term column experiment 99% of influent Ni was retained at pH 7.5 due to Ni adsorption (≈ 34%) and Ni-Al LDH precipitation (≈ 66%) based on mechanistic reactive transport modeling. The subsequent leaching at pH 6.5 could be largely attributed to desorption. Our results show that even in sandy aquifers with relatively low Al content, Ni-Al LDH precipitation is a promising mechanism to immobilize Ni.

  5. Cationic Pd(II-catalyzed C–H activation/cross-coupling reactions at room temperature: synthetic and mechanistic studies

    Directory of Open Access Journals (Sweden)

    Takashi Nishikata

    2016-05-01

    Full Text Available Cationic palladium(II complexes have been found to be highly reactive towards aromatic C–H activation of arylureas at room temperature. A commercially available catalyst [Pd(MeCN4](BF42 or a nitrile-free cationic palladium(II complex generated in situ from the reaction of Pd(OAc2 and HBF4, effectively catalyzes C–H activation/cross-coupling reactions between aryl iodides, arylboronic acids and acrylates under milder conditions than those previously reported. The nature of the directing group was found to be critical for achieving room temperature conditions, with the urea moiety the most effective in promoting facile coupling reactions at an ortho C–H position. This methodology has been utilized in a streamlined and efficient synthesis of boscalid, an agent produced on the kiloton scale annually and used to control a range of plant pathogens in broadacre and horticultural crops. Mechanistic investigations led to a proposed catalytic cycle involving three steps: (1 C–H activation to generate a cationic palladacycle; (2 reaction of the cationic palladacycle with an aryl iodide, arylboronic acid or acrylate, and (3 regeneration of the active cationic palladium catalyst. The reaction between a cationic palladium(II complex and arylurea allowed the formation and isolation of the corresponding palladacycle intermediate, characterized by X-ray analysis. Roles of various additives in the stepwise process have also been studied.

  6. Mechanistic studies of cyclohexanone monooxygenase: chemical properties of intermediates involved in catalysis.

    Science.gov (United States)

    Sheng, D; Ballou, D P; Massey, V

    2001-09-18

    Cyclohexanone monooxygenase (CHMO), a bacterial flavoenzyme, carries out an oxygen insertion reaction on cyclohexanone to form a seven-membered cyclic product, epsilon-caprolactone. The reaction catalyzed involves the four-electron reduction of O2 at the expense of a two-electron oxidation of NADPH and a two-electron oxidation of cyclohexanone to form epsilon-caprolactone. Previous studies suggested the participation of either a flavin C4a-hydroperoxide or a flavin C4a-peroxide intermediate during the enzymatic catalysis [Ryerson, C. C., Ballou, D. P., and Walsh, C. (1982) Biochemistry 21, 2644-2655]. However, there was no kinetic or spectral evidence to distinguish between these two possibilities. In the present work we used double-mixing stopped-flow techniques to show that the C4a-flavin-oxygen adduct, which is formed rapidly from the reaction of oxygen with reduced enzyme in the presence of NADP, can exist in two states. When the reaction is carried out at pH 7.2, the first intermediate is a flavin C4a-peroxide with maximum absorbance at 366 nm; this intermediate becomes protonated at about 3 s(-1) to form what is believed to be the flavin C4a-hydroperoxide with maximum absorbance at 383 nm. These two intermediates can be interconverted by altering the pH, with a pK(a) of 8.4. Thus, at pH 9.0 the flavin C4a-peroxide persists mainly in the deprotonated form. Further kinetic studies also demonstrated that only the flavin C4a-peroxide intermediate could oxygenate the substrate, cyclohexanone. The requirement in catalysis of the deprotonated flavin C4a-peroxide, a nucleophile, is consistent with a Baeyer-Villiger rearrangement mechanism for the enzymatic oxygenation of cyclohexanone. In the course of these studies, the Kd for cyclohexanone to the C4a-peroxyflavin form of CHMO was determined to be approximately 1 microM. The rate-determining step in catalysis was shown to be the release of NADP from the oxidized enzyme.

  7. Degradation of atrazine in aqueous medium by electrocatalytically generated hydroxyl radicals. A kinetic and mechanistic study.

    Science.gov (United States)

    Balci, Beytul; Oturan, Nihal; Cherrier, Richard; Oturan, Mehmet A

    2009-04-01

    Oxidative degradation of atrazine by hydroxyl radicals (()OH) was studied in aqueous medium. ()OH were formed in situ from electrochemically generating Fenton's reagent by an indirect electrochemical advanced oxidation process. Identification and evolution of seven main aromatic metabolites and four short-chain carboxylic acids were performed by using liquid chromatography analyses. Total organic carbon (TOC) and ionic chromatography were used in order to evaluate the mineralization efficiency of treated aqueous solutions. A high mineralization rate of 82% (never reported until now) was obtained. The oxidative degradation of cyanuric acid, the ultimate product of atrazine degradation, was highlighted for the first time. The absolute rate constant of the reaction between atrazine and hydroxyl radicals was evaluated by competition kinetics method as (2.54+/-0.22)x10(9)M(-1)s(-1). Considering all oxidation reaction intermediates and end products a general reaction sequence for atrazine degradation by hydroxyl radicals was proposed.

  8. Deterioration of ancient Korean paper (Hanji), treated with beeswax: a mechanistic study.

    Science.gov (United States)

    Jeong, Myung-Joon; Bogolitsyna, Anna; Jo, Byoung-Muk; Kang, Kyu-Young; Rosenau, Thomas; Potthast, Antje

    2014-01-30

    In the early 15th century, beeswax coating was applied to some of the cellulosic documents in a futile attempt to better conserve the paper. However, this treatment caused much more severe degradation compared to untreated Hanji. In the current study, the degradation pathway of this beeswax-treated Hanji has been clarified for the first time. The degradation of cellulose was investigated by labeling of oxidized groups combined with gel permeation chromatography, providing profiles of carbonyl and carboxyl groups relative to the molar mass distribution. The beeswax caused purely hydrolytic damage, leading to a decrease in molar mass to about one fifth of the original value. Oxidative degradation, by contrast, did not occur to any significant extent. Hydrolysis was not caused by acids but by microorganism feeding on the beeswax and excreting cellulolytic enzymes, which cause similar cellulose damage patterns. The hydrolytic enzymes were identified by typical metabolites present in the Hanji. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Very Efficient Nucleophilic Aromatic Fluorination Reaction in Molten Salts: A Mechanistic Study

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Sung Woo; Park, Sung Woo; Lee, Sung Yul [Kyung Hee University, Seoul (Korea, Republic of); Lee, Byoung Se; Chi, Dae Yoon [Sogang University, Seoul (Korea, Republic of); Song, Choong Eui [Sungkyunkwan University, Suwon (Korea, Republic of)

    2012-03-15

    We report a quantum chemical study of an extremely efficient nucleophilic aromatic fluorination in molten salts. We describe that the mechanism involves solvent anion interacting with the ion pair nucleophile M{sup +}F{sup -} (M = Na, K, Rb, Cs) to accelerate the reaction. We show that our proposed mechanism may well explain the excellent efficiency of molten salts for S{sub N}Ar reactions, the relative efficacy of the metal cations, and also the observed large difference in rate constants in two molten salts (n-C{sub 4}H{sub 9}){sub 4}N{sup +} CX{sub 3}SO{sub 3}{sup -}, (X=H, F) with slightly different sidechain (-CH{sub 3} vs. -CF{sub 3})

  10. Mechanistic studies of the structure-photostability relationship of organic conjugated polymers

    Science.gov (United States)

    Sanow, Logan Paul

    Organic Conjugated polymers (CPs) are a subject of intense research for their application in organic photovoltaics (OPVs), organic light emitting diodes (OLEDs), solid-state dye lasing, biological imaging and sensing, chemical sensing and remote sensing. CPs are key materials in the quest for more sustainable forms of renewable energy, making electronics more versatile and light weight, and increasing the functionality of everyday materials. For these applications and others that use CPs as the photoactive material, one of their main drawbacks is their susceptibility to photodegradation. Photodegradation occurs when the material is exposed to light leading to irreversible changes in the materials, most often resulting from photoxidation. These irreversible changes cause loss of mechanical, electronic and photophysical characteristics. For practical applications of CP devices, lifetime is as important as device efficiency. The following research is focused on studying the photodegradation mechanisms in various CPs to better understand the relationship between structure and stability, which may lead to the design of CPs which are more intrinsically photostable. To study how dependent photostability is on a polymer's chemical structure and frontier orbital energies, two series of CPs were studied. The first series contained two dicyano-substituted polyphenylenevinylene polymers with different side chains: poly(2,5-dioctyl-1,4-phenylene-1,2-dicyanovinylene) (C8-diCN-PPV) and poly(2,5-bis(decyloxy)-1,4-phenylene-1,2-dicyanovinylene) (RO-diCN-PPV). The second series included a well-known polymer, poly(3-hexylthiophene) (P3HT), and a newly synthesized CP, Poly(3,5-didodecyl-cyclopenta[2,1-b;3,4-b']dithiophen-4-one) (C6-CPDTO). The photodegradation mechanisms were studied through a combination of UV-Vis, PL, FTIR and NMR spectroscopy as well as gel permeation chromatography. There are two main degradation mechanisms that lead to photodegradation of CPs, the radical

  11. Mechanistic study of macrophage activation by LPS stimulation using fluorescence imaging techinques

    Science.gov (United States)

    Lu, Cuixia; Zhou, Feifan; Chen, Wei R.; Xing, Da

    2012-03-01

    Lipopolysaccharide (LPS), a structural component of the outer membrane of gram negative bacteria, has been suggested that stimulates macrophages secrete a wide variety of inflammatory mediators, such as nitric oxide (NO). However, the cellular mechanisms of NO generation in macrophage by LPS stimulation are not well known. In this study, LPS stimulated NO generation in macrophage was determined by measuring fluorescence changes with a NO specific probe DAF-FM DA. Using the fluorescence resonance energy transfer (FRET) techniques, we found an increase of protein kinase C (PKC) activation was dynamically monitored in macrophages treated with LPS. Nuclear factor kappa B (NF-κB) translocated from the cytoplasm to the nucleus in macrophage was measured by confocal laser scanning microscopy. Moreover, the PKC inhibitor GÖ6983 inhibited LPS-stimulated NF-κB activation and NO production. These results indicated that LPS stimulated NF-κB mediated NO production by activating PKC.

  12. Kinetic and Mechanistic Study of the Reduction of Chromium(VI by Lactic Acid

    Directory of Open Access Journals (Sweden)

    Jinhuan Shan

    2008-01-01

    Full Text Available The kinetics and mechanism of the reduction of chromium(VI by lactic acid (Lac in aqueous acidic medium was studied with spectrophotometry in a temperature range of 298.15 K~313.15 K. Under the conditions of the pseudo-first order ([Lac]0≫[Cr(VI]0, the observed rate constant (obs increased with the increase in [Lac] and [H+]. There is no salt effect. Based on the experimental results, a probable reaction mechanism of oxidation was proposed. The rate equation derived from the mechanism could explain all the experimental phenomena. Activation parameters along with rate constant of the rate-determining step have been evaluated.

  13. KINETIC AND MECHANISTIC STUDY OF OXIDATION OF ATENOLOL BY CERIUM (IV IN SULPHURIC ACIDIC MEDIUM

    Directory of Open Access Journals (Sweden)

    Fadnis G Anand

    2012-03-01

    Full Text Available The kinetics of oxidation of antihypertensive drug, atenolol by cerium (IV in sulphuric acidic medium has been studied spectrophotometrically at 360 nm. The reaction between cerium (IV and atenolol in acidic medium has exhibited 2:1 stoichiometry. The order of the reaction with respect to atenolol has been found to be one. The observed pseudo first order rate constants kobs increased with sulphuric acid and hydrogen ion concentrations where as decreased bisulphate ion concentration indicating the formation bisulphato reactive species of cerium (IV in the present reaction. The thermodynamic parameters have been evaluated from the temperature variation kinetic data. A possible mechanism is proposed which has been validated by derived rate law. An attempt has been made to use rate data for kinetic estimation of atenolol.KEYWORDS:

  14. Mechanistic study of fulvic acid assisted propranolol photodegradation in aqueous solution.

    Science.gov (United States)

    Makunina, Maria P; Pozdnyakov, Ivan P; Chen, Yong; Grivin, Vyacheslav P; Bazhin, Nikolay M; Plyusnin, Victor F

    2015-01-01

    Laser flash (355 nm) and stationary (365 nm) photolysis were used to study the mechanisms of propranolol photolysis in the presence of fulvic acid in aqueous solutions. The FA-assisted photodegradation of propranolol was observed using UV-A irradiation (where propranolol is stable). Direct evidence indicated that the photodegradation resulted from the static quenching of the FA triplet state by propranolol via the electron transfer mechanism. The triplet state yield (ϕT≈0.6%) and the T-T absorption coefficient (ɛT(620 nm)≈5×10(4) M(-1) cm(-1)) were estimated for the first time by modeling the yields of the FA triplet state in the presence of propranolol. Thus, fulvic acid is a promising agent for accelerating propranolol photodegradation in aqueous solutions under UV-A light irradiation.

  15. Adsorptive stripping voltammetry of trimethoprim: mechanistic studies and application to the fast determination in pharmaceutical suspensions.

    Science.gov (United States)

    Carapuça, Helena M; Cabral, David J; Rocha, Luciana S

    2005-06-15

    The adsorptive stripping voltammetric behaviour of trimethoprim (TMP) was studied at pH 3.8 and 7.0 by linear-sweep (LS) and cyclic voltammetry at the hanging mercury drop electrode. The charges and surface concentrations of the protonated TMP species were determined at both pH values. Taking advantage of the adsorption features of TMP fast voltammetric techniques (LS and square-wave (SW) voltammetry) were applied to the determination of TMP at the 10(-7)mol dm(-3) concentration level (pH 3.8). For these concentrations the relative standard deviations were cathodic stripping voltammetry originated a very fast and sensitive method for the direct analysis of TMP in pharmaceutical suspensions without any matrix effects or interference from sulfamethoxazole. No sample pre-treatments or solvent extraction procedures were needed. The quantitative results were in agreement with the data supplied by the manufacturer.

  16. Model system-based mechanistic studies of black tea thearubigin formation.

    Science.gov (United States)

    Yassin, Ghada H; Koek, Jan H; Kuhnert, Nikolai

    2015-08-01

    Thearubigins are the most abundant pigments found in black tea, comprising polyphenolic oxidation products, whose composition and chemical nature have remained unresolved until recently. In the course of studying the mechanism of thearubigin formation from green tea flavan-3-ols, a model system, based on electrochemical oxidation of one of the main tea flavan-3-ol substrates, epigallocatechin gallate (EGCG), was employed. Reaction intermediates and products were subsequently analysed using mass spectrometry techniques, allowing for the identification of key intermediates and products. The results provided, for the first time, spectroscopic evidence for the structures of primary oxidation products, and led to the conclusion that oxidation is mainly taking place on the B-ring and the galloyl group, where the oxidized components undergo oxidative coupling for the formation of theaflavins, theasinensins and polyhydroxylated flavan-3-ols, all precursors for thearubigin formation. Furthermore, density functional theory (DFT) calculations were carried out to support key findings.

  17. Inhibition of carbonic anhydrase II by thioxolone: a mechanistic and structural study.

    Science.gov (United States)

    Barrese, Albert A; Genis, Caroli; Fisher, S Zoe; Orwenyo, Jared N; Kumara, Mudalige Thilak; Dutta, Subodh K; Phillips, Eric; Kiddle, James J; Tu, Chingkuang; Silverman, David N; Govindasamy, Lakshmanan; Agbandje-McKenna, Mavis; McKenna, Robert; Tripp, Brian C

    2008-03-11

    This paper examines the functional mechanism of thioxolone, a compound recently identified as a weak inhibitor of human carbonic anhydrase II by Iyer et al. (2006) J. Biomol. Screening 11, 782-791 . Thioxolone lacks sulfonamide, sulfamate, or hydroxamate functional groups that are typically found in therapeutic carbonic anhydrase (CA) inhibitors, such as acetazolamide. Analytical chemistry and biochemical methods were used to investigate the fate of thioxolone upon binding to CA II, including Michaelis-Menten kinetics of 4-nitrophenyl acetate esterase cleavage, liquid chromatography-mass spectrometry (LC-MS), oxygen-18 isotope exchange studies, and X-ray crystallography. Thioxolone is proposed to be a prodrug inhibitor that is cleaved via a CA II zinc-hydroxide mechanism known to catalyze the hydrolysis of esters. When thioxolone binds in the active site of CA II, it is cleaved and forms 4-mercaptobenzene-1,3-diol via the intermediate S-(2,4-thiophenyl)hydrogen thiocarbonate. The esterase cleavage product binds to the zinc active site via the thiol group and is therefore the active CA inhibitor, while the intermediate is located at the rim of the active-site cavity. The time-dependence of this inhibition reaction was investigated in detail. Because this type of prodrug inhibitor mechanism depends on cleavage of ester bonds, this class of inhibitors may have advantages over sulfonamides in determining isozyme specificity. A preliminary structure-activity relationship study with a series of structural analogues of thioxolone yielded similar estimates of inhibition constants for most compounds, although two compounds with bromine groups at the C1 carbon of thioxolone were not inhibitory, suggesting a possible steric effect.

  18. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    Directory of Open Access Journals (Sweden)

    A. W. Birdsall

    2014-08-01

    Full Text Available Recently, methacrylic acid epoxide (MAE has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA: 2-methylglyceric acid (2-MG and a set of oligomers, nitric acid esters and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG, and acids (including MAE and 2-MG in their reactions with MAE were found to be of a similar magnitude, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water; this finding is consistent with previous environmental chamber investigations of the relative humidity-dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  19. Mechanistic study of wettability alteration of oil-wet sandstone surface using different surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Bao-feng, E-mail: hbf370283@163.com; Wang, Ye-fei; Huang, Yong

    2015-03-01

    Graphical abstract: Zeta potential of oil-wet quartz powder treated with different surfactants at different concentrations. - Highlights: • Mechanisms of wettability alteration during surfactant flooding were studied. • Different analytical instruments were used to study sandstone wettability alteration. • Surfactants’ structure plays a great role in wettability alteration of solid surface. • CTAB irreversibly desorbs carboxylic acid from solid surface by ionic interaction. • Cationic surfactant is more effective in wettability alteration of sandstone surface. - Abstract: Different analytical methods including Fourier transform infrared (FTIR), atomic force microscopy (AFM), zeta potential measurements, contact angle measurements and spontaneous imbibition tests were utilized to make clear the mechanism for wettability alteration of oil-wet sandstone surface using different surfactants. Results show that among three types of surfactants including cationic surfactants, anionic surfactants and nonionic surfactants, the cationic surfactant CTAB demonstrates the best effect on the wettability alteration of oil-wet sandstone surface. The positively charged head groups of CTAB molecules and carboxylic acid groups from crude oil could interact to form ion pairs, which could be desorbed from the solid surface and solubilized into the micelle formed by CTAB. Thus, the water-wetness of the solid surface is improved. Nonionic surfactant TX-100 could be adsorbed on oil-wet sandstone surface through hydrogen bonds and hydrophobic interaction to alter the wettability of oil-wet solid surface. The wettability alteration of oil-wet sandstone surface using the anionic surfactant POE(1) is caused by hydrophobic interaction. Due to the electrostatic repulsion between the anionic surfactant and the negatively charged surface, POE(1) shows less effect on the wettability alteration of oil-wet sandstone surface.

  20. Rational and Mechanistic Perspectives on Reinforcement Learning

    Science.gov (United States)

    Chater, Nick

    2009-01-01

    This special issue describes important recent developments in applying reinforcement learning models to capture neural and cognitive function. But reinforcement learning, as a theoretical framework, can apply at two very different levels of description: "mechanistic" and "rational." Reinforcement learning is often viewed in mechanistic terms--as…

  1. A Mechanistic Study of Nucleate Boiling Heat Transfer Under Microgravity Conditions

    Science.gov (United States)

    Dhir, V. K.; Hasan, M. M.

    2000-01-01

    Experimental studies of growth and detachment processes of a single bubble and multiple bubbles formed on a heated surface have been conducted in the parabola flights of KC-135 aircraft. Distilled water and PF5060 were used as the test liquids. A micro-fabricated test surface was designed and built. Artificial cavities of diameters 10 microns, 7 microns and 4 microns were made on a thin polished Silicon wafer that was electrically heated by a number of small heating elements on the back side in order to control the surface superheat. Bubble growth period, bubble size and shape from nucleation to departure were measured under subcooled and saturation conditions. Significantly larger bubble departure diameters and bubble growth periods than those at earth normal gravity were observed. Bubble departure diameters as large as 20 mm for water and 6 mm for PF5060 were observed as opposed to about 3 mm for water and less than 1 mm for PF5060 at earth normal gravity respectively. It is found that the bubble departure diameter can be approximately related to the gravity level through the relation D(sub d) proportional 1/g(exp 1/2). For water,the effect of wall superheat and liquid subcooling on bubble departure diameter is found to be small.The growth periods are found to be very sensitive to liquid subcooling at a given wall superheat. However,the preliminary results of single bubble dynamics using PF5060 showed that the departure diameter increases when wall superheat is elevated at the same gravity and subcooling. Growth period of single bubbles in water has been found to vary as t(sub g) proportional g(exp -.93). For water, when the magnitude of horizontal gravitational components was comparable to that of gravity normal to the surface, single bubbles slid along the heater surface and departed with smaller diameter at the same gravity level in the direction normal to the surface. For PF5060, even a very small horizontal gravitational component caused the sliding of

  2. Structural and Mechanistic Studies on Klebsiella pneumoniae 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline Decarboxylase

    Energy Technology Data Exchange (ETDEWEB)

    French, Jarrod B.; Ealick, Steven E. (Cornell)

    2010-11-12

    The stereospecific oxidative degradation of uric acid to (S)-allantoin was recently shown to proceed via three enzymatic steps. The final conversion is a decarboxylation of the unstable intermediate 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and is catalyzed by OHCU decarboxylase. Here we present the structures of Klebsiella pneumoniae OHCU decarboxylase in unliganded form and with bound allantoin. These structures provide evidence that ligand binding organizes the active site residues for catalysis. Modeling of the substrate and intermediates provides additional support for this hypothesis. In addition we characterize the steady state kinetics of this enzyme and report the first OHCU decarboxylase inhibitor, allopurinol, a structural isomer of hypoxanthine. This molecule is a competitive inhibitor of K. pneumoniae OHCU decarboxylase with a K{sub i} of 30 {+-} 2 {micro}m. Circular dichroism measurements confirm structural observations that this inhibitor disrupts the necessary organization of the active site. Our structural and biochemical studies also provide further insights into the mechanism of catalysis of OHCU decarboxylation.

  3. Mechanistic Studies of Anti-Hyperpigmentary Compounds: Elucidating Their Inhibitory and Regulatory Actions

    Directory of Open Access Journals (Sweden)

    Rosanna Y. Y. Lam

    2014-08-01

    Full Text Available Searching for depigmenting agents from natural sources has become a new direction in the cosmetic industry as natural products are generally perceived as relatively safer. In our previous study, selected Chinese medicines traditionally used to treat hyperpigmentation were tested for anti-hyperpigmentary effects using a melan-a cell culture model. Among the tested chemical compounds, 4-ethylresorcinol, 4-ethylphenol and 1-tetradecanol were found to possess hypopigmentary effects. Western blot analysis, reverse transcriptase polymerase chain reaction (RT-PCR, cyclic adenosine monophosphate (cAMP assay, protein kinase A (PKA activity assay, tyrosinase inhibition assay and lipid peroxidation inhibition assay were performed to reveal the underlying cellular and molecular mechanisms of the hypopigmentary effects. 4-Ethylresorcinol and 4-ethylphenol attenuated mRNA and protein expression of tyrosinase-related protein (TRP-2, and possessed antioxidative effect by inhibiting lipid peroxidation. 1-Tetradecanol was able to attenuate protein expression of tyrosinase. The hypopigmentary actions of 4-ethylresorcinol, 4-ethylphenol and 1-tetradecanol were associated with regulating downstream proteins along the PKA pathway. 4-Ethylresorcinol was more effective in inhibiting melanin synthesis when compared to 4-ethylphenol and 1-tetradecanol.

  4. Mechanistic study on the replacement reaction between silver nanostructures and chloroauric acid in aqueous medium.

    Science.gov (United States)

    Sun, Yugang; Xia, Younan

    2004-03-31

    The replacement reaction between silver nanostructures and an aqueous HAuCl(4) solution has recently been demonstrated as a versatile method for generating metal nanostructures with hollow interiors. Here we describe the results of a systematic study detailing the morphological, structural, compositional, and spectral changes involved in such a heterogeneous reaction on the nanoscale. Two distinctive steps have been resolved through a combination of microscopic and spectroscopic methods. In the first step, silver nanostructure (i.e., the template) is dissolved to generate gold atoms that are deposited epitaxially on the surface of each template. Silver atoms also diffuse into the gold shell (or sheath) to form a seamless, hollow nanostructure with its wall made of Au-Ag alloys. The second step involves dealloying, a process that selectively removes silver atoms from the alloyed wall, induces morphological reconstruction, and finally leads to the formation of pinholes in the walls. Reaction temperature was found to play an important role in the replacement reaction because the solubility constant of AgCl and the diffusion coefficients of Ag and Au atoms were both strongly dependent on this parameter. This work has enabled us to prepare metal nanostructures with controllable geometric shapes and structures, and thus optical properties (for example, the surface plasmon resonance peaks could be readily shifted from 500 to 1200 nm by controlling the ratio between Ag and HAuCl(4)).

  5. Mechanistic Study of the Inhibitory Effect of Kaempferol on Uterine Fibroids In Vitro.

    Science.gov (United States)

    Li, Yanxia; Ding, Zhaoxia; Wu, Chuanzhong

    2016-12-08

    BACKGROUND This study examined the effect of kaempferol on uterine fibroids in vitro and the underlying mechanism, and investigated the potential of kaempferol as a clinical drug for the treatment of uterine fibroids. MATERIAL AND METHODS Uterine fibroid tissue and surrounding smooth muscle tissue were collected for primary culture. Different concentrations of kaempferol (12 μM, 24 μM, and 48 μM) were used to treat the cells for 24, 48, and 72 hours. Ethanol was used in the control group. A CCK-8 colorimetric assay was used to detect cell proliferation. Real-time PCR and immunoblot were used to detect estrogen receptor (ER), insulin-like growth factor-1 (IGF-1), and vascular endothelial growth factor (VEGF) levels in mRNA and protein. RESULTS The differences in proliferation at different time points and concentrations of kaempferol were statistically significant. The inhibitory effect of kaempferol on mRNA levels of ER and IGF, and protein levels of ER, VEGF, and IGF-1 were positively correlated with kaempferol concentration. Changes in kaempferol concentration showed no effect on VEGF mRNA expression. Treatment with kaempferol significantly lowered myocardin levels in uterine fibroid tissue compared to normal uterine smooth muscle (PKaempferol might be used for clinical treatment of uterine fibroids due to its inhibitory effect on the proliferation of uterine fibroids cells.

  6. Mechanistic study of ozonation of p-nitrophenol in aqueous solution

    Institute of Scientific and Technical Information of China (English)

    SHI Hui-xiang; XU Xian-wen; XU Xin-hua; WANG Da-hui; WANG Qi-da

    2005-01-01

    Ozonlysis in the treatment of p-nitrophenol solution was studied in this paper. The results indicated that the decomposition of pnitrophenol was accelerated as the gas flow rate or pH value increased. When gaseous ozone concentration was 20.11 mg/L and pH was 3, after 24 min reaction, the removal rate of p-nitrophenol reached 73.04%, 86. 11%, 91.71 % and 95 % at the gas flow rate of 32, 40, 48and 56 ml/min respectively. And when pH was 3, 4, 5, 6, the decomposition rate was 66.38%, 82.09%, 90.46%, 97.50% after a 20min reaction respectively. It was mainly O3 molecule that took part in the decomposition when pH was 3. The main intermediates during the decomposition include catechol, o-benzoquinone, hydroquinone, p-benzoquinone, phenol, fumaric acid, maleic acid, oxalic acid and formic acid. The decomposition mechanism of p-nitrophenol was also discussed.

  7. Enhanced oral absorption of insulin-loaded liposomes containing bile salts: a mechanistic study.

    Science.gov (United States)

    Niu, Mengmeng; Tan, Ya'nan; Guan, Peipei; Hovgaard, Lars; Lu, Yi; Qi, Jianping; Lian, Ruyue; Li, Xiaoyang; Wu, Wei

    2014-01-01

    Liposomes containing bile salts (BS-liposomes) significantly enhanced the oral bioavailability of insulin (rhINS). However, the underlying absorption mechanisms have not been well understood yet. In this study, the transiting fate of the liposomes was first investigated using fluorescent imaging tools to confirm the effect of enhanced gastrointestinal stability. In order to obtain evidence of enhanced transcellular permeation, the interaction between BS-liposomes and the biomembrane was investigated in Caco-2 cell lines. BS-liposomes were found to be more stable in the gastrointestinal tract by showing prolonged residence time in comparison with conventional liposomes. BS-liposomes were significantly more effective for cellular uptake and transport of rhINS; and this effect was found to be size- and concentration-dependent. A good linear correlation was observed between the concentration of the liposomes and uptake/transport of rhINS. Confocal laser scanning microscopy visualization further validated the transcellular transit of BS-liposomes. The BS-liposomes showed little effect on cytotoxicity and did not induce apoptosis within 24h investigation. It was concluded that BS-liposomes showed improved in vivo residence time and enhanced permeation across the biomemebranes. Mechanisms of trans-enterocytic internalization could be proposed as an interpretation for enhanced absorption of insulin-loaded liposomes.

  8. Mechanistic Study of Silver Nanoparticle's Synthesis by Dragon's Blood Resin Ethanol Extract and Antiradiation Activity.

    Science.gov (United States)

    Hasan, Murtaza; Iqbal, Javed; Awan, Umer; Saeed, Yasmeen; Ranran, Yuan; Liang, Yanli; Dai, Rongji; Deng, Yulin

    2015-02-01

    Biological synthesis of nanoparticles is best way to avoid exposure of hazardous materials as compared to chemical manufacturing process which is a severe threat not only to biodiversity but also to environment. In present study, we reported a novel method of finding antiradiation compounds by bioreducing mechanism of silver nanoparticles formation using 50% ethanol extract of Dragons blood, a famous Chinese herbal plant. Color change during silver nanoparticles synthesis was observed and it was confirmed by ultra violet (UV) visible spectroscopy at wave length at 430 nm after 30 min of reaction at 60 °C. Well dispersed round shaped silver nanoparticles with approximate size (4 nm to 50 nm) were measured by TEM and particle size analyser. Capping of biomolecules on Ag nanoparticles was characterized by FTIR spectra. HPLC analysis was carried out to find active compounds in the extract. Furthermore, antiradiation activity of this extract was tested by MTT assay in vitro after incubating the SH-SY5Y cells for 24 h at 37 °C. The results indicate that presence of active compounds in plant extract not only involves in bioreduction process but also shows response against radiation. The dual role of plant extract as green synthesis of nanoparticles and exhibit activity against radiation which gives a new way of fishing out active compounds from complex herbal plants.

  9. Mechanistic Study of Adsorption of Acid Orange-7 over Aluminum Oxide Nanoparticles

    Directory of Open Access Journals (Sweden)

    Ekta Khosla

    2013-01-01

    Full Text Available The adsorption behavior of acid orange-7 (AO-7 on aluminum oxide nanoparticles (ANP generated by sol-gel method has been investigated to understand the physicochemical process involved and to explore the potential use of nano particles in textile effluent treatment and management. The results revealed that ANP can remove AO-7 dye up to 97.6 mg/g at 303 K. The adsorption process is found to be pH dependent and the optimum pH obtained is 2.0. The equilibrium was established in 1 h. Langmuir, Freundlich, and Temkin Isotherm models were applied on the system. Scanning electron microscopic analysis reveals eye-catching nanoporous morphology of the material. The results of FTIR spectroscopy reveal that the process is electrostatic complexation mechanism driven. XRD studies revealed nanocrystalline structure of ANP. BET surface area measurement suggests high pore volume and surface area of adsorbent. The kinetic measurements suggest pseudo-second-order kinetic processes. The thermodynamic measurements suggest that all processes are endothermic accompanied with negative ΔG° and positive ΔS°, ΔH°.

  10. A kinetic and mechanistic study into the formation of the Cu-Cr layered double hydroxide.

    Science.gov (United States)

    Williams, Gareth R; Clout, Alexander; Burley, Jonathan C

    2013-06-14

    The formation of the layered double hydroxide [Cu2Cr(OH)6]Cl·yH2O from the reaction between CuO and aqueous CrCl3·6H2O was explored using synchrotron X-ray diffraction and ex situ analyses. The use of hard X-rays permitted time-resolved in situ studies to be performed as the reaction proceeded under a range of conditions. Additional information was obtained from ex situ experiments in which aliquots of the reaction mixture were removed, quenched, and subsequently analysed by laboratory X-ray diffraction, IR, UV-visible, and atomic emission spectroscopies. On the basis of these data, it is proposed that the reaction involves three steps. First, the solid CuO starting material is hydrolysed to give Cu(OH)2 chains, releasing Cu(2+) ions into solution. The Cu hydroxide chains subsequently condense with aqueous Cr(3+) species, Cl(-) ions and water molecules to give a hydrated form of the LDH. This material then extrudes some water to form a phase with a reduced interlayer spacing.

  11. Mechanistic studies of sesquiterpene cyclases based on their carbon isotope ratios at natural abundance.

    Science.gov (United States)

    Tan, Wenhua; Bartram, Stefan; Boland, Wilhelm

    2017-01-03

    During the process of terpene biosynthesis, C-C bond breaking and forming steps are subjected to kinetic carbon isotope effects, leading to distinct carbon isotopic signatures of the products. Accordingly, carbon isotopic signatures could be used to reveal the 'biosynthetic history' of the produced terpenoids. Five known sesquiterpene cyclases, regulating three different pathways, representing simple to complex biosynthetic sequences, were heterologously expressed and used for in vitro assays with farnesyl diphosphate as substrate. Compound specific isotope ratio mass spectrometry measurements of the enzyme substrate farnesyl diphosphate (FDP) and the products of all the five cyclases were performed. The calculated δ(13) C value for FDP, based on δ(13) C values and relative amounts of the products, was identical with its measured δ(13) C value, confirming the reliability of the approach and the precision of measurements. The different carbon isotope ratios of the products reflect the complexity of their structure and are correlated with the frequency of carbon-carbon bond forming and breaking steps on their individual biosynthetic pathways. Thus, the analysis of carbon isotopic signatures of terpenes at natural abundance can be used as a powerful tool in elucidation of associated biosynthetic mechanisms of terpene synthases and in future in vivo studies even without 'touching' the plant. © 2017 John Wiley & Sons Ltd.

  12. Concave Cu-Pd bimetallic nanocrystals: Ligand-based Co-reduction and mechanistic study

    Institute of Scientific and Technical Information of China (English)

    Lan Zhang[1; Hongyang Su[1; Mei Sun[1; Youcheng Wang[1; Wenlong Wu[1; Taekyung Yu[2; Jie Zeng[1

    2015-01-01

    The synthesis of highly uniform alloy nanocrystals with a concave feature is desirable for applications in catalysis but is an arduous task. This article proposes an initiative protocol for the fabrication of novel Cu-Pd alloy nanocrystals, wherein the volume of decylamine (DA) in the reaction system was found to greatly influence the formation of different morphologies, including the tetrahedron (TH), concave tetrahedron (CTH), rhombohedral-tetrapod (RTP), and tetrapod (TP). The alloy structure of the products arises from the coordination interaction between the DA and metal ions, which affects the reduction potential of Cu and Pd species, and thus yields co-reduction. Other reaction parameters, such as the type of ligand, amount of reductant, and temperature, were also altered to study the growth mechanism, yielding consistent conclusions in the diffusion-controlled regime. As a catalyst, 48-nm Cu-Pd concave tetrahedral nanocrystals were highly active for the hydrogenation of 3-nitrostyrene and exhibited 〉99.9% chemoselectivity to C=C instead of-NO2.

  13. Kinetics, thermodynamics and mechanistic studies of carbofuran removal using biochars from tea waste and rice husks.

    Science.gov (United States)

    Vithanage, Meththika; Mayakaduwa, S S; Herath, Indika; Ok, Yong Sik; Mohan, Dinesh

    2016-05-01

    This study reports the thermodynamic application and non-linear kinetic models in order to postulate the mechanisms and compare the carbofuran adsorption behavior onto rice husk and tea waste derived biochars. Locally available rice husk and infused tea waste biochars were produced at 700 °C. Biochars were characterized by using proximate, ultimate and surface characterization methods. Batch experiments were conducted at 25, 35, and 45 °C for a series of carbofuran solutions ranging from 5 to 100 mg L(-1) with a biochar dose of 1 g L(-1) at pH 5.0 with acetate buffer. Molar O/C ratios indicated that rice husk biochar (RHBC700) is more hydrophilic than tea waste biochar (TWBC700). Negative ΔG (Gibbs free energy change) values indicated the feasibility of carbofuran adsorption on biochar. Increasing ΔG values with the rise in temperature indicated high favorability at higher temperatures for both RHBC and TWBC. Enthalpy values suggested the involvement of physisorption type interactions. Kinetic data modeling exhibited contribution of both physisorption, via pore diffusion, π*-π electron donor-acceptor interaction, H-bonding, and van der Waals dispersion forces and chemisorption via chemical bonding with phenolic, and amine groups. Equilibrium adsorption capacities of RHBC and TWBC determined by pseudo second order kinetic model were 25.2 and 10.2 mg g(-1), respectively.

  14. Removal of Chromium from Aqueous Solution Using Modified Pomegranate Peel:Mechanistic and Thermodynamic Studies

    Directory of Open Access Journals (Sweden)

    Tariq S. Najim

    2009-01-01

    Full Text Available Modified pomegranate peel (MPGP and formaldehyde modified pomegranate peel (FMPGP were prepared and used as adsorbent for removal of Cr(VI ions from aqueous solution using batch process. The temperature variation study of adsorption on both adsorbents revealed that the adsorption process is endothermic, from the positive values of ∆H˚. These values lie in the range of physisorption. The negative values of ∆G˚ show the adsorption is favorable and spontaneous. On the other hand, these negative values increases with increase in temperature on both adsorbents, which indicate that the adsorption is preferable at higher temperatures. ∆S˚ values showed that the process is accompanied by increase in disorder and randomness at the solid solution interface due to the reorientation of water molecules and Cr(VI ions around the adsorbent surface. The endothermic nature of the adsorption was also confirmed from the positive values of activation energy, Ea, the low values of Ea confirm the physisorption mechanism of adsorption. The sticking probability, S*, of Cr(VI ion on surface of both adsorbents showed that the adsorption is preferable due to low values of S* (0< S* < 1 , but S* values are lower for FMPGP indicating that the adsorption on FMPGP is more preferable .

  15. Kinetics and mechanistic study of competitive inhibition of thymidine phosphorylase by 5-fluoruracil derivatives.

    Science.gov (United States)

    Petaccia, Manuela; Gentili, Patrizia; Bešker, Neva; D'Abramo, Marco; Giansanti, Luisa; Leonelli, Francesca; La Bella, Angela; Gradella Villalva, Denise; Mancini, Giovanna

    2016-04-01

    In a previous investigation, cationic liposomes formulated with new 5-FU derivatives, differing for the length of the polyoxyethylenic spacer that links the N(3) position of 5-FU to an alkyl chain of 12 carbon atoms, showed a higher cytotoxicity compared to free 5-FU, the cytotoxic effect being directly related to the length of the spacer. To better understand the correlation of the spacer length with toxicity, we carried out initial rate studies to determine inhibition, equilibrium and kinetic constants (KI, KM, kcat), and get inside inhibition activity of the 5-FU derivatives and their mechanism of action, a crucial information to design structural variations for improving the anticancer activity. The experimental investigation was supported by docking simulations based on the X-ray structure of thymidine phosphorylase (TP) from Escherichia coli complexed with 3'-azido-2'-fluoro-dideoxyuridin. Theoretical and experimental results showed that all the derivatives exert the same inhibition activity of 5-FU either as monomer and when embedded in lipid bilayer.

  16. Mechanistic study of carvacrol processing and stabilization as glassy solid solution and microcapsule.

    Science.gov (United States)

    Tackenberg, Markus W; Geisthövel, Carola; Marmann, Andreas; Schuchmann, Heike P; Kleinebudde, Peter; Thommes, Markus

    2015-01-30

    Essential oils and other liquid active pharmaceutical ingredients (APIs) are frequently microencapsulated to improve shelf life, handling, and for tailoring release. A glassy solid solution (GSS), a single-phase system, where the excipient is plasticized by the API, could be an alternative formulation system. Thus this study focuses on the investigation of two formulation strategies using carvacrol as a model compound, namely a microcapsule (MC) and a glassy solid solution (GSS). Applying the solubility parameter approach, polyvinylpyrrolidone (PVP) was chosen as a suitable matrix material for a GSS system, whereas maltodextrin and sucrose served as excipients for a microcapsule (MC) system. Differential scanning calorimetry (DSC) measurements of the excipients' glass transition temperatures and the melting point of carvacrol verified plasticizing properties of carvacrol on PVP. Batch mixing processes, as preliminary experiments for future extrusion processes, were performed to prepare GSSs and MCs with various amounts of carvacrol, followed by crushing and sieving. Maximally 4.5% carvacrol was encapsulated in the carbohydrate material, whereas up to 16.3% were stabilized as GSS, which is an outstanding amount. However, grinding of the samples led to a loss of up to 30% of carvacrol.

  17. Peroxyoxalate-chemiluminescence of Tinopal CBS as a commercially important optical brightener: Mechanistic study and quantification

    Energy Technology Data Exchange (ETDEWEB)

    Shamsipur, Mojtaba, E-mail: mshamsipur@yahoo.co [Department of Chemistry, Razi University, Kermanshah (Iran, Islamic Republic of); Zargoosh, Kiomars [Department of Chemistry, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Javad Chaichi, Mohammad; Tajbakhsh, Mahmood; Parach, Ali [Department of Chemistry, Mazandaran University, Babolsar (Iran, Islamic Republic of)

    2010-05-15

    The peroxyoxalate-chemiluminescence arising from reaction of bis(2,4,6-trichlorophenyl)oxalate with hydrogen peroxide in the presence of a brightener Tinopal CBS (2,2'-((1,1'-biphenyl)-4,4'-diyldi-2.1-ethenediyl)bisbenzene sulfonic acid, disodium salt) has been studied. The relationship between the chemiluminescence intensity and concentrations of bis(2,4,6-trichlorophenyl)oxalate, sodium salicylate (as catalyst), hydrogen peroxide and Tinopal CBS is reported. The chemiluminescence parameters including intensity at maximum chemiluminescence, time at maximum intensity, total light yield, theoretical maximum level of intensity and pseudo-first-order rate constants for the rise and fall of the chemiluminescence burst (k{sub r} and k{sub f}) were evaluated from computer fitting of the resulting intensity-time plots. The activation parameters E{sub a}, DELTAH, DELTAS and DELTAG for the rise and fall steps were evaluated from the temperature dependence of k{sub r} and k{sub f} values. The results were discussed in terms of chemically initiated electron transfer between a reactive intermediate and Tinopal CBS as fluorescence activator. A possible mechanism involving dioxetanone derivatives as intermediates is proposed. Since there is a linear relationship between reciprocal of chemiluminescence intensity and reciprocal of fluorescer concentration, an analytical method based on partial least squares (PLS) regression was proposed for quantitative determination of Tinopal CBS. Satisfactory results were obtained with percent relative prediction error (RPE%) of 2.52 and detection limit of 2.7x10{sup -5} M.

  18. A mechanistic study on the synthesis of β-Sialon whiskers from coal fly ash

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, H.; Wang, P.Y. [Thermal Energy Research Centre, Shenyang Aerospace University, Shenyang 110136 (China); Yu, J.L., E-mail: jianglong.yu@newcastle.edu.au [Thermal Energy Research Centre, Shenyang Aerospace University, Shenyang 110136 (China); Chemical Engineering, University of Newcastle, Callaghan, NSW 2308 (Australia); Zhang, J. [Thermal Energy Research Centre, Shenyang Aerospace University, Shenyang 110136 (China)

    2015-05-15

    Graphical abstract: The appearance of bead-like whiskers indicated that the growth mechanism of the β-Sialon whiskers was different from the conventional one, in which a chain of droplets were formed and then consumed to participate in the formation of the whiskers. - Highlights: • β-Sialon whiskers were synthesized using waste fly ash by carbothemal reduction reaction under nitrogen atmosphere. • Rod-like β-Sialon whiskers with a diameter of 100–500 nm were formed. • Bead-like whiskers as intermediate morphology of the growing β-Sialon whiskers were found with increasing sintering time. • The growth mechanism of β-Sialon whiskers was different from the conventional VLS mechanism. • A chain of droplets were formed and participated in the formation of the whiskers. - Abstract: β-Sialon whiskers were produced at 1420 °C through carbothemal reduction reaction under nitrogen atmosphere using fly ash from coal-fired power plants. The effects of sintering time on the phase formation and morphology of the products were investigated by X-ray diffraction (XRD), scanning electron microscope (SEM) and energy dispersive spectrometer (EDS) techniques. Rod-like β-Sialon whiskers with the diameter of 100–500 nm were successfully formed. With increasing sintering time, bead-like morphology during the growth process of the whiskers was found, and growth mechanism of β-Sialon whiskers was also discussed in detail. The growth mechanism proposed in this study was different from the conventional vapor–liquid–solid (VLS) mechanism.

  19. Transcranial direct current stimulation to lessen neuropathic pain after spinal cord injury: a mechanistic PET study.

    Science.gov (United States)

    Yoon, Eun Jin; Kim, Yu Kyeong; Kim, Hye-Ri; Kim, Sang Eun; Lee, Youngjo; Shin, Hyung Ik

    2014-01-01

    It is suggested that transcranial direct current stimulation (tDCS) can produce lasting changes in corticospinal excitability and can potentially be used for the treatment of neuropathic pain. However, the detailed mechanisms underlying the effects of tDCS are unknown. We investigated the underlying neural mechanisms of tDCS for chronic pain relief using [(18)F]-fluorodeoxyglucose positron emission tomography ([(18)F]FDG-PET). Sixteen patients with neuropathic pain (mean age 44.1 ± 8.6 years, 4 females) due to traumatic spinal cord injury received sham or active anodal stimulation of the motor cortex using tDCS for 10 days (20 minutes, 2 mA, twice a day). The effect of tDCS on regional cerebral glucose metabolism was evaluated by [(18)F]FDG-PET before and after tDCS sessions. There was a significant decrease in the numeric rating scale scores for pain, from 7.6 ± 0.5 at baseline to 5.9 ± 1.8 after active tDCS (P = .016). We found increased metabolism in the medulla and decreased metabolism in the left dorsolateral prefrontal cortex after active tDCS treatment compared with the changes induced by sham tDCS. Additionally, an increase in metabolism after active tDCS was observed in the subgenual anterior cingulate cortex and insula. The results of this study suggest that anodal stimulation of the motor cortex using tDCS can modulate emotional and cognitive components of pain and normalize excessive attention to pain and pain-related information.

  20. Mechanistic and stereochemical studies of glycine oxidase from Bacillus subtilis strain R5.

    Science.gov (United States)

    Jamil, Farrukh; Gardner, Qurra-Tul-Ann Afza; Bashir, Qamar; Rashid, Naeem; Akhtar, Muhammad

    2010-08-31

    Glycine oxidase gene from a strain of Bacillus subtilis was cloned and expressed in Escherichia coli. The purified enzyme was found, by mass spectrometry, to have a protein M(r) of 40763 (value of 40761.6 predicted from DNA sequence) and a FAD prosthetic group M(r) of 785.1 (theoretical value of 785.5). Glycine oxidase optimally catalyzes the conversion of glycine and oxygen into glyoxylate, hydrogen peroxide, and ammonia. Using samples of [2-RS-(3)H(2),2-(14)C]-, [2-R-(3)H,2-(14)C]-, and [2-S-(3)H,2-(14)C]glycine, we found that in the overall process H(Si) is removed. Incubation of the enzyme with [2-RS-(3)H(2),2-(14)C]glycine under anaerobic conditions, when only the reducing half of the reaction can occur, led to the recovery of 98.5% of the original glycine, which had the same (3)H:(14)C ratio as the starting substrate. The primary isotope effect was studied using [2-(2)H(2)]glycine, and we found that the specificity constants, k(cat)/K(M), for the protio and deuterio substrates were 1.46 x 10(3) and 1.05 x 10(2) M(-1) s(-1), respectively. Two alternative mechanisms for FAD-containing oxidases that involve either the intermediacy of a FADH(2)-imino acid complex or an amino acid covalently linked to FAD, formed via a carbanion, have been considered. The current knowledge of the mechanisms is reviewed, and we argue that a mechanism involving the FADH(2)-imino acid complex can be dissected to satisfactorily explain some of puzzling observations for which the carbanion mechanism was originally conceived. Furthermore, our results, together with observations in the literature, suggest that the interaction of glycine with the enzyme occurs within a tight ternary complex, which is protected from the protons of the medium.

  1. Mechanistic studies of the spore photoproduct lyase via a single cysteine mutation.

    Science.gov (United States)

    Yang, Linlin; Lin, Gengjie; Nelson, Renae S; Jian, Yajun; Telser, Joshua; Li, Lei

    2012-09-11

    5-Thyminyl-5,6-dihydrothymine (also called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is repaired by a radical SAM (S-adenosylmethionine) enzyme, the spore photoproduct lyase (SPL), at the bacterial early germination phase. Our previous studies proved that SPL utilizes the 5'-dA• generated by the SAM cleavage reaction to abstract the H(6proR) atom to initiate the SP repair process. The resulting thymine allylic radical was suggested to take an H atom from an unknown protein source, most likely cysteine 141. Here we show that C141 can be readily alkylated in the native SPL by an iodoacetamide treatment, suggesting that it is accessible to the TpT radical. SP repair by the SPL C141A mutant yields TpTSO(2)(-) and TpT simultaneously from the very beginning of the reaction; no lag phase is observed for TpTSO(2)(-) formation. Should any other protein residue serve as the H donor, its presence would result in TpT being the major product at least for the first enzyme turnover. These observations provide strong evidence to support C141 as the direct H atom donor. Moreover, because of the lack of this intrinsic H donor, the C141A mutant produces TpT via an unprecedented thymine cation radical reduction (proton-coupled electron transfer) process, contrasting to the H atom transfer mechanism in the wild-type (WT) SPL reaction. The C141A mutant repairs SP at a rate that is ~3-fold slower than that of the WT enzyme. Formation of TpTSO(2)(-) and TpT exhibits a V(max) deuterium kinetic isotope effect (KIE) of 1.7 ± 0.2, which is smaller than the (D)V(max) KIE of 2.8 ± 0.3 determined for the WT SPL reaction. These findings suggest that removing the intrinsic H atom donor disturbs the rate-limiting process during enzyme catalysis. As expected, the prereduced C141A mutant supports only ~0.4 turnover, which is in sharp contrast to the >5 turnovers exhibited by the WT SPL reaction, suggesting that the enzyme catalytic cycle (SAM

  2. Inactivation of F-specific bacteriophages during flocculation with polyaluminum chloride - a mechanistic study.

    Science.gov (United States)

    Kreißel, Katja; Bösl, Monika; Hügler, Michael; Lipp, Pia; Franzreb, Matthias; Hambsch, Beate

    2014-03-15

    Bacteriophages are often used as surrogates for enteric viruses in spiking experiments to determine the efficiencies of virus removal of certain water treatment measures, like e.g. flocculation or filtration steps. Such spiking experiments with bacteriophages are indispensable if the natural virus concentrations in the raw water of water treatment plants are too low to allow the determination of elimination levels over several orders of magnitude. In order to obtain reliable results from such spiking tests, it is essential that bacteriophages behave comparable to viruses and remain stable during the experiments. To test this, the influence of flocculation parameters on the bacteriophages MS2, Qβ and phiX174 was examined. Notably, the F-specific phages MS2 and Qβ were found to be inactivated in flocculation processes with polyaluminum chloride (PACl). In contrast, other aluminum coagulants like AlCl3 or Al2(SO4)3 did not show a comparable effect on MS2 in this study. In experiments testing the influence of different PACl species on MS2 and Qβ inactivation during flocculation, it could be shown that cationic dissolved PACl species (Al13) interacted with the MS2 surface and hereby reduced the surviving phage fraction to c/c0 values below 1*10(-4) even at very low PACl concentrations of 7 μmol Al/L. Other inactivation mechanisms like the irreversible adsorption of phages to the floc structure or the damage of phage surfaces due to entrapment into the floc during coagulation and floc formation do not seem to contribute to the low surviving fraction found for both F-specific bacteriophages. Furthermore, no influence of phage agglomeration or pH drops during the flocculation process on phage inactivation could be observed. The somatic coliphage phiX174 in contrast did not show sensitivity to chemical stress and in accordance only slight interaction between Al13 and the phage surface was observed. Consequently, F-specific phages like MS2 should not be used as

  3. Mechanistic study of wettability alteration using surfactants with applications in naturally fractured reservoirs.

    Science.gov (United States)

    Salehi, Mehdi; Johnson, Stephen J; Liang, Jenn-Tai

    2008-12-16

    In naturally fractured reservoirs, oil recovery from waterflooding relies on the spontaneous imbibition of water to expel oil from the matrix into the fracture system. The spontaneous imbibition process is most efficient in strongly water-wet rock where the capillary driving force is strong. In oil- or mixed-wet fractured carbonate reservoirs, however, the capillary driving force for the spontaneous imbibition process is weak, and therefore the waterflooding oil recoveries are low. The recovery efficiency can be improved by dissolving low concentrations of surfactants in the injected water to alter the wettability of the reservoir rock to a more water-wet state. This wettability alteration accelerates the spontaneous imbibition of water into matrix blocks, thereby increasing the oil recovery during waterflooding. Several mechanisms have been proposed to explain the wettability alteration by surfactants, but none have been verified experimentally. Understanding of the mechanisms behind wettability alteration could help to improve the performance of the process and aid in identification of alternative surfactants for use in field applications. Results from this study revealed that ion-pair formation and adsorption of surfactant molecules through interactions with the adsorbed crude oil components on the rock surface are the two main mechanisms responsible for the wettability alteration. Previous researchers observed that, for a given rock type, the effectiveness of wettability alteration is highly dependent upon the ionic nature of the surfactant involved. Our experimental results demonstrated that ion-pair formation between the charged head groups of surfactant molecules and the adsorbed crude oil components on rock surface was more effective in changing the rock wettability toward a more water-wet state than the adsorption of surfactant molecules as a monolayer on the rock surface through hydrophobic interaction with the adsorbed crude oil components. By comparing

  4. Inhibition of lactoperoxidase-catalyzed oxidation by imidazole-based thiones and selones: a mechanistic study.

    Science.gov (United States)

    Roy, Gouriprasanna; Jayaram, P N; Mugesh, Govindasamy

    2013-08-01

    Herein, we describe the synthesis and biomimetic activity of a series of N,N-disubstituted thiones and selones that contain an imidazole pharmacophore. The N,N-disubstituted thiones do not show any inhibitory activity towards LPO-catalyzed oxidation reactions, but their corresponding N,N-disubstituted selones exhibit inhibitory activity towards LPO-catalyzed oxidation reactions. Substituents on the N atom of the imidazole ring appear to have a significant effect on the inhibition of LPO-catalyzed oxidation and iodination reactions. Selones 16, 17, and 19, which contain methyl, ethyl, and benzyl substituents, exhibit similar inhibition activities towards LPO-catalyzed oxidation reactions with IC50 values of 24.4, 22.5, and 22.5 μM, respectively. However, their activities are almost three-fold lower than that of the commonly used anti-thyroid drug methimazole (MMI). In contrast, selone 21, which contains a N-CH2CH2OH substituent, exhibits high inhibitory activity, with an IC50 value of 7.2 μM, which is similar to that of MMI. The inhibitory activity of these selones towards LPO-catalyzed oxidation/iodination reactions is due to their ability to decrease the concentrations of the co-substrates (H2O2 and I2), either by catalytically reducing H2O2 (anti-oxidant activity) or by forming stable charge-transfer complexes with oxidized iodide species. The inhibition of LPO-catalyzed oxidation/iodination reactions by N,N-disubstituted selones can be reversed by increasing the concentration of H2O2. Interestingly, all of the N,N-disubstituted selones exhibit high anti-oxidant activities and their glutathione peroxidase (GPx)-like activity is 4-12-fold higher than that of the well-known GPx-mimic ebselen. These experimental and theoretical studies suggest that the selones exist as zwitterions, in which the imidazole ring contains a positive charge and the selenium atom carries a large negative charge. Therefore, the selenium moieties of these selones possess highly

  5. Superhydrophobic photosensitizers. Mechanistic studies of (1)O2 generation in the plastron and solid/liquid droplet interface.

    Science.gov (United States)

    Aebisher, David; Bartusik, Dorota; Liu, Yang; Zhao, Yuanyuan; Barahman, Mark; Xu, QianFeng; Lyons, Alan M; Greer, Alexander

    2013-12-18

    We describe here a physical-organic study of the first triphasic superhydrophobic sensitizer for photooxidations in water droplets. Control of synthetic parameters enables the mechanistic study of "borderline" two- and three-phase superhydrophobic sensitizer surfaces where (1)O2 is generated in compartments that are wetted, partially wetted, or remain dry in the plastron (i.e., air layer beneath the droplet). The superhydrophobic surface is synthesized by partially embedding silicon phthalocyanine (Pc) sensitizing particles to specific locations on polydimethylsiloxane (PDMS) posts printed in a square array (1 mm tall posts on 0.5 mm pitch). In the presence of red light and oxygen, singlet oxygen is formed on the superhydrophobic surface and reacts with 9,10-anthracene dipropionate dianion (1) within a freestanding water droplet to produce an endoperoxide in 54-72% yields. Control of the (1)O2 chemistry was achieved by the synthesis of superhydrophobic surfaces enriched with Pc particles either at the PDMS end-tips or at PDMS post bases. Much of the (1)O2 that reacts with anthracene 1 in the droplets was generated by the sensitizer "wetted" at the Pc particle/water droplet interface and gave the highest endoperoxide yields. About 20% of the (1)O2 can be introduced into the droplet from the plastron. The results indicate that the superhydrophobic sensitizer surface offers a unique system to study (1)O2 transfer routes where a balance of gas and liquid contributions of (1)O2 is tunable within the same superhydrophobic surface.

  6. Polyester Textiles as a Source of Microplastics from Households: A Mechanistic Study to Understand Microfiber Release During Washing.

    Science.gov (United States)

    Hernandez, Edgar; Nowack, Bernd; Mitrano, Denise M

    2017-06-20

    Microplastic fibers make up a large proportion of microplastics found in the environment, especially in urban areas. There is good reason to consider synthetic textiles a major source of microplastic fibers, and it will not diminish since the use of synthetic fabrics, especially polyester, continues to increase. In this study we provide quantitative data regarding the size and mass of microplastic fibers released from synthetic (polyester) textiles during simulated home washing under controlled laboratory conditions. Consideration of fabric structure and washing conditions (use of detergents, temperature, wash duration, and sequential washings) allowed us to study the propensity of fiber shedding in a mechanistic way. Thousands of individual fibers were measured (number, length) from each wash solution to provide a robust data set on which to draw conclusions. Among all the variables tested, the use of detergent appeared to affect the total mass of fibers released the most, yet the detergent composition (liquid or powder) or overdosing of detergent did not significantly influence microplastic release. Despite different release quantities due to the addition of a surfactant (approximately 0.025 and 0.1 mg fibers/g textile washed, without and with detergent, respectively), the overall microplastic fiber length profile remained similar regardless of wash condition or fabric structure, with the vast majority of fibers ranging between 100 and 800 μm in length irrespective of wash cycle number. This indicates that the fiber staple length and/or debris encapsulated inside the fabric from the yarn spinning could be directly responsible for releasing stray fibers. This study serves as a first look toward understanding the physical properties of the textile itself to better understand the mechanisms of fiber shedding in the context of microplastic fiber release into laundry wash water.

  7. Assessing the ability of mechanistic volatilization models to simulate soil surface conditions: a study with the Volt'Air model.

    Science.gov (United States)

    Garcia, L; Bedos, C; Génermont, S; Braud, I; Cellier, P

    2011-09-01

    Ammonia and pesticide volatilization in the field is a surface phenomenon involving physical and chemical processes that depend on the soil surface temperature and water content. The water transfer, heat transfer and energy budget sub models of volatilization models are adapted from the most commonly accepted formalisms and parameterizations. They are less detailed than the dedicated models describing water and heat transfers and surface status. The aim of this work was to assess the ability of one of the available mechanistic volatilization models, Volt'Air, to accurately describe the pedo-climatic conditions of a soil surface at the required time and space resolution. The assessment involves: (i) a sensitivity analysis, (ii) an evaluation of Volt'Air outputs in the light of outputs from a reference Soil-Vegetation-Atmosphere Transfer model (SiSPAT) and three experimental datasets, and (iii) the study of three tests based on modifications of SiSPAT to establish the potential impact of the simplifying assumptions used in Volt'Air. The analysis confirmed that a 5 mm surface layer was well suited, and that Volt'Air surface temperature correlated well with the experimental measurements as well as with SiSPAT outputs. In terms of liquid water transfers, Volt'Air was overall consistent with SiSPAT, with discrepancies only during major rainfall events and dry weather conditions. The tests enabled us to identify the main source of the discrepancies between Volt'Air and SiSPAT: the lack of gaseous water transfer description in Volt'Air. They also helped to explain why neither Volt'Air nor SiSPAT was able to represent lower values of surface water content: current classical water retention and hydraulic conductivity models are not yet adapted to cases of very dry conditions. Given the outcomes of this study, we discuss to what extent the volatilization models can be improved and the questions they pose for current research in water transfer modeling and parameterization.

  8. Solution-phase mechanistic study and solid-state structure of a tris(bipyridinium radical cation) inclusion complex.

    Science.gov (United States)

    Fahrenbach, Albert C; Barnes, Jonathan C; Lanfranchi, Don Antoine; Li, Hao; Coskun, Ali; Gassensmith, Jeremiah J; Liu, Zhichang; Benítez, Diego; Trabolsi, Ali; Goddard, William A; Elhabiri, Mourad; Stoddart, J Fraser

    2012-02-15

    The ability of the diradical dicationic cyclobis(paraquat-p-phenylene) (CBPQT(2(•+))) ring to form inclusion complexes with 1,1'-dialkyl-4,4'-bipyridinium radical cationic (BIPY(•+)) guests has been investigated mechanistically and quantitatively. Two BIPY(•+) radical cations, methyl viologen (MV(•+)) and a dibutynyl derivative (V(•+)), were investigated as guests for the CBPQT(2(•+)) ring. Both guests form trisradical complexes, namely, CBPQT(2(•+))⊂MV(•+) and CBPQT(2(•+))⊂V(•+), respectively. The structural details of the CBPQT(2(•+))⊂MV(•+) complex, which were ascertained by single-crystal X-ray crystallography, reveal that MV(•+) is located inside the cavity of the ring in a centrosymmetric fashion: the 1:1 complexes pack in continuous radical cation stacks. A similar solid-state packing was observed in the case of CBPQT(2(•+)) by itself. Quantum mechanical calculations agree well with the superstructure revealed by X-ray crystallography for CBPQT(2(•+))⊂MV(•+) and further suggest an electronic asymmetry in the SOMO caused by radical-pairing interactions. The electronic asymmetry is maintained in solution. The thermodynamic stability of the CBPQT(2(•+))⊂MV(•+) complex was probed by both isothermal titration calorimetry (ITC) and UV/vis spectroscopy, leading to binding constants of (5.0 ± 0.6) × 10(4) M(-1) and (7.9 ± 5.5) × 10(4) M(-1), respectively. The kinetics of association and dissociation were determined by stopped-flow spectroscopy, yielding a k(f) and k(b) of (2.1 ± 0.3) × 10(6) M(-1) s(-1) and 250 ± 50 s(-1), respectively. The electrochemical mechanistic details were studied by variable scan rate cyclic voltammetry (CV), and the experimental data were compared digitally with simulated data, modeled on the proposed mechanism using the thermodynamic and kinetic parameters obtained from ITC, UV/vis, and stopped-flow spectroscopy. In particular, the electrochemical mechanism of association

  9. A Mechanistic study of Plasma Treatment Effects on Demineralized Dentin Surfaces for Improved Adhesive/Dentin Interface Bonding

    Science.gov (United States)

    Dong, Xiaoqing; Chen, Meng; Wang, Yong; Yu, Qingsong

    2014-01-01

    Our previous work has shown that non-thermal plasma treatment of demineralized dentin significantly (p<0.05) improved adhesive/dentin bonding strength for dental composite restoration as compared with the untreated controls. This study is to achieve mechanistic understanding of the plasma treatment effects on dentin surface through investigating the plasma treated dentin surfaces and their interaction with adhesive monomer, 2-Hydroxyethyl methacrylate (HEMA). The plasma treated dentin surfaces from human third molars were evaluated by water contact angle measurements and scanning electron microscopy (SEM). It was found that plasma-treated dentin surface with subsequent HEMA immersion (Plasma/HEMA Treated) had much lower water contact angle compared with only plasma-treated (Plasma Treated) or only HEMA immersed (HEMA Treated) dentin surfaces. With prolong water droplet deposition time, water droplets spread out completely on the Plasma/HEMA Treated dentin surfaces. SEM images of Plasma/HEMA Treated dentin surfaces verified that dentin tubules were opened-up and filled with HEMA monomers. Extracted type I collagen fibrils, which was used as simulation of the exposed dentinal collagen fibrils after acid etching step, were plasma treated and analyzed with Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) spectra. FT-IR spectra of the Plasma/HEMA Treated collage fibrils showed broadened amide I peak at 1660 cm−1 and amide II at 1550 cm−1, which indicate secondary structure changes of the collagen fibrils. CD spectra indicated that 67.4% collagen helix structures were denatured after plasma treatment. These experimental results demonstrate that non-thermal argon plasma treatment was very effective in loosing collagen structure and enhancing adhesive monomer penetration, which are beneficial to thicker hybrid layer and longer resin tag formation, and consequently enhance adhesive/dentin interface bonding. PMID:25267936

  10. Mechanistic study of TRPM2-Ca(2+)-CAMK2-BECN1 signaling in oxidative stress-induced autophagy inhibition.

    Science.gov (United States)

    Wang, Qian; Guo, Wenjing; Hao, Baixia; Shi, Xianli; Lu, Yingying; Wong, Connie W M; Ma, Victor W S; Yip, Timothy T C; Au, Joseph S K; Hao, Quan; Cheung, King-Ho; Wu, Wutian; Li, Gui-Rong; Yue, Jianbo

    2016-08-02

    Reactive oxygen species (ROS) have been commonly accepted as inducers of autophagy, and autophagy in turn is activated to relieve oxidative stress. Yet, whether and how oxidative stress, generated in various human pathologies, regulates autophagy remains unknown. Here, we mechanistically studied the role of TRPM2 (transient receptor potential cation channel subfamily M member 2)-mediated Ca(2+) influx in oxidative stress-mediated autophagy regulation. On the one hand, we demonstrated that oxidative stress triggered TRPM2-dependent Ca(2+) influx to inhibit the induction of early autophagy, which renders cells more susceptible to death. On the other hand, oxidative stress induced autophagy (and not cell death) in the absence of the TRPM2-mediated Ca(2+) influx. Moreover, in response to oxidative stress, TRPM2-mediated Ca(2+) influx activated CAMK2 (calcium/calmodulin dependent protein kinase II) at levels of both phosphorylation and oxidation, and the activated CAMK2 subsequently phosphorylated BECN1/Beclin 1 on Ser295. Ser295 phosphorylation of BECN1 in turn decreased the association between BECN1 and PIK3C3/VPS34, but induced binding between BECN1 and BCL2. Clinically, acetaminophen (APAP) overdose is the most common cause of acute liver failure worldwide. We demonstrated that APAP overdose also activated ROS-TRPM2-CAMK2-BECN1 signaling to suppress autophagy, thereby causing primary hepatocytes to be more vulnerable to death. Inhibiting the TRPM2-Ca(2+)-CAMK2 cascade significantly mitigated APAP-induced liver injury. In summary, our data clearly demonstrate that oxidative stress activates the TRPM2-Ca(2+)-CAMK2 cascade to phosphorylate BECN1 resulting in autophagy inhibition.

  11. Why did high-dose rosuvastatin not improve cardiac remodeling in chronic heart failure? Mechanistic insights from the UNIVERSE study.

    Science.gov (United States)

    Ashton, Emma; Windebank, Emma; Skiba, Marina; Reid, Christopher; Schneider, Hans; Rosenfeldt, Franklin; Tonkin, Andrew; Krum, Henry

    2011-02-03

    Statins are often prescribed for prevention of atherosclerotic outcomes in patients who have chronic heart failure (CHF), if this has an ischaemic etiology. These agents may also possess additional properties, independent of effects on blood lipid levels, which may have an effect on cardiac remodeling. However, beneficial effects were not observed in the recent UNIVERSE trial. We prospectively planned a sub-study of UNIVERSE to explore relevant mechanistic effects of rosuvastatin, including effects on collagen turnover and plasma coenzyme Q10 (CoQ) levels. Additionally, CoQ levels in CHF patients receiving chronic statin therapy were measured. CoQ levels were significantly reduced after 26 weeks of rosuvastatin statin therapy (n = 32), compared to placebo (n = 37) in CHF patients in UNIVERSE trial. Patients with CHF (n = 56) matched for age, gender and severity of disease who had been taking statins for 12 months or longer had CoQ levels of 847 ± 344 nmol/L, significantly lower than 1065.4 ± 394 nmol/L in UNIVERSE patients at baseline (p = 0.0001). Serum types I and III N-terminal procollagen peptide (PINP and PIIINP), measures of collagen turnover which can contribute to cardiac fibrosis were significantly increased in the rosuvastatin group compared to baseline in UNIVERSE patients (PINP: p = 0.03, PIIINP: p = 0.001). In conclusion putative beneficial effects of statin therapy on cardiac remodeling in UNIVERSE may have been negated by increases in collagen turnover markers as well as a reduction in plasma CoQ levels in these patients with CHF. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  12. Regioselective, borinic acid-catalyzed monoacylation, sulfonylation and alkylation of diols and carbohydrates: expansion of substrate scope and mechanistic studies.

    Science.gov (United States)

    Lee, Doris; Williamson, Caitlin L; Chan, Lina; Taylor, Mark S

    2012-05-16

    Synthetic and mechanistic aspects of the diarylborinic acid-catalyzed regioselective monofunctionalization of 1,2- and 1,3-diols are presented. Diarylborinic acid catalysis is shown to be an efficient and general method for monotosylation of pyranoside derivatives bearing three secondary hydroxyl groups (7 examples, 88% average yield). In addition, the scope of the selective acylation, sulfonylation, and alkylation is extended to 1,2- and 1,3-diols not derived from carbohydrates (28 examples); the efficiency, generality, and operational simplicity of this method are competitive with those of state-of-the-art protocols including the broadly applied organotin-catalyzed or -mediated reactions. Mechanistic details of the organoboron-catalyzed processes are explored using competition experiments, kinetics, and catalyst structure-activity relationships. These experiments are consistent with a mechanism in which a tetracoordinate borinate complex reacts with the electrophilic species in the turnover-limiting step of the catalytic cycle.

  13. Combining solvent isotope effects with substrate isotope effects in mechanistic studies of alcohol and amine oxidation by enzymes.

    Science.gov (United States)

    Fitzpatrick, Paul F

    2015-11-01

    Oxidation of alcohols and amines is catalyzed by multiple families of flavin- and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.

  14. Mechanistic studies of protein tyrosine phosphatases YopH and Cdc25A with m-nitrobenzyl phosphate.

    Science.gov (United States)

    McCain, Daniel F; Grzyska, Piotr K; Wu, Li; Hengge, Alvan C; Zhang, Zhong-Yin

    2004-06-29

    Protein tyrosine phosphatases (PTPs) constitute a large family of signaling enzymes that include both tyrosine specific and dual-specificity phosphatases that hydrolyze pSer/Thr in addition to pTyr. Previous mechanistic studies of PTPs have relied on the highly activated substrate p-nitrophenyl phosphate (pNPP), an aryl phosphate with a leaving group pK(a) of 7. In the study presented here, we employ m-nitrobenzyl phosphate (mNBP), an alkyl phosphate with a leaving group pK(a) of 14.9, which mimics the physiological substrates of the PTPs. We have carried out pH dependence and kinetic isotope effect measurements to characterize the mechanism of two important members of the PTP superfamily: Yersinia PTP (YopH) and Cdc25A. Both YopH and Cdc25A exhibit bell-shaped pH-rate profiles for the hydrolysis of mNBP, consistent with general acid catalysis. The slightly inverse (18)(V/K)(nonbridge) isotope effects (0.9999 for YopH and 0.9983 for Cdc25A) indicate a loose transition state with little nucleophilic participation for both enzymes. The smaller (18)(V/K)(bridge) primary isotope effects (0.9995 for YopH and 1.0012 for Cdc25A) relative to the corresponding isotope effects for pNPP hydrolysis suggest that protonation of the leaving group oxygen at the transition state by the general acid is ahead of P-O bond fission with the alkyl substrate, while general acid catalysis of pNPP by YopH is more synchronous with P-O bond fission. The isotope effect data also confirm findings from previous studies that Cdc25A utilizes general acid catalysis for substrates with a leaving group pK(a) of >8, but not for pNPP. Interestingly, the difference in the kinetic isotope effects for the reactions of aryl phosphate pNPP and alkyl phosphate mNBP by the PTPs parallels what is observed in the uncatalyzed reactions of their monoanions. In these reactions, the leaving group is protonated in the transition state, as is the case in PTP-catalyzed reactions. Also, the phosphoryl group in the

  15. Rapid radiosynthesis of [11C] and [14C]azelaic, suberic, and sebacic acids for in vivo mechanistic studies of systemic acquired resistance in plants

    Energy Technology Data Exchange (ETDEWEB)

    Best M.; Fowler J.; Best, M.; Gifford, A.N.; Kim, S.W.; Babst, B.; Piel, M.; Roesch, F.; Fowler, J.S.

    2011-11-25

    A recent report that the aliphatic dicarboxylic acid, azelaic acid (1,9-nonanedioic acid) but not related acids, suberic acid (1,8-octanedioic acid) or sebacic (1,10-decanedioic acid) acid induces systemic acquired resistance to invading pathogens in plants stimulated the development of a rapid method for labeling these dicarboxylic acids with {sup 11}C and {sup 14}C for in vivo mechanistic studies in whole plants. {sup 11}C-labeling was performed by reaction of ammonium [{sup 11}C]cyanide with the corresponding bromonitrile precursor followed by hydrolysis with aqueous sodium hydroxide solution. Total synthesis time was 60 min. Median decay-corrected radiochemical yield for [{sup 11}C]azelaic acid was 40% relative to trapped [{sup 11}C]cyanide, and specific activity was 15 GBq/{micro}mol. Yields for [{sup 11}C]suberic and sebacic acids were similar. The {sup 14}C-labeled version of azelaic acid was prepared from potassium [{sup 14}C]cyanide in 45% overall radiochemical yield. Radiolabeling procedures were verified using {sup 13}C-labeling coupled with {sup 13}C-NMR and liquid chromatography-mass spectrometry analysis. The {sup 11}C and {sup 14}C-labeled azelaic acid and related dicarboxylic acids are expected to be of value in understanding the mode-of-action, transport, and fate of this putative signaling molecule in plants.

  16. Radical behaviorism and scientific frameworks. From mechanistic to relational accounts.

    Science.gov (United States)

    Chiesa, M

    1992-11-01

    A substantial portion of B. F. Skinner's scholarship was devoted to developing methods and terms for a scientific study of behavior. Three concepts central to scientific accounts--cause, explanation, and theory--are examined to illustrate the distinction between mechanistic and relational frameworks and radical behaviorism's relationship to those frameworks. Informed by a scientific tradition that explicitly rejects mechanistic interpretations, radical behaviorism provides a distinctive stance in contemporary psychology. The present analysis suggests that radical behaviorism makes closer contact with the "new world view" advocated by physicists and philosophers of science than does much of contemporary psychology.

  17. Mechanistic Studies and Modeling Reveal the Origin of Differential Inhibition of Gag Polymorphic Viruses by HIV-1 Maturation Inhibitors.

    Science.gov (United States)

    Lin, Zeyu; Cantone, Joseph; Lu, Hao; Nowicka-Sans, Beata; Protack, Tricia; Yuan, Tian; Yang, Hong; Liu, Zheng; Drexler, Dieter; Regueiro-Ren, Alicia; Meanwell, Nicholas A; Cockett, Mark; Krystal, Mark; Lataillade, Max; Dicker, Ira B

    2016-11-01

    HIV-1 maturation inhibitors (MIs) disrupt the final step in the HIV-1 protease-mediated cleavage of the Gag polyprotein between capsid p24 capsid (CA) and spacer peptide 1 (SP1), leading to the production of infectious virus. BMS-955176 is a second generation MI with improved antiviral activity toward polymorphic Gag variants compared to a first generation MI bevirimat (BVM). The underlying mechanistic reasons for the differences in polymorphic coverage were studied using antiviral assays, an LC/MS assay that quantitatively characterizes CA/SP1 cleavage kinetics of virus like particles (VLPs) and a radiolabel binding assay to determine VLP/MI affinities and dissociation kinetics. Antiviral assay data indicates that BVM does not achieve 100% inhibition of certain polymorphs, even at saturating concentrations. This results in the breakthrough of infectious virus (partial antagonism) regardless of BVM concentration. Reduced maximal percent inhibition (MPI) values for BVM correlated with elevated EC50 values, while rates of HIV-1 protease cleavage at CA/SP1 correlated inversely with the ability of BVM to inhibit HIV-1 Gag polymorphic viruses: genotypes with more rapid CA/SP1 cleavage kinetics were less sensitive to BVM. In vitro inhibition of wild type VLP CA/SP1 cleavage by BVM was not maintained at longer cleavage times. BMS-955176 exhibited greatly improved MPI against polymorphic Gag viruses, binds to Gag polymorphs with higher affinity/longer dissociation half-lives and exhibits greater time-independent inhibition of CA/SP1 cleavage compared to BVM. Virological (MPI) and biochemical (CA/SP1 cleavage rates, MI-specific Gag affinities) data were used to create an integrated semi-quantitative model that quantifies CA/SP1 cleavage rates as a function of both MI and Gag polymorph. The model outputs are in accord with in vitro antiviral observations and correlate with observed in vivo MI efficacies. Overall, these findings may be useful to further understand antiviral

  18. Why did Jacques Monod make the choice of mechanistic determinism?

    Science.gov (United States)

    Loison, Laurent

    2015-06-01

    The development of molecular biology placed in the foreground a mechanistic and deterministic conception of the functioning of macromolecules. In this article, I show that this conception was neither obvious, nor necessary. Taking Jacques Monod as a case study, I detail the way he gradually came loose from a statistical understanding of determinism to finally support a mechanistic understanding. The reasons of the choice made by Monod at the beginning of the 1950s can be understood only in the light of the general theoretical schema supported by the concept of mechanistic determinism. This schema articulates three fundamental notions for Monod, namely that of the rigidity of the sequence of the genetic program, that of the intrinsic stability of macromolecules (DNA and proteins), and that of the specificity of molecular interactions.

  19. In vitro solubility, dissolution and permeability studies combined with semi-mechanistic modeling to investigate the intestinal absorption of desvenlafaxine from an immediate- and extended release formulation

    DEFF Research Database (Denmark)

    Franek, F; Jarlfors, A; Larsen, F.

    2015-01-01

    Desvenlafaxine is a biopharmaceutics classification system (BCS) class 1 (high solubility, high permeability) and biopharmaceutical drug disposition classification system (BDDCS) class 3, (high solubility, poor metabolism; implying low permeability) compound. Thus the rate-limiting step for desve......Desvenlafaxine is a biopharmaceutics classification system (BCS) class 1 (high solubility, high permeability) and biopharmaceutical drug disposition classification system (BDDCS) class 3, (high solubility, poor metabolism; implying low permeability) compound. Thus the rate-limiting step...... for desvenlafaxine absorption (i.e. intestinal dissolution or permeation) is not fully clarified. The aim of this study was to investigate whether dissolution and/or intestinal permeability rate-limit desvenlafaxine absorption from an immediate-release formulation (IRF) and Pristiq®, an extended release formulation...... (ERF). Semi-mechanistic models of desvenlafaxine were built (using SimCyp®) by combining in vitro data on dissolution and permeation (mechanistic part of model) with clinical data (obtained from literature) on distribution and clearance (non-mechanistic part of model). The model predictions...

  20. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    Energy Technology Data Exchange (ETDEWEB)

    Carraher, Jack McCaslin [Iowa State Univ., Ames, IA (United States)

    2014-01-01

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding ‘greener’ sources of commodity chemicals and fuels.

  1. Hepatocyte composition-based model as a mechanistic tool for predicting the cell suspension: aqueous phase partition coefficient of drugs in in vitro metabolic studies.

    Science.gov (United States)

    Poulin, Patrick; Haddad, Sami

    2013-08-01

    This study is an extension of a previously published microsome composition-based model by Poulin and Haddad (Poulin and Haddad. 2011. J Pharm Sci 100:4501-4517), which was converted to the hepatocyte composition-based model. The first objective was to investigate the ability of the composition-based model to predict nonspecific binding of drugs in hepatocytes suspended in the incubation medium in in vitro metabolic studies. The hepatocyte composition-based model describes the cell suspension-aqueous phase partition coefficients, which were used to estimate fraction unbound in the incubation medium (fuinc ) for each drug. The second objective was to make a comparative analysis between the proposed hepatocyte composition-based model and an empirical regression equation published in the literature by Austin et al. (Austin RP, Barton P, Mohmed S, Riley RJ. 2004. Drug Metab Dispos 33:419-425). The assessment was confined by the availability of experimentally determined in vitro fuinc values at diverse hepatocyte concentrations for 92 drugs. The model that made use of hepatocyte composition data provides comparable or superior prediction performance compared with the regression equation that relied solely on physicochemical data; therefore, this demonstrates the ability of predicting fuinc also based on mechanisms of drug tissue distribution. The accuracy of the predictions differed depending on the class of drugs (neutrals vs. ionized drugs) and species (rat vs. human) for each method. This study for hepatocytes corroborates a previous study for microsomes. Overall, this work represents a significant first step toward the development of a generic and mechanistic calculation method of fuinc in incubations of hepatocytes, which should facilitate rational interindividual and interspecies extrapolations of fuinc by considering differences in lipid composition of hepatocytes, for clearance prediction in the physiologically-based pharmacokinetics (PBPK) models.

  2. How to use mechanistic effect models in environmental risk assessment of pesticides: Case studies and recommendations from the SETAC workshop MODELINK.

    Science.gov (United States)

    Hommen, Udo; Forbes, Valery; Grimm, Volker; Preuss, Thomas G; Thorbek, Pernille; Ducrot, Virginie

    2016-01-01

    Mechanistic effect models (MEMs) are useful tools for ecological risk assessment of chemicals to complement experimentation. However, currently no recommendations exist for how to use them in risk assessments. Therefore, the Society of Environmental Toxicology and Chemistry (SETAC) MODELINK workshop aimed at providing guidance for when and how to apply MEMs in regulatory risk assessments. The workshop focused on risk assessment of plant protection products under Regulation (EC) No 1107/2009 using MEMs at the organism and population levels. Realistic applications of MEMs were demonstrated in 6 case studies covering assessments for plants, invertebrates, and vertebrates in aquatic and terrestrial habitats. From the case studies and their evaluation, 12 recommendations on the future use of MEMs were formulated, addressing the issues of how to translate specific protection goals into workable questions, how to select species and scenarios to be modeled, and where and how to fit MEMs into current and future risk assessment schemes. The most important recommendations are that protection goals should be made more quantitative; the species to be modeled must be vulnerable not only regarding toxic effects but also regarding their life history and dispersal traits; the models should be as realistic as possible for a specific risk assessment question, and the level of conservatism required for a specific risk assessment should be reached by designing appropriately conservative environmental and exposure scenarios; scenarios should include different regions of the European Union (EU) and different crops; in the long run, generic MEMs covering relevant species based on representative scenarios should be developed, which will require EU-level joint initiatives of all stakeholders involved. The main conclusion from the MODELINK workshop is that the considerable effort required for making MEMs an integral part of environmental risk assessment of pesticides is worthwhile, because

  3. Inhibitory effect of natural organic matter or other background constituents on photocatalytic advanced oxidation processes: Mechanistic model development and validation.

    Science.gov (United States)

    Brame, Jonathon; Long, Mingce; Li, Qilin; Alvarez, Pedro

    2015-11-01

    The ability of reactive oxygen species (ROS) to interact with priority pollutants is crucial for efficient water treatment by photocatalytic advanced oxidation processes (AOPs). However, background compounds in water such as natural organic matter (NOM) can significantly hinder targeted reactions and removal efficiency. This inhibition can be complex, interfering with degradation in solution and at the photocatalyst surface as well as hindering illumination efficiency and ROS production. We developed an analytical model to account for various inhibition mechanisms in catalytic AOPs, including competitive adsorption of inhibitors, scavenging of produced ROS at the surface and in solution, and the inner filtering of the excitation illumination, which combine to decrease ROS-mediated degradation. This model was validated with batch experiments using a variety of ROS producing systems (OH-generating TiO2 photocatalyst and H2O2-UV; (1)O2-generating photosensitive functionalized fullerenes and rose bengal) and inhibitory compounds (NOM, tert-butyl alcohol). Competitive adsorption by NOM and ROS scavenging were the most influential inhibitory mechanisms. Overall, this model enables accurate simulation of photocatalytic AOP performance when one or more inhibitory mechanisms are at work in a wide variety of application scenarios, and underscores the need to consider the effects of background constituents on degradation efficiency.

  4. COMPARATIVE STUDY ON METAL IONS ADSORPTION ON A LOW COST CARBONACEOUS ADSORBENT KINETIC EQUILIBRIUM AND MECHANISTIC STUDIES

    Directory of Open Access Journals (Sweden)

    S. Arivoli, M. Hema, C. Barathiraja

    2008-01-01

    Full Text Available A carbonaceous adsorbent prepared from an indigenous waste and treated by acid was tested for its efficiency in removing metal ions of Fe(II, Co(II and Ni(II. The process parameters studied included agitation time, initial metal ion concentration, carbon dosage, pH, other ions and temperature. The kinetics of adsorption followed first order reaction equation and the rate was mainly controlled by intraparticle diffusion. Freundlich and Langmuir isotherm models were applied to the equilibrium data. The adsorption capacity obtained from the Langmuir isotherm plots was found around 28mg/g for all selected metal ions at an initial pH of 6. The temperature variation study showed that the metal ions adsorption is endothermic and spontaneous with increased randomness at the solid solution interface. Significant effect on adsorption was observed on varying pH of the metal ion solutions. The type I and II isotherms obtained, positive H0 values, pH dependent results and desorption of metal ions in mineral acid suggests that the adsorption of metal ions on this type of adsorbent involves both chemisorption and physical adsorption mechanisms.

  5. Opening the black box—Development, testing and documentation of a mechanistically rich agent-based model

    DEFF Research Database (Denmark)

    Topping, Chris J.; Høye, Toke; Olesen, Carsten Riis

    2010-01-01

    Although increasingly widely used in biology, complex adaptive simulation models such as agent-based models have been criticised for being difficult to communicate and test. This study demonstrates the application of pattern-oriented model testing, and a novel documentation procedure to present a...... be compared to real-world data allows the formulation and testing of varied hypotheses in ways not tractable to experimentation. In the case of the brown hare the results provide a new insight into population regulation and the causes of the declines...

  6. Tear gas: an epidemiological and mechanistic reassessment

    Science.gov (United States)

    Rothenberg, Craig; Achanta, Satyanarayana; Svendsen, Erik R.

    2016-01-01

    Deployments of tear gas and pepper spray have rapidly increased worldwide. Large amounts of tear gas have been used in densely populated cities, including Cairo, Istanbul, Rio de Janeiro, Manama (Bahrain), and Hong Kong. In the United States, tear gas was used extensively during recent riots in Ferguson, Missouri. Whereas tear gas deployment systems have rapidly improved—with aerial drone systems tested and requested by law enforcement—epidemiological and mechanistic research have lagged behind and have received little attention. Case studies and recent epidemiological studies revealed that tear gas agents can cause lung, cutaneous, and ocular injuries, with individuals affected by chronic morbidities at high risk for complications. Mechanistic studies identified the ion channels TRPV1 and TRPA1 as targets of capsaicin in pepper spray, and of the tear gas agents chloroacetophenone, CS, and CR. TRPV1 and TRPA1 localize to pain‐sensing peripheral sensory neurons and have been linked to acute and chronic pain, cough, asthma, lung injury, dermatitis, itch, and neurodegeneration. In animal models, transient receptor potential inhibitors show promising effects as potential countermeasures against tear gas injuries. On the basis of the available data, a reassessment of the health risks of tear gas exposures in the civilian population is advised, and development of new countermeasures is proposed. PMID:27391380

  7. Tear gas: an epidemiological and mechanistic reassessment.

    Science.gov (United States)

    Rothenberg, Craig; Achanta, Satyanarayana; Svendsen, Erik R; Jordt, Sven-Eric

    2016-08-01

    Deployments of tear gas and pepper spray have rapidly increased worldwide. Large amounts of tear gas have been used in densely populated cities, including Cairo, Istanbul, Rio de Janeiro, Manama (Bahrain), and Hong Kong. In the United States, tear gas was used extensively during recent riots in Ferguson, Missouri. Whereas tear gas deployment systems have rapidly improved-with aerial drone systems tested and requested by law enforcement-epidemiological and mechanistic research have lagged behind and have received little attention. Case studies and recent epidemiological studies revealed that tear gas agents can cause lung, cutaneous, and ocular injuries, with individuals affected by chronic morbidities at high risk for complications. Mechanistic studies identified the ion channels TRPV1 and TRPA1 as targets of capsaicin in pepper spray, and of the tear gas agents chloroacetophenone, CS, and CR. TRPV1 and TRPA1 localize to pain-sensing peripheral sensory neurons and have been linked to acute and chronic pain, cough, asthma, lung injury, dermatitis, itch, and neurodegeneration. In animal models, transient receptor potential inhibitors show promising effects as potential countermeasures against tear gas injuries. On the basis of the available data, a reassessment of the health risks of tear gas exposures in the civilian population is advised, and development of new countermeasures is proposed.

  8. Plasma-based water treatment: development of a general mechanistic model to estimate the treatability of different types of contaminants

    Science.gov (United States)

    Mededovic Thagard, Selma; Stratton, Gunnar R.; Dai, Fei; Bellona, Christopher L.; Holsen, Thomas M.; Bohl, Douglas G.; Paek, Eunsu; Dickenson, Eric R. V.

    2017-01-01

    To determine the types of applications for which plasma-based water treatment (PWT) is best suited, the treatability of 23 environmental contaminants was assessed through treatment in a gas discharge reactor with argon bubbling, termed the enhanced-contact reactor. The contaminants were treated in a mixture to normalize reaction conditions and convective transport limitations. Treatability was compared in terms of the observed removal rate constant (k obs). To characterize the influence of interfacial processes on k obs, a model was developed that accurately predicts k obs for each compound, as well as the contributions to k obs from each of the three general degradation mechanisms thought to occur at or near the gas-liquid interface: ‘sub-surface’, ‘surface’ and ‘above-surface’. Sub-surface reactions occur just underneath the gas-liquid interface between the contaminants and dissolved plasma-generated radicals, contributing significantly to the removal of compounds that lack surfactant-like properties and so are not highly concentrated at the interface. Surface reactions occur at the interface between the contaminants and dissolved radicals, contributing significantly to the removal of surfactant-like compounds that have high interfacial concentrations. The contaminants’ interfacial concentrations were calculated using surface-activity parameters determined through surface tension measurements. Above-surface reactions are proposed to take place in the plasma interior between highly energetic plasma species and exposed portions of compounds that extend out of the interface. This mechanism largely accounts for the degradation of surfactant-like contaminants that contain highly hydrophobic perfluorocarbon groups, which are most likely to protrude from the interface. For a few compounds, the degree of exposure to the plasma interior was supported by new and previously reported molecular dynamics simulations results. By reviewing the predicted

  9. Mechanistic understanding of the nonlinear pharmacokinetics and intersubject variability of simeprevir: A PBPK-guided drug development approach.

    Science.gov (United States)

    Snoeys, J; Beumont, M; Monshouwer, M; Ouwerkerk-Mahadevan, S

    2016-02-01

    Simeprevir, a hepatitis C virus (HCV) NS3/4A protease inhibitor, displays nonlinear pharmacokinetics (PK) at therapeutic doses. Using physiologically based PK modeling, various drug-drug interactions were simulated with simeprevir as victim drug to identify whether saturation of the predominant metabolic enzyme (CYP3A4) or the active hepatic transporters (organic anion-transporting polypeptide (OATP)1B1/3) could account for the nonlinear PK. Interactions with ritonavir, a strong CYP3A4 inhibitor that does not affect OATP (at 100 mg dose), erythromycin, a moderate CYP3A4 inhibitor, and efavirenz, a moderate CYP3A inducer that does not affect OATP, demonstrated the involvement of CYP3A4. Interaction studies with low-dose cyclosporine confirmed the role of OATP. The interplay between hepatic uptake and CYP3A4 metabolism was verified by simulations with rifampicin, a potent CYP3A4 inducer and OATP1B1/3 inhibitor, and maintenance doses of cyclosporine. Saturation of gut and liver metabolism by CYP3A4, and saturation of hepatic uptake by OATP1B1/3, seem to account for the observed nonlinear PK of simeprevir.

  10. A semi-mechanistic model to characterize the pharmacokinetics and pharmacodynamics of brodalumab in healthy volunteers and subjects with psoriasis in a first-in-human single ascending dose study.

    Science.gov (United States)

    Salinger, David H; Endres, Christopher J; Martin, David A; Gibbs, Megan A

    2014-07-01

    Pharmacokinetic-pharmacodynamic (PK-PD) modeling can provide a framework for quantitative "learning and confirming" from studies in all phases of drug development. Brodalumab is a human monoclonal antibody (IgG2 ) targeting the IL-17 receptor A that blocks signaling by cytokines thought to play a central role in the pathogenesis of psoriasis (IL-17A, IL-17F, and IL-17A/F). We used semi-mechanistic modeling of single dose, first-in-human data to characterize the exposure-response relationship between brodalumab and the Psoriasis Area and Severity Index (PASI) in a Phase 1 clinical trial. Fifty-seven healthy volunteers and 25 subjects with moderate to severe psoriasis received single intravenous or subcutaneous administration of placebo or brodalumab (7-700 mg). A two-compartment model with parallel linear and nonlinear (Michaelis-Menten) elimination pathways described brodalumab PK. The PK-PASI relationship was characterized by linking a signaling compartment with an indirect response model of psoriatic plaques, where signaling suppressed plaque formation. The concentration of half-maximal inhibition IC50 was 2.86 µg/mL (SE: 50%). The endogenous psoriatic plaque formation rate of 0.862 (SE: 40%) PASI units/day was comparable with literature precedent. Despite the small sample size and single administration data, this semi-mechanistic modeling approach provided a quantitative framework to inform design of dose-ranging Phase 2 studies of brodalumab in psoriasis.

  11. Atmospheric reactivity of vinyl acetate: kinetic and mechanistic study of its gas-phase oxidation by OH, O3, and NO3.

    Science.gov (United States)

    Picquet-Varrault, B; Scarfogliero, M; Doussin, J-F

    2010-06-15

    Vinyl acetate is widely used in industry. It has been classified as a high-production volume (HPV) chemical in the United States. To evaluate its impact on the environment and air quality, its atmospheric reactivity toward the three main tropospheric oxidants (OH, NO(3), and O(3)) has been investigated. Kinetic and mechanistic experiments have been conducted at room temperature and atmospheric pressure using an indoor Pyrex simulation chamber coupled to Fourier transform infrared (FTIR) and UV-visible spectrometers. Rate constants for the reactions of vinyl acetate with OH, NO(3), and O(3) were equal to (2.3 +/- 0.3) x 10(-11), (7.3 +/- 1.8) x 10(-15), and (3.0 +/- 0.4) x 10(-18) cm(3) molecule(-1) s(-1), respectively. From these data, tropospheric lifetimes of vinyl acetate have been estimated as follows: tau(OH) = 6 h, tau(NO(3)) = 6 days, and tau(O(3)) = 5 days. This demonstrates that reaction with OH radicals is the main tropospheric loss process of this compound. From the mechanistic experiments, main oxidation products have been identified and quantified and oxidation schemes have been proposed for each studied reaction.

  12. In vitro solubility, dissolution and permeability studies combined with semi-mechanistic modeling to investigate the intestinal absorption of desvenlafaxine from an immediate- and extended release formulation.

    Science.gov (United States)

    Franek, F; Jarlfors, A; Larsen, F; Holm, P; Steffansen, B

    2015-09-18

    Desvenlafaxine is a biopharmaceutics classification system (BCS) class 1 (high solubility, high permeability) and biopharmaceutical drug disposition classification system (BDDCS) class 3, (high solubility, poor metabolism; implying low permeability) compound. Thus the rate-limiting step for desvenlafaxine absorption (i.e. intestinal dissolution or permeation) is not fully clarified. The aim of this study was to investigate whether dissolution and/or intestinal permeability rate-limit desvenlafaxine absorption from an immediate-release formulation (IRF) and Pristiq(®), an extended release formulation (ERF). Semi-mechanistic models of desvenlafaxine were built (using SimCyp(®)) by combining in vitro data on dissolution and permeation (mechanistic part of model) with clinical data (obtained from literature) on distribution and clearance (non-mechanistic part of model). The model predictions of desvenlafaxine pharmacokinetics after IRF and ERF administration were compared with published clinical data from 14 trials. Desvenlafaxine in vivo dissolution from the IRF and ERF was predicted from in vitro solubility studies and biorelevant dissolution studies (using the USP3 dissolution apparatus), respectively. Desvenlafaxine apparent permeability (Papp) at varying apical pH was investigated using the Caco-2 cell line and extrapolated to effective intestinal permeability (Peff) in human duodenum, jejunum, ileum and colon. Desvenlafaxine pKa-values and octanol-water partition coefficients (Do:w) were determined experimentally. Due to predicted rapid dissolution after IRF administration, desvenlafaxine was predicted to be available for permeation in the duodenum. Desvenlafaxine Do:w and Papp increased approximately 13-fold when increasing apical pH from 5.5 to 7.4. Desvenlafaxine Peff thus increased with pH down the small intestine. Consequently, desvenlafaxine absorption from an IRF appears rate-limited by low Peff in the upper small intestine, which "delays" the predicted

  13. Oxidation of alginate and pectate biopolymers by cerium(IV) in perchloric and sulfuric acid solutions: A comparative kinetic and mechanistic study.

    Science.gov (United States)

    Fawzy, Ahmed

    2016-03-15

    The kinetics of oxidation of alginate (Alg) and pectate (Pec) carbohydrate biopolymers was studied by spectrophotometry in aqueous perchloric and sulfuric acid solutions at fixed ionic strengths and temperature. In both acids, the reactions showed a first order dependence on [Ce(IV)], whereas the orders with respect to biopolymer concentrations are less than unity. In perchloric acid, the reactions exhibited less than unit orders with respect to [H(+)] whereas those proceeded in sulfuric acid showed negative fractional-first order dependences on [H(+)]. The effect of ionic strength and dielectric constant was studied. Probable mechanistic schemes for oxidation reactions were proposed. In both acids, the final oxidation products were characterized as mono-keto derivatives of both biopolymers. The activation parameters with respect to the slow step of the mechanisms were computed and discussed. The rate laws were derived and the reaction constants involved in the different steps of the mechanisms were calculated.

  14. Revealing the Mechanistic Pathway of Acid Activation of Proton Pump Inhibitors To Inhibit the Gastric Proton Pump: A DFT Study.

    Science.gov (United States)

    Jana, Kalyanashis; Bandyopadhyay, Tusar; Ganguly, Bishwajit

    2016-12-29

    Acid-related gastric diseases are associated with disorder of digestive tract acidification due to the acid secretion by gastric proton pump, H(+),K(+)-ATPase. Omeprazole is one of the persuasive irreversible inhibitor of the proton pump H(+),K(+)-ATPase. However, the reports on the mechanistic pathway of irreversible proton pump inhibitors (PPIs) on the acid activation and formation of disulfide complex are scarce in the literature. We have examined the acid activation PPIs, i.e., timoprazole, S-omeprazole and R-omeprazole using M062X/6-31++G(d,p) in aqueous phase with SMD solvation model. The proton pump inhibitor is a prodrug and activated in the acidic canaliculi of the gastric pump H(+),K(+)-ATPase to sulfenic acid which can either form another acid activate intermediate sulfenamide or a disulfide complex with cysteine amino acid of H(+),K(+)-ATPase. The quantum chemical calculations suggest that the transition state (TS5) for the disulfide complex formation is the rate-determining step of the multistep acid inhibition process by PPIs. The free energy barrier of TS5 is 5.5 kcal/mol higher for timoprazole compared to the S-omeprazole. The stability of the transition state for the formation of disulfide bond between S-omeprazole and cysteine amino acid of H(+),K(+)-ATPase is governed by inter- and intramolecular hydrogen bonding. The disulfide complex for S-omeprazole is thermodynamically more stable by 4.5 kcal/mol in aqueous phase compared to disulfide complex of timoprazole, which corroborates the less efficacy of timoprazole as irreversible PPI for acid inhibition process. It has been speculated that sulfenic acid can either form sulfenamide or a stable disulfide complex with cysteine amino acid residue of H(+),K(+)-ATPase. The M062X/6-31++G(d,p) level of theory calculated results reveal that the formation of tetra cyclic sulfenamide is unfavored by ∼17 kcal/mol for S-omeprazole and 11.5 kcal/mol for timoprazole compared to the disulfide complex formation

  15. Photodynamic therapy with the phthalocyanine photosensitizer Pc 4: the case experience with preclinical mechanistic and early clinical-translational studies.

    Science.gov (United States)

    Miller, Janine D; Baron, Elma D; Scull, Heather; Hsia, Andrew; Berlin, Jeffrey C; McCormick, Thomas; Colussi, Valdir; Kenney, Malcolm E; Cooper, Kevin D; Oleinick, Nancy L

    2007-11-01

    Photodynamic therapy (PDT) is emerging as a promising non-invasive treatment for cancers. PDT involves either local or systemic administration of a photosensitizing drug, which preferentially localizes within the tumor, followed by illumination of the involved organ with light, usually from a laser source. Here, we provide a selective overview of our experience with PDT at Case Western Reserve University, specifically with the silicon phthalocyanine photosensitizer Pc 4. We first review our in vitro studies evaluating the mechanism of cell killing by Pc 4-PDT. Then we briefly describe our clinical experience in a Phase I trial of Pc 4-PDT and our preliminary translational studies evaluating the mechanisms behind tumor responses. Preclinical work identified (a) cardiolipin and the anti-apoptotic proteins Bcl-2 and Bcl-xL as targets of Pc 4-PDT, (b) the intrinsic pathway of apoptosis, with the key participation of caspase-3, as a central response of many human cancer cells to Pc 4-PDT, (c) signaling pathways that could modify apoptosis, and (d) a formulation by which Pc 4 could be applied topically to human skin and penetrate at least through the basal layer of the epidermis. Clinical-translational studies enabled us to develop an immunohistochemical assay for caspase-3 activation, using biopsies from patients treated with topical Pc 4 in a Phase I PDT trial for cutaneous T-cell lymphoma. Results suggest that this assay may be used as an early biomarker of clinical response.

  16. Characterization of a new chronic lymphocytic leukemia cell line for mechanistic in vitro and in vivo studies relevant to disease.

    Directory of Open Access Journals (Sweden)

    Erin Hertlein

    Full Text Available Studies of chronic lymphocytic leukemia (CLL have yielded substantial progress, however a lack of immortalized cell lines representative of the primary disease has hampered a full understanding of disease pathogenesis and development of new treatments. Here we describe a novel CLL cell line (OSU-CLL generated by EBV transformation, which displays a similar cytogenetic and immunophenotype observed in the patient's CLL (CD5 positive with trisomy 12 and 19. A companion cell line was also generated from the same patient (OSU-NB. This cell line lacked typical CLL characteristics, and is likely derived from the patient's normal B cells. In vitro migration assays demonstrated that OSU-CLL exhibits migratory properties similar to primary CLL cells whereas OSU-NB has significantly reduced ability to migrate spontaneously or towards chemokine. Microarray analysis demonstrated distinct gene expression patterns in the two cell lines, including genes on chromosomes 12 and 19, which is consistent with the cytogenetic profile in this cell line. Finally, OSU-CLL was readily transplantable into NOG mice, producing uniform engraftment by three weeks with leukemic cells detectable in the peripheral blood spleen and bone marrow. These studies describe a new CLL cell line that extends currently available models to study gene function in this disease.

  17. Renal tubular and adrenal medullary tumors in the 2-year rat study with canagliflozin confirmed to be secondary to carbohydrate (glucose) malabsorption in the 15-month mechanistic rat study.

    Science.gov (United States)

    De Jonghe, Sandra; Johnson, Mark D; Mamidi, Rao N V S; Vinken, Petra; Feyen, Bianca; Lammens, Godelieve; Proctor, Jim

    2017-09-12

    During preclinical development of canagliflozin, an SGLT2 inhibitor, treatment-related pheochromocytomas, renal tubular tumors (RTT), and testicular Leydig cell tumors were reported in the 2-year rat toxicology study. In a previous 6-month rat mechanistic study, feeding a glucose free diet prevented canagliflozin effects on carbohydrate malabsorption as well as the increase in cell proliferation in adrenal medulla and kidneys, implicating carbohydrate malabsorption as the mechanism for tumor formation. In this chronic study male Sprague-Dawley rats were dosed orally with canagliflozin at high dose-levels (65 or 100 mg/kg/day) for 15 months and received either a standard diet or a glucose-free diet. Canagliflozin-dosed rats on standard diet showed presence of basophilic renal tubular tumors (6/90) and an increased incidence of adrenal medullary hyperplasia (35/90), which was fully prevented by feeding a glucose-free diet (no RTT's; adrenal medullary hyperplasia in ≤5/90). These data further confirm that kidney and adrenal medullary tumors in the 2-year rat study were secondary to carbohydrate (glucose) malabsorption and were not due to a direct effect of canagliflozin on these target tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Mechanistic Studies of Charge Injection from Metallic Electrodes into Organic Semiconductors Mediated by Ionic Functionalities: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Thuc-Quyen [UCSB; Bazan, Guillermo [UCSB; Mikhailovsky, Alexander [UCSB

    2014-04-15

    cost. During the execution of the project, main efforts were focused on the synthesis of new charge-bearing organic materials, such as CPEs and COEs, and block copolymers with neutral and ionic segments, studies of mechanisms responsible for the charge injection modulation in devices with ionic interlayers, and use of naturally occurring charged molecules for creation of enhanced devices. The studies allowed PIs to demonstrate the usefulness of the proposed approach for the improvement of operational parameters in model OLED and FET systems resulting in increased efficiency, decreased contact resistance, and possibility to use stable metals for fabrication of device electrodes. The successful proof-of-the-principle results potentially promise development of light-weight, low fabrication cost devices which can be used in consumer applications such as displays, solar cells, and printed electronic devices. Fundamental mechanisms responsible for the phenomena observed have been identified thus advancing the fundamental knowledgebase.

  19. Mechanistic models in computational social science

    Science.gov (United States)

    Holme, Petter; Liljeros, Fredrik

    2015-09-01

    Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes—to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to explore emergent phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influences from the natural and formal sciences. We argue that mechanistic computational models form a natural common ground for social and natural sciences, and look forward to possible future information flow across the social-natural divide.

  20. Mechanistic Models in Computational Social Science

    CERN Document Server

    Holme, Petter

    2015-01-01

    Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes -- to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to explore emerging phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influences from natural and formal sciences. We argue that mechanistic computational models form a natural common ground for social and natural sciences, and look forward to possible future information flow across the social-natural divide.

  1. Peptide inhibitor of complement C1 (PIC1, a novel suppressor of classical pathway activation: mechanistic studies and clinical potential

    Directory of Open Access Journals (Sweden)

    Julia A Sharp

    2014-08-01

    Full Text Available The classical pathway of complement plays multiple physiological roles including modulating immunological effectors initiated by adaptive immune responses as well as an essential homeostatic role in the clearance of damaged self-antigens. However, dysregulated classical pathway activation is associated with antibody-initiated, inflammatory diseases processes like cold agglutinin disease (CAD, acute intravascular hemolytic transfusion reaction (AIHTR and acute/hyperacute transplantation rejection. To date, only one putative classical pathway inhibitor, C1 esterase inhibitor (C1-INH, is currently commercially available and its only approved indication is for replacement treatment in hereditary angioedema (HAE, which is predominantly a kinin pathway disease. Given the variety of disease conditions in which the classical pathway is implicated, development of therapeutics that specifically inhibit complement initiation represents a major unmet medical need. Our laboratory has identified a peptide that specifically inhibits the classical and lectin pathways of complement. In vitro studies have demonstrated that these Peptide Inhibitors of Complement C1 (PIC1 bind to the collagen-like region of the initiator molecule of the classical pathway, C1q. PIC1 binding to C1q blocks activation of the associated serine proteases (C1s-C1r-C1r-C1s and subsequent downstream complement activation. Rational design optimization of PIC1 has resulted in the generation of a highly potent derivative of fifteen amino acids. PIC1 inhibits classical pathway mediated complement activation in ABO incompatibility in vitro as well as inhibiting classical pathway activation in vivo in rats. This review will focus on the pre-clinical development of PIC1 and discuss its potential as a therapeutic in antibody-mediated classical pathway disease, specifically AIHTR.

  2. Mechanistic species distribution modelling as a link between physiology and conservation.

    Science.gov (United States)

    Evans, Tyler G; Diamond, Sarah E; Kelly, Morgan W

    2015-01-01

    Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

  3. Controlled oxidation of aliphatic CH bonds in metallo-monooxygenases: mechanistic insights derived from studies on deuterated and fluorinated hydrocarbons.

    Science.gov (United States)

    Chen, Yao-Sheng; Luo, Wen-I; Yang, Chung-Ling; Tu, Yi-Jung; Chang, Chun-Wei; Chiang, Chih-Hsiang; Chang, Chi-Yao; Chan, Sunney I; Yu, Steve S-F

    2014-05-01

    The control over the regio- and/or stereo-selective aliphatic CH oxidation by metalloenzymes is of great interest to scientists. Typically, these enzymes invoke host-guest chemistry to sequester the substrates within the protein pockets, exploiting sizes, shapes and specific interactions such as hydrogen-bonding, electrostatic forces and/or van der Waals interactions to control the substrate specificity, regio-specificity and stereo-selectivity. Over the years, we have developed a series of deuterated and fluorinated variants of these hydrocarbon substrates as probes to gain insights into the controlled CH oxidations of hydrocarbons facilitated by these enzymes. In this review, we illustrate the application of these designed probes in the study of three monooxygenases: (i) the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath), which oxidizes straight-chain C1-C5 alkanes and alkenes to form their corresponding 2-alcohols and epoxides, respectively; (ii) the recombinant alkane hydroxylase (AlkB) from Pseudomonas putida GPo1, which oxidizes the primary CH bonds of C5-C12 linear alkanes; and (iii) the recombinant cytochrome P450 from Bacillus megaterium, which oxidizes C12-C20 fatty acids at the ω-1, ω-2 or ω-3 CH positions.

  4. Numerical simulation in steam injection process by a mechanistic approach

    Energy Technology Data Exchange (ETDEWEB)

    De Souza, J.C.Jr.; Campos, W.; Lopes, D.; Moura, L.S.S. [Petrobras, Rio de Janeiro (Brazil)

    2008-10-15

    Steam injection is a common thermal recovery method used in very viscous oil reservoirs. The method involves the injection of heat to reduce viscosity and mobilize oil. A steam generation and injection system consists primarily of a steam source, distribution lines, injection wells and a discarding tank. In order to optimize injection and improve the oil recovery factor, one must determine the parameters of steam flow such as pressure, temperature and steam quality. This study focused on developing a unified mathematical model by means of a mechanistic approach for two-phase steam flow in pipelines and wells. The hydrodynamic and heat transfer mechanistic model was implemented in a computer simulator to model the parameters of steam injection while trying to avoid the use of empirical correlations. A marching algorithm was used to determine the distribution of pressure and temperature along the pipelines and wellbores. The mathematical model for steam flow in injection systems, developed by a mechanistic approach (VapMec) performed well when the simulated values of pressures and temperatures were compared with the values measured during field tests. The newly developed VapMec model was incorporated in the LinVap-3 simulator that constitutes an engineering supporting tool for steam injection wells operated by Petrobras. 23 refs., 7 tabs., 6 figs.

  5. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    Science.gov (United States)

    Carraher, Jack McCaslin

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding 'greener' sources of commodity chemicals and fuels. High-valent Chromium from Hydroperoxido-Chromium(III). The decomposition of pentaaquahydroperoxido chromium(III) ion (hereafter Cr aqOOH2+) in acidic aqueous solutions is kinetically complex and generates mixtures of products (Craq3+, HCrO 4-, H2O2, and O2). The yield of high-valent chromium products (known carcinogens) increased from a few percent at pH 1 to 70 % at pH 5.5 (near biological pH). Yields of H 2O2 increased with acid concentration. The reproducibility of the kinetic data was poor, but became simplified in the presence of H2O2 or 2,2‧-azinobis(3-ethylbenzothiazoline-6-sulfonate) dianion (ABTS2-). Both are capable of scavenging strongly oxidizing intermediates). The observed rate constants (pH 1, [O2] ≤ 0.03 mM) in the presence of these scavengers are independent of [scavenger] and within the error are the same (k,ABTS2- = (4.9 +/- 0.2) x 10-4 s-1 and kH2O2 = (5.3 +/- 0.7) x 10-4 s-1); indicating involvement of the scavengers in post-rate determining steps. In the presence of either scavenger, decomposition of CrOOH2+ obeyed a two-term rate law, k obs / s-1 = (6.7 +/- 0.7) x 10-4 + (7.6 +/- 1.1) x 10-4 [H+]. Effect of [H+] on the kinetics and the product distribution, cleaner kinetics in the presence of scavengers, and independence of kobs on [scavenger] suggest a dual-pathway mechanism for the decay of Craq OOH2+. The H+-catalyzed path

  6. DFT mechanistic study of the selective terminal C–H activation of n-pentane with a tungsten allyl nitrosyl complex

    National Research Council Canada - National Science Library

    Lee, Richmond; Tan, Davin; Liu, Chaoli; Li, Huaifeng; Guo, Hao; Shyue, Jing-Jong; Huang, Kuo-Wei

    2017-01-01

    Mechanistic insights into the selective C–H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using...

  7. Mechanistic studies on the lipid-raising coffee diterpenes cafestol and kahweol in monkeys, mice and man

    NARCIS (Netherlands)

    Roos, de B.

    2000-01-01

    Cafestol and kahweol are lipid-raising diterpenes present in unfiltered coffee. The objective of this thesis was to study their lipid-raising action in man. Unravelling this action might lead to new insights into the regulation of serum cholesterol levels.We first studied the absorption and urinary

  8. Gold-Catalyzed β-Regioselective Formal [3 + 2] Cycloaddition of Ynamides with Pyrido[1,2-b]indazoles: Reaction Development and Mechanistic Insights.

    Science.gov (United States)

    Yu, Yinghua; Chen, Gui; Zhu, Lei; Liao, Yun; Wu, Yufeng; Huang, Xueliang

    2016-09-16

    Here, we report an unprecedented gold(I)-induced β-site regioselective formal [3 + 2] cycloaddition of ynamides with pyrido[1,2-b]indazoles, giving 3-amido-7-(pyrid-2'-yl)indoles in good to excellent yields. A complex of gold(I) catalyst with ynamide was isolated and characterized by X-ray diffraction analysis for the first time. Mechanistic investigations suggest the reaction pathway involves a gold-stabilized carbocation intermediate, which in turn participated in sequential C-H bond functionalization of the ortho-position of the phenyl ring.

  9. Lanthanide-Doped KLu2F7 Nanoparticles with High Upconversion Luminescence Performance: A Comparative Study by Judd-Ofelt Analysis and Energy Transfer Mechanistic Investigation

    Science.gov (United States)

    Xu, Dekang; Li, Anming; Yao, Lu; Lin, Hao; Yang, Shenghong; Zhang, Yueli

    2017-02-01

    The development, design and the performance evaluation of rare-earth doped host materials is important for further optical investigation and industrial applications. Herein, we successfully fabricate KLu2F7 upconversion nanoparticles (UCNPs) through hydrothermal synthesis by controlling the fluorine-to-lanthanide-ion molar ratio. The structural and morphological results show that the samples are orthorhombic-phase hexagonal-prisms UCNPs, with average side length of 80 nm and average thickness of 110 nm. The reaction time dependent crystal growth experiment suggests that the phase transformation is a thermo-dynamical process and the increasing F-/Ln3+ ratio favors the formation of the thermo-dynamical stable phase - orthorhombic KLu2F7 structure. The upconversion luminescence (UCL) spectra display that the orthorhombic KLu2F7:Yb/Er UCNPs present stronger UCL as much as 280-fold than their cubic counterparts. The UCNPS also display better UCL performance compared with the popular hexagonal-phase NaREF4 (RE = Y, Gd). Our mechanistic investigation, including Judd-Ofelt analysis and time decay behaviors, suggests that the lanthanide tetrad clusters structure at sublattice level accounts for the saturated luminescence and highly efficient UCL in KLu2F7:Yb/Er UCNPs. Our research demonstrates that the orthorhombic KLu2F7 is a promising host material for UCL and can find potential applications in lasing, photovoltaics and biolabeling techniques.

  10. Biological dosimetry: Mechanistic concepts

    Energy Technology Data Exchange (ETDEWEB)

    Preston, R.J.

    1990-01-01

    The study of the induction of chromosome aberrations by ionizing radiations has a 50 year history, having its initiation in the pioneering work of Karl Sax. Lea and his colleagues provided a more mathematical description of dose response curves and the effects of split doses, that allowed for the development of studies to better understand the process by which radiation induced chromosome aberrations. Subsequent studies have refined our understanding of the mechanism of induction, but many of the questions raised by these original studies still remain unanswered. It is the intention of this short review to revisit some of the questions pertinent to the mechanism of induction of chromosome aberrations and provide a personal view of what I think is happening. 19 refs.

  11. Flattened-Top Domical Water Drops Formed through Self-Organization of Hydrophobin Membranes: A Structural and Mechanistic Study Using Atomic Force Microscopy.

    Science.gov (United States)

    Yamasaki, Ryota; Takatsuji, Yoshiyuki; Asakawa, Hitoshi; Fukuma, Takeshi; Haruyama, Tetsuya

    2016-01-26

    The Trichoderma reesei hydrophobin, HFBI, is a unique structural protein. This protein forms membranes by self-organization at air/water or water/solid interfaces. When HFBI forms a membrane at an air/water interface, the top of the water droplet is flattened. The mechanism underlying this phenomenon has not been explored. In this study, this unique phenomenon has been investigated. Self-organized HFBI membranes form a hexagonal structured membrane on the surface of water droplets; the structure was confirmed by atomic force microscopy (AFM) measurement. Assembled hexagons can form a planar sheet or a tube. Self-organized HFBI membranes on water droplets form a sheet with an array of hexagonal structures or a honeycomb structure. This membrane, with its arrayed hexagonal structures, has very high buckling strength. We hypothesized that the high buckling strength is the reason that water droplets containing HFBI form flattened domes. To test this hypothesis, the strength of the self-organized HFBI membranes was analyzed using AFM. The buckling strength of HFBI membranes was measured to be 66.9 mN/m. In contrast, the surface tension of water droplets containing dissolved HFBI is 42 mN/m. Thus, the buckling strength of a self-organized HFBI membrane is higher than the surface tension of water containing dissolved HFBI. This mechanistic study clarifies why the water droplets formed by self-organized HFBI membranes have a flattened top.

  12. Palladium(II)-catalyzed desulfitative synthesis of aryl ketones from sodium arylsulfinates and nitriles: scope, limitations, and mechanistic studies.

    Science.gov (United States)

    Skillinghaug, Bobo; Sköld, Christian; Rydfjord, Jonas; Svensson, Fredrik; Behrends, Malte; Sävmarker, Jonas; Sjöberg, Per J R; Larhed, Mats

    2014-12-19

    A fast and efficient protocol for the palladium(II)-catalyzed production of aryl ketones from sodium arylsulfinates and various organic nitriles under controlled microwave irradiation has been developed. The wide scope of the reaction has been demonstrated by combining 14 sodium arylsulfinates and 21 nitriles to give 55 examples of aryl ketones. One additional example illustrated that, through the choice of the nitrile reactant, benzofurans are also accessible. The reaction mechanism was investigated by electrospray ionization mass spectrometry and DFT calculations. The desulfitative synthesis of aryl ketones from nitriles was also compared to the corresponding transformation starting from benzoic acids. Comparison of the energy profiles indicates that the free energy requirement for decarboxylation of 2,6-dimethoxybenzoic acid and especially benzoic acid is higher than the corresponding desulfitative process for generating the key aryl palladium intermediate. The palladium(II) intermediates detected by ESI-MS and the DFT calculations provide a detailed understanding of the catalytic cycle.

  13. Ni adsorption and Ni-Al LDH precipitation in a sandy aquifer: An experimental and mechanistic modeling study

    NARCIS (Netherlands)

    Regelink, I.C.; Temminghoff, E.J.M.

    2011-01-01

    Mining activities and industries have created nickel (Ni) contaminations in many parts of the world. The objective of this study is to increase our understanding of Ni adsorption and Nickel-Aluminium Layered Double Hydroxide (Ni-Al LDH) precipitation to reduce Ni mobility in a sandy soil aquifer. At

  14. Intermanual Transfer Effect in Young Children After Training in a Complex Skill : Mechanistic, Pseudorandomized, Pretest-Posttest Study

    NARCIS (Netherlands)

    Romkema, Sietske; Bongers, Raoul M.; van der Sluis, Corry K.

    2015-01-01

    Background. Intermanual transfer implies that motor skills learned on one side of the body transfer to the untrained side. This effect was previously noted in adults practicing with a prosthesis simulator. Objective. The study objective was to determine whether intermanual transfer is present in chi

  15. Intermanual Transfer in Training With an Upper-Limb Myoelectric Prosthesis Simulator : A Mechanistic, Randomized, Pretest-Posttest Study

    NARCIS (Netherlands)

    Romkema, Sietske; Bongers, Raoul M.; van der Sluis, Corry K.

    2013-01-01

    Background. Intermanual transfer may improve prosthetic handling and acceptance if used in training soon after an amputation. Objective. The purpose of this study was to determine whether intermanual transfer effects can be detected after training with a myoelectric upper-limb prosthesis simulator.

  16. Mechanistic studies of flux variability of neutral and ionic permeants during constant current dc iontophoresis with human epidermal membrane.

    Science.gov (United States)

    Li, S Kevin; Higuchi, William I; Kochambilli, Rajan P; Zhu, Honggang

    2004-04-01

    Although constant current iontophoresis is supposed to provide constant transdermal transport, significant flux variability and/or time-dependent flux drifts are observed during iontophoresis with human skin in vitro and human studies in vivo. The objectives of the present study were to determine (a) the causes of flux variability in constant current dc transdermal iontophoresis and (b) the relationships of flux variabilities among permeants of different physicochemical properties. Changes in the human epidermal membrane (HEM) effective pore size and/or electroosmosis during constant current dc iontophoresis were examined. Tetraethylammonium ion (TEA), urea, and mannitol were the model permeants. For the neutral permeants, the results in the present study showed a significant increase of fluxes with time in a given experiment and large HEM sample-to-sample variability. Although both effective pore size and pore charge density variations contributed to the time-dependent flux drifts observed in electroosmotic transport, the significant flux drifts observed were found to be primarily a result of the time-dependent increase in effective pore charge density. For the ionic permeant, the observed flux variability was smaller than that of the neutral permeants and was believed to be primarily due to effective pore size alteration in HEM during iontophoresis as suggested in a previous study. The different extents of flux variability observed between neutral and ionic permeants are consistent with the different iontophoretically enhanced transport mechanisms for the neutral and ionic permeants (i.e. electroosmosis and electrophoresis, respectively). The results of the present study also demonstrate that flux variability of two neutral permeants are inter-related, so the flux of one neutral permeant can be predicted if the permeability coefficient of the other neutral permeant is known.

  17. Isotopic effects in mechanistic studies of biotransformations of fluorine derivatives of L-alanine catalysed by L-alanine dehydrogenase.

    Science.gov (United States)

    Szymańska-Majchrzak, Jolanta; Pałka, Katarzyna; Kańska, Marianna

    2017-05-01

    Synthesis of 3-fluoro-[2-(2)H]-L-alanine (3-F-[(2)H]-L-Ala) in reductive amination of 3-fluoropyruvic acid catalysed by L-alanine dehydrogenase (AlaDH) was described. Fluorine derivative was used to study oxidative deamination catalysed by AlaDH applied kinetic (for 3-F-L-Ala in H2O - KIE's on Vmax: 1.1; on Vmax/KM: 1.2; for 3-F-L-Ala in (2)H2O - on Vmax: 1.4; on Vmax/KM: 2.1) and solvent isotope effect methods (for 3-F-L-Ala - SIE's on Vmax: 1.0; on Vmax/KM: 0.87; for 3-F-[2-(2)H]-L-Ala - on Vmax: 1.4; on Vmax/KM: 1.5). Studies explain some details of reaction mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Mechanistic study of programmed cell death of root border cells of cucumber (Cucumber sativus L.) induced by copper.

    Science.gov (United States)

    Sun, Lijuan; Song, Jie; Peng, Cheng; Xu, Chen; Yuan, Xiaofeng; Shi, Jiyan

    2015-12-01

    Programmed cell death (PCD) in root border cells (RBCs) induced by Copper (Cu) has been little studied. This study explored whether Cu induced PCD in RBCs of cucumber or not and investigated the possible mechanisms. The results showed that the percentage of apoptotic and necrotic RBCs increased with increasing concentration of Cu treatment. A quick burst of ROS in RBCs was detected, while mitochondrial membrane potential (ΔΨm) decreased sharply with Cu treatment. Caspase-3 like protease activity showed a tendency of increase with Cu treatment. The potential of Cu to induce PCD in RBCs of cucumber was first proved. Our results showed that ROS generation and mitochondrial membrane potential loss played important roles in Cu-induced caspase-3-like activation and PCD in RBCs of cucumber, which provided new insight into the signaling cascades that modulate Cu phytotoxicity mechanism.

  19. Mechanistic studies of the oxygen evolution reaction by a cobalt-phosphate catalyst at neutral pH.

    Science.gov (United States)

    Surendranath, Yogesh; Kanan, Matthew W; Nocera, Daniel G

    2010-11-24

    The mechanism of the oxygen evolution reaction (OER) by catalysts prepared by electrodepositions from Co(2+) solutions in phosphate electrolytes (Co-Pi) was studied at neutral pH by electrokinetic and (18)O isotope experiments. Low-potential electrodepositions enabled the controlled preparation of ultrathin Co-Pi catalyst films (oxygen from water in neutral solutions. The electrochemical rate law exhibits an inverse first order dependence on proton activity and a zeroth order dependence on phosphate for [Pi] ≥ 0.03 M. In the absence of phosphate buffer, the Tafel slope is increased ∼3-fold and the overall activity is greatly diminished. Together, these electrokinetic studies suggest a mechanism involving a rapid, one electron, one proton equilibrium between Co(III)-OH and Co(IV)-O in which a phosphate species is the proton acceptor, followed by a chemical turnover-limiting process involving oxygen-oxygen bond coupling.

  20. Achieving Reversible H2/H+ Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study

    Energy Technology Data Exchange (ETDEWEB)

    Priyadarshani, Nilusha; Dutta, Arnab; Ginovska-Pangovska, Bojana; Buchko, Garry W.; O' Hagan, Molly J.; Raugei, Simone; Shaw, Wendy J.

    2016-09-02

    Inspired by the contribution of the protein scaffold to the efficiency with which enzymes function, we report the first molecular complex that is reversible for electrocatalytic H2 production/oxidation at room temperature in methanol. [Ni(PCy2NPhe2)2]2+ (CyPhe; PR2NR’2 = 1,5-diaza-3,7-diphosphacyclooctane, Cy=cyclohexyl, Phe=phenylalanine), shows reversible behavior in acidic methanol with peripheral phenylalanine groups providing key contributions to the catalytic behavior. The importance of the aromatic rings is implicated in achieving reversibility, based on the lack of reversibility of similar complexes, [Ni(PCy2NAmino Acid2)2]2+, containing arginine (CyArg) or glycine (CyGly). A complex with an added OH group on the ring, (CyTyr; Tyr=Tyrosine), also shows similar behavior. NMR studies reveal a significantly slower rate of chair-boat isomerization for the CyPhe relative to other derivatives, suggesting that the aromatic groups provide structural control by interacting with each other, an observation supported by molecular dynamics studies. NMR studies also show extremely fast proton movement, with a proton pathway from the Ni-H through the pendant amine to the –COOH group. Further, studies of acomplex without the –COOH group, [Ni(PCy2NTym2)2]2+ (CyTym; Tym=Tyramine), are not reversible and have slow proton movement from the pendant amine, demonstrating the essential nature of the –COOH group in achieving reversibility. Finally, methanol is demonstrated to play a critical contributing role. The influence of multiple factors on reversibility for this synthetic catalyst is a demonstration of the intricate interplay between the first, second, and outer coordination spheres and resembles the complexity observed in metalloenzymes.

  1. Mechanistic and conformational studies on the interaction of anti-inflammatory drugs, isoxicam and tenoxicam with bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Punith, Reeta; Katrahalli, Umesha; Kalanur, Shankara S. [Department of Chemistry, Karnatak University, Dharwad 580 003 (India); Jaldappagari, Seetharamappa, E-mail: jseetharam@yahoo.co [Department of Chemistry, Karnatak University, Dharwad 580 003 (India)

    2010-11-15

    The mechanism of interaction of the non-steroidal anti-inflammatory drugs, isoxicam (IXM) and tenoxicam (TXM) with bovine serum albumin (BSA) has been studied using spectroscopic techniques, viz., spectrofluorescence, circular dichroism (CD), UV-visible absorption and FT-IR under simulative physiological conditions. Stern-Volmer analysis of fluorescence quenching data shows the presence of the static quenching mechanism. Thermodynamic parameters (negative {Delta}H{sup 0} and positive {Delta}S{sup 0} values obtained in the present study) revealed that the hydrophobic interactions played a major role in the interaction of these drugs with BSA. The distance, r between the donor (BSA) and acceptor (IXM/TXM) was calculated based on the Forster's theory of non-radiation energy transfer and the values were observed to be 3.85 nm and 2.60 nm in IXM-BSA and TXM-BSA system, respectively. CD and FT-IR studies indicated that the binding of IXM/TXM to BSA induced conformational changes in BSA. The effect of common ions on the binding of IXM/TXM to BSA has been investigated.

  2. Oxidation of tricyclic antidepressant drugs with chloramine-T in acidic solutions: kinetic, mechanistic and thermodynamic studies.

    Science.gov (United States)

    Sukhdev, Anu; Puttaswamy, Puttaswamy

    2013-12-01

    The kinetics of the oxidation of two tricyclic antidepressants (TCA) namely, imipramine (IMP) and clomipramine (CLM) with sodium N-chloro-p-toluenesulfonamide or chloramine-T (CAT) in HClO4 medium was studied at 300 K. The two reactions followed identical kinetics with a first-order dependence of rate on [CAT]o and fractional order dependence on [TCA]o. The reaction is catalyzed by H(+) ions with a fractional order dependence. The reaction was studied at different temperatures and activation parameters were evaluated. The reaction constants involved in the mechanism were computed. The solvent isotope effect was studied using D2O. Addition of p-toluenesulfonamide retards the reaction rate. The rate increased with decreasing dielectric constant of the medium. Variation of ionic strength of the medium and addition of halide ions (Cl(-) or Br(-)) showed no effect on the rate. The stoichiometry of the reaction was found to be 1:1 and the oxidation products were identified as imipramine-5-N-oxide and clomipramine-5-N-oxide. The rate of oxidation of IMP is faster than CLM. The observed results have been explained in terms of a mechanism and a relevant rate law has been deduced.

  3. Chelated Nitrogen-Sulphur-Codoped TiO2: Synthesis, Characterization, Mechanistic, and UV/Visible Photocatalytic Studies

    Directory of Open Access Journals (Sweden)

    Hayat Khan

    2017-01-01

    Full Text Available This study presents in detail the physicochemical, photoluminescent, and photocatalytic properties of carboxylic acid chelated nitrogen-sulphur-codoped TiO2. From the Fourier transform infrared spectroscopic study, it was revealed that the formate group formed bidentate bridging linkage while the acetate group coordinated in a bidentate chelating mode with a titanium precursor. In compliance with X-ray diffraction data, the anatase to rutile transformation temperature was extended due to carboxylic acid chelation and NS codoping. Raman analysis indicated four Raman peaks at 146, 392, 512, and 632 cm−1 for the precalcined chelated TiO2; on incorporation with NS dopants, an increase in Raman intensity for these peaks was recorded, indicating the structure stability of the anatase phase. Furthermore, X-ray photoelectron spectroscopic study revealed the presence of anionic doping of nitrogen and cationic doping of sulphur in the lattice of TiO2. When evaluating the UV-visible photodegradation rate of 4-chlorophenol, the modified TiO2 (NS0.06-TFA showed the highest photocatalytic activity. In connection with the activity tests, several scavenger agents were employed to elucidate the significance of the different reactive oxidizing species during the photocatalytic process. Moreover, the transfer pathways of photogenerated carriers and the photocatalytic reaction mechanism of modified TiO2 were also explained in detail.

  4. Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch

    Science.gov (United States)

    Howe, John A.; Xiao, Li; Fischmann, Thierry O.; Wang, Hao; Tang, Haifeng; Villafania, Artjohn; Zhang, Rumin; Barbieri, Christopher M.; Roemer, Terry

    2016-01-01

    ABSTRACT Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil is structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs. PMID:27485612

  5. Antihypertensive Effects of Hydroalcoholic Extract of Crataegus Azarolus Subspecies Aronia Fruit in Rats with Renovascular Hypertension: An Experimental Mechanistic Study.

    Science.gov (United States)

    Haydari, Mohammad Reza; Panjeshahin, Mohammad Reza; Mashghoolozekr, Elaheh; Nekooeian, Ali Akbar

    2017-05-01

    Hawthorn species decreases blood pressure and relaxes precontracted vessels. This study aimed at examining the antihypertensive effect and related mechanisms of hydroalcoholic extract of Crataegus azarolus subspecies aronia fruit in rats with renovascular hypertension. Six groups of male Sprague-Dawley rats, each containing 6 to 8 rats, were studied. The groups comprised of one sham group and 5 renal artery-clipped groups. The sham group received vehicle (distilled water 0.5 ml/day) and the renal artery-clipped groups received vehicle or the extract at 5, 10, 20 or 30 mg/kg/day. Oral vehicle or extract was administered daily for 4 weeks following sham-operation or induction of hypertension. Systolic blood pressure and heart rate were measured weekly. Isolated aorta study was performed by last week and serum superoxide dismutase and glutathione reductase were measured. The findings were analyzed using one-way analysis of variance and Duncan's multiple range tests at P≤0.05 using SigmaStat software. The data obtained after 4 weeks of treatment showed that the renal artery-clipped group receiving vehicle had significantly higher systolic blood pressure (P=0.002) and phenylephrine maximal response (P=0.01); and lower acetylcholine maximal response (P=0.01), serum superoxide dismutase (P=0.006) and serum glutathione reductase (P=0.006) than those of the sham group. The renal artery-clipped group receiving extract had significantly lower systolic blood pressure (P=0.03) and phenylephrine maximal response (P=0.01); and significantly higher acetylcholine maximal response (P=0.01), serum superoxide dismutase (P=0.015), and serum glutathione reductase (P=0.015) than those of the renal artery-clipped group receiving vehicle. Our findings show that the hydroalcoholic extract of Crataegus azarolus subspecies aronia fruit has antihypertensive effects, which may be partly due to antioxidant and nitric oxide releasing effects.

  6. Antihypertensive Effects of Hydroalcoholic Extract of Crataegus Azarolus Subspecies Aronia Fruit in Rats with Renovascular Hypertension: An Experimental Mechanistic Study

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Haydari

    2017-05-01

    Full Text Available Background: Hawthorn species decreases blood pressure and relaxes precontracted vessels. This study aimed at examining the antihypertensive effect and related mechanisms of hydroalcoholic extract of Crataegus azarolus subspecies aronia fruit in rats with renovascular hypertension. Methods: Six groups of male Sprague-Dawley rats, each containing 6 to 8 rats, were studied. The groups comprised of one sham group and 5 renal artery-clipped groups. The sham group received vehicle (distilled water 0.5 ml/day and the renal artery-clipped groups received vehicle or the extract at 5, 10, 20 or 30 mg/kg/day. Oral vehicle or extract was administered daily for 4 weeks following sham-operation or induction of hypertension. Systolic blood pressure and heart rate were measured weekly. Isolated aorta study was performed by last week and serum superoxide dismutase and glutathione reductase were measured. The findings were analyzed using one-way analysis of variance and Duncan’s multiple range tests at P≤0.05 using SigmaStat software. Results: The data obtained after 4 weeks of treatment showed that the renal artery-clipped group receiving vehicle had significantly higher systolic blood pressure (P=0.002 and phenylephrine maximal response (P=0.01; and lower acetylcholine maximal response (P=0.01, serum superoxide dismutase (P=0.006 and serum glutathione reductase (P=0.006 than those of the sham group. The renal artery-clipped group receiving extract had significantly lower systolic blood pressure (P=0.03 and phenylephrine maximal response (P=0.01; and significantly higher acetylcholine maximal response (P=0.01, serum superoxide dismutase (P=0.015, and serum glutathione reductase (P=0.015 than those of the renal artery-clipped group receiving vehicle. Conclusion: Our findings show that the hydroalcoholic extract of Crataegus azarolus subspecies aronia fruit has antihypertensive effects, which may be partly due to antioxidant and nitric oxide releasing effects.

  7. Effective Chirality Transfer in [3+2] Reaction between Allenyl-Rhodium and Enal: Mechanistic Study Based on DFT Calculations.

    Science.gov (United States)

    Qi, Xiaotian; Liu, Song; Zhang, Tao; Long, Rong; Huang, Jun; Gong, Jianxian; Yang, Zhen; Lan, Yu

    2016-09-16

    Theoretical calculation was performed to study the chirality transfer in a newly reported intramolecular [3+2] cycloaddition of enal and alleno rhodium species, generated in situ from an enynol precursor. [3.3.0] bicyclic system which contains two bridgehead quaternary carbons that can be achieved, the chirality of which are controlled by those of the starting material, and the product stereoselectivity is only determined by the α-position of the acetylene moiety. Density functional theory calculations predicted that only the cis [3.3.0] bicyclic product could be generated, regardless of either erythro or threo substrate, which was also confirmed by experimental observations.

  8. Synthetic Applications and Mechanistic Studies of the Hydroxide-Mediated Cleavage of Carbon-Carbon Bonds in Ketones

    DEFF Research Database (Denmark)

    Mazziotta, Andrea; Makarov, Ilya S.; Fristrup, Peter

    2017-01-01

    The hydroxide-mediated cleavage of ketones into alkanes and carboxylic acids has been reinvestigated and the substrate scope extended to benzyl carbonyl compounds. The transformation is performed with a 0.05 M ketone solution in refluxing xylene in the presence of 10 equiv of potassium hydroxide....... The studies were complemented by a theoretical investigation where two possible pathways were characterized by DFT/M06-2X. The calculations showed that the scission takes place by nucleophilic attack of hydroxide on the ketone followed by fragmentation of the resulting oxyanion into the carboxylic acid...

  9. Mechanistic and comparative studies of melatonin and classic antioxidants in terms of their interactions with the ABTS cation radical.

    Science.gov (United States)

    Tan, Dun-xian; Hardeland, Rüdiger; Manchester, Lucien C; Poeggeler, Burkhard; Lopez-Burillo, Silvia; Mayo, Juan C; Sainz, Rosa M; Reiter, Russel J

    2003-05-01

    Melatonin and classic antioxidants possess the capacity to scavenge ABTSb+ with IC50s of 4, 11, 15.5, 15.5, 17 and 21 microm for melatonin, glutathione, vitamin C, trolox, NADH and NADPH, respectively. In terms of scavenging ABTSb+, melatonin exhibits a different profile than that of the classic antioxidants. Classic antioxidants scavenge one or less ABTSb+, while each melatonin molecule can scavenge more than one ABTSb+, probably with a maximum of four. Classic antioxidants do not synergize when combined in terms of scavenging ABTSb+. However, a synergistic action is observed when melatonin is combined with any of the classic antioxidants. Cyclic voltammetry indicates that melatonin donates an electron at the potential of 715 mV. The scavenging mechanism of melatonin on ABTSb+ may involve multiple-electron donations via intermediates through a stepwise process. Intermediates including the melatoninyl cation radical, the melatoninyl neutral radical and cyclic 3-hydroxymelatonin (cyclic 3-OHM) and N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK) seem to participate in these reactions. More interestingly, the pH of the solution dramatically modifies the ABTSb+ scavenging capacity of melatonin while pH changes have no measurable influence on the scavenging activity of classic antioxidants. An acidic pH markedly reduces the ABTSb+ scavenging capacity of melatonin while an increased pH promotes the interaction of melatonin and ABTSb+. The major melatonin metabolites that develop when melatonin interacts with ABTSb+ are cyclic 3-OHM and AFMK. Cyclic 3-OHM is the intermediate between melatonin and AFMK, and cyclic 3-OHM also has the ability to scavenge ABTSb+. Melatonin and the metabolites which are generated via the interaction of melatonin with ABTSb+, i.e. the melatoninyl cation radical, melatoninyl neutral radical and cyclic 3-OHM, all scavenge ABTSb+. This unique cascade action of melatonin, in terms of scavenging, increases its efficiency to neutralized ABTSb+; this

  10. Experimental and Computational Mechanistic Studies Guiding the Rational Design of Molecular Electrocatalysts for Production and Oxidation of Hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Raugei, Simone; Helm, Monte L.; Hammes-Schiffer, Sharon; Appel, Aaron M.; O' Hagan, Molly J.; Wiedner, Eric S.; Bullock, R. Morris

    2016-01-19

    Understanding how to control the movement of protons and electrons is crucial to the design of fast, efficient electrocatalysts for hydrogen production and oxidation based on earth-abundant metals. Our work seeks to elucidate fundamental questions about proton movement. We have demonstrated that incorporating a pendant amine functioning as a proton relay in the second coordination sphere of a metal complex helps proton mobility, resulting in faster and more energy efficient catalysts. Proton transfer reactions are often rate limiting, and are influenced by several factors, such as pKa values, steric effects, hydrogen bonding, and solvation/desolvation of the exogenous base and acid employed. The presence of multiple protonation sites introduces branching points along the catalytic cycle, making less productive pathways accessible, or leading to the formation of stable off-cycle species. Using ligands with only one pendant amine mitigates this problem and results in catalysts with high rates for production of H2. For H2 oxidation catalysts, iron complexes with a high H2 binding affinity were developed. However, the improvement of H2 binding enthalpy resulted in a pKa mismatch between the protonated metal center and the protonated pendant amine, and consequently to rate-limiting intramolecular proton movement. Taken altogether, our results demonstrate the necessity of optimizing the entire catalytic cycle, as the optimization of a specific catalytic step can negatively influence another step, and not necessarily lead to better catalytic performance. We discuss a general procedure, based on thermodynamic arguments, which allows the simultaneous minimization of the free energy change of each catalytic step, yielding a nearly flat free energy surface, with no large barriers due to energy mismatches from either high- or low-energy intermediates. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by

  11. Kinetics and Mechanistic Studies on Oxidation of Levocarnitine by Bromamine-T in HCl Medium Catalyzed by Ru(III

    Directory of Open Access Journals (Sweden)

    R. Ramachandrappa

    2013-01-01

    Full Text Available A kinetic study on RuCl3-catalysed oxidation of levocarnitine (LC by sodium N-bromo-p-toluenesulphonamide or bromamine-T (BAT has been carried out in HCl medium at 303 K. The reaction rate shows a first order dependence on [BAT]0 and fractional order with respect to both [LC]0 and [H+]. Addition of the reaction product, p-toluenesulphonamide, retards the rate. The addition of RuCl3 and chloride ions to the reaction mixture shows an increase in the rate of the reaction. The dielectric effect is positive. The variation of ionic strength of the medium has no significant effect on the rate of the reaction. The reaction fails to initiate polymerization of acrylamide. Michaelis-Menten type of kinetics has been proposed. Thermodynamic parameters have been computed from Arrhenius plot by studying the reaction at different temperatures. The reaction stoichiometry and oxidation products were identified. Based on the experimental observations a suitable mechanism was proposed and rate law deduced.

  12. Theoretical Mechanistic and Kinetic Studies on Homogeneous Gas-Phase Formation of Polychlorinated Naphthalene from 2-Chlorophenol as Forerunner

    Directory of Open Access Journals (Sweden)

    Fei Xu

    2015-10-01

    Full Text Available Polychlorinated naphthalenes (PCNs are dioxins-like compounds and are formed along with polychlorinated dibenzo-p-dioxins (PCDDs and polychlorinated dibenzofurans (PCDFs in thermal and combustion procedures. Chlorophenols (CPs are the most important forerunners of PCNs. A comprehensive comprehension of PCN formation procedure from CPs is a precondition for reducing the discharge of PCNs. Experiments on the formation of PCNs from CPs have been hindered by PCN toxicity and short of precise detection methods for active intermediate radicals. In this work, PCN formation mechanism in gas-phase condition from 2-chlorophenol (2-CP as forerunner was studied by quantum chemistry calculations. Numbers of energetically advantaged formation routes were proposed. The rate constants of key elementary steps were calculated over 600–1200 K using canonical variational transition-state theory (CVT with small curvature tunneling contribution (SCT method. This study illustrates formation of PCNs with one chlorine atom loss from 2-CP is preferred over that without chlorine atom loss. In comparison with formation of PCDFs from 2-CP, PCN products are less chlorinated and have lower formation potential.

  13. Temperature-dependent spectroscopic evidences of curcumin in aqueous medium: a mechanistic study of its solubility and stability.

    Science.gov (United States)

    Jagannathan, Ramya; Abraham, Priya Mary; Poddar, Pankaj

    2012-12-20

    In curcumin, keto-enol-enolate equilibrium of the heptadiene-dione moiety determines its physiochemical and antioxidant properties. However, its poor solubility in water at neutral pH and room temperature decreases its bioavailability. Potential therapeutic applications have triggered an interest in manipulating the solubility of curcumin in water as its stability and solubility in water remains poorly understood. Here, the mechanism behind its solubility at various temperatures and the influence of interplay of temperature, intramolecular H-bonding, and intermolecular forces is reported, which leads to aggregation-disaggregation at various temperatures. Remarkable change is observed in temperature-dependent electronic transition behavior of curcumin, however, the absorption spectra after cooling and heating cycles remain unchanged, hinting much better thermal stability of curcumin in water than previously thought. This study indicates that it is perhaps the breaking of intramolecular hydrogen bonding which leads to exposure of polar groups and hence responsible for the dissolution of curcumin at higher temperature. The formation of intermolecular aggregates might be responsible behind a better room temperature stability of the molecules after cooling its aqueous suspension from 90 to 25 °C. These curcumin solubility studies have great application in biological research with reference to bioavailability and to understand target oriented mode of action of curcumin.

  14. Mechanistic study of ruthenium (III) catalysed oxidation of L-lysine by diperiodatoargentate (III) in aqueous alkaline medium

    Indian Academy of Sciences (India)

    R R Hosamani; S T Nandibewoor

    2009-05-01

    The kinetics of Ru(III) catalysed oxidation of L-lysine by diperiodatoargentate (III) (DPA) in alkaline medium at 298 K and a constant ionic strength of 0.50 mol dm-3 was studied spectrophotometrically. The oxidation products are aldehyde (5-aminopentanal) and Ag (I). The stoichiometry is i.e. [L-lysine] : [DPA] = 1 : 1. The reaction is of first order in [Ru(III)] and [DPA] and is less than unit order in both [L-lys] and [alkali]. Addition of periodate had a retarding effect on the reaction. The oxidation reaction in alkaline medium has been shown to proceed via a Ru(III)-L-lysine complex, which further reacts with one molecule of monoperiodatoargentate(III) (MPA) in a rate determining step followed by other fast steps to give the products. The main products were identified by spot test, IR, GC-MS studies. The activation parameters with respect to slow step of the mechanism are computed and discussed and thermodynamic quantities are also determined. The active species of catalyst and oxidant have been identified.

  15. Adsorption of Chromium Ion by Acid Activated Low Cost Carbon-Kinetic, Mechanistic, Thermodynamic and Equilibrium Studies

    Directory of Open Access Journals (Sweden)

    S. Arivoli

    2008-01-01

    Full Text Available A carbonaceous adsorbent prepared from an indigenous waste by acid treatment was tested for its efficiency in removing chromium ion. The parameters studied include agitation time, initial chromium ion concentration, carbon dose, pH and temperature. The adsorption followed first order reaction equation and the rate is mainly controlled by intra-particle diffusion. Freundlich and Langmuir isotherm models were applied to the equilibrium data. The adsorption capacity (Qm obtained from the Langmuir isotherm plots were 27.40, 26.06, 26.06 and 26.17 mg/g respectively at an initial pH of 7.0 at 30, 40, 50 and 60°C. The temperature variation study showed that the chromium ion adsorption is endothermic and spontaneous with increased randomness at the solid solution interface. Significant effect on adsorption was observed on varying the pH of the chromium ion solutions. Almost 70% removal of chromium ion was observed at 60°C. The Langmuir and Freundlich isotherms obtained, positive ∆H0 value, pH dependent results and desorption of dye in mineral acid suggest that the adsorption of chromium ion on PDC involves physisorption mechanism.

  16. Kinetic, Mechanistic, Thermodynamic and Equilibrium Studies on the Adsorption of Rhodamine B by Acid Activated Low Cost Carbon

    Directory of Open Access Journals (Sweden)

    S. Arivoli

    2008-01-01

    Full Text Available A carbonaceous adsorbent prepared from an indigenous waste by acid treatment was tested for its efficiency in removing Rhodamine B (RDB. The parameters studied include agitation time, initial dye concentration, carbon dose, pH and temperature. The adsorption followed first order reaction equation and the rate is mainly controlled by intra-particle diffusion. Freundlich and Langmuir isotherm models were applied to the equilibrium data. The adsorption capacity (Qm obtained from the Langmuir isotherm plots were 51.546, 47.236, 44.072 and 41.841 mg/g respectively at an initial pH of 7.0 at 30, 40, 50 and 60°C. The temperature variation study showed that the Rhodamine B adsorption is endothermic and spontaneous with increased randomness at the solid solution interface. Significant effect on adsorption was observed on varying the pH of the Rhodamine B solutions. Almost 90% removal of Rhodamine B was observed at 60°C. The Langmuir and Freundlich isotherms obtained, positive ΔH0 value, pH dependent results and desorption of dye in mineral acid suggest that the adsorption of Rhodamine B on PSC involves physisorption mechanism.

  17. The EpiDerm™ 3D human reconstructed skin micronucleus (RSMN) assay: Historical control data and proof of principle studies for mechanistic assay adaptations.

    Science.gov (United States)

    Roy, Shambhu; Kulkarni, Rohan; Hewitt, Nicola J; Aardema, Marilyn J

    2016-07-01

    The in vitro human reconstructed skin micronucleus (RSMN) assay in EpiDerm™ is a promising novel animal alternative for evaluating genotoxicity of topically applied chemicals. It is particularly useful for assessing cosmetic ingredients that can no longer be tested using in vivo assays. To advance the use of this test especially for regulatory decision-making, we have established the RSMN assay in our laboratory according to Good Laboratory Practice and following the principles of the OECD test guideline 487 in vitro mammalian cell micronucleus test. Proficiency with the assay was established by correctly identifying direct-acting genotoxins and genotoxins requiring metabolism, as well as non-genotoxic/non-carcinogenic chemicals. We also report the analysis of our historical control data that demonstrate vehicle control and positive control values for %micronuclei in binucleated cells are in the ranges reported previously. Technical issues including evaluating various solvents with both 48h and 72h treatment regimens were investigated. For the first time, mechanistic studies using CREST analysis revealed that the RSMN assay is suitable for distinguishing aneugens and clastogens. Moreover, the assay is also suitable for measuring cytokines as markers for proliferative and toxic effects of chemicals.

  18. Mechanistic insight into self-propagation of organo-mediated Beckmann rearrangement: a combined experimental and computational study.

    Science.gov (United States)

    An, Na; Tian, Bo-Xue; Pi, Hong-Jun; Eriksson, Leif A; Deng, Wei-Ping

    2013-05-03

    Organo-mediated Beckmann rearrangement in the liquid phase, which has the advantage of high efficiency and straightforward experimental procedures, plays an important role in the synthesis of amides from oximes. However, the catalytic mechanisms of these organic-based promoters are still not well understood. In this work, we report a combined experimental and computational study on the mechanism of Beckmann rearrangement mediated by organic-based promoters, using TsCl as an example. A novel self-propagating cycle is proposed, and key intermediates of this self-propagating cycle are confirmed by both experiments and DFT calculations. In addition, the reason why cyclohexanone oxime is not a good substrate of the organo-mediated Beckmann rearrangement is discussed, and a strategy for improving the yield is proposed.

  19. Atmospheric chemistry of HFC-134a. Kinetic and mechanistic study of the CF3CFHO2 + NO2 reaction

    DEFF Research Database (Denmark)

    Møgelberg, T.E.; Nielsen, O.J.; Sehested, J.;

    1994-01-01

    A pulse radiolysis system was used to study the kinetics of the reaction of CF3CFHO2 with NO2. By monitoring the rate of the decay of NO2 using its absorption at 400 nm the reaction rate constant was determined to be k = (5.0 +/- 0.5) x 10(-12) cm3 molecule-1 s-1. A long path length Fourier......-transform infrared technique was used to investigate the thermal decomposition of the product CF3CFHO2NO2. At 296 K in the presence of 700 Torr of air, decomposition of CF3CFHO2NO2 was rapid (greater than 90% decomposition within 3 min). The results are discussed in the context of atmospheric chemistry of CF3CFH2...

  20. Application of a Pyroprobe-Deuterium NMR System: Deuterium Tracing and Mechanistic Study of Upgrading Process for Lignin Model Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Ben, Haoxi; Jarvis, Mark W.; Nimlos, Mark R.; Gjersing, Erica L.; Sturgeon, Matthew R.; Foust, Thomas D.; Ragauskas, Arthur J.; Biddy, Mary J.

    2016-04-21

    In this study, a pyroprobe-deuterium (2H) NMR system has been used to identify isotopomer products formed during the deuteration and ring opening of lignin model compounds. Several common model compounds for lignin and its upgraded products, including guaiacol, syringol, toluene, p-xylene, phenol, catechol, cyclohexane, methylcyclohexane, and methylcyclopentane, have been examined for selective ring opening. Similar pathways for upgrading of toluene and p-xylene has been found, which will undergo hydrogenation, methyl group elimination, and ring opening process, and benzene, cyclohexane, and methylcyclohexane have been found as major intermediates before ring opening. Very interestingly, the 2H NMR analysis for the deuterium-traced ring opening of catechol on Ir/..gamma..-Al2O3 is almost identical to the ring opening process for phenol. The ring opening processes for guaiacol and syringol appeared to be very complicated, as expected. Benzene, phenol, toluene, cyclohexane, and methylcyclohexane have been determined to be the major products.

  1. Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions

    Science.gov (United States)

    Cordes, Thorben; Blum, Suzanne A.

    2013-12-01

    In recent years, single-molecule and single-particle fluorescence microscopy has emerged as a tool to investigate chemical systems. After an initial lag of over a decade with respect to biophysical studies, this powerful imaging technique is now revealing mechanisms of 'classical' organic reactions, spatial distribution of chemical reactivity on surfaces and the phase of active catalysts. The recent advance into commercial imaging systems obviates the need for home-built laser systems and thus opens this technique to traditionally trained synthetic chemists. We discuss the requisite photophysical and chemical properties of fluorescent reporters and highlight the main challenges in applying single-molecule techniques to chemical questions. The goal of this Perspective is to provide a snapshot of an emerging multidisciplinary field and to encourage broader use of this young experimental approach that aids the observation of chemical reactions as depicted in many textbooks: molecule by molecule.

  2. Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions.

    Science.gov (United States)

    Cordes, Thorben; Blum, Suzanne A

    2013-12-01

    In recent years, single-molecule and single-particle fluorescence microscopy has emerged as a tool to investigate chemical systems. After an initial lag of over a decade with respect to biophysical studies, this powerful imaging technique is now revealing mechanisms of 'classical' organic reactions, spatial distribution of chemical reactivity on surfaces and the phase of active catalysts. The recent advance into commercial imaging systems obviates the need for home-built laser systems and thus opens this technique to traditionally trained synthetic chemists. We discuss the requisite photophysical and chemical properties of fluorescent reporters and highlight the main challenges in applying single-molecule techniques to chemical questions. The goal of this Perspective is to provide a snapshot of an emerging multidisciplinary field and to encourage broader use of this young experimental approach that aids the observation of chemical reactions as depicted in many textbooks: molecule by molecule.

  3. Oxidation of aliphatic alcohols by triethylammonium chlorochromate in non-aqueous medium – A kinetic and mechanistic study

    Directory of Open Access Journals (Sweden)

    S. Sheik Mansoor

    2014-07-01

    Full Text Available The oxidation of some aliphatic alcohols by triethylammonium chlorochromate (TriEACC in dimethyl sulfoxide leads to the formation of the corresponding carbonyl compounds. The reaction is first order with respect to TriEACC. The reaction exhibited Michaelis–Menten type kinetics with respect to alcohol. The reaction is catalyzed by hydrogen ions. The hydrogen-ion dependence has the form: kobs = a + b[H+]. The oxidation of [1,1-2H2] ethanol (MeCD2OH exhibits a substantial primary kinetic isotope effect. Oxidation of aliphatic alcohol was studied in 19 different organic solvents. The solvent effect has been analysed using Kamlet’s and Swain’s multi-parametric equation. A suitable mechanism has been proposed.

  4. Mechanistic study on ultrasound assisted pretreatment of sugarcane bagasse using metal salt with hydrogen peroxide for bioethanol production.

    Science.gov (United States)

    Ramadoss, Govindarajan; Muthukumar, Karuppan

    2016-01-01

    This study presents the ultrasound assisted pretreatment of sugarcane bagasse (SCB) using metal salt with hydrogen peroxide for bioethanol production. Among the different metal salts used, maximum holocellulose recovery and delignification were achieved with ultrasound assisted titanium dioxide (TiO2) pretreatment (UATP) system. At optimum conditions (1% H2O2, 4 g SCB dosage, 60 min sonication time, 2:100 M ratio of metal salt and H2O2, 75°C, 50% ultrasound amplitude and 70% ultrasound duty cycle), 94.98 ± 1.11% holocellulose recovery and 78.72 ± 0.86% delignification were observed. The pretreated SCB was subjected to dilute acid hydrolysis using 0.25% H2SO4 and maximum xylose, glucose and arabinose concentration obtained were 10.94 ± 0.35 g/L, 14.86 ± 0.12 g/L and 2.52 ± 0.27 g/L, respectively. The inhibitors production was found to be very less (0.93 ± 0.11 g/L furfural and 0.76 ± 0.62 g/L acetic acid) and the maximum theoretical yield of glucose and hemicellulose conversion attained were 85.8% and 77%, respectively. The fermentation was carried out using Saccharomyces cerevisiae and at the end of 72 h, 0.468 g bioethanol/g holocellulose was achieved. Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analysis of pretreated SCB was made and its morphology was studied using scanning electron microscopy (SEM). The compounds formed during the pretreatment were identified using gas chromatography-mass spectrometry (GC-MS) analysis.

  5. A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs

    Science.gov (United States)

    Uzawa, Takanori; Cheng, Ryan R.; White, Ryan J.; Makarov, Dmitrii E.; Plaxco, Kevin W

    2010-01-01

    Electrode-bound, redox-reporter-modified oligonucleotides play roles in the functioning of a number of electrochemical biosensors, and thus the question of electron transfer through or from such molecules has proven of significant interest. In response, we have experimentally characterized the rate with which electrons are transferred between a methylene blue on the distal end of a short, single-stranded polythymine DNAs to a monolayer-coated gold electrode to which the other end of the DNA is site-specifically attached. We find that this rate scales with oligonucleotide length to the −1.16±0.09 power. This weak, approximately inverse length dependence differs dramatically from the much stronger dependencies observed for the rates of end-to-end collisions in single-stranded DNA and through-oligonucleotide electron hopping. It instead coincides with the expected length dependence of a reaction-limited process in which the overall rate is proportional to the equilibrium probability that the end of the oligonucleotide chain approaches the surface. Studies of the ionic strength and viscosity dependencies of electron transfer further support this “chain-flexibility” mechanism, and studies of the electron transfer rate of methylene blue attached to the hexanethiol monolayer suggest that heterogeneous electron transfer through the monolayer is rate limiting. Thus, under the circumstances we have employed, the flexibility (i.e., the equilibrium statistical properties) of the oligonucleotide chain defines the rate with which an attached redox reporter transfers electrons to an underlying electrode, an observation that may be of utility in the design of new biosensor architectures. PMID:20964337

  6. Mechanistic Investigations of Oxidation of Some Dipeptides by Sodium N-chloro-p-toluenesulfonamide in Alkaline Medium: A Kinetic Study

    Institute of Scientific and Technical Information of China (English)

    PUTTASWAMY; VAZ Nirmala; RAJENAHALLY VGOWDA Jagadeesh

    2008-01-01

    The kinetics of oxidation of five dipeptides (DPP) viz., glycylglycine (Gly-Gly), L-alanyl-L-alanine (Ala-Ala),L-valyl-L-valine (Val-Val), L-leucyl-L-leucine (Leu-Leu) and phenylglycyl-phenylglycine (Phg-Phg) by sodium N-chloro-p-toluenesuifonamide or chloramine-T (CAT) in NaOH medium was studied at 308 K. The reactions follow identical kinetics for all the dipeptides, being first-order dependence each on [CAT]o, [DPP]o and fractional-order on [OH-]. Addition of p-toluenesulfonamide or halide ions (CI- or Br-) has no significant effect on the rate of reaction. The reaction rate was found to increase with increase in ionic strength of the medium. The solvent isotope effect was studied using D2O. The activation parameters for the reaction were computed from Arrhenius plots. Equilibrium and decomposition constants were evaluated. The oxidation products of the dipeptides were identiffed as their corresponding aldehydes. An isokinetic relationship was observed with β=352 K, indicating that enthalpy factors control the reaction rate. CH3C6H4SO2NCl- of the oxidant has been postulated as the reactive oxidizing species. Under comparable experimental conditions, the rate of oxidation of the dipeptides increases in the order: Phg-Phg>Ala-Ala>Val-Val>Leu-Leu>Gly-Gly. The kinetics of oxidation of the dipeptides have also been compared with those of their corresponding monomer amino acids. The observed results have been explained by a plausible mechanism and the related rate law has been deduced.

  7. Reversing the reduced level of endometrial GLUT4 expression in polycystic ovary syndrome: a mechanistic study of metformin action.

    Science.gov (United States)

    Li, Xin; Cui, Peng; Jiang, Hong-Yuan; Guo, Yan-Rong; Pishdari, Bano; Hu, Min; Feng, Yi; Billig, Håkan; Shao, Ruijin

    2015-01-01

    Conflicting results have been reported regarding whether or not insulin-regulated glucose transporter 4 (GLUT4) is expressed in human and rodent endometria. There is an inverse relationship between androgen levels and insulin-dependent glucose metabolism in women. Hyperandrogenemia, hyperinsulinemia, and insulin resistance are believed to contribute to endometrial abnormalities in women with polycystic ovary syndrome (PCOS). However, it has been unclear in previous studies if endometrial GLUT4 expression is regulated by androgen-dependent androgen receptors (ARs) and/or the insulin receptor/Akt/mTOR signaling network. In this study, we demonstrate that GLUT4 is expressed in normal endometrial cells (mainly in the epithelial cells) and is down-regulated under conditions of hyperandrogenemia in tissues from PCOS patients and in a 5α-dihydrotestosterone-induced PCOS-like rat model. Western blot analysis revealed reduced endometrial GLUT4 expression and increased AR expression in PCOS patients. However, the reduced GLUT4 level was not always associated with an increase in AR in PCOS patients when comparing non-hyperplasia with hyperplasia. Using a human tissue culture system, we investigated the molecular basis by which GLUT4 regulation in endometrial hyperplasia tissues is affected by metformin in PCOS patients. We show that specific endogenous organic cation transporter isoforms are regulated by metformin, and this suggests a direct effect of metformin on endometrial hyperplasia. Moreover, we demonstrate that metformin induces GLUT4 expression and inhibits AR expression and blocks insulin receptor/PI3K/Akt/mTOR signaling in the same hyperplasia human tissues. These findings indicate that changes in endometrial GLUT4 expression in PCOS patients involve the androgen-dependent alteration of AR expression and changes in the insulin receptor/PI3K/Akt/mTOR signaling network.

  8. Interaction of 2-aminopyrimidine with dichloro-[1-alkyl-2-(naphthylazo imidazole]palladium(II complexes : Kinetic and mechanistic studies

    Directory of Open Access Journals (Sweden)

    Saha Sushanta

    2007-10-01

    Full Text Available Abstract Background The anticancer properties of cisplatin and palladium(II complexes stem from the ability of the cis-MCl2 fragment to bind to DNA bases. However, cisplatin also interacts with non-cancer cells, mainly through bonding molecules containing -SH groups, resulting in nephrotoxicity. This has aroused interest in the design of palladium(II complexes of improved activity and lower toxicity. The reaction of DNA bases with palladium(II complexes with chelating N,N/donors of the cis-MCl2 configuration constitutes a model system that may help explore the mechanism of cisplatin's anticancer activity. Heterocyclic compounds are found widely in nature and are essential to many biochemical processes. Amongst these naturally occurring compounds, the most thoroughly studied is that of pyrimidine. This was one of the factors that encouraged this study into the kinetics and mechanism of the interaction of 2-aminopyrimidine (2-NH2-Pym with dichloro-{1-alkyl-2-(α-naphthylazoimidazole}palladium(II [Pd(α-NaiRCl2, 1] and dichloro-{1-alkyl-2-(β-naphthylazoimidazole}palladium(II [Pd(β-NaiRCl2, 2] complexes where the alkyl R = Me (a, Et (b, or Bz (c. Results 2-NH2-Pym reacts with 1a, 1b, and 1c to yield [{1-alkyl-2-(α-naphthylazoimidazole}bis(2-aminopyrimidine]palladium(II (3a, 3b, 3c dichloride and with 2a, 2b, and 2c to yield [{1-alkyl-2-(β-naphthylazoimidazole}bis(2-aminopyrimidine]palladium(II (4a, 4b, 4c dichloride in an acetonitrile (MeCN medium. The products were characterized using spectroscopic techniques (FT-IR, UV-Vis, NMR. The ligand substitution reactions follow second order kinetics – first order dependence on the concentration of the Pd(II complex and 2-NH2-Pym. Addition of LiCl to the reaction does not influence its rate. The thermodynamic parameters (standard enthalpy of activation, Δ‡H° and standard entropy of activation, Δ‡S° were determined from variable temperature kinetic studies. The magnitude of the second order

  9. The Reductive Activation of CO2 Across a Ti=Ti Double Bond: Synthetic, Structural, and Mechanistic Studies

    Science.gov (United States)

    2015-01-01

    The reactivity of the bis(pentalene)dititanium double-sandwich compound Ti2Pn†2 (1) (Pn† = 1,4-{SiiPr3}2C8H4) with CO2 is investigated in detail using spectroscopic, X-ray crystallographic, and computational studies. When the CO2 reaction is performed at −78 °C, the 1:1 adduct 4 is formed, and low-temperature spectroscopic measurements are consistent with a CO2 molecule bound symmetrically to the two Ti centers in a μ:η2,η2 binding mode, a structure also indicated by theory. Upon warming to room temperature the coordinated CO2 is quantitatively reduced over a period of minutes to give the bis(oxo)-bridged dimer 2 and the dicarbonyl complex 3. In situ NMR studies indicated that this decomposition proceeds in a stepwise process via monooxo (5) and monocarbonyl (7) double-sandwich complexes, which have been independently synthesized and structurally characterized. 5 is thermally unstable with respect to a μ-O dimer in which the Ti–Ti bond has been cleaved and one pentalene ligand binds in an η8 fashion to each of the formally TiIII centers. The molecular structure of 7 shows a “side-on” bound carbonyl ligand. Bonding of the double-sandwich species Ti2Pn2 (Pn = C8H6) to other fragments has been investigated by density functional theory calculations and fragment analysis, providing insight into the CO2 reaction pathway consistent with the experimentally observed intermediates. A key step in the proposed mechanism is disproportionation of a mono(oxo) di-TiIII species to yield di-TiII and di-TiIV products. 1 forms a structurally characterized, thermally stable CS2 adduct 8 that shows symmetrical binding to the Ti2 unit and supports the formulation of 4. The reaction of 1 with COS forms a thermally unstable complex 9 that undergoes scission to give mono(μ-S) mono(CO) species 10. Ph3PS is an effective sulfur transfer agent for 1, enabling the synthesis of mono(μ-S) complex 11 with a double-sandwich structure and bis(μ-S) dimer 12 in which the Ti

  10. A mechanistic study on Decontamination of Methyl Orange Dyes from Aqueous Phase by Mesoporous Pulp Waste and Polyaniline.

    Science.gov (United States)

    Li, Donglin; Yang, Yonggang; Li, Chaozheng; Liu, Yufang

    2017-04-01

    The dispersion-corrected density functional theory (DFT-D3) is used to investigate the mechanism of mesoporous pulp waste (MPW) and polyaniline (PANI) adsorptive removal methyl orange (MO) dye from their aqueous solutions. The results are absolutely reliable because of the sufficiently accurate method although such big systems are studied. It is demonstrated that hydrogen bond and Van Der Waals interactions play a significant role in MO adsorption by MPW and PANI. For MO adsorption by MPW, hydrogen bond and Van Der Waals interactions are both weakened in S1 state. In contrast, hydrogen bond and Van Der Waals interactions between PANI and MO are both enhanced in S1 state. The thermodynamic parameters such as enthalpy and free energy change reveal that the MO adsorption by MPW and PANI are spontaneous and exothermic. The adsorption of MO on MPW is less favorable in S1 state and the adsorption of MO on PANI is more favorable in S1 state. Therefore, the photoexcitation should be controlled during the MO adsorption by MPW and applied for MO adsorption by PANI. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate.

    Science.gov (United States)

    Song, Heng; Hu, Wen; Naowarojna, Nathchar; Her, Ampon Sae; Wang, Shu; Desai, Rushil; Qin, Li; Chen, Xiaoping; Liu, Pinghua

    2015-01-01

    Ergothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond formation reaction and a PLP-mediated C-S lyase (EgtE) reaction results in a net sulfur transfer from cysteine to histidine side-chain. This demonstrates a new sulfur transfer strategy in the biosynthesis of sulfur-containing natural products. Due to difficulties associated with the overexpression of Mycobacterium smegmatis EgtE protein, the proposed EgtE functionality remained to be verified biochemically. In this study, we have successfully overexpressed and purified M. smegmatis EgtE enzyme and evaluated its activities under different in vitro conditions: C-S lyase reaction using either thioether or sulfoxide as a substrate in the presence or absence of reductants. Results from our biochemical characterizations support the assignment of sulfoxide 4 as the native EgtE substrate and the involvement of a sulfenic acid intermediate in the ergothioneine C-S lyase reaction.

  12. Mechanistic studies of Ser/Thr dehydration catalyzed by a member of the LanL lanthionine synthetase family.

    Science.gov (United States)

    Goto, Yuki; Okesli, Ayşe; van der Donk, Wilfred A

    2011-02-08

    Members of the LanL family of lanthionine synthetases consist of three catalytic domains, an N-terminal pSer/pThr lyase domain, a central Ser/Thr kinase domain, and a C-terminal lanthionine cyclase domain. The N-terminal lyase domain has sequence homology with members of the OspF family of effector proteins. In this study, the residues in the lyase domain of VenL that are conserved in the active site of OspF proteins were mutated to evaluate their importance for catalysis. In addition, residues that are fully conserved in the LanL family but not in the OspF family were mutated. Activity assays with these mutant proteins are consistent with a model in which Lys80 in VenL deprotonates the α-proton of pSer/pThr residues to initiate the elimination reaction. Lys51 is proposed to activate this proton by coordination to the carbonyl of the pSer/pThr, and His53 is believed to protonate the phosphate leaving group. These functions are very similar to the corresponding homologous residues in OspF proteins. On the other hand, recognition of the phosphate group of pSer/pThr appears to be achieved differently in VenL than in the OspF proteins. Arg156 and Lys103 are thought to interact with the phosphate group on the basis of a structural homology model.

  13. Mechanistic Studies of Ser/Thr Dehydration Catalyzed by a Member of the LanL Lanthionine Synthetase Family†

    Science.gov (United States)

    2011-01-01

    Members of the LanL family of lanthionine synthetases consist of three catalytic domains, an N-terminal pSer/pThr lyase domain, a central Ser/Thr kinase domain, and a C-terminal lanthionine cyclase domain. The N-terminal lyase domain has sequence homology with members of the OspF family of effector proteins. In this study, the residues in the lyase domain of VenL that are conserved in the active site of OspF proteins were mutated to evaluate their importance for catalysis. In addition, residues that are fully conserved in the LanL family but not in the OspF family were mutated. Activity assays with these mutant proteins are consistent with a model in which Lys80 in VenL deprotonates the α-proton of pSer/pThr residues to initiate the elimination reaction. Lys51 is proposed to activate this proton by coordination to the carbonyl of the pSer/pThr, and His53 is believed to protonate the phosphate leaving group. These functions are very similar to the corresponding homologous residues in OspF proteins. On the other hand, recognition of the phosphate group of pSer/pThr appears to be achieved differently in VenL than in the OspF proteins. Arg156 and Lys103 are thought to interact with the phosphate group on the basis of a structural homology model. PMID:21229987

  14. Long-term habituation (LTH in the crab Chasmagnathus: a model for behavioral and mechanistic studies of memory

    Directory of Open Access Journals (Sweden)

    H. Maldonado

    1997-07-01

    Full Text Available A decade of studies on long-term habituation (LTH in the crab Chasmagnathus is reviewed. Upon sudden presentation of a passing object overhead, the crab reacts with an escape response that habituates promptly and for at least five days. LTH proved to be an instance of associative memory and showed context, stimulus frequency and circadian phase specificity. A strong training protocol (STP (³15 trials, intertrial interval (ITI of 171 s invariably yielded LTH, while a weak training protocol (WTP (£10 trials, ITI = 171 s invariably failed. STP was used with a presumably amnestic agent and WTP with a presumably hypermnestic agent. Remarkably, systemic administration of low doses was effective, which is likely to be due to the lack of an endothelial blood-brain barrier. LTH was blocked by inhibitors of protein and RNA synthesis, enhanced by protein kinase A (PKA activators and reduced by PKA inhibitors, facilitated by angiotensin II and IV and disrupted by saralasin. The presence of angiotensins and related compounds in the crab brain was demonstrated. Diverse results suggest that LTH includes two components: an initial memory produced by spaced training and mainly expressed at an initial phase of testing, and a retraining memory produced by massed training and expressed at a later phase of testing (retraining. The initial memory would be associative, context specific and sensitive to cycloheximide, while the retraining memory would be nonassociative, context independent and insensitive to cycloheximide

  15. Coagulation-adsorption of reactive orange from aqueous solution by freshly formed magnesium hydroxide: mixing time and mechanistic study.

    Science.gov (United States)

    Zhao, Jianhai; Shi, Huanhuan; Liu, Meile; Lu, Jingfang; Li, Wenpu

    2017-04-01

    The utilization of magnesium hydroxide was successfully carried out to remove reactive orange by coagulation-adsorption from aqueous solution. The coagulation-adsorption mechanisms and magnesium hydroxide-reactive orange floc property were analyzed through zeta potential, scanning electron microscope (SEM), X-ray diffraction and Fourier transform infrared spectroscopy (FT-IR). Flocculation Index was then discussed with controlled experiments using intelligent Particle Dispersion Analyzer (iPDA) and optimum rapid mixing time of 90 s was obtained for pH 12. The results of this study indicate that charge neutralization and adsorption are proposed to be the main coagulation mechanisms. The FT-IR spectra and SEM showed that reactive orange was adsorbed on the magnesium hydroxide surface during coagulation and adsorption. Freshly generated magnesium hydroxide can effectively remove reactive orange and the removal efficiency can reach 96.7% and 46.3% for coagulation and adsorption, respectively. Adsorption process accounts for 48% of the whole coagulation experiment. The removal efficiency decreased significantly with increasing magnesium hydroxide formation time.

  16. Boron doped diamond sensor for sensitive determination of metronidazole: Mechanistic and analytical study by cyclic voltammetry and square wave voltammetry

    Energy Technology Data Exchange (ETDEWEB)

    Ammar, Hafedh Belhadj, E-mail: hbelhadjammar@yahoo.fr; Brahim, Mabrouk Ben; Abdelhédi, Ridha; Samet, Youssef

    2016-02-01

    The performance of boron-doped diamond (BDD) electrode for the detection of metronidazole (MTZ) as the most important drug of the group of 5-nitroimidazole was proven using cyclic voltammetry (CV) and square wave voltammetry (SWV) techniques. A comparison study between BDD, glassy carbon and silver electrodes on the electrochemical response was carried out. The process is pH-dependent. In neutral and alkaline media, one irreversible reduction peak related to the hydroxylamine derivative formation was registered, involving a total of four electrons. In acidic medium, a prepeak appears probably related to the adsorption affinity of hydroxylamine at the electrode surface. The BDD electrode showed higher sensitivity and reproducibility analytical response, compared with the other electrodes. The higher reduction peak current was registered at pH 11. Under optimal conditions, a linear analytical curve was obtained for the MTZ concentration in the range of 0.2–4.2 μmol L{sup −1}, with a detection limit of 0.065 μmol L{sup −1}. - Highlights: • SWV for the determination of MTZ • Boron-doped diamond as a new electrochemical sensor • Simple and rapid detection of MTZ • Efficiency of BDD for sensitive determination of MTZ.

  17. Boron doped diamond sensor for sensitive determination of metronidazole: Mechanistic and analytical study by cyclic voltammetry and square wave voltammetry.

    Science.gov (United States)

    Ammar, Hafedh Belhadj; Brahim, Mabrouk Ben; Abdelhédi, Ridha; Samet, Youssef

    2016-02-01

    The performance of boron-doped diamond (BDD) electrode for the detection of metronidazole (MTZ) as the most important drug of the group of 5-nitroimidazole was proven using cyclic voltammetry (CV) and square wave voltammetry (SWV) techniques. A comparison study between BDD, glassy carbon and silver electrodes on the electrochemical response was carried out. The process is pH-dependent. In neutral and alkaline media, one irreversible reduction peak related to the hydroxylamine derivative formation was registered, involving a total of four electrons. In acidic medium, a prepeak appears probably related to the adsorption affinity of hydroxylamine at the electrode surface. The BDD electrode showed higher sensitivity and reproducibility analytical response, compared with the other electrodes. The higher reduction peak current was registered at pH11. Under optimal conditions, a linear analytical curve was obtained for the MTZ concentration in the range of 0.2-4.2μmolL(-1), with a detection limit of 0.065μmolL(-1). Copyright © 2015 Elsevier B.V. All rights reserved.

  18. OXIDATION OF PROPRANOLOL USING CHLORAMINE – T IN HClO4 MEDIUM: A KINETIC AND MECHANISTIC STUDY

    Directory of Open Access Journals (Sweden)

    Range Gowda Ramachandrappa

    2012-06-01

    Full Text Available Kinetics and oxidation of Propranolol (PPL ((RS-1-(1-methylethylamino-3-(1-naphthyloxypropan-2-ol by sodium – N- chloro – p- toluenesulphonamide (Chloramine – T or CAT in HClO4 medium at 298K have been studied. The rate was first order in [CAT]o, fractional order in [PPL] and zero order in [H+]. Addition of p-toluenesulphonamide, NaCl and NaBr did not affect the rate of the reaction. Variation in ionic strength did not affect the rate of the reaction indicating that non – ionic species are involved in the rate limiting step. The dielectric effect of the medium was positive. Rate increased with increase in temperature from 288K to 318K. From the linear Arrhenius plot, activation parameters were computed. Addition of reaction mixture to aqueous acrylonitrile solution did not initiate polymerization, showing the absence of free radicals species. Oxidation products were identified. TsNClNa, the reactive species, oxidizes the substrate. Based on kinetic results, reaction stoichiometry and oxidation products, a suitable mechanism have been proposed.

  19. Peroxydisulfate activation by [RuII(tpy)(pic)(H2O)]+. Kinetic, mechanistic and anti-microbial activity studies.

    Science.gov (United States)

    Chatterjee, Debabrata; Banerjee, Priyabrata; Bose, Jagadeesh C K; Mukhopadhyay, Sudit

    2012-03-07

    The oxidation of [Ru(II)(tpy)(pic)H(2)O](+) (tpy = 2,2',6',2''-terpyridine; pic(-) = picolinate) by peroxidisulfate (S(2)O(8)(2-)) as precursor oxidant has been investigated kinetically by UV-VIS, IR and EPR spectroscopy. The overall oxidation of Ru(II)- to Ru(IV)-species takes place in a consecutive manner involving oxidation of [Ru(II)(tpy)(pic)H(2)O](+) to [Ru(III)(tpy)(pic)(OH)](+), and its further oxidation of to the ultimate product [Ru(IV)(tpy)(pic)(O)](+) complex. The time course of the reaction was followed as a function of [S(2)O(8)(2-)], ionic strength (I) and temperature. Kinetic data and activation parameters are interpreted in terms of an outer-sphere electron transfer mechanism. Anti-microbial activity of Ru(II)(tpy)(pic)H(2)O](+) complex by inhibiting the growth of Escherichia coli DH5α in presence of peroxydisulfate has been explored, and the results of the biological studies have been discussed in terms of the [Ru(IV)(tpy)(pic)(O)](+) mediated cleavage of chromosomal DNA of the bacteria.

  20. Comparative analysis of quercetin oxidation by electrochemical, enzymatic, autoxidation, and free radical generation techniques: a mechanistic study.

    Science.gov (United States)

    Zhou, Ailing; Sadik, Omowunmi A

    2008-12-24

    Quercetin, the most abundant flavonoid in dietary fruits and vegetables, acts as antioxidant or prooxidant depending on the environmental conditions. The antioxidant behavior is believed to involve initial oxidative steps with subsequent changes in the flavonoid skeleton, which ultimately alters the chemical and biological properties of these molecules. Although the mechanism is still unclear, it has been suggested to be strongly influenced by the surrounding media. This paper reports the oxidation of quercetin by air oxygen or autoxidation, bulk electrolysis, mushroom tyrosinase, and azodiisobutyronitrile (AIBN). The central aim of this study is to systematically examine how the similarities and differences of quercetin transformation can be affected by the nature of the oxidation systems. Using a range of molecular and structural characterization techniques (UV-vis, LC-MS, GC-MS, and NMR), the oxidation of quercetin was found to result in the generation of somewhat similar metabolites including depside, phenolic acids, and quercetin-solvent adducts, although the transformation process and quantities of each product depend on the type of oxidation method employed. The rate of quercetin autoxidation can be fitted to a monoexponential first-order decay with a k value of 6.45 x 10(-2) M(-1) s(-1). Comparison of quercetin oxidative products in the different systems provides a deeper insight into the underlying mechanism involved in the oxidation process. This work demonstrates that the presence of water and/or nucleophiles as well as different catalysts (tyrosinase, AIBN, or air oxygen in solution) may have very important implications for the formation of quinone with subsequent oxidative cleavage or polymerization. Moreover, the apparent first-order kinetics of autoxidation can indicate a rate-determining, one-electron oxidation of quercetin anions followed by two fast steps of radical disproportionation and solvent addition on the resulting quinone.

  1. A functional mechanistic study of the effect of emollients on the structure and function of the skin barrier.

    Science.gov (United States)

    Danby, S G; Chalmers, J; Brown, K; Williams, H C; Cork, M J

    2016-11-01

    Preventing relapses of atopic dermatitis (AD) through the regular use of topical products to repair the skin barrier defect is an emerging concept. It is still unclear if some commonly used emollients exert a positive effect on the skin barrier. To determine the skin barrier effects of emollients commonly prescribed in the U.K. Two cohorts of volunteers with quiescent AD undertook observer-blind forearm-controlled studies. The first cohort (18 volunteers) treated the volar side of one forearm with two fingertip units of Doublebase(™) gel twice daily for 4 weeks. The second cohort (19 volunteers) undertook the same regimen using Diprobase(®) cream. Transepidermal water loss (TEWL), stratum corneum integrity and hydration, skin surface pH and redness were determined at the test sites before and after treatment. Neither Diprobase(®) cream nor Doublebase(™) gel significantly affected the underlying skin barrier function. Both emollients were associated with significantly increased skin surface pH immediately after application (by 0·8 ± 0·19 and 1·0 ± 0·18 units, respectively), and no erythema. Diprobase(®) cream artificially and transiently (6 h) improved permeability barrier function by 2·9-3·1 g m(-2)  h(-1) TEWL and increased skin hydration by 6·0-6·2 units. Doublebase(™) gel, containing humectants, was associated with a greater (between 10·1 and 13·0 units during the first 6 h) and more sustained increase in hydration, lasting more than 12 h following repeated use. Diprobase(®) cream and Doublebase(™) gel are not associated with skin barrier harm and appear to be appropriate for AD treatment. While displaying emollient properties, neither formulation displayed an ability to actively improve sustained skin barrier function. © 2016 British Association of Dermatologists.

  2. Mechanistic study of the anti-cancer effect of Gynostemma pentaphyllum saponins in the Apc(Min/+) mouse model.

    Science.gov (United States)

    Tai, William Chi-Shing; Wong, Wing-Yan; Lee, Magnolia Muk-Lan; Chan, Brandon Dow; Lu, Cheng; Hsiao, Wen-Luan Wendy

    2016-05-01

    Gynostemma pentaphyllum saponins (GpS) have been shown to have anti-cancer activity. However, the underlying mechanisms remain unclear. In this study, we used the Apc(Min) (/+) colorectal cancer (CRC) mouse model to investigate the anti-cancer effect of GpS and we demonstrated that GpS treatment could significantly reduce the number and size of intestinal polyps in Apc(Min) (/+) mice. In order to identify the potential targets and mechanisms involved, a comparative proteomics analysis was performed and 40 differentially expressed proteins after GpS treatment were identified. Bioinformatics analyses suggested a majority of these proteins were involved in processes related to cellular redox homeostasis, and predicted Raf-1 as a potential target of GpS. The upregulation of two proteins known to be involved in redox homeostasis, peroxiredoxin-1 (Prdx1) and peroxiredoxin-2 (Prdx2), and the downregulation of Raf-1 were validated using Western blot analysis. After further investigation of the associated signaling networks, we postulated that the anti-cancer effect of GpS was mediated through the upregulation of Prdx1 and Prdx2, suppression of Ras, RAF/MEK/ERK/STAT, PI3K/AKT/mTOR signaling and modulation of JNK/p38 MAPK signaling. We also examined the potential combinatorial effect of GpS with the chemotherapeutic 5-fluorouracil (5-FU) and found that GpS could enhance the anti-cancer efficacy of 5-FU, further suppressing the number of polyps in Apc(Min/+) mice. Our findings highlight the potential of GpS as an anti-cancer agent, the potential mechanisms of its anti-cancer activities, and its effect as an adjuvant of 5-FU in the chemotherapy of CRC. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Mechanistic studies for the role of cellular nucleic-acid-binding protein (CNBP) in regulation of c-myc transcription.

    Science.gov (United States)

    Chen, Siqi; Su, Lijuan; Qiu, Jun; Xiao, Nannan; Lin, Jing; Tan, Jia-Heng; Ou, Tian-Miao; Gu, Lian-Quan; Huang, Zhi-Shu; Li, Ding

    2013-10-01

    Guanine-rich sequence of c-myc nuclease hypersensitive element (NHE) III1 is known to fold in G-quadruplex and subsequently serves as a transcriptional silencer. Cellular nucleic-acid-binding protein (CNBP), a highly conserved zinc-finger protein with multiple biological functions, could bind to c-myc NHE III1 region, specifically to the single strand G-rich sequence. In the present study, a variety of methods, including cloning, expression and purification of protein, EMSA, CD, FRET, Ch-IP, RNA interference, luciferase reporter assay, SPR, co-immunoprecipitation, and co-transfection, were applied to investigate the mechanism for the role of CNBP in regulating c-myc transcription. We found that human CNBP specifically bound to the G-rich sequence of c-myc NHE III1 region both in vitro and in cellulo, and subsequently promoted the formation of G-quadruplex. CNBP could induce a transient decrease followed by an increase in c-myc transcription in vivo. The interaction of CNBP with NM23-H2 was responsible for the increase of c-myc transcription. Based on above experimental results, a new mechanism, involving G-quadruplex related CNBP/NM23-H2 interaction, for the regulation of c-myc transcription was proposed. These findings indicated that the regulation of c-myc transcription through NHE III1 region might be governed by mechanisms involving complex protein-protein interactions, and suggested a new possibility of CNBP as a potential anti-cancer target based on CNBP's biological function in c-myc transcription. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Mechanistic studies of copper(II)-aminoglycoside mediated DNA damage and magnesium catalyzed nuclease activity of hammerhead ribozyme

    Science.gov (United States)

    Patwardhan, Anjali A.

    The antibacterial activity of aminoglycosides stems from their high affinity binding to the 16S rRNA in bacteria resulting in inhibition of protein synthesis. Used to treat acute bacterial infections these antibiotics have limited applications due to their high dosage requirements and the emergence of resistant strains. We have synthesized and characterized Cu(II) derivatives of the aminoglycosides, kanamycin A, tobramycin, neamine, kanamycin B, neomycin B, and paromomycin. The first three exhibit preferential and tight binding to Cu(II) as against neomycin B and kanamycin B and paromomycin. EPR of frozen solutions and UV-visible spectroscopy suggest a change in geometry around the Cu(II) but the stabilities of the complexes in water differ. These copper derivatives efficiently cleave plasmid DNA at micromolar concentrations (hydrolytic) and at nanomolar concentrations in the presence co-reactants like hydrogen peroxide or ascorbic acid. Hydrolysis is multi turnover and exhibits Michelis-Menten kinetics with enzyme-like behavior whereas oxidative cleavage is highly specific with C-4' H abstraction resulting in characteristic base propenal and nucleotide base products. Hydroxyl radicals generated are copper based and are generated in close proximity of the substrate. Hammerhead ribozymes are selectively hydrolyzed in the presence of divalent ions with Mg2+ being the metal ion of choice in vivo . Our studies with complex ions like cobalt hexaammine and fac-triamminetriaquochromium(III) establish outer sphere interactions of Mg2+ with the hammerhead in the catalytic site. There are two sets of sites, one structural and one catalytic. Complex ions in the catalytic site and divalent ions in the structural site result in a slow but active hammerhead ribozyme suggesting that the complex ions are not inhibitory, contrary to what was suggested previously.

  5. Adsorption of chromium(VI) and Rhodamine B by surface modified tannery waste: Kinetic, mechanistic and thermodynamic studies

    Energy Technology Data Exchange (ETDEWEB)

    Anandkumar, J. [Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati 781039, Assam (India); Mandal, B., E-mail: bpmandal@iitg.ernet.in [Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam (India)

    2011-02-28

    In this study, various activation methods have been employed to examine the potential reuse of tannery residual biomass (TRB) obtained from vegetable tanning process for the removal of Cr(VI) and Rhodamine B (RB) from aqueous solution. The maximum BET surface area (10.42 m{sup 2}/g), honey comb pore distribution and uptake of both Cr(VI) and RB were achieved when only 3-fold volume of HCl was used to activate the biomass. The pH and temperature experiment showed that they have considerable impact on the adsorption capacity of the used adsorbent. The presence of other ions (Na{sup +}, Ca{sup 2+} and NH{sub 4}{sup +}) significantly reduces the metal uptake but marginal enhancement in the dye removal was observed when Na{sup +} and NH{sub 4}{sup +} ions were present in the solution. The equilibrium data fitted satisfactorily with the Langmuir model and monolayer sorption capacity obtained as 177-217 and 213-250 mg/g for Cr(VI) and RB at 30-50 deg. C, respectively. The sorption kinetics was found to follow the pseudo-second-order kinetic model. The increase in adsorption capacity for both metal and dye with increase in temperature indicates that the uptake was endothermic in nature. The results indicate that the HCl modified TRB (A-TRB) could be employed as a low cost adsorbent for the removal of both Cr(VI) and RB from the aqueous solution including industrial wastewater.

  6. Effect of Garlic, Gingko and St. John's Wort Extracts on the Pharmacokinetics of Fexofenadine: A Mechanistic Study.

    Science.gov (United States)

    Turkanovic, Jasmina; Gerber, Jacobus P; Ward, Michael B; Milne, Robert W

    2017-02-10

    The aim of this study was to determine the effects of garlic and ginkgo herbal extracts on the pharmacokinetics of the P-glycoprotein (P-gp)/Organic anion transporting polypeptides (Oatps) substrate fexofenadine. Male rats were dosed orally with garlic (120 mg/kg), ginkgo (17 mg/kg), St. John's wort (SJW; 1000 mg/kg; positive control) or milli Q water for 14 days. On day 15, rats were either administered fexofenadine (orally or intravenously), had their livers isolated and perfused with fexofenadine, or the small intestine divided into four segments (SI-SIV) and analysed for P-gp and Oatp1a5. In vivo, SJW increased the CL of fexofenadine by 28%. Garlic increased the AUC0-∞ and Cmax of fexofenadine by 47% and 85%, respectively. Ginkgo and SJW had no effect on the oral absorption of fexofenadine. In the perfused liver, garlic, ginkgo and SJW increased the biliary clearance of fexofenadine with respect to perfusate by 71%, 121% and 234%, respectively. SJW increased the biliary clearance relative to the liver concentration by 64%. The ratio of liver to perfusate concentrations significantly increased in all treated groups. The expression of Oatp1a5 in SI was increased by garlic (88%) and SJW (63%). There were no significant changes in the expression of P-gp. Induction of intestinal Oatp1a5 by garlic may explain the increased absorption of orally administered fexofenadine. Ginkgo had no effect on the expression of intestinal P-gp or Oatp1a5. A dual inductive effect by SJW on opposing intestinal epithelial transport by Oatp1a5 and P-gp remains a possibility.

  7. Impaired circulating CD4+ LAP+ regulatory T cells in patients with acute coronary syndrome and its mechanistic study.

    Directory of Open Access Journals (Sweden)

    Zheng-Feng Zhu

    Full Text Available OBJECTIVE: CD4(+ latency-associated peptide (LAP(+ regulatory T cells (Tregs are a newly discovered T cell subset in humans and the role of these cells in patients with acute coronary syndrome (ACS has not been explored. We designed to investigate whether circulating frequency and function of CD4(+LAP(+ Tregs are defective in ACS. METHODS: One hundred eleven ACS patients (acute myocardial infarction and unstable angina and 117 control patients were enrolled in the study. The control patients consisted of chronic stable angina (CSA and chest pain syndrome (CPS. The frequencies of circulating CD4(+LAP(+ Tregs and the expression of the transmembrane protein glycoprotein-A repetitions predominant (GARP on CD4(+ T cells were determined by flow cytometry. The function of CD4(+LAP(+ Tregs was detected using thymidine uptake. Serum interleukin-10 (IL-10 and transforming growth factor-β protein (TGF-β levels were detected using ELISA and expression of GARP mRNA in peripheral blood mononuclear cells (PBMCs was measured by real time-polymerase chain reaction. RESULTS: We found ACS patients had a significantly lower frequency of circulating CD4(+LAP(+ Tregs, and the function of these cells was reduced compared to controls. The expression of GARP in CD4(+ T cells and the serum levels of TGF-β in ACS patients were lower than those of control patients. The serum levels of IL-10 were similar between the two cohorts. CONCLUSIONS: A novel regulatory T cell subset, defined as CD4(+LAP(+ T cells is defective in ACS patients.

  8. Mechanistic studies on the intramolecular one-electron transfer between the two flavins in the human endothelial NOS reductase domain.

    Science.gov (United States)

    Nishino, Yoshitaka; Yamamoto, Keita; Kimura, Shigenobu; Kikuchi, Akihiro; Shiro, Yoshitsugu; Iyanagi, Takashi

    2007-09-01

    The object of this study was to clarify the mechanism of electron transfer in the human endothelial nitric oxide synthase (eNOS) reductase domain using recombinant eNOS reductase domains; the FAD/NADPH domain containing FAD- and NADPH-binding sites and the FAD/FMN domain containing FAD/NADPH-, FMN-, and a calmodulin-binding sites. In the presence of molecular oxygen or menadione, the reduced FAD/NADPH domain is oxidized via the neutral (blue) semiquinone (FADH(*)), which has a characteristic absorption peak at 520 nm. The FAD/NADPH and FAD/FMN domains have high activity for ferricyanide, but the FAD/FMN domain has low activity for cytochrome c. In the presence or absence of calcium/calmodulin (Ca(2+)/CaM), reduction of the oxidized flavins (FAD-FMN) and air-stable semiquinone (FAD-FMNH(*)) with NADPH occurred in at least two phases in the absorbance change at 457nm. In the presence of Ca(2+)/CaM, the reduction rate of both phases was significantly increased. In contrast, an absorbance change at 596nm gradually increased in two phases, but the rate of the fast phase was decreased by approximately 50% of that in the presence of Ca(2+)/CaM. The air-stable semiquinone form was rapidly reduced by NADPH, but a significant absorbance change at 520 nm was not observed. These findings indicate that the conversion of FADH(2)-FMNH(*) to FADH(*)-FMNH(2) is unfavorable. Reduction of the FAD moiety is activated by CaM, but the formation rate of the active intermediate, FADH(*)-FMNH(2) is extremely low. These events could cause a lowering of enzyme activity in the catalytic cycle.

  9. Glyoxylate as a reducing agent for manganese(III) in salen scaffold: A kinetics and mechanistic study

    Indian Academy of Sciences (India)

    Akshaya K Kar; Achyutananda Acharya; Guru C Pradhan; Anadi C Dash

    2014-05-01

    The kinetics of oxidation of glyoxylic acid (HGl) by MnIII(salen)(OH2)$^{+}_{2}$ ((H2salen = N,N'- bis(salicylidene)ethane-1,2-diamine) is investigated at 30.0-45.0°C, 1.83 ≤ pH ≤ 6.10, I = 0.3 mol dm-3(NaClO4). The products are identified as formic acid, CO2 and MnII with the reaction stoichiometry, |[MnIII]/[HGl]| = 2. The overall reaction involves fast equilibrium pre-association of MnIII(salen)(OH2)$^{+}_{2}$ with HGl and its conjugate base Gl− forming the corresponding inner sphere complexes (both HGl and Gl− being the monohydrate gem-diol forms) followed by the slow electron transfer steps. In addition, the second order electron transfer reactions involving the inner-sphere complexes and HGl/Gl− are also observed. The rate, equilibrium constants and activation parameters for various steps are presented. MnIII(salen)(OH2)(Gl) is virtually inert to intra molecular electron transfer while the process is facile for MnIII(salen)(OH2)(HGl)+ (105ket} = 2.8 ± 0.3 s-1 at 35.0°C) reflecting the involvement of proton coupled electron transfer mechanism in the latter case. A computational study of the structure optimization of the complexes, trans-MnIII(salen)(OH2)$^{+}_{2}$, trans-MnIII(salen)(OH2)(Gl), and trans- MnIII(salen)(OH2)(HGl)+ (all high spin MnIII(d4) systems), reveals strongest axial distortion for the (aqua)(Gl) complex ; HGl bound to MnIII centre by the C=O function of the carboxyl group in the (aqua)(HGl) complex facilitates the formation of a hydrogen bond between the proton of the carboxyl group and the coordinated phenoxide moiety ((O-H…O hydrogen bond distance 1.745 Å) and the gem-diols are not involved in H-bonding in either case. A rate comparison for the second order paths: MnIII(salen)(OH2)(HGl)/Gl)+/0 + HGl/Gl− → products, shows that HGl for the (aqua)(HGl) complex is a better reducing agent than Gl− for the (aqua)(Gl) complex (HG ∼ 5 Gl). The high values of activation enthalpy (H≠ = 93-119 kJ mol-1) are indicative of

  10. Mechanistic studies of anticancer aptamer AS1411 reveal a novel role for nucleolin in regulating Rac1 activation.

    Science.gov (United States)

    Reyes-Reyes, E Merit; Šalipur, Francesca R; Shams, Mitra; Forsthoefel, Matthew K; Bates, Paula J

    2015-08-01

    AS1411 is a G-rich quadruplex-forming oligodeoxynucleotide that binds specifically to nucleolin, a protein found on the surface and in the cytoplasm of most malignant cells but absent from the surface/cytoplasm of most normal cells. AS1411 has shown promising clinical activity and is being widely used as a tumor-targeting agent, but its mechanism of action is not fully understood. Previously, we showed that AS1411 is taken up in cancer cells by macropinocytosis (fluid phase endocytosis) and subsequently stimulates further macropinocytosis by a nucleolin-dependent mechanism. In the current study, we have investigated the significance and molecular mechanisms of AS1411-induced macropinocytosis. Our results indicate that the antiproliferative activity of AS1411 in various cell lines correlated with its capacity to stimulate macropinocytosis. In DU145 prostate cancer cells, AS1411 induced activation of EGFR, Akt, p38, and Rac1. Activation of Akt and p38 were not critical for AS1411 activity because Akt activation was not observed in all AS1411-responsive cell lines and knockdown of p38 had no effect on AS1411's ability to inhibit proliferation. On the other hand, activation of EGFR and Rac1 appeared to play a role in AS1411 activity in all cancer cell lines examined (DU145, MDA-MB-468, A549, LNCaP) and their inhibition significantly reduced AS1411-mediated macropinocytosis and AS1411 antiproliferative activity. Interestingly, downregulation of nucleolin expression by siRNA also produced a substantial increase in activated Rac1, revealing a previously unknown role for nucleolin as a negative regulator of Rac1 activation. Our results are consistent with a model whereby AS1411 binding to nucleolin leads to sustained activation of Rac1 and causes methuosis, a novel type of nonapoptotic cell death characterized by hyperstimulation of macropinocytosis. We speculate that methuosis is a tumor/metastasis suppressor mechanism that opposes the malignant functions of Rac1 and that

  11. Mechanistic studies on cyclohexanone oxygenase.

    Science.gov (United States)

    Ryerson, C C; Ballou, D P; Walsh, C

    1982-05-25

    The bacterial flavoprotein monooxygenase carries out an oxygen insertion reaction on cyclohexanone, with ring expansion to form the seven-membered cyclic product epsilon-caprolactone, a transformation quite distinct from the phenol leads to catechol transformation carried out by the bacterial flavoprotein aromatic hydroxylases. Cyclohexanone oxygenase catalysis involves the four-electron of O2 at the expense of a two-electron oxidation of NADPH, concomitant with a two-electron oxidation of cyclohexanone to epsilon-caprolactone. NADPH oxidase activity is fully coupled with oxygen transfer to substrate. Steady-state kinetic assays demonstrate a ter-ter mechanism for this enzyme. Pre-steady-state kinetic assays demonstrate the participation of a 4a-hydroperoxyflavin intermediate during catalysis. In addition to its ketolactonizing activity, cyclohexanone oxygenase carries out S-oxygenation of thiane to thiane 1-oxide, a reaction which represents a nucleophilic displacement by the sulfur upon the terminal oxygen of the hydroperoxide. This is in contrast to cyclohexanone oxygenations where the flavin hydroperoxide acts as a nucleophile. In addition, a stable apoenzyme form is accessible and can be reconstituted with various FAD analogues with up to 100% recovery of enzyme activity. The accumulated results presented here support a Baeyer-Villiger rearrangement mechanism for the enzymatic oxygenation of cyclohexanone.

  12. Mechanistic models in computational social science

    OpenAIRE

    Petter eHolme; Fredrik eLiljeros

    2015-01-01

    Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes—to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to explore emergent phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influenc...

  13. Mechanistic models in computational social science

    OpenAIRE

    Holme, Petter; Liljeros, Fredrik

    2015-01-01

    Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes -- to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to explore emergent phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influ...

  14. The role of vitamin B6 as an antioxidant in the presence of vitamin B2-photogenerated reactive oxygen species. A kinetic and mechanistic study.

    Science.gov (United States)

    Natera, José; Massad, Walter; García, Norman A

    2012-06-01

    We report on the photostability of a mixture of vitamins B6 and B2 (riboflavin, Rf) upon visible light irradiation and on the possible role of the vitamin B6 family (B6D) as deactivators of reactive oxygen species (ROS). The work is a systematic kinetic and mechanistic study under conditions in which only Rf absorbs photoirradiation. Pyridoxine, pyridoxal hydrochloride, pyridoxal phosphate and pyridoxamine dihydrochloride were studied as representative members of the vitamin B6 family. The visible light irradiation of dissolved Rf and B6D in pH 7.4 aqueous medium under aerobic conditions induces photoprocesses that mainly produce B6D degradation. The overall oxidative mechanism involves the participation of ROS. Photogenerated (3)Rf* is quenched either by oxygen, giving rise to O(2)((1)Δ(g)) by electronic energy transfer to dissolved ground state oxygen, or by B6D yielding, through an electron transfer process, the neutral radical RfH˙, and O(2)˙(-) in an subsequent step. B6D act as quenchers of O(2)((1)Δ(g)) and O(2)˙(-), the former in a totally reactive event that also inhibits Rf photoconsumption. The common chromophoric moiety of B6D represented by 3-hydroxypyridine, constitutes an excellent model that mimics the kinetic behavior of the vitamin as an antioxidant towards Rf-generated ROS. The protein lysozyme, taken as an O(2)((1)Δ(g))-mediated oxidizable biological target, is photoprotected by B6D from Rf-sensitized photodegradation through the quenching of electronically excited triplet state of the pigment, in a process that competes with O(2)((1)Δ(g)) generation.

  15. Acridone derivative 8a induces oxidative stress-mediated apoptosis in CCRF-CEM leukemia cells: application of metabolomics in mechanistic studies of antitumor agents.

    Directory of Open Access Journals (Sweden)

    Yini Wang

    Full Text Available A new acridone derivative, 2-aminoacetamido-10-(3, 5-dimethoxy-benzyl-9(10H-acridone hydrochloride (named 8a synthesized in our lab shows potent antitumor activity, but the mechanism of action remains unclear. Herein, we report the use of an UPLC/Q-TOF MS metabolomic approach to study the effects of three compounds with structures optimized step-by-step, 9(10H-acridone (A, 10-(3,5-dimethoxybenzyl-9(10H-acridone (I, and 8a, on CCRF-CEM leukemia cells and to shed new light on the probable antitumor mechanism of 8a. Acquired data were processed by principal component analysis (PCA and orthogonal partial least squares discriminant analysis (OPLS-DA to identify potential biomarkers. Comparing 8a-treated CCRF-CEM leukemia cells with vehicle control (DMSO, 23 distinct metabolites involved in five metabolic pathways were identified. Metabolites from glutathione (GSH and glycerophospholipid metabolism were investigated in detail, and results showed that GSH level and the reduced/oxidized glutathione (GSH/GSSG ratio were significantly decreased in 8a-treated cells, while L-cysteinyl-glycine (L-Cys-Gly and glutamate were greatly increased. In glycerophospholipid metabolism, cell membrane components phosphatidylcholines (PCs were decreased in 8a-treated cells, while the oxidative products lysophosphatidylcholines (LPCs were significantly increased. We further found that in 8a-treated cells, the reactive oxygen species (ROS and lipid peroxidation product malondialdehyde (MDA were notably increased, accompanied with decrease of mitochondrial transmembrane potential, release of cytochrome C and activation of caspase-3. Taken together our results suggest that the acridone derivative 8a induces oxidative stress-mediated apoptosis in CCRF-CEM leukemia cells. The UPLC/Q-TOF MS based metabolomic approach provides novel insights into the mechanistic studies of antitumor drugs from a point distinct from traditional biological investigations.

  16. Mechanistic study of CBT-Cys click reaction and its application for identifying bioactive N-terminal cysteine peptides in amniotic fluid.

    Science.gov (United States)

    Zheng, Zhen; Chen, Peiyao; Li, Gongyu; Zhu, Yunxia; Shi, Zhonghua; Luo, Yufeng; Zhao, Chun; Fu, Ziyi; Cui, Xianwei; Ji, Chenbo; Wang, Fuqiang; Huang, Guangming; Liang, Gaolin

    2017-01-01

    CBT-Cys click condensation reaction has a high second-order reaction rate constant and has found wide applicability in recent years. However, its reaction mechanism has not been experimentally validated and its application for identifying bioactive N-terminal Cys peptides in real clinical samples has not been reported. Herein, firstly, by employing induced nanoelectrospray ionization-mass spectrometry (InESI-MS) and a home-built micro-reactor, we successfully intercepted and structurally characterized the crucial intermediate in this click reaction for the first time. With the intermediate, the proposed mechanism of this reaction was corroborated. Moreover, we also applied this MS setup to monitor the reaction in real time and obtained the second-order reaction rate constants of this reaction at different pH values. After mechanistic study, we applied this click reaction for identifying bioactive N-terminal cysteine peptides in amniotic fluid (AF). Eight unique N-terminal Cys peptides in AF, three of which are located in the functional domain regions of their corresponding proteins, were identified with a false positive rate less than 1%. One of the three peptides was found able to inhibit the growth of uterine endometrial cancer HEC-1-B cells but not the endometrial normal cells via a typical apoptotic pathway. With its mechanism satisfactorily elucidated, the kinetic parameters obtained, as well as its application for fishing bioactive N-terminal Cys peptides from vast complex clinical samples, we anticipate that this CBT-Cys click reaction could be applied more widely for the facile isolation, site-specific identification, and quantification of N-terminal Cys-containing peptides in complex biological samples.

  17. Tryptophan oxygenation: mechanistic considerations.

    Science.gov (United States)

    Naismith, James H

    2012-06-01

    From a protein structural viewpoint, tryptophan is often considered an inert structural amino acid, playing a role as a hydrophobic anchor in membrane proteins or as part of the hydrophobic core of soluble proteins. However, tryptophan is the only polyaromatic amino acid and, from a chemical viewpoint, possesses unique reactivity owing to the electron-richness of the indole system. This reactivity is seen in the area of natural products and metabolites which have exquisite modifications of the indole ring system. Enzymes have evolved multiple strategies to break or modify the indole ring; one particular class is the IDO/TDO (indoleamine/tryptophan dioxygenase) superfamily. A new member of this family, PrnB, on the surface catalyses a very different reaction, but actually shares much of the early chemistry with the tryptophan dioxygenases. Studies on PrnB have contributed to our understanding of the wider superfamily. In the present mini-review, recent developments in our understanding of how the TDO class of enzymes use activated molecular oxygen to break the indole ring are discussed.

  18. Evolutionary and mechanistic theories of aging.

    Science.gov (United States)

    Hughes, Kimberly A; Reynolds, Rose M

    2005-01-01

    Senescence (aging) is defined as a decline in performance and fitness with advancing age. Senescence is a nearly universal feature of multicellular organisms, and understanding why it occurs is a long-standing problem in biology. Here we present a concise review of both evolutionary and mechanistic theories of aging. We describe the development of the general evolutionary theory, along with the mutation accumulation, antagonistic pleiotropy, and disposable soma versions of the evolutionary model. The review of the mechanistic theories focuses on the oxidative stress resistance, cellular signaling, and dietary control mechanisms of life span extension. We close with a discussion of how an approach that makes use of both evolutionary and molecular analyses can address a critical question: Which of the mechanisms that can cause variation in aging actually do cause variation in natural populations?

  19. Mechanistic models in computational social science

    Directory of Open Access Journals (Sweden)

    Petter eHolme

    2015-09-01

    Full Text Available Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes—to test scenarios, to test the consistency of descriptive theories (proof-of-concept models, to explore emergent phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influences from the natural and formal sciences. We argue that mechanistic computational models form a natural common ground for social and natural sciences, and look forward to possible future information flow across the social-natural divide.

  20. Understanding and Exploitation of Neighboring Heteroatom Effect for the Mild N-Arylation of Heterocycles with Diaryliodonium Salts under Aqueous Conditions: A Theoretical and Experimental Mechanistic Study.

    Science.gov (United States)

    Bihari, Tamás; Babinszki, Bence; Gonda, Zsombor; Kovács, Szabolcs; Novák, Zoltán; Stirling, András

    2016-07-01

    The mechanism of arylation of N-heterocycles with unsymmetric diaryliodonium salts is elucidated. The fast and efficient N-arylation reaction is interpreted in terms of the bifunctionality of the substrate: The consecutive actions of properly oriented Lewis base and Brønsted acid centers in sufficient proximity result in the fast and efficient N-arylation. The mechanistic picture points to a promising synthetic strategy where suitably positioned nucleophilic and acidic centers enable functionalization, and it is tested experimentally.

  1. Systems toxicology approaches enable mechanistic comparison of spontaneous and cigarette smoke-related lung tumor development in the A/J mouse model

    OpenAIRE

    2014-01-01

    The A/J mouse is highly susceptible to lung tumor induction and has been widely used as a screening model in carcinogenicity testing and chemoprevention studies. However, the A/J mouse model has several disadvantages. Most notably, it develops lung tumors spontaneously. Moreover, there is a considerable gap in our understanding of the underlying mechanisms of pulmonary chemical carcinogenesis in the A/J mouse. Therefore, we examined the differences between spontaneous and cigarette smoke-rela...

  2. Mechanistic study of aerosol dry deposition on vegetated canopies; Etude mecaniste du depot sec d'aerosols sur les couverts vegetaux

    Energy Technology Data Exchange (ETDEWEB)

    Petroff, A

    2005-04-15

    The dry deposition of aerosols onto vegetated canopies is modelled through a mechanistic approach. The interaction between aerosols and vegetation is first formulated by using a set of parameters, which are defined at the local scale of one surface. The overall deposition is then deduced at the canopy scale through an up-scaling procedure based on the statistic distribution parameters. This model takes into account the canopy structural and morphological properties, and the main characteristics of the turbulent flow. Deposition mechanisms considered are Brownian diffusion, interception, initial and turbulent impaction, initially with coniferous branches and then with entire canopies of different roughness, such as grass, crop field and forest. (author)

  3. Legitimising neural network river forecasting models: a new data-driven mechanistic modelling framework

    Science.gov (United States)

    Mount, N. J.; Dawson, C. W.; Abrahart, R. J.

    2013-01-01

    In this paper we address the difficult problem of gaining an internal, mechanistic understanding of a neural network river forecasting (NNRF) model. Neural network models in hydrology have long been criticised for their black-box character, which prohibits adequate understanding of their modelling mechanisms and has limited their broad acceptance by hydrologists. In response, we here present a new, data-driven mechanistic modelling (DDMM) framework that incorporates an evaluation of the legitimacy of a neural network's internal modelling mechanism as a core element in the model development process. The framework is exemplified for two NNRF modelling scenarios, and uses a novel adaptation of first order, partial derivate, relative sensitivity analysis methods as the means by which each model's mechanistic legitimacy is explored. The results demonstrate the limitations of standard, goodness-of-fit validation procedures applied by NNRF modellers, by highlighting how the internal mechanisms of complex models that produce the best fit scores can have much lower legitimacy than simpler counterparts whose scores are only slightly inferior. The study emphasises the urgent need for better mechanistic understanding of neural network-based hydrological models and the further development of methods for elucidating their mechanisms.

  4. Trichloroethylene: Mechanistic, Epidemiologic and Other Supporting Evidence of Carcinogenic Hazard

    Science.gov (United States)

    Rusyn, Ivan; Chiu, Weihsueh A.; Lash, Lawrence H.; Kromhout, Hans; Hansen, Johnni; Guyton, Kathryn Z.

    2013-01-01

    The chlorinated solvent trichloroethylene (TCE) is a ubiquitous environmental pollutant. The carcinogenic hazard of TCE was the subject of a 2012 evaluation by a Working Group of the International Agency for Research on Cancer (IARC). Information on exposures, relevant data from epidemiologic studies, bioassays in experimental animals, and toxicity and mechanism of action studies was used to conclude that TCE is carcinogenic to humans (Group 1). This article summarizes the key evidence forming the scientific bases for the IARC classification. Exposure to TCE from environmental sources (including from hazardous waste sites and contaminated water) is common throughout the world. While workplace use of TCE has been declining, occupational exposures remain of concern, especially in developing countries. Strongest human evidence is from studies of occupational TCE exposure and kidney cancer. Positive, although less consistent, associations were reported for liver cancer and non-Hodgkin's lymphoma. TCE is carcinogenic at multiple sites in multiple species and strains of experimental animals. The mechanistic evidence includes extensive data on the toxicokinetics and genotoxicity of TCE and its metabolites. Together, available evidence provided a cohesive database supporting the human cancer hazard of TCE, particularly in the kidney. For other target sites of carcinogenicity, mechanistic and other data were found to be more limited. Important sources of susceptibility to TCE toxicity and carcinogenicity were also reviewed by the Working Group. In all, consideration of the multiple evidence streams presented herein informed the IARC conclusions regarding the carcinogenicity of TCE. PMID:23973663

  5. Trichloroethylene: Mechanistic, epidemiologic and other supporting evidence of carcinogenic hazard.

    Science.gov (United States)

    Rusyn, Ivan; Chiu, Weihsueh A; Lash, Lawrence H; Kromhout, Hans; Hansen, Johnni; Guyton, Kathryn Z

    2014-01-01

    The chlorinated solvent trichloroethylene (TCE) is a ubiquitous environmental pollutant. The carcinogenic hazard of TCE was the subject of a 2012 evaluation by a Working Group of the International Agency for Research on Cancer (IARC). Information on exposures, relevant data from epidemiologic studies, bioassays in experimental animals, and toxicity and mechanism of action studies was used to conclude that TCE is carcinogenic to humans (Group 1). This article summarizes the key evidence forming the scientific bases for the IARC classification. Exposure to TCE from environmental sources (including hazardous waste sites and contaminated water) is common throughout the world. While workplace use of TCE has been declining, occupational exposures remain of concern, especially in developing countries. The strongest human evidence is from studies of occupational TCE exposure and kidney cancer. Positive, although less consistent, associations were reported for liver cancer and non-Hodgkin lymphoma. TCE is carcinogenic at multiple sites in multiple species and strains of experimental animals. The mechanistic evidence includes extensive data on the toxicokinetics and genotoxicity of TCE and its metabolites. Together, available evidence provided a cohesive database supporting the human cancer hazard of TCE, particularly in the kidney. For other target sites of carcinogenicity, mechanistic and other data were found to be more limited. Important sources of susceptibility to TCE toxicity and carcinogenicity were also reviewed by the Working Group. In all, consideration of the multiple evidence streams presented herein informed the IARC conclusions regarding the carcinogenicity of TCE.

  6. Mechanistic individualism versus organistic totalitarianism

    Directory of Open Access Journals (Sweden)

    J.J. Venter

    1997-03-01

    Full Text Available Mechanistic individualism versus organistic totalitarianismIn this article it is argued that the organistic world picture, when functioning as a world view, is associated with a totalitarian view of social relationships, usually promoting the interests o f the state or the ethnic group as the interests which should dominate. This is illustrated by referring to the social ideas of Hobbes, Rousseau, D.H. Lawrence and Mussolini. The mechanistic world picture, however, when functioning as a world view, is associated with individualism, according to which the individuals have a relatively independent existence; it suggests that justice and morality are the automatic products of the equilibrating process. Cases in point: Hobbes, Adam Smith, Kant, Darwin, New-Classical and Monetarist economics. Finally (in Neo-Calvinist vein it is argued that the application o f such worldviewish metaphors should be limited, so that justice can be done to both the differentiation of social relationships and their integration.

  7. New web-based applications for mechanistic case diagramming

    Directory of Open Access Journals (Sweden)

    Fred R. Dee

    2014-07-01

    Full Text Available The goal of mechanistic case diagraming (MCD is to provide students with more in-depth understanding of cause and effect relationships and basic mechanistic pathways in medicine. This will enable them to better explain how observed clinical findings develop from preceding pathogenic and pathophysiological events. The pedagogic function of MCD is in relating risk factors, disease entities and morphology, signs and symptoms, and test and procedure findings in a specific case scenario with etiologic pathogenic and pathophysiological sequences within a flow diagram. In this paper, we describe the addition of automation and predetermined lists to further develop the original concept of MCD as described by Engelberg in 1992 and Guerrero in 2001. We demonstrate that with these modifications, MCD is effective and efficient in small group case-based teaching for second-year medical students (ratings of ~3.4 on a 4.0 scale. There was also a significant correlation with other measures of competency, with a ‘true’ score correlation of 0.54. A traditional calculation of reliability showed promising results (α =0.47 within a low stakes, ungraded environment. Further, we have demonstrated MCD's potential for use in independent learning and TBL. Future studies are needed to evaluate MCD's potential for use in medium stakes assessment or self-paced independent learning and assessment. MCD may be especially relevant in returning students to the application of basic medical science mechanisms in the clinical years.

  8. New web-based applications for mechanistic case diagramming

    Science.gov (United States)

    Dee, Fred R.; Haugen, Thomas H.; Kreiter, Clarence D.

    2014-01-01

    The goal of mechanistic case diagraming (MCD) is to provide students with more in-depth understanding of cause and effect relationships and basic mechanistic pathways in medicine. This will enable them to better explain how observed clinical findings develop from preceding pathogenic and pathophysiological events. The pedagogic function of MCD is in relating risk factors, disease entities and morphology, signs and symptoms, and test and procedure findings in a specific case scenario with etiologic pathogenic and pathophysiological sequences within a flow diagram. In this paper, we describe the addition of automation and predetermined lists to further develop the original concept of MCD as described by Engelberg in 1992 and Guerrero in 2001. We demonstrate that with these modifications, MCD is effective and efficient in small group case-based teaching for second-year medical students (ratings of ~3.4 on a 4.0 scale). There was also a significant correlation with other measures of competency, with a ‘true’ score correlation of 0.54. A traditional calculation of reliability showed promising results (α =0.47) within a low stakes, ungraded environment. Further, we have demonstrated MCD's potential for use in independent learning and TBL. Future studies are needed to evaluate MCD's potential for use in medium stakes assessment or self-paced independent learning and assessment. MCD may be especially relevant in returning students to the application of basic medical science mechanisms in the clinical years. PMID:25059836

  9. Elucidation of mechanisms in manganese and iron based oxidation catalysis : Mechanistic insights and development of novel approaches applied to transition metal catalyzed oxidations catalysis

    NARCIS (Netherlands)

    Angelone, Davide

    2016-01-01

    Oxidation chemistry is central to life and to the modern chemical industry and hence understanding chemical oxidation is essential to developing new processes and elucidating biological oxidation mechanisms. Elucidating mechanisms in inorganic oxidation catalysis and simultaneously developing new to

  10. Mechanistic modeling of pesticide exposure: The missing keystone of honey bee toxicology.

    Science.gov (United States)

    Sponsler, Douglas B; Johnson, Reed M

    2017-04-01

    The role of pesticides in recent honey bee losses is controversial, partly because field studies often fail to detect effects predicted by laboratory studies. This dissonance highlights a critical gap in the field of honey bee toxicology: there exists little mechanistic understanding of the patterns and processes of exposure that link honey bees to pesticides in their environment. The authors submit that 2 key processes underlie honey bee pesticide exposure: 1) the acquisition of pesticide by foraging bees, and 2) the in-hive distribution of pesticide returned by foragers. The acquisition of pesticide by foraging bees must be understood as the spatiotemporal intersection between environmental contamination and honey bee foraging activity. This implies that exposure is distributional, not discrete, and that a subset of foragers may acquire harmful doses of pesticide while the mean colony exposure would appear safe. The in-hive distribution of pesticide is a complex process driven principally by food transfer interactions between colony members, and this process differs importantly between pollen and nectar. High priority should be placed on applying the extensive literature on honey bee biology to the development of more rigorously mechanistic models of honey bee pesticide exposure. In combination with mechanistic effects modeling, mechanistic exposure modeling has the potential to integrate the field of honey bee toxicology, advancing both risk assessment and basic research. Environ Toxicol Chem 2017;36:871-881. © 2016 SETAC. © 2016 SETAC.

  11. Mechanistic aspects of ionic reactions in flames

    DEFF Research Database (Denmark)

    Egsgaard, H.; Carlsen, L.

    1993-01-01

    Some fundamentals of the ion chemistry of flames are summarized. Mechanistic aspects of ionic reactions in flames have been studied using a VG PlasmaQuad, the ICP-system being substituted by a simple quartz burner. Simple hydrocarbon flames as well as sulfur-containing flames have been investigated....... The simple hydrocarbon flames are dominated by a series of hydrocarbonic ions and, to a minor extent, protonated oxo-compounds. The introduction of sulfur to the flames leads to significant changes in the ion composition, as sulfur-containing species become dominant. The ability of the technique to study...

  12. Systems toxicology approaches enable mechanistic comparison of spontaneous and cigarette smoke-related lung tumor development in the A/J mouse model

    Directory of Open Access Journals (Sweden)

    Luettich Karsta

    2014-06-01

    Full Text Available The A/J mouse is highly susceptible to lung tumor induction and has been widely used as a screening model in carcinogenicity testing and chemoprevention studies. However, the A/J mouse model has several disadvantages. Most notably, it develops lung tumors spontaneously. Moreover, there is a considerable gap in our understanding of the underlying mechanisms of pulmonary chemical carcinogenesis in the A/J mouse. Therefore, we examined the differences between spontaneous and cigarette smokerelated lung tumors in the A/J mouse model using mRNA and microRNA (miRNA profiling. Male A/J mice were exposed whole-body to mainstream cigarette smoke (MS for 18 months. Gene expression interaction term analysis of lung tumors and surrounding nontumorous parenchyma samples from animals that were exposed to either 300 mg/m3 MS or sham-exposed to fresh air indicated significant differential expression of 296 genes. Ingenuity Pathway Analysis® (IPA® indicated an overall suppression of the humoral immune response, which was accompanied by a disruption of sphingolipid and glycosaminoglycan metabolism and a deregulation of potentially oncogenic miRNA in tumors of MS-exposed A/J mice. Thus, we propose that MS exposure leads to severe perturbations in pathways essential for tumor recognition by the immune system, thereby potentiating the ability of tumor cells to escape from immune surveillance. Further, exposure to MS appeared to affect expression of miRNA, which have previously been implicated in carcinogenesis and are thought to contribute to tumor progression. Finally, we identified a 50-gene expression signature and show its utility in distinguishing between cigarette smoke-related and spontaneous lung tumors

  13. DFT Mechanistic Study of the Selective Terminal C-H Activation of n-Pentane with a Tungsten Allyl Nitrosyl Complex

    KAUST Repository

    Lee, Richmond

    2017-01-17

    Mechanistic insights into the selective C-H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using Bader’s atom in molecules (AIM) analysis on the elementary steps of the hydrogen transfer process, TS1 and TS2, it was observed that the calculated H-transfer models were closely similar to Hall’s metal-assisted σ-bond metathesis through bond critical point (BCP) comparisons. One distinguishable feature was the fact that the formal oxidation state of the W changed in the concerted H-transfer process. To better differentiate, we term these processes as ‘Formal Reductive Hydrogen Transfer’ (FRHT) for TS1 and ‘Formal Oxidative Hydrogen Transfer’ (FOHT) for TS2.

  14. DFT mechanistic study of the selective terminal C–H activation of n-pentane with a tungsten allyl nitrosyl complex

    Directory of Open Access Journals (Sweden)

    Richmond Lee

    2017-07-01

    Full Text Available Mechanistic insights into the selective C–H terminal activation of n-pentane with tungsten allyl nitrosyl complex reported by Legzdins were gained by employing density functional theory with B3LYP hybrid functional. Using Bader’s atom in molecules (AIM analysis on the elementary steps of the hydrogen transfer process, TS1 and TS2, it was observed that the calculated H-transfer models were closely similar to Hall’s metal-assisted σ-bond metathesis through bond critical point (BCP comparisons. One distinguishable feature was the fact that the formal oxidation state of the W changed in the concerted H-transfer process. To better differentiate, we term these processes as ‘Formal Reductive Hydrogen Transfer’ (FRHT for TS1 and ‘Formal Oxidative Hydrogen Transfer’ (FOHT for TS2.

  15. Collective cell migration: a mechanistic perspective.

    Science.gov (United States)

    Vedula, Sri Ram Krishna; Ravasio, Andrea; Lim, Chwee Teck; Ladoux, Benoit

    2013-11-01

    Collective cell migration is fundamental to gaining insights into various important biological processes such as wound healing and cancer metastasis. In particular, recent in vitro studies and in silico simulations suggest that mechanics can explain the social behavior of multicellular clusters to a large extent with minimal knowledge of various cellular signaling pathways. These results suggest that a mechanistic perspective is necessary for a comprehensive and holistic understanding of collective cell migration, and this review aims to provide a broad overview of such a perspective.

  16. Elucidation of mechanisms in manganese and iron based oxidation catalysis: Mechanistic insights and development of novel approaches applied to transition metal catalyzed oxidations catalysis

    OpenAIRE

    Angelone, Davide

    2016-01-01

    Oxidation chemistry is central to life and to the modern chemical industry and hence understanding chemical oxidation is essential to developing new processes and elucidating biological oxidation mechanisms. Elucidating mechanisms in inorganic oxidation catalysis and simultaneously developing new tools to do so is the theme of this thesis. Spectroscopic techniques, especially Raman and UV-vis absorption, are used, together with Density Functional theory (DFT), to observe and characterise the ...

  17. From patterns to emerging processes in mechanistic urban ecology.

    Science.gov (United States)

    Shochat, Eyal; Warren, Paige S; Faeth, Stanley H; McIntyre, Nancy E; Hope, Diane

    2006-04-01

    Rapid urbanization has become an area of crucial concern in conservation owing to the radical changes in habitat structure and loss of species engendered by urban and suburban development. Here, we draw on recent mechanistic ecological studies to argue that, in addition to altered habitat structure, three major processes contribute to the patterns of reduced species diversity and elevated abundance of many species in urban environments. These activities, in turn, lead to changes in animal behavior, morphology and genetics, as well as in selection pressures on animals and plants. Thus, the key to understanding urban patterns is to balance studying processes at the individual level with an integrated examination of environmental forces at the ecosystem scale.

  18. Mechanistic Perspectives on Organic Photoredox Catalysis for Aromatic Substitutions.

    Science.gov (United States)

    Majek, Michal; Jacobi von Wangelin, Axel

    2016-10-18

    Photoredox catalysis has emerged as a powerful tool for the utilization of visible light to drive chemical reactions between organic molecules that exhibit two rather ubiquitous properties: colorlessness and redox-activity. The photocatalyst, however, requires significant absorption in the visible spectrum and reversible redox activity. This very general framework has led to the development of several new modes of reactivity based on electron and energy transfer steps between photoexcited catalyst states and various organic molecules. In the past years, major effort has been devoted to photoredox-catalytic aromatic substitutions involving an initial reductive activation of various aryl electrophiles by the photocatalyst, which opens a new entry into selective arene functionalizations within organic synthesis endeavors. This, however, has led to a unilateral emphasis of synthetic developments including catalyst modifications, substrate scope studies, and combinations with other chemical processes. This Account summarizes recent reports of new protocols for the synthesis of aromatic esters, thioethers, boronates, sulfonates, heterobiaryls, deuteroarenes, and other functionalized arenes under mild photoredox conditions with organic dyes. On the other hand, mechanistic studies were largely neglected. This Account emphasizes the most relevant experiments and techniques, which can greatly assist in the exploration of the mechanistic foundation of aromatic photoredox substitutions and the design of new chemical reactivities. The nature and physicochemical properties of the employed organic dyes, the control of its acid-base chemistry, the choice of the irradiation sources, and the concentrations of substrates and dyes are demonstrated to decisively affect the activity of organic photocatalysts, the chemo- and regioselectivities of reactions, and the operating mechanisms. Several methods of distinction between photocatalytic and radical chain processes are being discussed

  19. Development of multiple QSAR models for consensus predictions and unified mechanistic interpretations of the free-radical scavenging activities of chromone derivatives.

    Science.gov (United States)

    Mitra, Indrani; Saha, Achintya; Roy, Kunal

    2012-05-01

    Antioxidants are important defenders of the human body against nocive free radicals, which are the causative agents of most life-threatening diseases. The immense biomedicinal utility of antioxidants necessitates the development and design of new synthetic antioxidant molecules. The present report deals with the modeling of a series of chromone derivatives, which was done to provide detailed insight into the main structural fragments that impart antioxidant activity to these molecules. Four different quantitative structure-property relationship (QSAR) techniques, namely 3D pharmacophore mapping, comparative molecular similarity indices analysis (CoMSIA 3D-QSAR), hologram QSAR (HQSAR), and group-based QSAR (G-QSAR) techniques, were employed to obtain statistically significant models with encouraging external predictive potentials. Moreover, the visual contribution maps obtained for the different models signify the importance of different structural features in specific regions of the chromone nucleus. Additionally, the G-QSAR models determine the composite influence of pairs of substituent fragments on the overall antioxidant activity profiles of the molecules. Multiple models with different strategies for assessing structure-activity relationships were applied to reach a unified conclusion regarding the antioxidant mechanism and to provide consensus predictions, which are more reliable than values derived from a single model. The structural information obtained from the various QSAR models developed in the present work can thus be effectively utilized to design and predict the activities of new molecules belonging to the class of chromone derivatives.

  20. Mechanistic study of electrocatalytic oxidation of formic acid at platinum in acidic solution by time-resolved surface-enhanced infrared absorption spectroscopy.

    Science.gov (United States)

    Samjeské, Gabor; Miki, Atsushi; Ye, Shen; Osawa, Masatoshi

    2006-08-24

    Surface-enhanced infrared absorption spectroscopy (SEIRAS) combined with cyclic voltammetry or chronoamperometry has been utilized to examine kinetic and mechanistic aspects of the electrocatalytic oxidation of formic acid on a polycrystalline Pt surface at the molecular scale. Formate is adsorbed on the electrode in a bridge configuration in parallel to the adsorption of linear and bridge CO produced by dehydration of formic acid. A solution-exchange experiment using isotope-labeled formic acids (H(12)COOH and H(13)COOH) reveals that formic acid is oxidized to CO(2) via adsorbed formate and the decomposition (oxidation) of formate to CO(2) is the rate-determining step of the reaction. The adsorption/oxidation of CO and the oxidation/reduction of the electrode surface strongly affect the formic acid oxidation by blocking active sites for formate adsorption and also by retarding the decomposition of adsorbed formate. The interplay of the involved processes also affects the kinetics and complicates the cyclic voltammograms of formic acid oxidation. The complex voltammetric behavior is comprehensively explained at the molecular scale by taking all these effects into account.

  1. Rational Design in Catalysis: A Mechanistic Study of β-Hydride Eliminations in Gold(I) and Gold(III) Complexes Based on Features of the Reaction Valley.

    Science.gov (United States)

    Castiñeira Reis, Marta; López, Carlos Silva; Kraka, Elfi; Cremer, Dieter; Faza, Olalla Nieto

    2016-09-01

    β-Hydride eliminations for ethylgold(III) dichloride complexes are identified as reactions with an unusually long prechemical stage corresponding to the conformational preparation of the reaction complex and spanning six phases. The prechemical process is characterized by a geared rotation of the L-Au-L group (L = Cl) driving methyl group rotation and causing a repositioning of the ligands. This requires more than 28 kcal/mol of the total barrier of 34.0 kcal/mol, according to the unified reaction valley approach, which also determines that the energy requirements of the actual chemical process leading to the β-elimination product are only about 5.5 kcal/mol. A detailed mechanistic analysis was used as a basis for a rational design of substrates (via substituents on the ethyl group) and/or ligands, which can significantly reduce the reaction barrier. This strategy takes advantage of either a higher trans activity of the ligands or a tuned electronic demand of the ethyl group. The β-hydride elimination of gold(I) was found to suffer from strong Coulomb and exchange repulsion when a positively charged hydrogen atom enforces a coordination position in a d(10)-configured gold atom, thus triggering an unassisted σ-π Au(I)-C conversion.

  2. The Role of Parathyroid Hormone-Related Protein (PTHrP) in Osteoblast Response to Microgravity: Mechanistic Implications for Osteoporosis Development.

    Science.gov (United States)

    Camirand, Anne; Goltzman, David; Gupta, Ajay; Kaouass, Mohammadi; Panda, Dibyendu; Karaplis, Andrew

    2016-01-01

    Prolonged skeletal unloading through bedrest results in bone loss similar to that observed in elderly osteoporotic patients, but with an accelerated timeframe. This rapid effect on weight-bearing bones is also observed in astronauts who can lose up to 2% of their bone mass per month spent in Space. Despite the important implications for Spaceflight travelers and bedridden patients, the exact mechanisms involved in disuse osteoporosis have not been elucidated. Parathyroid hormone-related protein (PTHrP) regulates many physiological processes including skeletal development, and has been proposed as a mechanosensor. To investigate the role of PTHrP in microgravity-induced bone loss, trabecular and calvarial osteoblasts (TOs and COs) from Pthrp +/+ and -/- mice were subjected to actual Spaceflight for 6 days (Foton M3 satellite). Pthrp +/+, +/- and -/- osteoblasts were also exposed to simulated microgravity for periods varying from 6 days to 6 weeks. While COs displayed little change in viability in 0g, viability of all TOs rapidly decreased in inverse proportion to PTHrP expression levels. Furthermore, Pthrp+/+ TOs displayed a sharp viability decline after 2 weeks at 0g. Microarray analysis of Pthrp+/+ TOs after 6 days in simulated 0g revealed expression changes in genes encoding prolactins, apoptosis/survival molecules, bone metabolism and extra-cellular matrix composition proteins, chemokines, insulin-like growth factor family members and Wnt-related signalling molecules. 88% of 0g-induced expression changes in Pthrp+/+ cells overlapped those caused by Pthrp ablation in normal gravity, and pulsatile treatment with PTHrP1-36 not only reversed a large proportion of 0g-induced effects in Pthrp+/+ TOs but maintained viability over 6-week exposure to microgravity. Our results confirm PTHrP efficacy as an anabolic agent to prevent microgravity-induced cell death in TOs.

  3. The Role of Parathyroid Hormone-Related Protein (PTHrP in Osteoblast Response to Microgravity: Mechanistic Implications for Osteoporosis Development.

    Directory of Open Access Journals (Sweden)

    Anne Camirand

    Full Text Available Prolonged skeletal unloading through bedrest results in bone loss similar to that observed in elderly osteoporotic patients, but with an accelerated timeframe. This rapid effect on weight-bearing bones is also observed in astronauts who can lose up to 2% of their bone mass per month spent in Space. Despite the important implications for Spaceflight travelers and bedridden patients, the exact mechanisms involved in disuse osteoporosis have not been elucidated. Parathyroid hormone-related protein (PTHrP regulates many physiological processes including skeletal development, and has been proposed as a mechanosensor. To investigate the role of PTHrP in microgravity-induced bone loss, trabecular and calvarial osteoblasts (TOs and COs from Pthrp +/+ and -/- mice were subjected to actual Spaceflight for 6 days (Foton M3 satellite. Pthrp +/+, +/- and -/- osteoblasts were also exposed to simulated microgravity for periods varying from 6 days to 6 weeks. While COs displayed little change in viability in 0g, viability of all TOs rapidly decreased in inverse proportion to PTHrP expression levels. Furthermore, Pthrp+/+ TOs displayed a sharp viability decline after 2 weeks at 0g. Microarray analysis of Pthrp+/+ TOs after 6 days in simulated 0g revealed expression changes in genes encoding prolactins, apoptosis/survival molecules, bone metabolism and extra-cellular matrix composition proteins, chemokines, insulin-like growth factor family members and Wnt-related signalling molecules. 88% of 0g-induced expression changes in Pthrp+/+ cells overlapped those caused by Pthrp ablation in normal gravity, and pulsatile treatment with PTHrP1-36 not only reversed a large proportion of 0g-induced effects in Pthrp+/+ TOs but maintained viability over 6-week exposure to microgravity. Our results confirm PTHrP efficacy as an anabolic agent to prevent microgravity-induced cell death in TOs.

  4. Serum Albumin Binding and Esterase Activity: Mechanistic Interactions with Organophosphates

    Directory of Open Access Journals (Sweden)

    Nikolay V. Goncharov

    2017-07-01

    Full Text Available The albumin molecule, in contrast to many other plasma proteins, is not covered with a carbohydrate moiety and can bind and transport various molecules of endogenous and exogenous origin. The enzymatic activity of albumin, the existence of which many scientists perceive skeptically, is much less studied. In toxicology, understanding the mechanistic interactions of organophosphates with albumin is a special problem, and its solution could help in the development of new types of antidotes. In the present work, the history of the issue is briefly examined, then our in silico data on the interaction of human serum albumin with soman, as well as comparative in silico data of human and bovine serum albumin activities in relation to paraoxon, are presented. Information is given on the substrate specificity of albumin and we consider the possibility of its affiliation to certain classes in the nomenclature of enzymes.

  5. A General Mechanistic Model of Solid Oxide Fuel Cells

    Institute of Scientific and Technical Information of China (English)

    SHI Yixiang; CAI Ningsheng

    2006-01-01

    A comprehensive model considering all forms of polarization was developed. The model considers the intricate interdependency among the electrode microstructure, the transport phenomena, and the electrochemical processes. The active three-phase boundary surface was expressed as a function of electrode microstructure parameters (porosity, coordination number, contact angle, etc.). The exchange current densities used in the simulation were obtained by fitting a general formulation to the polarization curves proposed as a function of cell temperature and oxygen partial pressure. A validation study shows good agreement with published experimental data. Distributions of overpotentials, gas component partial pressures, and electronic/ionic current densities have been calculated. The effects of a porous electrode structure and of various operation conditions on cell performance were also predicted. The mechanistic model proposed can be used to interpret experimental observations and optimize cell performance by incorporating reliable experimental data.

  6. Mechanistic models of animal migration behaviour--their diversity, structure and use.

    Science.gov (United States)

    Bauer, Silke; Klaassen, Marcel

    2013-05-01

    1. Migration is a widespread phenomenon in the animal kingdom, including many taxonomic groups and modes of locomotion. Developing an understanding of the proximate and ultimate causes for this behaviour not only addresses fundamental ecological questions but has relevance to many other fields, for example in relation to the spread of emerging zoonotic diseases, the proliferation of invasive species, aeronautical safety as well as the conservation of migrants. 2. Theoretical methods can make important contributions to our understanding of migration, by allowing us to integrate findings on this complex behaviour, identify caveats in our understanding and to guide future empirical research efforts. Various mechanistic models exist to date, but their applications seem to be scattered and far from evenly distributed across taxonomic units. 3. Therefore, we provide an overview of the major mechanistic modelling approaches used in the study of migration behaviour and characterize their fundamental features, assumptions and limitations and discuss their typical data requirements both for model parameterization and for scrutinizing model predictions. 4. Furthermore, we review 155 studies that have used mechanistic models to study animal migration and analyse them with regard to the approaches used and the focal species, and also explore their contribution to advancing current knowledge within six broad migration ecology research themes. 5. This identifies important gaps in our present knowledge, which should be tackled in future research using existing and to-be developed theoretical approaches.

  7. Facile synthesis of 1-alkoxy-1H-benzo- and 7-azabenzotriazoles from peptide coupling agents, mechanistic studies, and synthetic applications

    Directory of Open Access Journals (Sweden)

    Mahesh K. Lakshman

    2014-08-01

    Full Text Available (1H-Benzo[d][1,2,3]triazol-1-yloxytris(dimethylaminophosphonium hexafluorophosphate (BOP, 1H-benzo[d][1,2,3]triazol-1-yl 4-methylbenzenesulfonate (Bt-OTs, and 3H-[1,2,3]triazolo[4,5-b]pyridine-3-yl 4-methylbenzenesulfonate (At-OTs are classically utilized in peptide synthesis for amide-bond formation. However, a previously undescribed reaction of these compounds with alcohols in the presence of a base, leads to 1-alkoxy-1H-benzo- (Bt-OR and 7-azabenzotriazoles (At-OR. Although BOP undergoes reactions with alcohols to furnish 1-alkoxy-1H-benzotriazoles, Bt-OTs proved to be superior. Both, primary and secondary alcohols undergo reaction under generally mild reaction conditions. Correspondingly, 1-alkoxy-1H-7-azabenzotriazoles were synthesized from At-OTs. Mechanistically, there are three pathways by which these peptide-coupling agents can react with alcohols. From 31P{1H}, [18O]-labeling, and other chemical experiments, phosphonium and tosylate derivatives of alcohols seem to be intermediates. These then react with BtO− and AtO− produced in situ. In order to demonstrate broader utility, this novel reaction has been used to prepare a series of acyclic nucleoside-like compounds. Because BtO− is a nucleofuge, several Bt-OCH2Ar substrates have been evaluated in nucleophilic substitution reactions. Finally, the possible formation of Pd π–allyl complexes by departure of BtO− has been queried. Thus, alpha-allylation of three cyclic ketones was evaluated with 1-(cinnamyloxy-1H-benzo[d][1,2,3]triazole, via in situ formation of pyrrolidine enamines and Pd catalysis.

  8. DFT functional benchmarking on the energy splitting of chromium spin states and mechanistic study of acetylene cyclotrimerization over the Phillips Cr(II)/silica catalyst.

    Science.gov (United States)

    Liu, Zhen; Cheng, Ruihua; He, Xuelian; Wu, Xiaojun; Liu, Boping

    2012-07-19

    In this work, a two-state reaction mechanism for the acetylene cyclotrimerization over a cluster model for the Phillips Cr(II)/silica catalyst were systematically investigated using density functional theory (DFT). Since spin crossover phenomenon was confirmed in the catalytic cycle, an accurate prediction of the energy gap between low- and high-spin states is crucial for the description of a reaction involving a two-state reactivity. Therefore, a massive DFT functional benchmarking test has been conducted on the cluster model by taking a CASPT2 energy gap as a reference. Consequently, B3PW91* with 28% Hartree-Fock exchange energy was selected for the following mechanistic investigation. Each of the possible potential energy surface including singlet, triplet, and quintet surfaces was explored. On the quintet surface, the reaction begins with a coordination of an acetylene on the chromium center to generate a π-coordinated complex. The following oxidative coupling through further coordination with a second acetylene was predicted to be a two-step reaction to generate a chromacyclopentadiene species. This transformation was found to be energetically prohibitive by the presence of the transition state (5)TS[C-E] (ΔG(‡) = 31.1 kcal/mol). On the triplet surface, however, the coordination of an acetylene generates a chromacyclopropene species without showing any activation barrier. The second acetylene incorporation proceeding via a coordination on the chromium center followed by an insertion into a Cr-C σ-bond of the chromacyclopropene was predicted to be a facile reaction pathway (ΔG(‡) = 10.2 kcal/mol). The third acetylene was captured by the cluster model through the formation of a hydrogen bond. The later transformation on the triplet surface was found to be an intermolecular [4 + 2] cycloaddition to finish the cyclization. The lack of the aromaticity of the benzene ring in (3)L results in an uncompleted reaction pathway on a single triplet surface

  9. Mechanistic approach to the pathophysiology of target organ damage in hypertension from studies in a human model with characteristics opposite to hypertension: Bartter's and Gitelman's syndromes.

    Science.gov (United States)

    Calò, L A; Maiolino, G

    2015-07-01

    Extensive studies using Bartter's/Gitelman's syndrome patients have provided insights into the angiotensin II (Ang II) signaling pathways involved in the regulation of vascular tone and cardiovascular-renal remodeling. The renin-angiotensin-aldosterone system is activated in these syndromes, however, patients do not develop hypertension and cardiovascular remodeling and clinically manifest conditions opposite to hypertension. The short- and the long-term signaling of Ang II remains an important matter of investigation to shed light on mechanisms responsible for the pathophysiology of hypertension and its long-term complications. The long-term signaling of Ang II is involved in the pathophysiology of cardiovascular-renal remodeling and inflammatory responses in which the balance between RhoA/Rho kinase pathway and NO system plays a crucial role. In this brief review, the results of our studies in Bartter's and Gitelman's syndromes are reported on these processes. The information obtained from these studies can clarify, confirm or be used to extend the biochemical mechanisms responsible for the pathophysiology of hypertension and its long-term complications and could offer further chances to identify additional potential significant targets of therapy.

  10. Potential pharmacokinetic interactions of therapeutic cytokines or cytokine modulators on small-molecule drugs: mechanistic understanding via studies using in vitro systems.

    Science.gov (United States)

    Zhou, Jin; Li, Feng

    2014-01-01

    The potential pharmacokinetic interactions between macromolecules and small-molecule drugs have received more and more attention with the increasing development of macromolecule therapeutics. Studies have shown that cytokines can differentially modulate drug-metabolizing enzymes and transporters, which raises concerns on the potential interactions of therapeutic cytokines and cytokine modulators on the disposition of small-molecule drugs. Although many in vitro studies have been conducted to characterize the effects of cytokines on drug-metabolizing enzymes and transporters, these studies were limited to only a handful of cytokines, such as interleukin-1 (IL-1), IL-6, tumor necrosis factor-α, and interferon. It is also challenging to translate these in vitro results to in vivo. In addition, information on the impact of cytokine modulators on drug-metabolizing enzymes and transporters is rather limited. More research is needed in this area. The present review is to provide a summary of the in vitro findings on the pharmacokinetic interactions of therapeutic cytokines and cytokine modulators on small-molecule drugs. Discussion on current challenges in assessing these interactions is also included.

  11. Mechanistic Fermentation Models for Process Design, Monitoring, and Control

    DEFF Research Database (Denmark)

    Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla

    2017-01-01

    Mechanistic models require a significant investment of time and resources, but their application to multiple stages of fermentation process development and operation can make this investment highly valuable. This Opinion article discusses how an established fermentation model may be adapted...... for application to different stages of fermentation process development: planning, process design, monitoring, and control. Although a longer development time is required for such modeling methods in comparison to purely data-based model techniques, the wide range of applications makes them a highly valuable tool...... for fermentation research and development. In addition, in a research environment, where collaboration is important, developing mechanistic models provides a platform for knowledge sharing and consolidation of existing process understanding....

  12. Palladium-catalyzed microwave-assisted direct arylation of imidazo[2,1-b]thiazoles with aryl bromides: synthesis and mechanistic study.

    Science.gov (United States)

    Zhu, Yi-Shuo; Shi, Benyi; Fang, Ran; Wang, Xiaoxuan; Jing, Huanwang

    2014-08-14

    A palladium-catalyzed direct C-H arylation of various imidazo[2,1-b]thiazoles with a range of aryl bromides under microwave irradiation is described. 6-Phenyl substituted imidazo[2,1-b]thiazoles could be regioselectively C-5 arylated using the developed protocol. The utility of this method enables the representative coupling product to be achieved by a sequential one-pot reaction. Density functional theory (DFT) calculations show that this arylation proceeds via a concerted metalation-deprotonation (CMD) pathway, which is in agreement with our experimental results. This work provides a convenient access to a variety of biologically active imidazo[2,1-b]thiazole derivatives. Also, it enriches the mechanism study of site-selective C-H arylation in fused heterocycles, and offers a valuable guide to design highly efficient catalytic systems for the preparation of similar compounds.

  13. The role of plasma-surface interactions in process chemistry: Mechanistic studies of a-carbon nitride deposition and sulfur fluoride/oxygen etching of silicon

    Science.gov (United States)

    Stillahn, Joshua M.

    The molecular level chemistry of a-CNx deposition in plasma discharges was studied with emphasis on the use of CH 3CN and BrCN as single source precursors for these films. Characterization of the global deposition behavior in these systems indicates that the resulting films are relatively smooth and contain significant levels of N-content, with N/C > 0.3. Notably, films obtained from BrCN plasmas are observed to delaminate upon their exposure to atmosphere, and preliminary investigation of this behavior is presented. Detailed chemical investigation of the deposition process focuses primarily on the contributions of CN radicals, which were characterized from their origin in the gas phase to their reaction at the a-CNx film surface. Laser-induced fluorescence studies suggest that CN is formed through electron impact dissociation of the precursor species and that this breakdown process produces CN with high internal energies, having rotational and vibrational temperatures on the order of 1000 K and 5000 K, respectively. Measurement of CN surface reactivity coefficients in CH3CN plasmas show that CN reacts with a probability of ˜94%, irrespective of the deposition conditions; this information, combined with gas phase and film characterization data, leads to the conclusion that CN internal energies exert a strong influence on their surface reactivity and that these surface reactions favor their incorporation into the a-CN x film. Moreover, this correlation is shown to hold for several other plasma radicals studied in our lab, suggesting the potential for developing a general model for predicting surface interactions of activated gas phase species. This dissertation also presents results from studies of SF6/O 2 etching of Si. Addition of O2 to the feed gas leads to the generation of SO2, among other species, and gas phase characterization data suggest that SO2 may act as a sink for atomic S, preventing the reformation of SOxFy (y > 0) and thus promoting generation of

  14. Biomimetic oxidation studies. 9. Mechanistic aspects of the oxidation of alcohols with functional,active site methane monooxygenase enzyme models in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Rabion, A. [Lawrence Berkeley National Lab., CA (United States)]|[Univ. of California, Berkeley, CA (United States)]|[Groupement de Recherche de Lacq, Artix (France); Chen, S.; Wang, J.; Buchanan, R.M. [Univ. of Louisville, KY (United States); Seris, J.L. [Groupement de recherche de Lacq, Artix (France); Fish, R.H. [Lawrence Berkeley National Lab., CA (United States)]|[Univ. of California, Berkeley, CA (United States)

    1995-12-13

    The syntheses of biomimetic complexes that mimic the major structural features of the hydroxylase component of methane monooxygenase enzyme (MMO) and, more importantly, that provide similar alkane functionalization activity, in the presence of an oxidant, have been of great interest to the discipline of bioinorganic chemistry. In this communication, we will demonstrate the feasibility of conducting biomimetic oxidation studies in H{sub 2}O with soluble substrates, i.e., alcohols (cyclohexanol, benzyl alcohol), using H{sub 2}O-stable MMO mimics at pH 4.2, and the oxidant, tert-butyl hydroperoxide (TBHP). Both the Mitusunobu procedure and the mesylate displacement reaction proceeded with complete inversion of the stereo-center and provided optically pure penultimate intermediate (>99.9% ee). The synthesis was completed by reduction of the nitro group under standard conditions to deliver LY300164 in 87%. In summary, we have developed an efficient and environmentally benign synthesis of the 5H-2,3-benzodiazepine LY300164 that provides the optically pure compound in 51% overall yield. Intramolecular hydrazone alkylation led to a remarkably facile and selective formation of the benzodiazepine. Furthermore, the application of resins to whole-cell-based biotransformations should find general utility for similar reactions that are complicated by component inhibition and product isolation. 11 refs., 1 fig.

  15. Mechanistic Studies of Wacker-Type Amidocyclization of Alkenes Catalyzed by (IMes)Pd(TFA)2(H2O): Kinetic and Stereochemical Implications of Proton Transfer†

    Science.gov (United States)

    Ye, Xuan; White, Paul B.

    2012-01-01

    The stereochemical course of the amidopalladation of alkenes has important implications for the development of enantioselective Pd-catalyzed “Wacker-type” oxidative amination of alkenes. We have recently shown that the addition of base (Na2CO3) can alter the stereochemical course of amidopalladation in the (IMes)Pd(TFA)2(H2O)-catalyzed aerobic oxidative amidation of alkene. In this study, the mechanism of (IMes)Pd(TFA)2(H2O)-catalyzed oxidative heterocyclization of (Z)-4-hexenyltosylamide was investigated in the presence and absence of exogenous base Na2CO3. The results reveal two parallel pathways in the absence of base: a cis-amidopalladation pathway with turnover-limiting deprotonation of the sulfonamide nucleophile, and a trans-amidopalladation pathway with turnover-limiting nucleophilic attack of sulfonamide on the coordinated alkene. The addition of base (Na2CO3) lowers the energy barrier associated with the proton transfer, leading to an overall faster turnover rate and exclusive cis-amidopalladation of alkene. PMID:23157332

  16. Mechanistic studies of Wacker-type amidocyclization of alkenes catalyzed by (IMes)Pd(TFA)2(H2O): kinetic and stereochemical implications of proton transfer.

    Science.gov (United States)

    Ye, Xuan; White, Paul B; Stahl, Shannon S

    2013-03-01

    The stereochemical course of the amidopalladation of alkenes has important implications for the development of enantioselective Pd-catalyzed "Wacker-type" oxidative amidation of alkenes. We have recently shown that the addition of base (Na2CO3) can alter the stereochemical course of amidopalladation in the (IMes)Pd(TFA)2(H2O)-catalyzed aerobic oxidative amidation of alkene. In this study, the mechanism of (IMes)Pd(TFA)2(H2O)-catalyzed oxidative heterocyclization of (Z)-4-hexenyltosylamide was investigated in the presence and absence of exogenous base Na2CO3. The results reveal two parallel pathways in the absence of base: a cis-amidopalladation pathway with turnover-limiting deprotonation of the sulfonamide nucleophile and a trans-amidopalladation pathway with turnover-limiting nucleophilic attack of sulfonamide on the coordinated alkene. The addition of base (Na2CO3) lowers the energy barrier associated with the proton transfer, leading to an overall faster turnover rate and exclusive cis-amidopalladation of alkene.

  17. Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics

    Directory of Open Access Journals (Sweden)

    Jaehee V. Shim

    2017-09-01

    Full Text Available Tyrosine kinase inhibitors (TKIs are highly potent cancer therapeutics that have been linked with serious cardiotoxicity, including left ventricular dysfunction, heart failure, and QT prolongation. TKI-induced cardiotoxicity is thought to result from interference with tyrosine kinase activity in cardiomyocytes, where these signaling pathways help to control critical processes such as survival signaling, energy homeostasis, and excitation–contraction coupling. However, mechanistic understanding is limited at present due to the complexities of tyrosine kinase signaling, and the wide range of targets inhibited by TKIs. Here, we review the use of TKIs in cancer and the cardiotoxicities that have been reported, discuss potential mechanisms underlying cardiotoxicity, and describe recent progress in achieving a more systematic understanding of cardiotoxicity via the use of mechanistic models. In particular, we argue that future advances are likely to be enabled by studies that combine large-scale experimental measurements with Quantitative Systems Pharmacology (QSP models describing biological mechanisms and dynamics. As such approaches have proven extremely valuable for understanding and predicting other drug toxicities, it is likely that QSP modeling can be successfully applied to cardiotoxicity induced by TKIs. We conclude by discussing a potential strategy for integrating genome-wide expression measurements with models, illustrate initial advances in applying this approach to cardiotoxicity, and describe challenges that must be overcome to truly develop a mechanistic and systematic understanding of cardiotoxicity caused by TKIs.

  18. Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage

    Science.gov (United States)

    McMahon, Stephen J.; Schuemann, Jan; Paganetti, Harald; Prise, Kevin M.

    2016-09-01

    Characterising and predicting the effects of ionising radiation on cells remains challenging, with the lack of robust models of the underlying mechanism of radiation responses providing a significant limitation to the development of personalised radiotherapy. In this paper we present a mechanistic model of cellular response to radiation that incorporates the kinetics of different DNA repair processes, the spatial distribution of double strand breaks and the resulting probability and severity of misrepair. This model enables predictions to be made of a range of key biological endpoints (DNA repair kinetics, chromosome aberration and mutation formation, survival) across a range of cell types based on a set of 11 mechanistic fitting parameters that are common across all cells. Applying this model to cellular survival showed its capacity to stratify the radiosensitivity of cells based on aspects of their phenotype and experimental conditions such as cell cycle phase and plating delay (correlation between modelled and observed Mean Inactivation Doses R2 > 0.9). By explicitly incorporating underlying mechanistic factors, this model can integrate knowledge from a wide range of biological studies to provide robust predictions and may act as a foundation for future calculations of individualised radiosensitivity.

  19. Human Glycinamide Ribonucleotide Transformylase: Active Site Mutants as Mechanistic Probes†

    OpenAIRE

    Manieri, Wanda; Moore, Molly E.; Soellner, Matthew B.; Tsang, Pearl; Caperelli, Carol A.

    2007-01-01

    Human glycinamide ribonucleotide transformylase (GART) (EC2.1.2.2) is a validated target for cancer chemotherapy, but mechanistic studies of this therapeutically important enzyme are limited. Site-directed mutagenesis, initial velocity studies, pH-rate studies, and substrate binding studies have been employed to probe the role of the strictly conserved active site residues, N106, H108, D144, and the semi-conserved K170 in substrate binding and catalysis. Only two conservative substitutions, N...

  20. Mechanistic modeling of aberrant energy metabolism in human disease

    Directory of Open Access Journals (Sweden)

    Vineet eSangar

    2012-10-01

    Full Text Available Dysfunction in energy metabolism—including in pathways localized to the mitochondria—has been implicated in the pathogenesis of a wide array of disorders, ranging from cancer to neurodegenerative diseases to type II diabetes. The inherent complexities of energy and mitochondrial metabolism present a significant obstacle in the effort to understand the role that these molecular processes play in the development of disease. To help unravel these complexities, systems biology methods have been applied to develop an array of computational metabolic models, ranging from mitochondria-specific processes to genome-scale cellular networks. These constraint-based models can efficiently simulate aspects of normal and aberrant metabolism in various genetic and environmental conditions. Development of these models leverages—and also provides a powerful means to integrate and interpret—information from a wide range of sources including genomics, proteomics, metabolomics, and enzyme kinetics. Here, we review a variety of mechanistic modeling studies that explore metabolic functions, deficiency disorders, and aberrant biochemical pathways in mitochondria and related regions in the cell.

  1. Applying Mechanistic Dam Breach Models to Historic Levee Breaches

    Directory of Open Access Journals (Sweden)

    Risher Paul

    2016-01-01

    Full Text Available Hurricane Katrina elevated levee risk in the US national consciousness, motivating agencies to assess and improve their levee risk assessment methodology. Accurate computation of the flood flow magnitude and timing associated with a levee breach remains one of the most difficult and uncertain components of levee risk analysis. Contemporary methods are largely empirical and approximate, introducing substantial uncertainty to the damage and life loss models. Levee breach progressions are often extrapolated to the final width and breach formation time based on limited experience with past breaches or using regression equations developed from a limited data base of dam failures. Physically based embankment erosion models could improve levee breach modeling. However, while several mechanistic embankment breach models are available, they were developed for dams. Several aspects of the levee breach problem are distinct, departing from dam breach assumptions. This study applies three embankments models developed for dam breach analysis (DL Breach, HR BREACH, and WinDAM C to historic levee breaches with observed (or inferred breach rates, assessing the limitations, and applicability of each model to the levee breach problem.

  2. Recent STM, DFT and HAADF-STEM studies of sulfide-based hydrotreating catalysts: Insight into mechanistic, structural and particle size effects

    DEFF Research Database (Denmark)

    Besenbacher, Flemming; Brorson, M.; Clausen, B.S.

    2008-01-01

    -angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) studies which have provided insight into the detailed atomic structure. In accordance with earlier theoretical studies, the experimental studies show that the Ni-Mo-S structures may in some instances differ from the Co...

  3. Newly constructed stable reporter cell lines for mechanistic studies on electrophile-responsive element-mediated gene expression reveal a role for flavonoid planarity

    NARCIS (Netherlands)

    Boerboom, A.M.J.F.; Vermeulen, M.; Woude, van der H.; Bremer, B.I.; Lee, Y.Y.; Kampman, E.; Bladeren, van P.J.; Rietjens, I.M.C.M.; Aarts, J.M.M.J.G.

    2006-01-01

    The electrophile-responsive element (EpRE) is a transcriptional enhancer involved in cancer-chemoprotective gene expression modulation by certain food components. Two stably transfected luciferase reporter cell lines were developed, EpRE(hNQO1)-LUX and EpRE(mGST-Ya)-LUX, based on EpRE sequences from

  4. Newly constructed stable reporter cell lines for mechanistic studies on electrophile-responsive element-mediated gene expression reveal a role for flavonoid planarity.

    NARCIS (Netherlands)

    Boerboom, A.M.A.; Vermeulen, M.; Woude, H. van der; Bremer, B.I.; Lee-Hilz, Y.Y.; Kampman, E.; Bladeren, P.J. van; Rietjens, I.M.C.M.; Aarts, J.

    2006-01-01

    The electrophile-responsive element (EpRE) is a transcriptional enhancer involved in cancer-chemoprotective gene expression modulation by certain food components. Two stably transfected luciferase reporter cell lines were developed, EpRE(hNQO1)-LUX and EpRE(mGST-Ya)-LUX, based on EpRE sequences from

  5. Fine particulate matter air pollution and atherosclerosis: Mechanistic insights.

    Science.gov (United States)

    Bai, Yuntao; Sun, Qinghua

    2016-12-01

    Atherosclerosis is a progressive disease characterized by the accumulation of lipids and fibrous plaque in the arteries. Its etiology is very complicated and its risk factors primarily include genetic defects, smoking, hyperlipidemia, hypertension, lack of exercise, and infection. Recent studies suggest that fine particulate matter (PM2.5) air pollution may also contribute to the development of atherosclerosis. The present review integrates current experimental evidence with mechanistic pathways whereby PM2.5 exposure can promote the development of atherosclerosis. PM2.5-mediated enhancement of atherosclerosis is likely due to its pro-oxidant and pro-inflammatory effects, involving multiple organs, different cell types, and various molecular mediators. Studies about the effects of PM2.5inhalation on atherosclerosis may yield a better understanding of the link between air pollution and major cardiovascular diseases, and provide useful information for policy makers to determine acceptable levels of PM2.5 air quality. This article is part of a Special Issue entitled Air Pollution, edited by Wenjun Ding, Andrew J. Ghio and Weidong Wu. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. The copper catalysed reaction of sodium methoxide with aryl bromides. A mechanistic study leading to a facile synthesis of anisole derivatives

    NARCIS (Netherlands)

    Koten, G. van; Aalten, H.L.; Grove, D.M.; Kuilman, T.; Piekstra, O.G.; Hulshof, L.A.; Sheldon, R.A.

    1989-01-01

    The copper catalysed reaction of unactivated aryl bromides with sodium methoxide has been investigated by studying a number of parameters (copper catalyst, cosolvent, concentration and relative ratio of the reactants, additives and aryl bromide substituents) which influence this reaction. The

  7. Mechanistic Studies of Viral Entry: An Overview of Dendrimer-Based Microbicides As Entry Inhibitors Against Both HIV and HSV-2 Overlapped Infections.

    Science.gov (United States)

    Sepúlveda-Crespo, Daniel; Ceña-Díez, Rafael; Jiménez, José Luis; Ángeles Muñoz-Fernández, Ma

    2017-01-01

    This review provides an overview of the development of different dendrimers, mainly polyanionic, against human immunodeficiency virus (HIV) and genital herpes (HSV-2) as topical microbicides targeting the viral entry process. Vaginal topical microbicides to prevent sexually transmitted infections such as HIV and HSV-2 are urgently needed. To inhibit HIV/HSV-2 entry processes, new preventive targets have been established to maximize the current therapies against wild-type and drug-resistant viruses. The entry of HIV/HSV-2 into target cells is a multistep process that triggers a cascade of molecular interactions between viral envelope proteins and cell surface receptors. Polyanionic dendrimers are highly branched nanocompounds with potent activity against HIV/HSV-2. Inhibitors of each entry step have been identified with regard to generations and surface groups, and possible roles for these agents in anti-HIV/HSV-2 therapies have also been discussed. Four potential binding sites for impeding HIV infection (HSPG, DC-SIGN, GSL, and CD4/gp120 inhibitors) and HSV-2 infection (HS, gB, gD, and gH/gL inhibitors) exist according to their mechanisms of action and structures. This review clarifies that inhibition of HIV/HSV-2 entry continues to be a promising target for drug development because nanotechnology can transform the field of HIV/HSV-2 prevention by improving the efficacy of the currently available antiviral treatments.

  8. Complexes of vitamin B6XX: equilibrium and mechanistic studies of the reaction of pyridoxal-5'-phosphate with pyridoxamine-5'-phosphate in the presence of copper(II).

    Science.gov (United States)

    Marafie, H M; el-Ezaby, M S; Fareed, S

    1989-09-01

    The interaction of Cu(II) with pyridoxamine-5'-phosphate (PMP) and pyridoxal-5'-phosphate (PLP) was studied potentiometrically. The titration data were assessed by MINIQUAD program. Several protonated and nonprotonated complexes have been found to exist in solution. The reaction of PLP with Cu(II)-PMP has been studied kinetically, using the stopped-flow technique. Two rate steps have been observed. The first step has been attributed to the formation of a Schiff's base metal complex. The second step may be due to the formation of a ternary complex formation. A mechanism was suggested.

  9. Analytical techniques for mechanistic characterization of EUV photoresists

    Science.gov (United States)

    Grzeskowiak, Steven; Narasimhan, Amrit; Murphy, Michael; Ackerman, Christian; Kaminsky, Jake; Brainard, Robert L.; Denbeaux, Greg

    2017-03-01

    Extreme ultraviolet (EUV, 13.5 nm) lithography is the prospective technology for high volume manufacturing by the microelectronics industry. Significant strides towards achieving adequate EUV source power and availability have been made recently, but a limited rate of improvement in photoresist performance still delays the implementation of EUV. Many fundamental questions remain to be answered about the exposure mechanisms of even the relatively well understood chemically amplified EUV photoresists. Moreover, several groups around the world are developing revolutionary metal-based resists whose EUV exposure mechanisms are even less understood. Here, we describe several evaluation techniques to help elucidate mechanistic details of EUV exposure mechanisms of chemically amplified and metal-based resists. EUV absorption coefficients are determined experimentally by measuring the transmission through a resist coated on a silicon nitride membrane. Photochemistry can be evaluated by monitoring small outgassing reaction products to provide insight into photoacid generator or metal-based resist reactivity. Spectroscopic techniques such as thin-film Fourier transform infrared (FTIR) spectroscopy can measure the chemical state of a photoresist system pre- and post-EUV exposure. Additionally, electrolysis can be used to study the interaction between photoresist components and low energy electrons. Collectively, these techniques improve our current understanding of photomechanisms for several EUV photoresist systems, which is needed to develop new, better performing materials needed for high volume manufacturing.

  10. Reduction of ketones and alkyl iodides by SmI(2) and Sm(II)-HMPA complexes. Rate and mechanistic studies.

    Science.gov (United States)

    Prasad, E; Flowers, Robert A

    2002-06-19

    The effect of HMPA on the electron transfer (ET) rate of samarium diiodide reduction reactions in THF was analyzed for a series of ketones (2-butanone, methyl acetoacetate, and N,N-dimethylacetoacetamide) and alkyl iodides (1-iodobutane and 2-iodobutane) with stopped flow spectrophotometric studies. Activation parameters for the ET processes were determined by temperature-dependence studies over a range of 30-50 degrees C. The ET rate constants and the activation parameters obtained for the above systems in the presence of different equivalents of HMPA were compared to understand the mechanism of action of HMPA on various substrates. The results obtained from these studies indicate that coordination or chelation is possible in the transition state geometry for SmI(2)/ketone systems even in the presence of the sterically demanding ligand HMPA. After the addition of 4 equiv of HMPA the ET rate and activation parameters for ketone reduction by Sm is unaffected by further HMPA addition while a linear dependence of ET rate on the equivalents of HMPA was found in the SmI(2)/alkyl iodide system. The results of these studies are consistent with an inner-sphere-type ET for the reduction of ketones by SmI(2) (and SmI(2)[bond]HMPA complexes) and an outer-sphere-type ET for the reduction of alkyl iodides by SmI(2) or SmI(2)[bond]HMPA complexes.

  11. Mechanistic Studies on Chabazite-Type Methanol-to-Olefin Catalysts: Insights from Time-Resolved UV/Vis Microspectroscopy Combined with Theoretical Simulations

    NARCIS (Netherlands)

    Van Speybroeck, V.; Hemelsoet, K.L.J.; De Wispelaere, K.; Qian, Q.; Van der Mynsbrugge, J.; De Sterck, B.; Weckhuysen, B.M.; Waroquier, M.

    2013-01-01

    The formation and nature of active sites for methanol conversion over solid acid catalyst materials are studied by using a unique combined spectroscopic and theoretical approach. A working catalyst for the methanol-to-olefin conversion has a hybrid organic–inorganic nature in which a cocatalytic org

  12. Elucidating the interplay between DNA-condensing and free polycations in gene transfection through a mechanistic study of linear and branched PEI

    DEFF Research Database (Denmark)

    Dai, Zhuojun; Gjetting, Torben; Mattebjerg, Maria Ahlm;

    2011-01-01

    In the present study we compare LPEI and BPEI characteristics related to DNA condensation and their role as free polycation chains in gene transfection. Using radioactive 32P labeled DNA, we investigated the effect of free PEI chains on the cellular uptake of polyplexes. Our investigations show d...

  13. Role of Re in Pt–Re/TiO2 catalyst for water gas shift reaction: A mechanistic and kinetic study

    NARCIS (Netherlands)

    Azzam, K.G.; Babich, I.V.; Seshan, K.; Lefferts, L.

    2008-01-01

    Transient kinetic studies and in situ FTIR spectroscopy were used to follow the reaction sequences that occur during water gas shift (WGS) reaction over Pt–Re/TiO2 catalyst. Results pointed to contributions of an associative formate route with redox regeneration and two classical redox routes involv

  14. Brincidofovir Is Not a Substrate for the Human Organic Anion Transporter 1: A Mechanistic Explanation for the Lack of Nephrotoxicity Observed in Clinical Studies

    Science.gov (United States)

    Morrison, Marion E.; Brundage, Thomas M.; Momméja-Marin, Hervé

    2016-01-01

    Background: Brincidofovir (BCV) is an orally bioavailable lipid conjugate of cidofovir (CDV) with increased in vitro potency relative to CDV against all 5 families of double-stranded DNA viruses that cause human disease. After intravenous (IV) administration of CDV, the organic anion transporter 1 (OAT1) transports CDV from the blood into the renal proximal tubule epithelial cells with resulting dose-limiting nephrotoxicity. Objective: To study whether OAT1 transports BCV and to evaluate the pharmacokinetic and renal safety profile of oral BCV compared with IV CDV. Methods: The cellular uptake of BCV and its major metabolites was assessed in vitro. Renal function at baseline and during and after treatment in subjects in BCV clinical studies was examined. Results: In OAT1-expressing cells, uptake of BCV and its 2 major metabolites (CMX103 and CMX064) was the same as in mock-transfected control cells and was not inhibited by the OAT inhibitor probenecid. In human pharmacokinetic studies, BCV administration at therapeutic doses resulted in detection of CDV as a circulating metabolite; peak CDV plasma concentrations after oral BCV administration in humans were <1% of those observed after IV CDV administration at therapeutic doses. Analysis of renal function and adverse events from 3 BCV clinical studies in immunocompromised adult and pediatric subjects indicated little to no evidence of associated nephrotoxicity. Over 80% of subjects who switched from CDV or foscarnet to BCV experienced an improvement in renal function as measured by maximum on-treatment estimated glomerular filtration rate. Conclusions: The lack of BCV uptake through OAT1, together with lower CDV concentrations after oral BCV compared with IV CDV administration, likely explains the superior renal safety profile observed in immunocompromised subjects receiving BCV compared with CDV. PMID:27851688

  15. Mechanistic studies on the phosphoramidite coupling reaction in oligonucleotide synthesis. I. Evidence for nudeophilic catalysis by tetrazole and rate variations with the phosphorus substituents

    DEFF Research Database (Denmark)

    Dahl, Bjarne H.; Nielsen, John; Dahl, Otto

    1987-01-01

    Tetrazole catalyzed reactions of a series of phosphoramidites, 5′ -O- DMTdT-3′-O-P(OR 1)NRNR22 (1a-h), with 3′ O-SiBu tPh 2-6-N-benzoyl-dA (2a) in acetonitrite solution have been studied. It is found that the coupling rate depends very much on whether tetrazole is added before or after 2a, and th...

  16. From Rate Measurements to Mechanistic Data for Condensed Matter Reactions: A Case Study Using the Crystallization of [Zn(OH26][ZnCl4

    Directory of Open Access Journals (Sweden)

    Berkley G. Hillis

    2016-12-01

    Full Text Available The kinetics of crystallization of the R = 3 hydrate of zinc chloride, [Zn(OH26][ZnCl4], is measured by time-resolved synchrotron x-ray diffraction, time-resolved neutron diffraction, and by differential scanning calorimetry. It is shown that analysis of the rate data using the classic Kolmogorov, Johnson, Mehl, Avrami (KJMA kinetic model affords radically different rate constants for equivalent reaction conditions. Reintroducing the amount of sample measured by each method into the kinetic model, using our recently developed modified-KJMA model (M-KJMA, it is shown that each of these diverse rate measurement techniques can give the intrinsic, material specific rate constant, the velocity of the phase boundary, vpb. These data are then compared to the velocity of the crystallization front directly measured optically. The time-resolved diffraction methods uniquely monitor the loss of the liquid reactant and formation of the crystalline product demonstrating that the crystallization of this hydrate phase proceeds through no intermediate phases. The temperature dependent vpb data are then well fit to transition zone theory to extract activation parameters. These demonstrate that the rate-limiting component to this crystallization reaction is the ordering of the waters (or protons of hydration into restricted positions of the crystalline lattice resulting in large negative entropy of activation.

  17. A mechanistic model of hydrogen-methanogen dynamics in the rumen.

    Science.gov (United States)

    Wang, Yuancheng; Janssen, Peter H; Lynch, Tammy A; Brunt, Bruce van; Pacheco, David

    2016-03-21

    Existing mathematical models to estimate methane production in the rumen are based on calculation of hydrogen balances without considering the presence of methanogens. In this study, a mechanistic model of methane production is proposed that depicts the interaction between hydrogen concentration and methanogens in the rumen. Analytical results show that it meets biological expectations, namely increased fractional passage rate leads to a greater growth rate of methanogens, and a greater steady state hydrogen concentration. This model provides a basis on which to develop a more comprehensive model of methane production in the rumen that includes thermodynamics and feed fermentation pathways.

  18. Comparative Molecular Mechanistic Modelling of a Tubular Thermal Cracker in Two and Three Dimensions

    OpenAIRE

    Olufemi, B. A.; O.O. Famuyide

    2014-01-01

    This study aimed at the modelling of a tubular thermal cracker in two and three dimensions using 0.15 kg/h of ethane and 1.5 kg/h of nitrogen in laminar flow using a molecular mechanistic model for ethane cracking, followed by the solution and comparison of the results obtained. This was used to find the effect that spatial development had on the generated profiles. The purpose was achieved by deriving the requisite model equations from mass, energy and momentum balances consisting of nine co...

  19. Aqueous-phase photooxidation of levoglucosan - a mechanistic study using aerosol time-of-flight chemical ionization mass spectrometry (Aerosol ToF-CIMS)

    Science.gov (United States)

    Zhao, R.; Mungall, E. L.; Lee, A. K. Y.; Aljawhary, D.; Abbatt, J. P. D.

    2014-09-01

    Levoglucosan (LG) is a widely employed tracer for biomass burning (BB). Recent studies have shown that LG can react rapidly with hydroxyl (OH) radicals in the aqueous phase despite many mass balance receptor models assuming it to be inert during atmospheric transport. In the current study, aqueous-phase photooxidation of LG by OH radicals was performed in the laboratory. The reaction kinetics and products were monitored by aerosol time-of-flight chemical ionization mass spectrometry (Aerosol ToF-CIMS). Approximately 50 reaction products were detected by the Aerosol ToF-CIMS during the photooxidation experiments, representing one of the most detailed product studies yet performed. By following the evolution of mass defects of product peaks, unique trends of adding oxygen (+O) and removing hydrogen (-2H) were observed among the products detected, providing useful information for determining potential reaction mechanisms and sequences. Additionally, bond-scission reactions take place, leading to reaction intermediates with lower carbon numbers. We introduce a data analysis framework where the average oxidation state (OSc) is plotted against a novel molecular property: double-bond-equivalence-to-carbon ratio (DBE/#C). The trajectory of LG photooxidation on this plot suggests formation of polycarbonyl intermediates and their subsequent conversion to carboxylic acids as a general reaction trend. We also determined the rate constant of LG with OH radicals at room temperature to be 1.08 ± 0.16 × 109 M-1 s-1. By coupling an aerosol mass spectrometer (AMS) to the system, we observed a rapid decay of the mass fraction of organic signals at mass-to-charge ratio 60 (f60), corresponding closely to the LG decay monitored by the Aerosol ToF-CIMS. The trajectory of LG photooxidation on a f44-f60 correlation plot matched closely to literature field measurement data. This implies that aqueous-phase photooxidation might be partially contributing to aging of BB particles in the

  20. Aqueous-phase photooxidation of levoglucosan - a mechanistic study using Aerosol Time of Flight Chemical Ionization Mass Spectrometry (Aerosol-ToF-CIMS)

    Science.gov (United States)

    Zhao, R.; Mungall, E. L.; Lee, A. K. Y.; Aljawhary, D.; Abbatt, J. P. D.

    2014-04-01

    Levoglucosan (LG) is a widely employed tracer for biomass burning (BB). Recent studies have shown that LG can react rapidly with hydroxyl (OH) radicals in the aqueous phase, despite many mass balance receptor models assuming it to be inert during atmospheric transport. In the current study, aqueous-phase photooxidation of LG by OH radicals was performed in the laboratory. The reaction kinetics and products were monitored by Aerosol Time of Flight Chemical Ionization Mass Spectrometry (Aerosol-ToF-CIMS). Approximately 50 reaction products were detected by the Aerosol-ToF-CIMS during the photooxidation experiments, representing one of the most detailed product studies yet performed. By following the evolution of mass defects of product peaks, unique trends of adding oxygen (+O) and removing hydrogen (-2H) were observed among the products detected, providing useful information to determine potential reaction mechanisms and sequences. As well, bond scission reactions take place, leading to reaction intermediates with lower carbon numbers. We introduce a data analysis framework where the average oxidation state (OSc) is plotted against a novel molecular property: double bond equivalence to carbon ratio (DBE / #C). The trajectory of LG photooxidation on this plot suggests formation of poly-carbonyl intermediates and their subsequent conversion to carboxylic acids as a general reaction trend. We also determined the rate constant of LG with OH radicals at room temperature to be 1.08 ± 0.16 × 109 M-1 s-1. By coupling an Aerosol Mass Spectrometer (AMS) to the system, we observed a rapid decay of the mass fraction of organic signals at mass-to-charge ratio 60 (f60), corresponding closely to the LG decay monitored by the Aerosol-ToF-CIMS. The trajectory of LG photooxidation on a f44-f60 correlation plot matched closely to literature field measurement data. This implies that aqueous-phase photooxidation might be partially contributing to aging of BB particles in the ambient

  1. Mechanistic studies on activation of ubiquitin and di-ubiquitin-like protein, FAT10, by ubiquitin-like modifier activating enzyme 6, Uba6.

    Science.gov (United States)

    Gavin, James M; Chen, Jesse J; Liao, Hua; Rollins, Neil; Yang, Xiaofeng; Xu, Qing; Ma, Jingya; Loke, Huay-Keng; Lingaraj, Trupti; Brownell, James E; Mallender, William D; Gould, Alexandra E; Amidon, Benjamin S; Dick, Lawrence R

    2012-05-01

    Uba6 is a homolog of the ubiquitin-activating enzyme, Uba1, and activates two ubiquitin-like proteins (UBLs), ubiquitin and FAT10. In this study, biochemical and biophysical experiments were performed to understand the mechanisms of how Uba6 recognizes two distinct UBLs and catalyzes their activation and transfer. Uba6 is shown to undergo a three-step activation process and form a ternary complex with both UBLs, similar to what has been observed for Uba1. The catalytic mechanism of Uba6 is further supported by inhibition studies using a mechanism-based E1 inhibitor, Compound 1, which forms covalent adducts with both ubiquitin and FAT10. In addition, pre-steady state kinetic analysis revealed that the rates of UBL-adenylate (step 1) and thioester (step 2) formation are similar between ubiquitin and FAT10. However, distinct kinetic behaviors were also observed for ubiquitin and FAT10. FAT10 binds Uba6 with much higher affinity than ubiquitin while demonstrating lower catalytic activity in both ATP-PP(i) exchange and E1-E2 transthiolation assays. Also, Compound 1 is less potent with FAT10 as the UBL compared with ubiquitin in ATP-PP(i) exchange assays, and both a slow rate of covalent adduct formation and weak adduct binding to Uba6 contribute to the diminished potency observed for FAT10. Together with expression level analysis in IM-9 cells, this study sheds light on the potential role of cytokine-induced FAT10 expression in regulating Uba6 pathways.

  2. Mechanistic insights into type III restriction enzymes.

    Science.gov (United States)

    Raghavendra, Nidhanapati K; Bheemanaik, Shivakumara; Rao, Desirazu N

    2012-01-01

    Type III restriction-modification (R-M) enzymes need to interact with two separate unmethylated DNA sequences in indirectly repeated, head-to-head orientations for efficient cleavage to occur at a defined location next to only one of the two sites. However, cleavage of sites that are not in head-to-head orientation have been observed to occur under certain reaction conditions in vitro. ATP hydrolysis is required for the long-distance communication between the sites prior to cleavage. Type III R-M enzymes comprise two subunits, Res and Mod that form a homodimeric Mod2 and a heterotetrameric Res2Mod2 complex. The Mod subunit in M2 or R2M2 complex recognizes and methylates DNA while the Res subunit in R2M2 complex is responsible for ATP hydrolysis, DNA translocation and cleavage. A vast majority of biochemical studies on Type III R-M enzymes have been undertaken using two closely related enzymes, EcoP1I and EcoP15I. Divergent opinions about how the long-distance interaction between the recognition sites exist and at least three mechanistic models based on 1D- diffusion and/or 3D- DNA looping have been proposed.

  3. Diacetoxyiodobenzene assisted C-O bond formation via sequential acylation and deacylation process: synthesis of benzoxazole amides and their mechanistic study by DFT.

    Science.gov (United States)

    Nahakpam, Lokendrajit; Chipem, Francis A S; Chingakham, Brajakishor S; Laitonjam, Warjeet S

    2016-08-10

    An efficient method for the transformation of N-substituted-N'-benzoylthioureas to substituted N-benzoxazol-2-yl-amides using diacetoxyiodobenzene (DIB) is described in this work. The transformation follows the C-O bond formation leading to the benzoxazole derivative, due to oxidative dehydrogenation by DIB, instead of the expected C-S bond formation of the benzothiazole moiety. The C-O bond formation leading to benzoxazole is due to consecutive acylation and deacylation in conjunction with the reduction of two moles of DIB. A plausible mechanism was proposed for the reaction and density functional calculations were also performed to study the reaction mechanism.

  4. Oxidative study of gabapentin by alkaline hexacyanoferrate(III) in room temperature in presence of catalytic amount of Ru(III) a mechanistic approach

    Science.gov (United States)

    Jose, Timy P.; Angadi, Mahantesh A.; Salunke, Manjalee S.; Tuwar, Suresh M.

    2008-12-01

    The kinetics of oxidation of gabapentin by hexacyanoferrate(III) in aqueous alkaline medium at a constant ionic strength of 0.5 mol dm -3 was studied spectrophotometrically. The reaction is of first order in [HCF(III)] and of less than unit order in [alkali]. The reaction rate is independent upon [gabapentin]. Effects of added products, ionic strength and dielectric constant of the reaction medium have been investigated. Oxidative product of gabapentin was identified. A suitable mechanism has been proposed. The reaction constants involved in the different steps of mechanism are calculated. The activation parameters of the mechanism are computed and discussed .

  5. Mechanistic Insight into the Cu-Catalyzed C-S Cross-Coupling of Thioacetate with Aryl Halides. A Joint Experimental-Computational Study.

    Science.gov (United States)

    Soria-Castro, Silvia M; Andrada, Diego M; Caminos, Daniel A; Argúello, Juan E; Robert, Marc; Peñeñory, Alicia B

    2017-09-29

    The mechanism of the Ullmann-type reaction between potassium thioacetate (KSAc) and iodobenzene (PhI) catalyzed by CuI associated with 1,10-phenanthroline (phen) as a ligand has been explored experimentally and computationally. The study on C-S bond formation has been investigated by UV-visible spectrophotometry, cyclic voltammetry, mass espectrometry and products assessment from radical probes. The results indicate that under experimental conditions the catalytically active species is [Cu(phen)(SAc)] regardless of the copper source. An examination of the aryl halide activation mechanism using radical probes was undertaken. No evidences of the presence of radical species have been found during the reaction process, which is consistent with an oxidative addition cross coupling pathway. The different reaction pathways leading to the experimentally observed reaction products have been studied by DFT calculation. The oxidative addition - reductive elimination mechanism via an unstable CuIII intermediate is energetically more feasible than other possible mechanisms such as Single Electron Transfer, Halogen Atom Transfer and σ-Bond Methatesis.

  6. Photocatalytical removal of fluorouracil using TiO2-P25 and N/S doped TiO2 catalysts: A kinetic and mechanistic study.

    Science.gov (United States)

    Koltsakidou, Α; Antonopoulou, M; Εvgenidou, Ε; Konstantinou, I; Giannakas, A E; Papadaki, M; Bikiaris, D; Lambropoulou, D A

    2017-02-01

    In the present study, the photocatalytic activity of TiO2-based photocatalysts toward degradation and mineralization of the anti-cancer drug 5-fluorouracil (5-FU) in aqueous phase was investigated under simulated solar and visible irradiation. Commercial TiO2 (P25) and N/S-doped TiO2 catalysts synthesized by a simple sol-gel method were used as photocatalysts. TiO2 P-25 was found to be the most photoactive catalyst for the removal of 5-FU, under simulated solar irradiation. Among N/S-doped TiO2 catalysts, the one with molar Ti:N/S ratio equal to 0.5 was the most efficient under simulated solar irradiation. In contrast, under visible irradiation the catalyst with equimolar Ti:N/S ratio showed the highest performance for the removal of 5-FU. Scavenging experiments revealed that HO radicals and h(+) were the major reactive species mediating photocatalytic degradation of 5-FU using TiO2 P-25 and N/S-doped TiO2 catalysts, under simulated solar irradiation. On the other hand, the essential contribution of (1)O2 and O2(-) in the degradation of 5-FU under visible light was proved. The transformation products (TPs) of 5-FU, were identified by LC-MS-TOF suggesting that defluorination followed by hydroxylation and oxidation are the main transformation pathways, under all the studied photocatalytic systems.

  7. A Mechanistic Study of CO2 Reduction at the Interface of a Gallium Phosphide (GaP) Surface using Core-level Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, Kristen [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-08-18

    Carbon dioxide (CO2) emission into the atmosphere has increased tremendously through burning of fossil fuels, forestry, etc.. The increased concentration has made CO2 reductions very attractive though the reaction is considered uphill. Utilizing the sun as a potential energy source, CO2 has the possibility to undergo six electron and four proton transfers to produce methanol, a useable resource. This reaction has been shown to occur selectively in an aqueous pyridinium solution with a gallium phosphide (GaP) electrode. Though this reaction has a high faradaic efficiency, it was unclear as to what role the GaP surface played during the reaction. In this work, we aim to address the fundamental role of GaP during the catalytic conversion, by investigating the interaction between a clean GaP surface with the reactants, products, and intermediates of this reaction using X-ray photoelectron spectroscopy. We have determined a procedure to prepare atomically clean GaP and our initial CO2 adsorption studies have shown that there is evidence of chemisorption and reaction to form carbonate on the clean surface at LN2 temperatures (80K), in contrast to previous theoretical calculations. These findings will enable future studies on CO2 catalysis.

  8. Mechanistic and Kinetic Studies on the Homogeneous Gas-Phase Formation of PCTA/DTs from 2,4-Dichlorothiophenol and 2,4,6-Trichlorothiophenol

    Directory of Open Access Journals (Sweden)

    Fei Xu

    2015-08-01

    Full Text Available Polychlorinated thianthrene/dibenzothiophenes (PCTA/DTs are sulfur analogues compounds to polychlorinated dibenzo-p-dioxin/dibenzofurans (PCDD/Fs. Chlorothiophenols (CTPs are key precursors to form PCTA/DTs. 2,4-DCTP has the minimum number of Cl atoms to form 2,4,6,8-tetrachlorinated dibenzothiophenes (2,4,6,8-TeCDT, which is the most important and widely detected of the PCDTs. In this paper, quantum chemical calculations were carried out to investigate the homogeneous gas-phase formation of PCTA/DTs from 2,4-DCTP and 2,4,6-TCTP precursors at the MPWB1K/6-311+G(3df,2p//MPWB1K/6-31+G(d,p level. Several energetically feasible pathways were revealed to compare the formation potential of PCTA/DT products. The rate constants of the crucial elementary reactions were evaluated by the canonical variational transition-state (CVT theory with the small curvature tunneling (SCT correction over a wide temperature range of 600–1200 K. This study shows that pathways that ended with elimination of Cl step were dominant over pathways ended with elimination of the H step. The water molecule has a negative catalytic effect on the H-shift step and hinders the formation of PCDTs from 2,4-DCTP. This study, together with works already published from our group, clearly illustrates an increased propensity for the dioxin formation from CTPs over the analogous CPs.

  9. Mechanistic studies of the copolymerization reaction of oxetane and carbon dioxide to provide aliphatic polycarbonates catalyzed by (Salen)CrX complexes.

    Science.gov (United States)

    Darensbourg, Donald J; Moncada, Adriana I; Choi, Wonsook; Reibenspies, Joseph H

    2008-05-21

    Chromium salen derivatives in the presence of anionic initiators have been shown to be very effective catalytic systems for the selective coupling of oxetane and carbon dioxide to provide the corresponding polycarbonate with a minimal amount of ether linkages. Optimization of the chromium(III) system was achieved utilizing a salen ligand with tert-butyl groups in the 3,5-positions of the phenolate rings and a cyclohexylene backbone for the diimine along with an azide ion initiator. The mechanism for the coupling reaction of oxetane and carbon dioxide has been studied. Based on binding studies done by infrared spectroscopy, X-ray crystallography, kinetic data, end group analysis done by (1)H NMR, and infrared spectroscopy, a mechanism of the copolymerization reaction is proposed. The formation of the copolymer is shown to proceed in part by way of the intermediacy of trimethylene carbonate, which was observed as a minor product of the coupling reaction, and by the direct enchainment of oxetane and CO 2. The parity of the determined free energies of activation for these two processes, namely 101.9 kJ x mol (-1) for ring-opening polymerization of trimethylene carbonate and 107.6 kJ x mol (-1) for copolymerization of oxetane and carbon dioxide supports this conclusion.

  10. A Mechanistic Study of CO2 Reduction at the Interface of a Gallium Phosphide (GaP) Surface using Core-level Spectroscopy - Oral Presentation

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, Kristen [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-08-19

    Carbon dioxide (CO2) emission into the atmosphere has increased tremendously through burning of fossil fuels, forestry, etc.. The increased concentration has made CO2 reductions very attractive though the reaction is considered uphill. Utilizing the sun as a potential energy source, CO2 has the possibility to undergo six electron and four proton transfers to produce methanol, a useable resource. This reaction has been shown to occur selectively in an aqueous pyridinium solution with a gallium phosphide (GaP) electrode. Though this reaction has a high faradaic efficiency, it was unclear as to what role the GaP surface played during the reaction. In this work, we aim to address the fundamental role of GaP during the catalytic conversion, by investigating the interaction between a clean GaP surface with the reactants, products, and intermediates of this reaction using X-ray photoelectron spectroscopy. We have determined a procedure to prepare atomically clean GaP and our initial CO2 adsorption studies have shown that there is evidence of chemisorption and reaction to form carbonate on the clean surface at LN2 temperatures (80K), in contrast to previous theoretical calculations. These findings will enable future studies on CO2 catalysis.

  11. Mechanistic study of atomic layer deposition of Al{sub x}Si{sub y}O thin film via in-situ FTIR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Jea; Kim, Taeseung; Seegmiller, Trevor; Chang, Jane P., E-mail: jpchang@ucla.edu [Department of Chemical and Biomolecular Engineering, UCLA, Los Angeles, California 90095 (United States)

    2015-09-15

    A study of surface reaction mechanism on atomic layer deposition (ALD) of aluminum silicate (Al{sub x}Si{sub y}O) was conducted with trimethylaluminum (TMA) and tetraethoxysilane (TEOS) as precursors and H{sub 2}O as the oxidant. In-situ Fourier transform infrared spectroscopy (FTIR) was utilized to elucidate the underlying surface mechanism that enables the deposition of Al{sub x}Si{sub y}O by ALD. In-situ FTIR study revealed that ineffective hydroxylation of the surface ethoxy (–OCH{sub 2}CH{sub 3}) groups prohibits ALD of SiO{sub 2} by TEOS/H{sub 2}O. In contrast, effective desorption of the surface ethoxy group was observed in TEOS/H{sub 2}O/TMA/H{sub 2}O chemistry. The presence of Al-OH* group in vicinity of partially hydroxylated ethoxy (–OCH{sub 2}CH{sub 3}) group was found to propagate disproportionation reaction, which results in ALD of Al{sub x}Si{sub y}O. The maximum thickness from incorporation of SiO{sub x} from alternating exposures of TEOS/H{sub 2}O chemistry in Al{sub x}Si{sub y}O was found to be ∼2 Å, confirmed by high resolution transmission electron microscopy measurements.

  12. Synthesis of Bridged Heterocycles via Sequential 1,4- and 1,2-Addition Reactions to α,β-Unsaturated N-Acyliminium Ions: Mechanistic and Computational Studies.

    Science.gov (United States)

    Yazici, Arife; Wille, Uta; Pyne, Stephen G

    2016-02-19

    Novel tricyclic bridged heterocyclic systems can be readily prepared from sequential 1,4- and 1,2-addition reactions of allyl and 3-substituted allylsilanes to indolizidine and quinolizidine α,β-unsaturated N-acyliminium ions. These reactions involve a novel N-assisted, transannular 1,5-hydride shift. Such a mechanism was supported by examining the reaction of a dideuterated indolizidine, α,β-unsaturated N-acyliminium ion precursor, which provided specifically dideuterated tricyclic bridged heterocyclic products, and from computational studies. In contrast, the corresponding pyrrolo[1,2-a]azepine system did not provide the corresponding tricyclic bridged heterocyclic product and gave only a bis-allyl adduct, while more substituted versions gave novel furo[3,2-d]pyrrolo[1,2-a]azepine products. Such heterocyclic systems would be expected to be useful scaffolds for the preparation of libraries of novel compounds for new drug discovery programs.

  13. Polyethylene Glycols as Efficient Media for Decarboxylative Nitration of α,β-Unsaturated Aromatic Carboxylic Acids by Ceric Ammonium Nitrate in Acetonitrile Medium: A Kinetic and Mechanistic Study

    Directory of Open Access Journals (Sweden)

    K. Ramesh

    2013-01-01

    Full Text Available Polyethylene glycols (PEGs were found to be efficient media for decarboxylative nitration of α,β-unsaturated aromatic carboxylic acids by ceric ammonium nitrate (CAN in acetonitrile to give β-nitrostyrene derivatives. Kinetics of the reaction exhibited second order kinetics with a first order dependence on [CAN] and [substrate]. Reactions were too sluggish to be studied in the absence of PEG; therefore detailed kinetics were not taken up. Reaction times were reduced from 24 hrs to few hours. The catalytic activity was found to be in the increasing order PEG-300 > PEG-400 > PEG-600 > PEG-200. Mechanism of PEG-mediated reactions was explained by Menger-Portnoy's scheme as applied in micellar kinetics.

  14. Mechanistic study of electrochemical oxidation of o-dihydroxybenzenes in the presence of 4-hydroxy-1-methyl-2(1H)-quinolone

    Energy Technology Data Exchange (ETDEWEB)

    Moghaddam, Abdolmajid Bayandori [Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran 1983963113 (Iran, Islamic Republic of)]. E-mail: bayandori@gmail.com; Kobarfard, Farzad [Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran 1983963113 (Iran, Islamic Republic of); Fakhari, Ali Reza [Department of Chemistry, Faculty of Science, University of Shahid Beheshti, Tehran (Iran, Islamic Republic of); Nematollahi, Davood [Department of Chemistry, Faculty of Science, University of Bu-Ali-Sina, Hamadan (Iran, Islamic Republic of); Davarani, Saied Saeed Hosseiny [Department of Chemistry, Faculty of Science, University of Shahid Beheshti, Tehran (Iran, Islamic Republic of)

    2005-11-01

    Electrochemical oxidation of o-dihydroxybenzenes (1a and 1b) has been studied in the presence of 4-hydroxy-1-methyl-2(1H)-quinolone (3) as a nucleophile in aqueous solution using cyclic voltammetry and controlled-potential coulometry. The results indicate that the o-quinones derived from o-dihydroxybenzenes (1a and 1b) participate in 1,4-(michael) addition reactions with 3 to form the corresponding new o-dihydroxybenzene derivatives (6a and 6b). We propose a mechanism for the electrode process. The efficient electrochemical synthesis of 6a and 6b has been successfully performed at carbon rod electrodes in an undivided cell in good yield and purity. The products have been characterized after purification by IR, {sup 1}H NMR, {sup 13}C NMR and MS.

  15. Mechanistic study of electrochemical oxidation of catechols in the presence of 4-hydroxy-1-methyl-2(1H)-quinolone

    Energy Technology Data Exchange (ETDEWEB)

    Fakhari, Ali Reza [Department of Chemistry, Faculty of Science, University of Shahid Beheshti, Tehran 19835389 (Iran, Islamic Republic of)]. E-mail: a-zavareh@sbu.ac.ir; Nematollahi, Davood [Department of Chemistry, Faculty of Science, University of Bu-Ali-Sina, Hamadan (Iran, Islamic Republic of); Moghaddam, Abdolmajid Bayandori [Department of Chemistry, Faculty of Science, University of Shahid Beheshti, Tehran 19835389 (Iran, Islamic Republic of)

    2005-09-20

    Electrochemical oxidation of catechols (1a-1c) has been studied in the presence of 4-hydroxy-1-methyl-2(1H)-quinolone (3) as a nucleophile in aqueous solution using cyclic voltammetry and controlled-potential coulometry. The results indicate that the quinones derived from catechols (1a-1c) participate in Michael addition reactions with 3 to form the corresponding benzofuran (or isochromeno[4,3-c]quinoline) derivatives (6a-6c). The electrochemical synthesis of (6a-6c) has been successfully performed in an undivided cell in good yield and purity. The oxidation mechanism was deduced from voltammetric data and by coulometry at controlled-potential. The products have been characterized after purification by IR, {sup 1}H NMR, {sup 13}C NMR and MS.

  16. Ultrasonic Synthesis, Molecular Structure and Mechanistic Study of 1,3-Dipolar Cycloaddition Reaction of 1-Alkynylpyridinium-3-olate and Acetylene Derivatives

    Directory of Open Access Journals (Sweden)

    Asmaa Aboelnaga

    2016-06-01

    Full Text Available Regioselectively, ethyl propiolate reacted with 1-(propergyl-pyridinium-3-olate to give two regioisomers; ethyl 4-oxo-8-(prop-2-ynyl-8-aza-bicyclo(3.2.1octa-2,6-diene-6-carboxylate 4, ethyl 2-oxo-8-(prop-2-ynyl-8-aza-bicyclo(3.2.1octa-3,6-diene-6-carboxylate 5 as well as ethyl 2,6-dihydro-6-(prop-2-ynylfuro(2,3-cpyridine-3-carboxylate 6. The obtained compounds were identified by their spectral (IR, mass and NMR data. Moreover, DFT quantum chemical calculations were used to study the mechanism of the cycloaddition reaction. The regioselectivity was explained using transition state calculations, where the calculations agreed with the formation of products 4 and 5 in almost the same ratio. The reaction was also extended for diphenylaceylene as dipolarophile to give only two products instead of three.

  17. The Oxidation of 2-(2-Methoxyethoxyethanol and 2-(2-Ethoxyethoxyethanol by Ditelluratocuprate(III: A Kinetic and Mechanistic Study

    Directory of Open Access Journals (Sweden)

    Jin-huan Shan

    2013-01-01

    Full Text Available The oxidation of 2-(2-methoxyethoxyethanol (MEE and 2-(2-ethoxyethoxyethanol (EEE by ditelluratocuprate(III (DTC had been studied spectrophotometrically in alkaline medium. The reaction between and showed first-order dependence in DTC and fractional order in MEE and EEE. The rate constant of the pseudo-first-order reaction decreased with an increase of [TeO4  2−], whereas adding [OH−] enhanced the constant. In addition, the reaction had a negative salt effect. The rate of EEE was higher than that of MEE. A suitable assumption involving preequilibriums before the rate-controlling step and a free radical mechanism was proposed, based on the kinetic data. Activation parameters and the rate constant of the rate-determining step were calculated.

  18. Activity of Bruton's tyrosine-kinase inhibitor ibrutinib in patients with CD117-positive acute myeloid leukaemia: a mechanistic study using patient-derived blast cells.

    Science.gov (United States)

    Rushworth, Stuart A; Pillinger, Genevra; Abdul-Aziz, Amina; Piddock, Rachel; Shafat, Manar S; Murray, Megan Y; Zaitseva, Lyubov; Lawes, Matthew J; MacEwan, David J; Bowles, Kristian M

    2015-05-01

    Roughly 80% of patients with acute myeloid leukaemia have high activity of Bruton's tyrosine-kinase (BTK) in their blast cells compared with normal haemopoietic cells, rendering the cells sensitive to the oral BTK inhibitor ibrutinib in vitro. We aimed to develop the biological understanding of the BTK pathway in acute myeloid leukaemia to identify clinically relevant diagnostic information that might define a subset of patients that should respond to ibrutinib treatment. We obtained acute myeloid leukaemia blast cells from unselected patients attending our UK hospital between Feb 19, 2010, and Jan 20, 2014. We isolated primary acute myeloid leukaemia blast cells from heparinised blood and human peripheral blood mononuclear cells to establish the activity of BTK in response to CD117 activation. Furthermore, we investigated the effects of ibrutinib on CD117-induced BTK activation, downstream signalling, adhesion to primary bone-marrow mesenchymal stromal cells, and proliferation of primary acute myeloid leukaemia blast cells. We used the Mann-Whitney U test to compare results between groups. We obtained acute myeloid leukaemia blast cells from 29 patients. Ibrutinib significantly inhibited CD117-mediated proliferation of primary acute myeloid leukaemia blast cells (p=0·028). CD117 activation increased BTK activity by inducing phosphorylated BTK in patients with CD117-positive acute myeloid leukaemia. Furthermore, ibrutinib inhibited CD117-induced activity of BTK and downstream kinases at a concentration of 100 nM or more. CD117-mediated adhesion of CD117-expressing blast cells to bone-marrow stromal cells was significantly inhibited by Ibrutinib at 500 nM (p=0·028) INTERPRETATION: As first-in-man clinical trials of ibrutinib in patients with acute myeloid leukaemia commence, the data suggest not all patients will respond. Our findings show that BTK has specific pro-tumoural biological actions downstream of surface CD117 activation, which are inhibited by ibrutinib

  19. Methyleneation of peptides by N,N,N,N-tetramethylethylenediamine (TEMED) under conditions used for free radical polymerization: a mechanistic study.

    Science.gov (United States)

    Shirangi, Mehrnoosh; Sastre Toraño, Javier; Sellergren, Börje; Hennink, Wim E; Somsen, Govert W; van Nostrum, Cornelus F

    2015-01-21

    Free radical polymerization is often used to prepare protein and peptide-loaded hydrogels for the design of controlled release systems and molecular imprinting materials. Peroxodisulfates (ammonium peroxodisulfates (APS) or potassium peroxodisulfates (KPS)) with N,N,N,N-tetramethylethylenediamine (TEMED) are frequently used as initiator and catalyst. However, exposure to these free radical polymerization reagents may lead to modification of the protein and peptide. In this work, we show the modification of lysine residues by ammonium peroxodisulfate (APS)/TEMED of the immunostimulant thymopentin (TP5). Parallel studies on a decapeptide and a library of 15 dipeptides were performed to reveal the mechanism of modification. LC-MS of APS/TEMED-exposed TP5 revealed a major reaction product with an increased mass (+12 Da) with respect to TP5. LC-MS(2) and LC-MS(3) were performed to obtain structural information on the modified peptide and localize the actual modification site. Interpretation of the obtained data demonstrates the formation of a methylene bridge between the lysine and arginine residue in the presence of TEMED, while replacing TEMED with a sodium bisulfite catalyst did not show this modification. Studies with the other peptides showed that the TEMED radical can induce methyleneation on peptides when lysine is next to arginine, proline, cysteine, aspargine, glutamine, histidine, tyrosine, tryptophan, and aspartic acid residues. Stability of peptides and protein needs to be considered when using APS/TEMED in in situ polymerization systems. The use of an alternative catalyst such as sodium bisulfite may preserve the chemical integrity of peptides during in situ polymerization.

  20. Anti-nociceptive Activity of Ethnomedicinally Important Analgesic Plant Isodon rugosus Wall. ex Benth: Mechanistic Study and Identifications of Bioactive Compounds.

    Science.gov (United States)

    Zeb, Anwar; Ahmad, Sajjad; Ullah, Farhat; Ayaz, Muhammad; Sadiq, Abdul

    2016-01-01

    Isodon rugosus Wall. ex Benth. is extensively used as traditional medicine for the management of various types of pain including tooth ache, gastric pain, abdominal pain, ear ache, and generalized body pain. The current study is designed to scientifically verify the purported uses of I. rugosus as analgesic agent and to figure out its possible mechanism of action. Bioactive compounds responsible for analgesic activity were identified using GC and GC-MS analysis. Analgesic potentials were evaluated using acetic acid induced writhing, hot plate test, and formalin induced paw licking test. In acetic acid induced writhing chloroform fraction (Ir.Chf) exhibited 53% analgesia while formalin test displayed 61% inhibition at phase-I and 45% at phase-II respectively at a dose of 100 mg/kg. Similarly, in hot plate test Ir.Chf displayed average reaction time of 7 min at 15, 30, 45, and 60 min intervals. The possible mechanism of action was found to be the central pathway via opioidergic receptors as the mice showed morphine like analgesic activity at pre-administration of naloxone (opioid antagonist) in hot plate and formalin tests. In GC-MS analysis, 83 compounds were identified among which eight compounds including benzyl alcohol, sebacic acid, myristic acid, phytol, sugiol, Tocopherol, α-Amyrin, and stigmasterol were sorted out as previously reported analgesic compounds. Current study revealed that analgesic potential of I. rugosus can attributed to the presence of analgesic compounds. It may also be concluded that opioids receptors are involved in the analgesic mechanism of I. rugosus due to effective antagonism of nalaxone.

  1. Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis.

    Science.gov (United States)

    Sleeman, Mark C; Sorensen, John L; Batchelar, Edward T; McDonough, Michael A; Schofield, Christopher J

    2005-10-14

    The first step in the biosynthesis of the medicinally important carbapenem family of beta-lactam antibiotics is catalyzed by carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily. CarB catalyzes formation of (2S,5S)-carboxymethylproline [(2S,5S)-t-CMP] from malonyl-CoA and l-glutamate semialdehyde. In addition to using a cosubstrate, CarB catalyzes C-C and C-N bond formation processes as well as an acyl-coenzyme A hydrolysis reaction. We describe the crystal structure of CarB in the presence and absence of acetyl-CoA at 2.24 A and 3.15 A resolution, respectively. The structures reveal that CarB contains a conserved oxy-anion hole probably required for decarboxylation of malonyl-CoA and stabilization of the resultant enolate. Comparison of the structures reveals that conformational changes (involving His(229)) in the cavity predicted to bind l-glutamate semialdehyde occur on (co)substrate binding. Mechanisms for the formation of the carboxymethylproline ring are discussed in the light of the structures and the accompanying studies using isotopically labeled substrates; cyclization via 1,4-addition is consistent with the observed labeling results (providing that hydrogen exchange at the C-6 position of carboxymethylproline does not occur). The side chain of Glu(131) appears to be positioned to be involved in hydrolysis of the carboxymethylproline-CoA ester intermediate. Labeling experiments ruled out the possibility that hydrolysis proceeds via an anhydride in which water attacks a carbonyl derived from Glu(131), as proposed for 3-hydroxyisobutyryl-CoA hydrolase. The structural work will aid in mutagenesis studies directed at altering the selectivity of CarB to provide intermediates for the production of clinically useful carbapenems.

  2. Mechanistic and computational studies of the reductive half-reaction of tyrosine to phenylalanine active site variants of D-arginine dehydrogenase.

    Science.gov (United States)

    Gannavaram, Swathi; Sirin, Sarah; Sherman, Woody; Gadda, Giovanni

    2014-10-21

    The flavin-mediated enzymatic oxidation of a CN bond in amino acids can occur through hydride transfer, carbanion, or polar nucleophilic mechanisms. Previous results with D-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) using multiple deuterium kinetic isotope effects (KIEs) and computational studies established preferred binding of the substrate protonated on the α-amino group, with cleavages of the NH and CH bonds occurring in asynchronous fashion, consistent with the three possible mechanisms. The hydroxyl groups of Y53 and Y249 are ≤4 Å from the imino and carboxylate groups of the reaction product iminoarginine, suggesting participation in binding and catalysis. In this study, we have investigated the reductive half-reactions of the Y53F and Y249F variants of PaDADH using substrate and solvent deuterium KIEs, solvent viscosity and pH effects, and quantum mechanical/molecular mechanical computational approaches to gain insights into the catalytic roles of the tyrosines and evaluate whether their mutations affect the transition state for substrate oxidation. Both Y53F and Y249F enzymes oxidized D-arginine with steady-state kinetic parameters similar to those of the wild-type enzyme. Rate constants for flavin reduction (k(red)) with D-leucine, a slow substrate amenable to rapid kinetics, were 3-fold smaller than the wild-type value with similar pKa values for an unprotonated group of ∼10.0. Similar pKa values were observed for (app)Kd in the variant and wild-type enzymes. However, cleavage of the substrate NH and CH bonds in the enzyme variants occurred in synchronous fashion, as suggested by multiple deuterium KIEs on k(red). These data can be reconciled with a hydride transfer mechanism, but not with carbanion and polar nucleophilic mechanisms.

  3. Mechanistic Features of Nanodiamonds in the Lapping of Magnetic Heads

    Directory of Open Access Journals (Sweden)

    Xionghua Jiang

    2014-01-01

    Full Text Available Nanodiamonds, which are the main components of slurry in the precision lapping process of magnetic heads, play an important role in surface quality. This paper studies the mechanistic features of nanodiamond embedment into a Sn plate in the lapping process. This is the first study to develop mathematical models for nanodiamond embedment. Such models can predict the optimum parameters for particle embedment. From the modeling calculations, the embedded pressure satisfies p0=3/2·W/πa2 and the indentation depth satisfies δ=k1P/HV. Calculation results reveal that the largest embedded pressure is 731.48 GPa and the critical indentation depth δ is 7 nm. Atomic force microscopy (AFM, scanning electron microscopy (SEM, and Auger electron spectroscopy (AES were used to carry out surface quality detection and analysis of the disk head. Both the formation of black spots on the surface and the removal rate have an important correlation with the size of nanodiamonds. The results demonstrate that an improved removal rate (21 nm·min−1 can be obtained with 100 nm diamonds embedded in the plate.

  4. Mechanistic rationales for targeting interleukin-17A in spondyloarthritis.

    Science.gov (United States)

    Raychaudhuri, Siba P; Raychaudhuri, Smriti K

    2017-03-08

    The term spondyloarthritis (SpA) is used to describe a group of inflammatory autoimmune diseases, including ankylosing spondylitis and psoriatic arthritis, with common genetic risk factors and clinical features. SpA is clinically distinct from rheumatoid arthritis and typically affects the spine, sacroiliac joints, entheses, and, less commonly, peripheral joints. Although the pathogenesis of SpA is not fully understood, recent findings have identified the interleukin (IL)-17 pathway as a key mediator of disease pathogenesis. Clinical evidence for the efficacy of IL-17A inhibition by biologic agents was initially shown in patients with chronic plaque psoriasis, another autoimmune disease mediated by the IL-17 pathway. Subsequently, similar positive efficacy for inhibition of IL-17A was seen in patients with ankylosing spondylitis and psoriatic arthritis. Inhibition of IL-17A may also improve cardiovascular and metabolic comorbidities often found in patients with SpA because studies have linked these disorders to the IL-17 pathway. In this review, we will examine key preclinical studies that demonstrated the mechanistic role of IL-17A in the development SpA and discuss how these observations were translated into clinical practice.

  5. Mechanistic studies of cancer cell mitochondria- and NQO1-mediated redox activation of beta-lapachone, a potentially novel anticancer agent

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jason Z. [Virginia Tech CRC, Blacksburg, VA (United States); Ke, Yuebin [Shenzhen Center for Disease Control and Prevention, Shenzhen 518055 (China); Misra, Hara P. [Virginia Tech CRC, Blacksburg, VA (United States); Trush, Michael A. [Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD (United States); Li, Y. Robert [Campbell University School of Osteopathic Medicine, Buies Creek, NC (United States); Virginia Tech-Wake Forest University SBES, Blacksburg, VA (United States); Department of Biology, University of North Carolina at Greensboro, NC (United States); Zhu, Hong, E-mail: zhu@campbell.edu [Campbell University School of Osteopathic Medicine, Buies Creek, NC (United States); Jia, Zhenquan, E-mail: z_jia@uncg.edu [Department of Biology, University of North Carolina at Greensboro, NC (United States)

    2014-12-15

    Beta-lapachone (beta-Lp) derived from the Lapacho tree is a potentially novel anticancer agent currently under clinical trials. Previous studies suggested that redox activation of beta-Lp catalyzed by NAD(P)H:quinone oxidoreductase 1 (NQO1) accounted for its killing of cancer cells. However, the exact mechanisms of this effect remain largely unknown. Using chemiluminescence and electron paramagnetic resonance (EPR) spin-trapping techniques, this study for the first time demonstrated the real-time formation of ROS in the redox activation of beta-lapachone from cancer cells mediated by mitochondria and NQO1 in melanoma B16–F10 and hepatocellular carcinoma HepG2 cancer cells. ES936, a highly selective NQO1 inhibitor, and rotenone, a selective inhibitor of mitochondrial electron transport chain (METC) complex I were found to significantly block beta-Lp meditated redox activation in B16–F10 cells. In HepG2 cells ES936 inhibited beta-Lp-mediated oxygen radical formation by ∼ 80% while rotenone exerted no significant effect. These results revealed the differential contribution of METC and NQO1 to beta-lapachone-induced ROS formation and cancer cell killing. In melanoma B16–F10 cells that do not express high NQO1 activity, both NOQ1 and METC play a critical role in beta-Lp redox activation. In contrast, in hepatocellular carcinoma HepG2 cells expressing extremely high NQO1 activity, redox activation of beta-Lp is primarily mediated by NQO1 (METC plays a minor role). These findings will contribute to our understanding of how cancer cells are selectively killed by beta-lapachone and increase our ability to devise strategies to enhance the anticancer efficacy of this potentially novel drug while minimizing its possible adverse effects on normal cells. - Highlights: • Both isolated mitochondria and purified NQO1 are able to generate ROS by beta-Lp. • The differential roles of mitochondria and NQO1 in mediating redox activation of beta-Lp • In cancer cells with

  6. Mechanistic studies of NO{sub x} reduction reactions under oxidative atmosphere on alumina supported 0.2wt% platinum catalyst treated under microwave. Part 2

    Energy Technology Data Exchange (ETDEWEB)

    Ringler, Sandrine; Girard, Paule; Maire, Gilbert; Garin, Francois [Laboratoire d`Etudes de la Reactivite Catalytique, des Surfaces et Interfaces (LERCSI), UMR 7515 du CNRS - ECPM, Universite Louis Pasteur - Institut Le Bel 4, rue Blaise Pascal 67, 070 Strasbourg Cedex (France); Hilaire, Stephanie; Roussy, Georges [Laboratoire de Spectroscopie et des Techniques Micro-Ondes LSTM, Universite de Nancy I, BP 239 54506, Vandoeuvre-les-Nancy Cedex (France)

    1999-03-08

    Reduction of nitrogen oxides under oxidative atmosphere is a very extensively studied reaction, but it is still very difficult to understand and to follow the various pathways of the reaction. Two alumina supported 0.2wt% platinum catalysts, reduced by hydrogen in an oven heated either by microwave irradiations or by Joule effect, with different metal dispersion of 60% and 90%, respectively, were studied. By the use of labelled compounds we were able to show the presence of an exchange reaction between 15N16O and 15N18O which occurred on both catalysts. It means that [15N16O18O] is the intermediate species. Such product, 15N18O, is less formed on the microwave catalyst `MW` than on the classical one `CT`. Experiments were performed at 22 and 550Torr, between 150C and 250C. Near atmospheric pressure, `MW` catalyst gives higher initial rates for 15N{sub 2} formation than the `CT` catalysts. At low temperature, the nitrogen selectivity is higher on `MW` catalyst than on the other catalyst. From the apparent activation energy values, one may deduce that several mechanisms are responsible for the 15N{sub 2} formation depending on the reaction temperature and the catalyst used. On the 0.2% Pt/Al{sub 2}O{sub 3} `CT` catalyst, an additive process between propene and 15NO takes place at low temperature giving nitroso and oxime intermediate species. At high temperature, a partial oxidation of propene occurs, giving a ketone, before the 15NO reduction to 15N{sub 2}. With this catalyst only two sites with different activity are involved. On the 0.2% Pt/Al{sub 2}O{sub 3} `MW` catalyst the reactants are seated on three sites with different activity. This particularity reinforce the proposals concerning the `MW` catalyst which may exhibit particular shapes for the aggregates having different crystallographic orientations. What is surprising, for this `MW` catalyst, is the fact that we already observed a specific reactivity under reductive atmosphere in reforming reactions and now

  7. Oxidation of 3,6-dioxa-1,8-octanedithiol by platinum(IV) anticancer prodrug and model complex: kinetic and mechanistic studies.

    Science.gov (United States)

    Huo, Shuying; Shen, Shigang; Liu, Dongzhi; Shi, Tiesheng

    2012-06-07

    Thioredoxins are small redox proteins and have the active sites of Cys-Xaa-Yaa-Cys; they are overexpressed by many different cancer cells. Cisplatin and Pt(II) analogues could bind to the active sites and inhibit the activities of the proteins, as demonstrated by other researchers. Platinum(IV) anticancer drugs are often regarded as prodrugs, but their interactions with thioredoxins have not been studied. In this work, 3,6-dioxa-1,8-octanedithiol (dithiol) was chosen as a model compound for the active sites of thioredoxins, and its reactions with cis-[Pt(NH(3))(2)Cl(4)] and trans-[PtCl(2)(CN)(4)](2-) (cisplatin prodrug and a model complex) were studied. The pK(a) values for the dithiol were characterized to be 8.7 ± 0.2 and 9.6 ± 0.2 at 25.0 °C and an ionic strength of 1.0 M. The reaction kinetics was followed by a stopped-flow spectrophotometer over a wide pH range. An overall second-order rate law was established, -d[Pt(IV)]/dt = k'[Pt(IV)][dithiol], where k' stands for the observed second-order rate constants. Values of k' increased several orders of magnitude when the solution pH was increased from 3 to 9. A stoichiometry of Δ[Pt(IV)]/Δ[dithiol] = 1:1 derived for the reduction process and product analysis by mass spectrometry indicated that the dithiol was oxidized to form an intramolecular disulfide, coinciding with the nature of thioredoxin proteins. All of the reaction features are rationalized in terms of a reaction mechanism, involving three parallel rate-determining steps depending on the pH of the reaction medium. Rate constants for the rate-determining steps were evaluated. It can be concluded that Pt(IV) anticancer prodrugs can oxidize the reduced thioredoxins, and the oxidation mechanism is similar to those of the oxidations of biologically important reductants by some reactive oxygen species (ROS) such as hypochlorous acid/hypochlorite and chloramines.

  8. Identifying mechanistic similarities in drug responses

    KAUST Repository

    Zhao, C.

    2012-05-15

    Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

  9. Kinetic and mechanistic study on the pyrolysis of 1,3-dihydroisothianaphthene-2,2-dioxide toward benzocyclobutene using RRKM and BET theories

    Science.gov (United States)

    Zahedi, Ehsan; Mozaffari, Majid; Yousefi, Leyla; Shiroudi, Abolfazl; Deleuze, Michael S.

    2017-02-01

    The kinetics and mechanisms of pyrolysis of 1,3-dihydroisothianaphthene-2,2-dioxide toward benzocyclobutene have been theoretically studied using canonical transition state theory (CTST), statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory, and bonding evolution theory (BET) in conjugation with M06-2X/aug-cc-pVTZ calculations. The CTST slightly breaks down to estimate the reaction rate of the cheletropic extrusion. RRKM results indicated that the cheletropic extrusion and electrocyclic reaction require energy barriers of 171.3 and 122.2 kJ/mol to be overcome; and can be characterized respectively by 7 and 3 phases associated to the sequence of catastrophes C8H8SO2 (1): 7-[FF]C†C†FFF-0: C8H8 + SO2 and C8H8 (2): 3-[F†F†]C-0: C8H8 (3). For the cheletropic extrusion, breaking of the C7-S and C8-S bonds begins respectively at Rx = -2.7434 amu1/2 Bohr and Rx = -1.7458 amu1/2 Bohr, and formation of the sulfur dioxide is completed at Rx = -0.2494 amu1/2 Bohr. For the electrocyclic reaction, formation of new C7-C8 bond occurs at Rx = 1.6214 amu1/2 Bohr from C- to C- coupling between the generated pseudoradical centers at Rx = 0.1474 amu1/2 Bohr on the terminal carbon atoms.

  10. A mechanistic study of the enhancing effect of Tween 80 on the mycelial growth and exopolysaccharide production by Pleurotus tuber-regium.

    Science.gov (United States)

    Zhang, Bo-Bo; Cheung, Peter C K

    2011-09-01

    Several new observations related to the enhancement effect of Tween 80 on the mycelial growth and exopolysaccharide production by the submerged fermentation of Pleurotus tuber-regium were reported in the present study. Firstly, it was found that the addition of Tween 80 on the 5th day could significantly increase the glucose consumption rate at the later stage of the fermentation compared to the control. Secondly, addition of Tween 80 could maintain the intact structure of the mycelial pellets of P. tuber-regium with little signs of disintegration as observed under microscope and kept the pH value of the fermentation broth at an acidic level lower than that of the control. Thirdly, the oleic acid (C18:1) composition in the mycelial cell membrane was significantly increased from 2.6% (in the control) to 18.5% (with addition of Tween 80) coincided with a decrease in the concentration of Tween 80 in the culture medium. These new findings provide some important insight to the elucidation of the detailed mechanism by which Tween 80 is used as a stimulatory agent in the submerged fermentation of mushroom mycelium.

  11. Fluorescence quenching of CdS quantum dots by 4-azetidinyl-7-nitrobenz-2-oxa-1,3-diazole: a mechanistic study.

    Science.gov (United States)

    Santhosh, Kotni; Patra, Satyajit; Soumya, S; Khara, Dinesh Chandra; Samanta, Anunay

    2011-10-24

    Fluorescence quenching of CdS quantum dots (QDs) by 4-azetidinyl-7-nitrobenz-2-oxa-1,3-diazole (NBD), where the two quenching partners satisfy the spectral overlap criterion necessary for Förster resonance energy transfer (FRET), is studied by steady-state and time-resolved fluorescence techniques. The fluorescence quenching of the QDs is accompanied by an enhancement of the acceptor fluorescence and a reduction of the average fluorescence lifetime of the donor. Even though these observations are suggestive of a dynamic energy transfer process, it is shown that the quenching actually proceeds through a static interaction between the quenching partners and is probably mediated by charge-transfer interactions. The bimolecular quenching rate constant estimated from the Stern-Volmer plot of the fluorescence intensities, is found to be exceptionally high and unrealistic for the dynamic quenching process. Hence, a kinetic model is employed for the estimation of actual quencher/QD ratio dependent exciton quenching rate constants of the fluorescence quenching of CdS by NBD. The present results point to the need for a deeper analysis of the experimental quenching data to avoid erroneous conclusions.

  12. Mechanistic study on the nuclear modifier gene MSS1 mutation suppressing neomycin sensitivity of the mitochondrial 15S rRNA C1477G mutation in Saccharomyces cerevisiae.

    Science.gov (United States)

    Zhou, Qiyin; Wang, Wei; He, Xiangyu; Zhu, Xiaoyu; Shen, Yaoyao; Yu, Zhe; Wang, Xuexiang; Qi, Xuchen; Zhang, Xuan; Fan, Mingjie; Dai, Yu; Yang, Shuxu; Yan, Qingfeng

    2014-01-01

    The phenotypic manifestation of mitochondrial DNA (mtDNA) mutations can be modulated by nuclear genes and environmental factors. However, neither the interaction among these factors nor their underlying mechanisms are well understood. The yeast Saccharomyces cerevisiae mtDNA 15S rRNA C1477G mutation (PR) corresponds to the human 12S rRNA A1555G mutation. Here we report that a nuclear modifier gene mss1 mutation suppresses the neomycin-sensitivity phenotype of a yeast C1477G mutant in fermentable YPD medium. Functional assays show that the mitochondrial function of the yeast C1477G mutant was impaired severely in YPD medium with neomycin. Moreover, the mss1 mutation led to a significant increase in the steady-state level of HAP5 (heme activated protein), which greatly up-regulated the expression of glycolytic transcription factors RAP1, GCR1, and GCR2 and thus stimulated glycolysis. Furthermore, the high expression of the key glycolytic enzyme genes HXK2, PFK1 and PYK1 indicated that enhanced glycolysis not only compensated for the ATP reduction from oxidative phosphorylation (OXPHOS) in mitochondria, but also ensured the growth of the mss1(PR) mutant in YPD medium with neomycin. This study advances our understanding of the phenotypic manifestation of mtDNA mutations.

  13. Antidiabetic effect of Ficus racemosa Linn. stem bark in high-fat diet and low-dose streptozotocin-induced type 2 diabetic rats: a mechanistic study.

    Science.gov (United States)

    Veerapur, V P; Prabhakar, K R; Thippeswamy, B S; Bansal, Punit; Srinivasan, K K; Unnikrishnan, M K

    2012-05-01

    The present study was designed to investigate the effects of the ethanol extract of Ficus racemosa (FRE) on biochemical parameters in type 2-like diabetes, induced by a combination of standardised high-fat diet and low-dose streptozotocin (25mgkg(-1), i.p.) in rats. To elucidate the mode of action of FRE, its effects on a battery of targets involved in glucose homeostasis was evaluated. FRE (200 and 400mgkg(-1), p.o.), in a dose-dependent manner, altered the biochemical parameters and significantly improved glucose tolerance and HDL-c levels. In different bioassays, FRE showed inhibition of PTP-1B (IC50 12.1μg/mL) and DPP-IV (42.5%). FRE exhibited 82.6% binding to PPAR-γ. Furthermore FRE exhibited stimulation of glucose uptake by skeletal muscles (hemi-diaphragm). Bergenin was quantified in bioactive-FRE by high-performance liquid chromatography (0.15%w/w). This is the first report demonstrating the effectiveness of F. racemosa stem bark in type 2 diabetes and targets involved in it.

  14. Modification-free and N-acetyl-L-cysteine-induced colorimetric response of AuNPs: A mechanistic study and sensitive Hg(2+) detection.

    Science.gov (United States)

    Tang, Jie; Wu, Peng; Hou, Xiandeng; Xu, Kailai

    2016-10-01

    A facile yet sensitive and selective method was proposed for Hg(2+) detection based on N-acetyl-L-cysteine(NAC)-induced colorimetric response of AuNPs. The proposed method can be easily performed by introducing the premixing of NAC and Hg(2+) into as-prepared citrate-capped AuNPs solution. A combination of experimental and theoretical studies was applied to illustrate the mechanism of this AuNPs colorimetric system. The strong interaction of NAC and AuNPs through Au-S bond could lead to the aggregation of AuNPs, but the formation of NAC-Hg-NAC complex decreased the affinity between NAC and AuNPs and resulted in an anti-aggregation effect. Therefore, the color of the AuNPs solution would progress from purple to red with the increase of Hg(2+) concentration. The proposed method had a high sensitivity with a limit of detection of 9.9nM. Coexistent metal ions, including Cd(2+), Mn(2+), Al(3+), Ag(+), K(+), Mg(2+), Ca(2+), Cr(3+), Cu(2+), Fe(3+), Pb(2+), Ni(2+) and Zn(2+), did not interfere with the detection of Hg(2+). This method can be used to monitor Hg(2+) in tap water.

  15. Ce(IV)- and light-driven water oxidation by [Ru(terpy)(pic)3]2+ analogues: catalytic and mechanistic studies.

    Science.gov (United States)

    Duan, Lele; Xu, Yunhua; Tong, Lianpeng; Sun, Licheng

    2011-02-18

    A series of mononuclear ruthenium polypyridyl complexes [Ru(Mebimpy)(pic)(3)](PF(6))(2) (2; Mebimpy = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine; pic = 4-picoline), Ru(bimpy)(pic)(3) (3; H(2)bimpy = 2,6-bis(benzimidazol-2-yl)pyridine), trans-[Ru(terpy)(pic)(2)Cl](PF(6)) (4; terpy = 2,2';6',2"-terpyridine), and trans-[Ru(terpy)(pic)(2)(OH(2))](ClO(4))(2) (5) are synthesized and characterized as analogues of the known Ru complex, [Ru(terpy)(pic)(3)](PF(6))(2) (1). The effect of the ligands on electronic and catalytic properties is studied and discussed. The negatively charged ligand, bimpy(2-), has a remarkable influence on the electrochemical events due to its strong electron-donating ability. The performance in light- and Ce(IV)-driven (Ce(IV) = Ce(NH(4))(2)(NO(3))(6)) water oxidation is successfully demonstrated. We propose that ligand exchange between pic and H(2)O occurs to form the real catalyst, a Ru-aqua complex. The synthesis and testing of trans-[Ru(terpy)(pic)(2)(OH(2))](ClO(4))(2) (5) confirmed our proposal. In addition, complex 5 possesses the best catalytic activity among these five complexes.

  16. Mechanistic and Structural Studies of Protein-Only RNase P Compared to Ribonucleoproteins Reveal the Two Faces of the Same Enzymatic Activity

    Directory of Open Access Journals (Sweden)

    Cédric Schelcher

    2016-06-01

    Full Text Available RNase P, the essential activity that performs the 5′ maturation of tRNA precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only RNase P (PRORP that occur in eukaryote nuclei and organelles. A fast growing list of studies has investigated three-dimensional structures and mode of action of PRORP proteins. Results suggest that similar to ribozymes, PRORP proteins have two main domains. A clear functional analogy can be drawn between the specificity domain of the RNase P ribozyme and PRORP pentatricopeptide repeat domain, and between the ribozyme catalytic domain and PRORP N4BP1, YacP-like Nuclease domain. Moreover, both types of enzymes appear to dock with the acceptor arm of tRNA precursors and make specific contacts with the corner of pre-tRNAs. While some clear differences can still be delineated between PRORP and ribonucleoprotein (RNP RNase P, the two types of enzymes seem to use, fundamentally, the same catalytic mechanism involving two metal ions. The occurrence of PRORP and RNP RNase P represents a remarkable example of convergent evolution. It might be the unique witness of an ongoing replacement of catalytic RNAs by proteins for enzymatic activities.

  17. Synthesis, GC-EIMS, ~1H NMR, ~(13)C NMR, Mechanistic and Thermal Studies of o-Xylylene-α,α'-bis(triphenylphosphinebromide)

    Institute of Scientific and Technical Information of China (English)

    Muddasir Hanif; LU Ping; XU Hai; TIAN Zhi-cheng; YANG Bing; WANG Zhi-ming; TIAN Lei-lei; XU Yuan-ze; XIE Zeng-qi; MA Yu-guang

    2009-01-01

    Organophosphorous compounds containing phosphorus as an integral part have been widely used in industry, organic synthesis and optoelectronics. o-Xylylene-α,α'-bis(triphenylphosphinebromide)(OXBTPPB) is a facile reagent to convert o-quinones(e.g., 9,10-phenanthrenequinone) into polycyclic aromatic hydrocarbons(PAHs). Herein lies an improved synthetic route to OXBTPPB. The resultant was carefully characterized with GC-EIMS, ~1H NMR, ~(13)C NMR, spectroscopic techniques. The EIMS shows characteristic peaks at m/z=262.4, 183.3, 108.2, 77.1 attributed to the [C_(18)H_(15)P]~+, [C_(18)H_8P]~+, [C_6H_5P]~+, [C_6H_5]~+ ions, respectively. The 1H and ~(13)C NMR spectrum shows well resolved peaks and all the hydrogens and carbons were well-assigned via a combined study of ~1H-~1H COSY, HMBC, and HMQC experiments. The mechanism for the formation of OXBTPPB was proposed based on literature and obtained experimental data. Meanwhile, the thermal stability of OXBTPPB was evaluated with TGA analysis, and an onset decomposition temperature(T_d) was recorded at 323.6℃.

  18. Mechanistic Evaluation for Mixed-field Agglutination in the K562 Cell Study Model with Exon 3 Deletion of A1 Gene.

    Science.gov (United States)

    Chen, Ding-Ping; Tseng, Ching-Ping; Lin, Chi-Jui; Wang, Wei-Ting; Sun, Chien-Feng

    2015-01-01

    In the case of blood type B3 with typical mixed-field agglutination of RBCs in the presence of anti-B or anti-AB antibody, a number of genetic alternations have been reported. It is well known that the IVS3+5G→A mutation in the B gene destroys the consensus of the splice donor site leading to exon 3 skipping during mRNA splicing. The lack of exon 3 likely causes a short stem region, producing an unstable B3 protein, and is concomitant with a decrease in B3 protein expression. Whether the phenomenon also appears in the type A blood group is of question. In this study, we evaluate whether exon 3 deletion in the blood type A gene also results in mixed-field phenotype. Site-directed mutagenesis was used to generate cDNA encoding A1 gene with exon 3 deletion. The cDNA was stably expressed in K562 cells. The expression of A antigen was compared with expression in parental K562 cells that did not express A antigen and in the stable K562 cell line expressing A(1) cDNA by flow cytometry analyses. The expression of A antigen in A1 stable cells and parental K562 cells was set as 100% and 0%, respectively. The mean relative percentage of A antigen expression for the cells of A1 with exon 3 deletion was 59.9% of A1 stable cells. Consistent with the observations of B3, which is B gene with exon 3 deletion, mixed field agglutination was observed for the cells expressing A1 with exon 3 deletion. Exon 3 deletion results in mixed field phenotype in both type A and B RBCs. However, the degree of antigen expression change for exon 3 deletion in A gene was less severe when compared with the deletion occurred in B gene.

  19. Hydroxy- and silyloxy-substituted TEMPO derivatives for the living free-radical polymerization of styrene and n-butyl acrylate: synthesis, kinetics, and mechanistic studies.

    Science.gov (United States)

    Knoop, Christoph Alexander; Studer, Armido

    2003-12-31

    The synthesis of new 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) styryl derivatives as mediators for the living free-radical polymerization is described. Two of the alpha-methyl groups at the 2- and 6-position of the parent TEMPO styryl alkoxyamine have been replaced by hydroxymethyl and silyloxymethyl groups. To further increase the steric hindrance around the alkoxyamine oxygen atom, the remaining two methyl groups have been substituted with larger ethyl groups. Styrene polymerizations using hydroxy-substituted TEMPO derivatives are fast, but are not well-controlled. As previously shown for other OH-substituted alkoxyamines, intramolecular H-bonding leads to an acceleration of the C-O bond homolysis and, hence, to an acceleration of the polymerization process. However, the OH groups also increase the alkoxyamine decomposition rate constant. The kinetics of the C-O bond homolysis have been determined using EPR spectroscopy. Decomposition studies have been conducted with the aid of 1H NMR spectroscopy. In contrast to the OH-substituted alkoxyamines, highly hindered silyloxy-substituted TEMPO alkoxyamines turned out to be excellent mediator/initiators for the controlled styrene polymerization. Polystyrene with M(n) of up to 80 000 g/mol and narrow polydispersities (PDI) has been prepared using the new alkoxyamines. Reactions have been conducted at 105 degrees C; however, even at 90 degrees C controlled but slow polymerizations can be achieved. Furthermore, and more importantly, poly(n-butyl acrylates) with narrow PDIs (acrylate polymerization can be conducted at temperatures as low as 90 degrees C. The silylated alkoxyamines presented belong to the most efficient initiator/mediators for the controlled acrylate polymerization known to date. The effect of the addition of free nitroxide on the acrylate polymerization is discussed. Moreover, the synthesis of diblock copolymers with narrow PDIs is described.

  20. Gigantol from Dendrobium chrysotoxum Lindl. binds and inhibits aldose reductase gene to exert its anti-cataract activity: An in vitro mechanistic study.

    Science.gov (United States)

    Wu, Jie; Li, Xue; Wan, Wencheng; Yang, Qiaohong; Ma, Weifeng; Chen, Dan; Hu, Jiangmiao; Chen, C-Y Oliver; Wei, Xiaoyong

    2017-02-23

    Dendrobium. chrysotoxum Lindl is a commonly used species of medicinal Dendrobium which belongs to the family of Orchidaceae, locally known as "Shihu" or "Huangcao". D. chrysotoxum Lindl is widely known for medicinal values in traditional Chinese medicine as it possesses anti-inflammatory, anti-hyperglycemic induction, antitumor and antioxidant properties. To characterize the interaction between gigantol extracted from D. chrysotoxum Lindl and the AR gene, and determine gigantol's efficacy against cataractogenesis. Human lens epithelial cells (HLECs) were induced by glucose as the model group. Reverse transcription polymerase chain reaction (RT-PCR) was used to assess AR gene expression. Then, the mode of interaction of gigantol with the AR gene was evaluated by UV-visible spectroscopy, atomic force microscope (AFM) and surface-enhanced Raman spectroscopy (SERS). The binding constant was determined by UV-visible. Gigantol depressed AR gene expression in HLECs. UV-visible spectra preliminarily indicated that interaction between the AR gene and gigantol may follow the groove mode, with a binding constant of 1.85×10(3)L/mol. Atomic force microscope (AFM) data indicated that gigantol possibly bound to insert AR gene base pairs of the double helix. Surface-enhanced Raman spectroscopy (SERS) studies further supported these observations. Gigantol extracted from D. chrysotoxum Lindl not only has inhibitory effects on aldose reductase, but also inhibits AR gene expression. These findings provide a more comprehensive theoretical basis for the use of Dendrobium for the treatment of diabetic cataract. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  1. Glutathione S-transferase omega genes in Alzheimer and Parkinson disease risk, age-at-diagnosis and brain gene expression: an association study with mechanistic implications.

    Science.gov (United States)

    Allen, Mariet; Zou, Fanggeng; Chai, High Seng; Younkin, Curtis S; Miles, Richard; Nair, Asha A; Crook, Julia E; Pankratz, V Shane; Carrasquillo, Minerva M; Rowley, Christopher N; Nguyen, Thuy; Ma, Li; Malphrus, Kimberly G; Bisceglio, Gina; Ortolaza, Alexandra I; Palusak, Ryan; Middha, Sumit; Maharjan, Sooraj; Georgescu, Constantin; Schultz, Debra; Rakhshan, Fariborz; Kolbert, Christopher P; Jen, Jin; Sando, Sigrid B; Aasly, Jan O; Barcikowska, Maria; Uitti, Ryan J; Wszolek, Zbigniew K; Ross, Owen A; Petersen, Ronald C; Graff-Radford, Neill R; Dickson, Dennis W; Younkin, Steven G; Ertekin-Taner, Nilüfer

    2012-04-11

    Glutathione S-transferase omega-1 and 2 genes (GSTO1, GSTO2), residing within an Alzheimer and Parkinson disease (AD and PD) linkage region, have diverse functions including mitigation of oxidative stress and may underlie the pathophysiology of both diseases. GSTO polymorphisms were previously reported to associate with risk and age-at-onset of these diseases, although inconsistent follow-up study designs make interpretation of results difficult. We assessed two previously reported SNPs, GSTO1 rs4925 and GSTO2 rs156697, in AD (3,493 ADs vs. 4,617 controls) and PD (678 PDs vs. 712 controls) for association with disease risk (case-controls), age-at-diagnosis (cases) and brain gene expression levels (autopsied subjects). We found that rs156697 minor allele associates with significantly increased risk (odds ratio = 1.14, p = 0.038) in the older ADs with age-at-diagnosis > 80 years. The minor allele of GSTO1 rs4925 associates with decreased risk in familial PD (odds ratio = 0.78, p = 0.034). There was no other association with disease risk or age-at-diagnosis. The minor alleles of both GSTO SNPs associate with lower brain levels of GSTO2 (p = 4.7 × 10-11-1.9 × 10-27), but not GSTO1. Pathway analysis of significant genes in our brain expression GWAS, identified significant enrichment for glutathione metabolism genes (p = 0.003). These results suggest that GSTO locus variants may lower brain GSTO2 levels and consequently confer AD risk in older age. Other glutathione metabolism genes should be assessed for their effects on AD and other chronic, neurologic diseases.

  2. n-Doping of organic electronic materials using air-stable organometallics: a mechanistic study of reduction by dimeric sandwich compounds.

    Science.gov (United States)

    Guo, Song; Mohapatra, Swagat K; Romanov, Alexander; Timofeeva, Tatiana V; Hardcastle, Kenneth I; Yesudas, Kada; Risko, Chad; Brédas, Jean-Luc; Marder, Seth R; Barlow, Stephen

    2012-11-12

    Several 19-electron sandwich compounds are known to exist as "2×18-electron" dimers. Recently it has been shown that, despite their air stability in the solid state, some of these dimers act as powerful reductants when co-deposited from either the gas phase or from solution and that this behavior can be useful in n-doping materials for organic electronics, including compounds with moderate electron affinities, such as 6,13-bis[tri(isopropyl)silylethynyl]pentacene (3). This paper addresses the mechanisms by which the dimers of 1,2,3,4,5-pentamethylrhodocene (1 b(2)), (pentamethylcyclopentadienyl)(1,3,5-trialkylbenzene)ruthenium (alkyl=Me, 2 a(2); alkyl=Et, 2 b(2)), and (pentamethylcyclopentadienyl)(benzene)iron (2 c(2)) react with 3 in solution. Vis/NIR and NMR spectroscopy, and X-ray crystallography indicate that the products of these solution reactions are 3(·-) salts of the monomeric sandwich cations. Vis/NIR kinetic studies for the Group 8 dimers are consistent with a mechanism whereby an endergonic electron transfer from the dimer to 3 is followed by rapid cleavage of the dimer cation. NMR crossover experiments with partially deuterated derivatives suggest that the C-C bond in the 1 b(2) dimer is much more readily broken than that in 2 a(2); consistent with this observation, Vis/NIR kinetic measurements suggest that the solution reduction of 3 by 1 b(2) can occur by both the mechanism established for the Group 8 species and by a mechanism in which an endergonic dissociation of the dimer is followed by rapid electron transfer from monomeric 1 b to 3.

  3. Mechanistic insights on the electronic properties and electronic/atomic structure aspects in orthorhombic SrVO3 thin films: XANES-EXAFS study.

    Science.gov (United States)

    Sharma, Aditya; Varshney, Mayora; Cheol Lim, Weon; Shin, Hyun-Joon; Pal Singh, Jitendra; Ok Won, Sung; Hwa Chae, Keun

    2017-03-01

    Correlations among the B-O6 octahedra distortions, existing polymorphous phases, band structures and electronic conductivities of ABO3 perovskites are matters for debate and require a deep understanding of their local atomic/electronic structures and diverse assets. In this study, to illustrate the distortion in V-O6 octahedra and its implication on the band structure and electronic properties, spectroscopic investigations on the RF-sputtering grown insulating SrVO3 thin films were employed using X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). V K-edge and V L3,2-edge XANES, along with atomic multiplet calculations, have confirmed the 4+ oxidation state of V ions in the pristine and annealed SrVO3 thin films. Lower t2g/eg peak intensity ratio and smaller energy separation between t2g and eg peaks in the O K-edge XANES spectra, compared to the VO2 reference sample, have confirmed a larger V-O6 distortion in the orthorhombic SrVO3 thin films. Moreover, from the EXAFS data analysis, the local orthorhombic structure has been identified in the pristine and annealed SrVO3 thin films, compelling significant distortion in the V-O6 octahedra. Dimerization in the vanadium chains and V-V twisting, caused by V-O6 octahedra distortion, manifests a miscellaneous ligand field interaction between O 2p and V 3d orbitals and facilitates (i) a larger separation between the bonding and antibonding d‖ orbitals and (ii) an upward shift of the π* band in the band structure, leading to larger band gaps in the insulating SrVO3 thin films. Our spectroscopy results may open up new avenues for the mechanism of insulating/conducting character in other complicated perovskite materials using XANES-EXAFS.

  4. Ascorbic acid prolongs the viability and stability of isolated perfused lungs: A mechanistic study using 31P and hyperpolarized 13C nuclear magnetic resonance.

    Science.gov (United States)

    Shaghaghi, Hoora; Kadlecek, Stephen; Siddiqui, Sarmad; Pourfathi, Mehrdad; Hamedani, Hooman; Clapp, Justin; Profka, Harrilla; Rizi, Rahim

    2015-12-01

    Ex vivo lung perfusion (EVLP) has recently shown promise as a means of more accurately gauging the health of lung grafts and improving graft performance post-transplant. However, reperfusion of ischemic lung promotes the depletion of high-energy compounds and a progressive loss of normal mitochondrial function, and it remains unclear how and to what extent the EVLP approach contributes to this metabolic decline. Although ascorbate has been used to mitigate the effects of ischemia-reperfusion injury, the nature of its effects during EVLP are also not clear. To address these uncertainties, this study monitored the energy status of lungs during EVLP and after the administration of ascorbate using (31)P and hyperpolarized (13)C NMR (nuclear magnetic resonance). Our experiments demonstrated that the oxidative phosphorylation capacity and pyruvate dehydrogenase flux of lungs decline during ex vivo perfusion. The addition of ascorbate to the perfusate prolonged lung viability by 80% and increased the hyperpolarized (13)C bicarbonate signal by a factor of 2.7. The effect of ascorbate is apparently due not to its antioxidant quality but rather to its ability to energize cellular respiration given that it increased the lung's energy charge significantly, whereas other antioxidants (glutathione and α-lipoic acid) did not alter energy metabolism. During ascorbate administration, inhibition of mitochondrial complex I with rotenone depressed energy charge and shifted the metabolic state of the lung toward glycolysis; reenergizing the electron transport chain with TMPD (N,N,N',N'-tetramethyl-p-phenylenediamine) recovered metabolic activity. This indicates that ascorbate slows the decline of the ex vivo perfused lung's mitochondrial activity through an independent interaction with the electron transport chain complexes.

  5. A mechanistic model of ion-exchange chromatography on polymer fiber stationary phases.

    Science.gov (United States)

    Winderl, Johannes; Hahn, Tobias; Hubbuch, Jürgen

    2016-12-02

    Fibers are prominent among novel stationary phase supports for preparative chromatography. Several recent studies have highlighted the potential of fiber-based adsorbents for high productivity downstream processing in both batch and continuous mode, but so far the development of these materials and of processes employing these materials has solely been based on experimental data. In this study we assessed whether mechanistic modeling can be performed on fiber-based adsorbents. With a column randomly filled with short cut hydrogel grafted anion exchange fibers, we tested whether tracer, linear gradient elution, and breakthrough data could be reproduced by mechanistic models. Successful modeling was achieved for all of the considered experiments, for both non-retained and retained molecules. For the fibers used in this study the best results were obtained with a transport-dispersive model in combination with a steric mass action isotherm. This approach accurately accounted for the convection and dispersion of non-retained tracers, and the breakthrough and elution behaviors of three different proteins with sizes ranging from 6 to 160kDa were accurately modeled, with simulation results closely resembling the experimental data. The estimated model parameters were plausible both from their physical meaning, and from an analysis of the underlying model assumptions. Parameters were determined within good confidence levels; the average confidence estimate was below 7% for confidence levels of 95%. This shows that fiber-based adsorbents can be modeled mechanistically, which will be valuable for the future design and evaluation of these novel materials and for the development of processes employing such materials.

  6. Mechanistic studies of semicarbazone triapine targeting human ribonucleotide reductase in vitro and in mammalian cells: tyrosyl radical quenching not involving reactive oxygen species.

    Science.gov (United States)

    Aye, Yimon; Long, Marcus J C; Stubbe, JoAnne

    2012-10-12

    Triapine® (3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP)) is a drug in Phase II trials. One of its established cellular targets is the β(2) subunit of ribonucleotide reductase that requires a diferric-tyrosyl-radical [(Fe(III)(2)-Y·)(Fe(III)(2))] cofactor for de novo DNA biosynthesis. Several mechanisms for 3-AP inhibition of β(2) have been proposed; one involves direct iron chelation from β(2), whereas a second involves Y· destruction by reactive oxygen species formed in situ in the presence of O(2) and reductant by Fe(II)-(3-AP). Inactivation of β(2) can thus arise from cofactor destruction by loss of iron or Y·. In vitro kinetic data on the rates of (55)Fe and Y· loss from [((55)Fe(III)(2)-Y·)((55)Fe(III)(2))]-β(2) under aerobic and anaerobic conditions reveal that Y· loss alone is sufficient for rapid β(2) inactivation. Oxyblot(TM) and mass spectrometric analyses of trypsin-digested inhibited β(2), and lack of Y· loss from H(2)O(2) and O(2)(•) treatment together preclude reactive oxygen species involvement in Y· loss. Three mammalian cell lines treated with 5 μm 3-AP reveal Y· loss and β(2) inactivation within 30-min of 3-AP-exposure, analyzed by whole-cell EPR and lysate assays, respectively. Selective degradation of apo- over [(Fe(III)(2)-Y·)(Fe(III)(2))]-β(2) in lysates, similar iron-content in β(2) immunoprecipitated from 3-AP-treated and untreated [(55)Fe]-prelabeled cells, and prolonged (12 h) stability of the inhibited β(2) are most consistent with Y· loss being the predominant mode of inhibition, with β(2) remaining iron-loaded and stable. A model consistent with in vitro and cell-based biochemical studies is presented in which Fe(II)-(3-AP), which can be cycled with reductant, directly reduces Y· of the [(Fe(III)(2)-Y·)(Fe(III)(2))] cofactor of β(2).

  7. Mechanistic PBPK Modeling of the Dissolution and Food Effect of a BCS IV Compound - the Venetoclax Story.

    Science.gov (United States)

    Emami Riedmaier, Arian; Lindley, David J; Hall, Jeffrey A; Castleberry, Steven; Slade, Russell T; Stuart, Patricia; Carr, Robert A; Borchardt, Thomas B; Bow, Daniel A J; Nijsen, Marjoleen

    2017-10-06

    Venetoclax, a selective B-cell lymphoma-2 inhibitor, is a biopharmaceutics classification system (BCS) class IV compound. The aim of this study was to develop a physiologically-based pharmacokinetic (PBPK) model to mechanistically describe absorption and disposition of an amorphous solid dispersion (ASD) formulation of venetoclax in humans. A mechanistic PBPK model was developed incorporating measured amorphous solubility, dissolution, metabolism and plasma protein binding. A middle-out approach was used to define permeability. Model predictions of oral venetoclax pharmacokinetics were verified against clinical studies of fed and fasted healthy volunteers, and clinical drug interaction studies with strong CYP3A inhibitor (ketoconazole) and inducer (rifampicin). Model verification demonstrated accurate prediction of the observed food effect following a low-fat diet. Ratios of predicted versus observed Cmax and AUC of venetoclax were within 0.8- to 1.25-fold of observed ratios for strong CYP3A inhibitor and inducer interactions, indicating that the venetoclax elimination pathway was correctly specified. The verified venetoclax PBPK model is one of the first examples mechanistically capturing absorption, food effect and exposure of an ASD formulated compound. This model allows evaluation of untested drug-drug interactions, especially those primarily occurring in the intestine, and paves the way for future modeling of BCS IV compounds. Copyright © 2017. Published by Elsevier Inc.

  8. Home range analysis using a mechanistic home range model

    Energy Technology Data Exchange (ETDEWEB)

    Moorcroft, P.R. (Princeton Univ., NJ (United States). Dept. of Ecology and Evolutionary Biology); Lewis, M.A. (Univ. of Utah, Salt Lake City, UT (United States). Dept. of Mathematics) Crabtree, R.L. (Univ. of Idaho, Moscow, ID (United States). Dept. of Fish and Wildlife Resources)

    1999-07-01

    The traditional models used to characterize animal home ranges have no mechanistic basis underlying their descriptions of space use, and as a result, the analysis of animal home ranges has primarily been a descriptive endeavor. In this paper, the authors characterize coyote (Canis latrans) home range patterns using partial differential equations for expected space use that are formally derived from underlying descriptions of individual movement behavior. To the authors' knowledge, this is the first time that mechanistic models have been used to characterize animal home ranges. The results provide empirical support for a model formulation of movement response to scent marks, and suggest that having relocation data for individuals in adjacent groups is necessary to capture the spatial arrangement of home range boundaries. The authors then show how the model fits can be used to obtain predictions for individual movement and scent marking behavior and to predict changes in home range patterns. More generally, the findings illustrate how mechanistic models permit the development of a predictive theory for the relationship between movement behavior and animal spatial distribution.

  9. Mechanistic studies on a sequential PDT protocol

    Science.gov (United States)

    Kessel, David

    2016-03-01

    A low (~LD15) PDT dose resulting in selective lysosomal photodamage can markedly promote photokilling by subsequent photodamage targeted to mitochondria. Experimental data are consistent with the proposal that cleavage of the autophagyassociated protein ATG5 to a pro-apoptotic fragment is responsible for this effect. This process is known to be dependent on the proteolytic activity of calpain. We have proposed that Ca2+ released from photodamaged lysosomes is the trigger for ATG5 cleavage. We can now document the conversion of ATG5 to the truncated form after lysosomal photodamage. Photofrin, a photosensitizer that targets both mitochondria and lysosomes, can be used for either phase of the sequential PDT process. The ability of Photofrin to target both loci may explain the well-documented efficacy of this agent.

  10. MECHANISTIC STUDIES OF IMPROVED FOAM EOR PROCESSES

    Energy Technology Data Exchange (ETDEWEB)

    William R. Rossen

    2005-03-16

    The objective of this research is to widen the application of foam to enhanced oil recovery (EOR) by investigating fundamental mechanisms of foams in porous media. This research is to lay the groundwork for more-applied research on foams for improved sweep efficiency in miscible gas, steam and surfactant-based EOR. Task 1 investigates the pore-scale interactions between foam bubbles and polymer molecules. Task 2 examines the mechanisms of gas trapping, and interaction between gas trapping and foam effectiveness. Task 3 investigates mechanisms of foam generation in porous media.

  11. Electrocatalytic carbon dioxide reduction - a mechanistic study

    NARCIS (Netherlands)

    Schouten, Klaas Jan Schouten

    2013-01-01

    This thesis presents new insights into the reduction of carbon dioxide to methane and ethylene on copper electrodes. This electrochemical process has great potential for the storage of surplus renewable electrical energy in the form of hydrocarbons. The research described in this thesis focuses on t

  12. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-08-31

    An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values.

  13. Black tea polyphenols: a mechanistic treatise.

    Science.gov (United States)

    Butt, M S; Imran, A; Sharif, M K; Ahmad, Rabia Shabir; Xiao, Hang; Imran, M; Rsool, H A

    2014-01-01

    Dietary interventions are among the emerging trends to curtail physiological malfunctioning like cancer, diabetes, cardiac complications, etc. The essence of phytonutrients has developed the concept of nutraceuticals at the junction of diet health linkages. In this context, theaflavin & thearubigins are the oxidized derivatives of black tea catechins during fermentation having nutraceutical potential owing to esterification of hydroxyl ring with digallate esters. Theaflavin may influence activation of transcription factors such as NFnB or AP-1 that ultimately hinder the formation of nitric oxide expression gene. Likewise, black tea contains a unique amino acid theanine acts as neurotransmitter owing to its ability to cross the blood-brain barrier. Moreover, it boasts immunity by enhancing the disease-fighting ability of gamma delta T cells. Theaflavin & thearubigins act as safeguard against oxidative stress thereby effective in the cardiac functioning. The mechanistic approach of these antioxidants is likely to be associated with inhibition of redox sensitive transcription factors & pro-oxidant enzymes such as xanthine oxidase or nitric oxide synthase. However, their involvement in antioxidative enzyme induction as in glutathione-S-transferases is also well documented. They act as curative agent against numerous pathological disorders by disrupting the electron chain thus inhibiting the progression of certain ailments. Black tea polyphenols established themselves as strong antioxidants due to their standard one-electron potential, and their vitality is dependent on the concentration of polyphenols and pH for their inclusive execution. Present review is an attempt to enrich the readers regarding the health promoting aspects of black tea polyphenols. Concomitantly, it needs core attention of researchers for the exploitations of black tea flavanols as an important dietary constituent for the vulnerable segment.

  14. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    Science.gov (United States)

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  15. Testing mechanistic models of growth in insects.

    Science.gov (United States)

    Maino, James L; Kearney, Michael R

    2015-11-22

    Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compared against other mechanistic growth models. Unlike the other mechanistic models, our growth model predicts energy reserves per biomass to increase with age, which implies a higher production efficiency and energy density of biomass in later instars. These predictions are tested against data compiled from the literature whereby it is confirmed that insects increase their production efficiency (by 24 percentage points) and energy density (by 4 J mg(-1)) between hatching and the attainment of full size. The model suggests that insects achieve greater production efficiencies and enhanced growth rates by increasing specific assimilation and increasing energy reserves per biomass, which are less costly to maintain than structural biomass. Our findings illustrate how the explanatory and predictive power of mechanistic growth models comes from their grounding in underlying biological processes.

  16. A mechanistic study of TiO2 nanoparticle toxicity on Shewanella oneidensis MR-1 with UV-containing simulated solar irradiation: Bacterial growth, riboflavin secretion, and gene expression.

    Science.gov (United States)

    Qiu, Tian A; Meyer, Ben M; Christenson, Ky G; Klaper, Rebecca D; Haynes, Christy L

    2017-02-01

    Toxicity of nanomaterials to ecological systems has recently emerged as an important field of research, and thus, many researchers are exploring the mechanisms of how nanoparticles impact organisms. Herein, we probe the mechanisms of bacteria-nanoparticle interaction by investigating how TiO2 nanoparticles impact a model organism, the metal-reducing bacterium Shewanella oneidensis MR-1. In addition to examining the effect of TiO2 exposure, the effect of synergistic simulated solar irradiation containing UV was explored in this study, as TiO2 nanoparticles are known photocatalysts. The data reveal that TiO2 nanoparticles cause an inhibition of S. oneidensis growth at high dosage without compromising cell viability, yet co-exposure of nanoparticles and illumination does not increase the adverse effects on bacterial growth relative to TiO2 alone. Measurements of intracellular reactive oxygen species and riboflavin secretion, on the same nanoparticle-exposed bacteria, reveal that TiO2 nanoparticles have no effect on these cell functions, but application of UV-containing illumination with TiO2 nanoparticles has an impact on the level of riboflavin outside bacterial cells. Finally, gene expression studies were employed to explore how cells respond to TiO2 nanoparticles and illumination, and these results were correlated with cell growth and cell function assessment. Together these data suggest a minimal impact of TiO2 NPs and simulated solar irradiation containing UV on S. oneidensis MR-1, and the minimal impact could be accounted for by the nutrient-rich medium used in this work. These measurements demonstrate a comprehensive scheme combining various analytical tools to enable a mechanistic understanding of nanoparticle-cell interactions and to evaluate the potential adverse effects of nanoparticles beyond viability/growth considerations.

  17. Mechanistic aspects of carotenoid biosynthesis

    KAUST Repository

    Moïse, Alexander R.

    2014-01-08

    Carotenoid synthesis is based on the analysis of the phenotype of several mutant strains of tomato lacking carotenoid synthetic genes. Carotenoids are tetraterpenes derived through the condensation of the five-carbon (C5) universal isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). A recently developed concept that could explain the role of the poly-cis pathway in carotenoid synthesis is that the intermediates of this pathway have additional physiological roles that extend beyond serving as precursors of lycopene. This concept is based on the analysis of the phenotype of several mutant strains of tomato lacking carotenoid synthetic genes. The feedback regulation of early carotenoid synthetic genes in response to a block in upstream metabolism represents a paradigm shift in our understanding of the mechanism and regulation of carotenoid synthesis and of metabolic regulation in general. The molecular details of a signaling pathway that regulates carotenogenesis in response to the levels of carotenoid precursors are still unclear.

  18. CYCLIC VOLTAMMETRY AND REDUCTION MECHANISTIC ...

    African Journals Online (AJOL)

    Preferred Customer

    Kinetic studies on platinum electrodes based on the variation of the peak potential at ... present potential applications as fluorescent probes for metals detection, adsorption of iodide anions [7] and homogeneous photocatalysts for the degradation of organic pollutants, such as phenolic compounds [8, 9] and pesticides [10].

  19. Numerical simulation in steam injection wellbores by mechanistic approach; Simulacao numerica do escoamento de vapor em pocos por uma abordagem mecanicista

    Energy Technology Data Exchange (ETDEWEB)

    Souza Junior, J.C. de; Campos, W.; Lopes, D.; Moura, L.S.S. [PETROBRAS, Rio de Janeiro, RJ (Brazil); Thomas, A. Clecio F. [Universidade Estadual do Ceara (UECE), CE (Brazil)

    2008-07-01

    This work addresses to the development of a hydrodynamic and heat transfer mechanistic model for steam flow in injection wellbores. The problem of two-phase steam flow in wellbores has been solved recently by using available empirical correlations from petroleum industry (Lopes, 1986) and nuclear industry (Moura, 1991).The good performance achieved by mechanistic models developed by Ansari (1994), Hasan (1995), Gomez (2000) and Kaya (2001) supports the importance of the mechanistic approach for the steam flow problem in injection wellbores. In this study, the methodology to solve the problem consists in the application of a numerical method to the governing equations of steam flow and a marching algorithm to determine the distribution of the pressure and temperature along the wellbore. So, a computer code has been formulated to get numerical results, which provides a comparative study to the main models found in the literature. Finally, when compared to available field data, the mechanistic model for downward vertical steam flow in wellbores gave better results than the empirical correlations. (author)

  20. Longer Left Ventricular Electric Delay Reduces Mitral Regurgitation After Cardiac Resynchronization Therapy: Mechanistic Insights From the SMART-AV Study (SmartDelay Determined AV Optimization: A Comparison to Other AV Delay Methods Used in Cardiac Resynchronization Therapy).

    Science.gov (United States)

    Chatterjee, Neal A; Gold, Michael R; Waggoner, Alan D; Picard, Michael H; Stein, Kenneth M; Yu, Yinghong; Meyer, Timothy E; Wold, Nicholas; Ellenbogen, Kenneth A; Singh, Jagmeet P

    2016-11-01

    Mitral regurgitation (MR) is associated with worse survival in those undergoing cardiac resynchronization therapy (CRT). Left ventricular (LV) lead position in CRT may ameliorate mechanisms of MR. We examine the association between a longer LV electric delay (QLV) at the LV stimulation site and MR reduction after CRT. QLV was assessed retrospectively in 426 patients enrolled in the SMART-AV study (SmartDelay Determined AV Optimization: A Comparison to Other AV Delay Methods Used in CRT). QLV was defined as the time from QRS onset to the first large peak of the LV electrogram. Linear regression and logistic regression were used to assess the association between baseline QLV and MR reduction at 6 months (absolute change in vena contracta width and odds of ≥1 grade reduction in MR). At baseline, there was no difference in MR grade, LV dyssynchrony, or LV volumes in those with QLV above versus below the median (95 ms). After multivariable adjustment, increasing QLV was an independent predictor of MR reduction at 6 months as reflected by an increased odds of MR response (odds ratio: 1.13 [1.03-1.25]/10 ms increase QLV; P=0.02) and a decrease in vena contracta width (P<0.001). At 3 months, longer QLV (≥median) was associated with significant decrease in LV end-systolic volume (ΔLV end-systolic volume -28.2±38.9 versus -4.9±33.8 mL, P<0.001). Adjustment for 3-month ΔLV end-systolic volume attenuated the association between QLV and 6-month MR reduction. In patients undergoing CRT, longer QLV was an independent predictor of MR reduction at 6 months and associated with interval 3-month LV reverse remodeling. These findings provide a mechanistic basis for using an electric-targeting LV lead strategy at the time of CRT implant. © 2016 American Heart Association, Inc.

  1. New Mexico renewable development study

    Energy Technology Data Exchange (ETDEWEB)

    Toole, Gasper [Los Alamos National Laboratory; Bent, Russell [Los Alamos National Laboratory; Ewers, Mary [Los Alamos National Laboratory

    2010-09-17

    Since the early 1990s, Los Alamos National Laboratory (LANL) has applied electric grid models and simulation software to problems of national significance. This effort continues with a variety of other projects funded by the Department of Energy (DOE), other federal and state agencies and private companies. Critical to the success of these programs is the ability to integrate regional-scale models of the electric grid, to assess the propagation of grid impacts, and to present interactively the effect of potential mitigating actions required to stabilize the grid. All of these capabilities are applied in this study, to accomplish the following goals and objectives: (1) Develop an AC power flow model representing future conditions within New Mexico's electric grid, using commercial tools accepted by the utility industry; (2) Conduct a 'screening' analysis of options for accelerating potential renewable energy development through the addition of a statewide transmission collector system; (3) Estimate total revenue needed, jobs created (temporary and permanent) plus indirect and direct impacts to the state's economy; (4) Evaluate potential cost allocation methodology; and (5) Issue a project report that will provide information for policy direction by state regulators, project developers, and legislators.

  2. Mechanistic determinants of MBNL activity

    Science.gov (United States)

    Sznajder, Łukasz J.; Michalak, Michał; Taylor, Katarzyna; Cywoniuk, Piotr; Kabza, Michał; Wojtkowiak-Szlachcic, Agnieszka; Matłoka, Magdalena; Konieczny, Patryk; Sobczak, Krzysztof

    2016-01-01

    Muscleblind-like (MBNL) proteins are critical RNA processing factors in development. MBNL activity is disrupted in the neuromuscular disease myotonic dystrophy type 1 (DM1), due to the instability of a non-coding microsatellite in the DMPK gene and the expression of CUG expansion (CUGexp) RNAs. Pathogenic interactions between MBNL and CUGexp RNA lead to the formation of nuclear complexes termed foci and prevent MBNL function in pre-mRNA processing. The existence of multiple MBNL genes, as well as multiple protein isoforms, raises the question of whether different MBNL proteins possess unique or redundant functions. To address this question, we coexpressed three MBNL paralogs in cells at equivalent levels and characterized both specific and redundant roles of these proteins in alternative splicing and RNA foci dynamics. When coexpressed in the same cells, MBNL1, MBNL2 and MBNL3 bind the same RNA motifs with different affinities. While MBNL1 demonstrated the highest splicing activity, MBNL3 showed the lowest. When forming RNA foci, MBNL1 is the most mobile paralog, while MBNL3 is rather static and the most densely packed on CUGexp RNA. Therefore, our results demonstrate that MBNL paralogs and gene-specific isoforms possess inherent functional differences, an outcome that could be enlisted to improve therapeutic strategies for DM1. PMID:27733504

  3. Mechanistic fracture criteria for the failure of human cortical bone

    Energy Technology Data Exchange (ETDEWEB)

    Nalla, Ravi K.; Kinney, John H.; Ritchie, Robert O.

    2002-12-13

    A mechanistic understanding of fracture in human bone is critical to predicting fracture risk associated with age and disease. Despite extensive work, a mechanistic framework for describing how the underlying microstructure affects the failure mode in bone is lacking.

  4. Precision and accuracy of mechanistic-empirical pavement design

    CSIR Research Space (South Africa)

    Theyse, HL

    2006-09-01

    Full Text Available The availability of mechanistic-empirical pavement design methods is increasing internationally. Although mechanistic-empirical design does offer some insight into pavement behaviour and performance, at least more so than empirical design methods...

  5. Mechanistic species distribution modeling reveals a niche shift during invasion.

    Science.gov (United States)

    Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

    2017-06-01

    Niche shifts of nonnative plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by reanalyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially invaded ranges of individual populations. Northern-origin populations that were established outside the generally accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially invaded range northward and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual

  6. STS Case Study Development Support

    Science.gov (United States)

    Rosa de Jesus, Dan A.; Johnson, Grace K.

    2013-01-01

    The Shuttle Case Study Collection (SCSC) has been developed using lessons learned documented by NASA engineers, analysts, and contractors. The SCSC provides educators with a new tool to teach real-world engineering processes with the goal of providing unique educational materials that enhance critical thinking, decision-making and problem-solving skills. During this third phase of the project, responsibilities included: the revision of the Hyper Text Markup Language (HTML) source code to ensure all pages follow World Wide Web Consortium (W3C) standards, and the addition and edition of website content, including text, documents, and images. Basic HTML knowledge was required, as was basic knowledge of photo editing software, and training to learn how to use NASA's Content Management System for website design. The outcome of this project was its release to the public.

  7. Simulating the Risk of Liver Fluke Infection using a Mechanistic Hydro-epidemiological Model

    Science.gov (United States)

    Beltrame, Ludovica; Dunne, Toby; Rose, Hannah; Walker, Josephine; Morgan, Eric; Vickerman, Peter; Wagener, Thorsten

    2016-04-01

    Liver Fluke (Fasciola hepatica) is a common parasite found in livestock and responsible for considerable economic losses throughout the world. Risk of infection is strongly influenced by climatic and hydrological conditions, which characterise the host environment for parasite development and transmission. Despite on-going control efforts, increases in fluke outbreaks have been reported in recent years in the UK, and have been often attributed to climate change. Currently used fluke risk models are based on empirical relationships derived between historical climate and incidence data. However, hydro-climate conditions are becoming increasingly non-stationary due to climate change and direct anthropogenic impacts such as land use change, making empirical models unsuitable for simulating future risk. In this study we introduce a mechanistic hydro-epidemiological model for Liver Fluke, which explicitly simulates habitat suitability for disease development in space and time, representing the parasite life cycle in connection with key environmental conditions. The model is used to assess patterns of Liver Fluke risk for two catchments in the UK under current and potential future climate conditions. Comparisons are made with a widely used empirical model employing different datasets, including data from regional veterinary laboratories. Results suggest that mechanistic models can achieve adequate predictive ability and support adaptive fluke control strategies under climate change scenarios.

  8. Tear gas: an epidemiological and mechanistic reassessment

    OpenAIRE

    Rothenberg, Craig; Achanta, Satyanarayana; Svendsen, Erik R.; Jordt, Sven‐Eric

    2016-01-01

    Deployments of tear gas and pepper spray have rapidly increased worldwide. Large amounts of tear gas have been used in densely populated cities, including Cairo, Istanbul, Rio de Janeiro, Manama (Bahrain), and Hong Kong. In the United States, tear gas was used extensively during recent riots in Ferguson, Missouri. Whereas tear gas deployment systems have rapidly improved—with aerial drone systems tested and requested by law enforcement—epidemiological and mechanistic research have lagged behi...

  9. Testing mechanistic models of growth in insects

    OpenAIRE

    Maino, James L.; Kearney, Michael R.

    2015-01-01

    Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compare...

  10. Mechanistic basis for overcoming platinum resistance using copper chelating agents.

    Science.gov (United States)

    Liang, Zheng D; Long, Yan; Tsai, Wen-Bin; Fu, Siqing; Kurzrock, Razelle; Gagea-Iurascu, Mihai; Zhang, Fan; Chen, Helen H W; Hennessy, Bryan T; Mills, Gordon B; Savaraj, Niramol; Kuo, Macus Tien

    2012-11-01

    Platinum-based antitumor agents are widely used in cancer chemotherapy. Drug resistance is a major obstacle to the successful use of these agents because once drug resistance develops, other effective treatment options are limited. Recently, we conducted a clinical trial using a copper-lowering agent to overcome platinum drug resistance in ovarian cancer patients and the preliminary results are encouraging. In supporting this clinical study, using three pairs of cisplatin (cDDP)-resistant cell lines and two ovarian cancer cell lines derived from patients who had failed in platinum-based chemotherapy, we showed that cDDP resistance associated with reduced expression of the high-affinity copper transporter (hCtr1), which is also a cDDP transporter, can be preferentially resensitized by copper-lowering agents because of enhanced hCtr1 expression, as compared with their drug-sensitive counterparts. Such a preferential induction of hCtr1 expression in cDDP-resistant variants by copper chelation can be explained by the mammalian copper homeostasis regulatory mechanism. Enhanced cell-killing efficacy by a copper-lowering agent was also observed in animal xenografts bearing cDDP-resistant cells. Finally, by analyzing a public gene expression dataset, we found that ovarian cancer patients with elevated levels of hCtr1 in their tumors, but not ATP7A and ATP7B, had more favorable outcomes after platinum drug treatment than those expressing low hCtr1 levels. This study reveals the mechanistic basis for using copper chelation to overcome cDDP resistance in clinical investigations.

  11. Student Development and Developmental Studies.

    Science.gov (United States)

    Champaigne, John

    1982-01-01

    Reviews the nine-stage Perry Scheme of Intellectual and Ethical Development, detailing three major student orientations--dualism, multiplicity, and commitments in relativism. Suggests techniques developmental educators can use to communicate with, support, and challenge students to promote intellectual development. Underscores the importance of…

  12. Induced polarization dependence on pore space geometry: Empirical observations and mechanistic predictions

    Science.gov (United States)

    Weller, A.; Slater, L. D.

    2015-12-01

    We use an extensive database to compare empirical observations and previously proposed empirical models against recently developed mechanistic formulations for the induced polarization (IP) response in porous media as a function of pore space geometry and interfacial chemistry. These comparisons support the argument that the pore-volume normalized internal surface (Spor) is the most important geometric parameter influencing the polarization. The specific polarizability derived from the empirical relationship between imaginary conductivity σ″ and Spor is independent of the porosity. By contrast, equivalent specific polarizability terms in recently proposed mechanistic models are found to be significantly correlated with porosity, and thus do not appear to represent an interfacial chemistry factor independent of the pore space geometry. Furthermore, the database shows no evidence for a significant decrease in the counterion mobility of clayey materials relative to clay-free materials, as postulated in recent studies. On the contrary, a single value of cp is consistent with no significant differences in ionic mobility given that all samples were saturated with a NaCl solution close to a common salinity of about 100 mS/m.

  13. Theories in Social Policy and Development Studies

    DEFF Research Database (Denmark)

    Schmidt, Johannes Dragsbæk

    Theories in Social Policy and Development Studies Presentation for the PhD Seminar - Theories, Concepts and Methods in Development Studies and Sociology......Theories in Social Policy and Development Studies Presentation for the PhD Seminar - Theories, Concepts and Methods in Development Studies and Sociology...

  14. Splicing in immune cells-mechanistic insights and emerging topics.

    Science.gov (United States)

    Schaub, Annalisa; Glasmacher, Elke

    2017-04-01

    Differential splicing of mRNAs not only enables regulation of gene expression levels, but also ensures a high degree of gene-product diversity. The extent to which splicing of mRNAs is utilized as a mechanism in immune cells has become evident within the last few years. Still, only a few of these mechanisms have been well studied. In this review, we discuss some of the best-understood mechanisms, for instance the differential splicing of CD45 in T cells, as well as immunoglobulin genes in B cells. Beyond that we provide general mechanistic insights on how, when and where this process takes place and discuss the current knowledge regarding these topics in immune cells. We also highlight some of the reported links to immune-related diseases, genome-wide sequencing studies that revealed thousands of differentially spliced transcripts, as well as splicing studies on immune cells that remain mechanistically not fully understood. We thereby display potential emerging topics for future studies centered on splicing mechanisms in immune cells. © The Author 2017. Published by Oxford University Press on behalf of The Japanese Society for Immunology.

  15. Shevchenko Study: "Eternal" Development Prospects

    Directory of Open Access Journals (Sweden)

    Varenikova Olena

    2016-09-01

    Full Text Available The article describes the definitions of some Ukrainian researchers in the field of Shevchenko study during the 1st third of XX – the beginning of XXI centuries, concerning the unlimited subject of studies, analyses some social-scientific correlation that contributes to the phenomenon of "always new Shevchenko study".

  16. Language Development in Social Studies.

    Science.gov (United States)

    Nelson, Lloyd; Phillips, Rick

    1987-01-01

    Describes a program in a tenth-grade geography class for helping students who speak English as a second language develop better writing skills. Specifically examines the use of English as a second language (ESC) teaching techniques to accomplish this task. (RKM)

  17. Noncanonical IFN Signaling: Mechanistic Linkage of Genetic and Epigenetic Events

    Directory of Open Access Journals (Sweden)

    Howard M. Johnson

    2016-01-01

    Full Text Available The canonical model of cytokine signaling via the JAK/STAT pathway dominates our view of signal transduction but provides no insight into the significance of the simultaneous presence of activated JAKs and STATs in the nucleus of cells treated with cytokines. Such a mechanistic shortcoming challenges the usefulness of the model in its present form. Focusing on the interferon (IFN cytokines, we have developed a noncanonical model of IFN signaling that naturally connects activated JAKs and STATs at or near response elements of genes that are activated by the IFNs. Specifically, cells treated with IFNγ showed association of activated STAT1α and JAK2 at the GAS element of genes activated by IFNγ. For IFNα treated cells, the association involved activated STAT1α and TYK2 JAK kinase at the ISRE promoter. The power of the noncanonical model is that it provides mechanistic insight into specific gene activation at the level of the associated epigenetics, akin to that of steroid/steroid receptor signaling.

  18. The Mechanistic Approach to Psychiatric Classification

    Directory of Open Access Journals (Sweden)

    Elisabetta Sirgiovanni

    2009-01-01

    Full Text Available A Kuhnian reformulation of the recent debate in psychiatric nosography suggested that the current psychiatric classification system (the DSM is in crisis and that a sort of paradigm shift is awaited (Aragona, 2009. Among possible revolutionary alternatives, the proposed fi ve-axes etiopathogenetic taxonomy (Charney et al., 2002 emphasizes the primacy of the genotype over the phenomenological level as the relevant basis for psychiatric nosography. Such a position is along the lines of the micro-reductionist perspective of E. Kandel (1998, 1999, which sees mental disorders reducible to explanations at a fundamental epistemic level of genes and neurotransmitters. This form of micro-reductionism has been criticized as a form of genetic-molecular fundamentalism (e.g. Murphy, 2006 and a multi-level approach, in the form of the burgeoning Cognitive Neuropsychiatry, was proposed. This article focuses on multi-level mechanistic explanations, coming from Cognitive Science, as a possible alternative etiopathogenetic basis for psychiatric classification. The idea of a mechanistic approach to psychiatric taxonomy is here defended on the basis of a better conception of levels and causality. Nevertheless some critical remarks of Mechanism as a psychiatric general view are also offered.

  19. Surgery for malignant gliomas: mechanistic reasoning and slippery statistics.

    Science.gov (United States)

    Mitchell, Patrick; Ellison, David W; Mendelow, A David

    2005-07-01

    Current surgical treatment of malignant gliomas largely depends on mechanistic reasoning and data collected in non-randomised studies. Technological advance has enabled more accurate resection of tumours and preservation of eloquent brain areas but ethical considerations have restricted randomised trials on the efficacy of surgery to one small trial that found a 3 month survival advantage for patients over age 65 years who received surgery and interim analysis of a larger trial. There is an argument for surgery as a palliative measure in patients with symptoms caused by mechanisms that are surgically remediable. Whether there is any survival advantage from surgery in patients other than those with immediately life-threatening, surgically remediable complications, such as raised intracranial pressure, is unclear. The available data show that if such an advantage does exist, it is modest at best. Adjuvant treatments given surgically are being studied. Chemotherapy wafers are the most prominent of the adjuvant treatments but the evidence available is insufficient to recommend their use in routine practice. In this review we examine the prevailing mechanistic model and observational data; we assess how these are applied and the priorities they indicate for future research.

  20. Mechanistic Multidimensional Modeling of Forced Convection Boiling Heat Transfer

    Directory of Open Access Journals (Sweden)

    Michael Z. Podowski

    2009-01-01

    Full Text Available Due to the importance of boiling heat transfer in general, and boiling crisis in particular, for the analysis of operation and safety of both nuclear reactors and conventional thermal power systems, extensive efforts have been made in the past to develop a variety of methods and tools to evaluate the boiling heat transfer coefficient and to assess the onset of temperature excursion and critical heat flux (CHF at various operating conditions of boiling channels. The objective of this paper is to present mathematical modeling concepts behind the development of mechanistic multidimensional models of low-quality forced convection boiling, including the mechanisms leading to temperature excursion and the onset of CHF.

  1. Measurement, geospatial, and mechanistic models of public health hazard vulnerability and jurisdictional risk.

    Science.gov (United States)

    Testa, Marcia A; Pettigrew, Mary L; Savoia, Elena

    2014-01-01

    County and state health departments are increasingly conducting hazard vulnerability and jurisdictional risk (HVJR) assessments for public health emergency preparedness and mitigation planning and evaluation to improve the public health disaster response; however, integration and adoption of these assessments into practice are still relatively rare. While the quantitative methods associated with complex analytic and measurement methods, causal inference, and decision theory are common in public health research, they have not been widely used in public health preparedness and mitigation planning. To address this gap, the Harvard School of Public Health PERLC's goal was to develop measurement, geospatial, and mechanistic models to aid public health practitioners in understanding the complexity of HVJR assessment and to determine the feasibility of using these methods for dynamic and predictive HVJR analyses. We used systematic reviews, causal inference theory, structural equation modeling (SEM), and multivariate statistical methods to develop the conceptual and mechanistic HVJR models. Geospatial mapping was used to inform the hypothetical mechanistic model by visually examining the variability and patterns associated with county-level demographic, social, economic, hazards, and resource data. A simulation algorithm was developed for testing the feasibility of using SEM estimation. The conceptual model identified the predictive latent variables used in public health HVJR tools (hazard, vulnerability, and resilience), the outcomes (human, physical, and economic losses), and the corresponding measurement subcomponents. This model was translated into a hypothetical mechanistic model to explore and evaluate causal and measurement pathways. To test the feasibility of SEM estimation, the mechanistic model path diagram was translated into linear equations and solved simultaneously using simulated data representing 192 counties. Measurement, geospatial, and mechanistic

  2. Causation at Different Levels: Tracking the Commitments of Mechanistic Explanations

    DEFF Research Database (Denmark)

    Fazekas, Peter; Kertész, Gergely

    2011-01-01

    This paper tracks the commitments of mechanistic explanations focusing on the relation between activities at different levels. It is pointed out that the mechanistic approach is inherently committed to identifying causal connections at higher levels with causal connections at lower levels. For th...... their autonomy at the same time than standard reductive accounts are, and that what mechanistic explanations are able to do at best is showing that downward causation does not exist....

  3. Mechanistic and Economical Characteristics of Asphalt Rubber Mixtures

    Directory of Open Access Journals (Sweden)

    Mena I. Souliman

    2016-01-01

    Full Text Available Load associated fatigue cracking is one of the major distress types occurring in flexible pavement systems. Flexural bending beam fatigue laboratory test has been used for several decades and is considered to be an integral part of the new superpave advanced characterization procedure. One of the most significant solutions to prolong the fatigue life for an asphaltic mixture is to utilize flexible materials as rubber. A laboratory testing program was performed on a conventional and Asphalt Rubber- (AR- gap-graded mixtures to investigate the impact of added rubber on the mechanical, mechanistic, and economical attributes of asphaltic mixtures. Strain controlled fatigue tests were conducted according to American Association of State Highway and Transportation Officials (AASHTO procedures. The results from the beam fatigue tests indicated that the AR-gap-graded mixtures would have much longer fatigue life compared with the reference (conventional mixtures. In addition, a mechanistic analysis using 3D-Move software coupled with a cost analysis study based on the fatigue performance on the two mixtures was performed. Overall, analysis showed that AR modified asphalt mixtures exhibited significantly lower cost of pavement per 1000 cycles of fatigue life per mile compared to conventional HMA mixture.

  4. Structure determines medication errors in nursing units: a mechanistic approach.

    Science.gov (United States)

    Hung, Chang-Chiao; Lee, Bih-O; Tsai, Shu-Ling; Tseng, Yun Shan; Chang, Chia-Hao

    2015-03-01

    Medication errors have long been considered critical in global health care systems. However, few studies have been conducted to explore the effects of nursing unit structure on medication errors. The purpose of this study, therefore, was to determine the effects of structural factors on medication errors in nursing units. A total of 977 staff nurses and 62 head nurses participated in this cross-sectional design study. The findings show that professional autonomy (β = .53, t = 6.03, p nursing experts (β = .52, t = 5.99, p medication error rates. This study shows that the structural factors influence medication administration and the mechanistic approach is specifically in relation of low medication error rates. The author suggests that head nurses should consider strategies that require adjustments to unit control mechanisms.

  5. Reaction Coordinates and Mechanistic Hypothesis Tests.

    Science.gov (United States)

    Peters, Baron

    2016-05-27

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.

  6. Reaction Coordinates and Mechanistic Hypothesis Tests

    Science.gov (United States)

    Peters, Baron

    2016-05-01

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.

  7. Mechanistic issues in asparagine synthetase catalysis.

    Science.gov (United States)

    Richards, N G; Schuster, S M

    1998-01-01

    The enzymatic synthesis of asparagine is an ATP-dependent process that utilizes the nitrogen atom derived from either glutamine or ammonia. Despite a long history of kinetic and mechanistic investigation, there is no universally accepted catalytic mechanism for this seemingly straightforward carboxyl group activating enzyme, especially as regards those steps immediately preceding amide bond formation. This chapter considers four issues dealing with the mechanism: (a) the structural organization of the active site(s) partaking in glutamine utilization and aspartate activation; (b) the relationship of asparagine synthetase to other amidotransferases; (c) the way in which ATP is used to activate the beta-carboxyl group; and (d) the detailed mechanism by which nitrogen is transferred.

  8. Fetal programming of CVD and renal disease: animal models and mechanistic considerations.

    Science.gov (United States)

    Langley-Evans, Simon C

    2013-08-01

    The developmental origins of health and disease hypothesis postulates that exposure to a less than optimal maternal environment during fetal development programmes physiological function, and determines risk of disease in adult life. Much evidence of such programming comes from retrospective epidemiological cohorts, which demonstrate associations between birth anthropometry and non-communicable diseases of adulthood. The assertion that variation in maternal nutrition drives these associations is supported by studies using animal models, which demonstrate that maternal under- or over-nutrition during pregnancy can programme offspring development. Typically, the offspring of animals that are undernourished in pregnancy exhibit a relatively narrow range of physiological phenotypes that includes higher blood pressure, glucose intolerance, renal insufficiency and increased adiposity. The observation that common phenotypes arise from very diverse maternal nutritional insults has led to the proposal that programming is driven by a small number of mechanistic processes. The remodelling of tissues during development as a consequence of maternal nutritional status being signalled by endocrine imbalance or key nutrients limiting processes in the fetus may lead to organs having irreversibly altered structures that may limit their function with ageing. It has been proposed that the maternal diet may impact upon epigenetic marks that determine gene expression in fetal tissues, and this may be an important mechanism connecting maternal nutrient intakes to long-term programming of offspring phenotype. The objective for this review is to provide an overview of the mechanistic basis of fetal programming, demonstrating the critical role of animal models as tools for the investigation of programming phenomena.

  9. Mechanistic Aspects in the Formation, Growth and Surface Functionalization of Metal Oxide Nanoparticles in Organic Solvents.

    Science.gov (United States)

    Niederberger, Markus; Deshmukh, Rupali

    2017-04-04

    The synthesis of metal oxide nanoparticles in organic solvents, so-called nonaqueous (or nonhydrolytic) processes represent powerful alternatives to aqueous approaches and have become an independent research field. 10 years ago, when we published our first review on organic reaction pathways in nonaqueous sol-gel approaches,[1] the number of examples was relatively limited. Nowadays, it is almost impossible to provide an exhaustive overview. Here we review the development of the last few years, without neglecting pioneering examples, which help to follow the historical development. The importance of a profound understanding of mechanistic aspects of nanoparticle crystallization and formation mechanisms can't be overestimated, when it comes to the design of rational synthesis concepts under minimization of trial-and-error experiments. The main reason for the progress in mechanistic understanding lies in the availability of characterization tools that make it possible to monitor chemical reactions from the dissolution of the precursor to the nucleation and growth of the nanoparticles, by ex-situ methods involving sampling after different reaction times, but more and more also by in-situ studies. After a short introduction to experimental aspects of nonaqueous sol-gel routes to metal oxide nanoparticles, we provide an overview of the main and basic organic reaction pathways in these approaches. Afterwards, we summarize the main characterization methods to study formation mechanisms, and then we discuss in great depth the chemical formation mechanisms of many different types of metal oxide nanoparticles. The review concludes with a paragraph on selected crystallization mechanisms reported for nonaqueous systems and a few illustrative examples of nonaqueous sol-gel concepts applied to surface chemistry.

  10. Slow component of VO2 kinetics: Mechanistic bases and practical applications

    DEFF Research Database (Denmark)

    Jones, Andrew M; Grassi, Bruno; Christensen, Peter Møller

    2011-01-01

    state of knowledge concerning the mechanistic bases of the V¿O2 slow component and describes practical interventions which can attenuate the slow componentand thus enhance exercise tolerance. There is strong evidence that, during CWR exercise, the development of the V¿O2 slow component is associated...

  11. Students' Interpretations of Mechanistic Language in Organic Chemistry before Learning Reactions

    Science.gov (United States)

    Galloway, Kelli R.; Stoyanovich, Carlee; Flynn, Alison B.

    2017-01-01

    Research on mechanistic thinking in organic chemistry has shown that students attribute little meaning to the electron-pushing (i.e., curved arrow) formalism. At the University of Ottawa, a new curriculum has been developed in which students are taught the electron-pushing formalism prior to instruction on specific reactions--this formalism is…

  12. Permanent deformation testing for a new South African mechanistic pavement design method

    CSIR Research Space (South Africa)

    Anochie-Boateng, Joseph

    2012-01-01

    Full Text Available The South Africa National Road Agency Limited together with the CSIR are undertaking a research and development project to support the revision of the South African mechanistic-empirical pavement design method. An important part of this project...

  13. [Relationships between climate change and rice development and its yield formation: a simulation study].

    Science.gov (United States)

    Liu, Taoju; Yin, Xinyou; Qi, Changhan; Tang, Jianjun; Chen, Meiqiu

    2005-03-01

    With the application of mechanistic model (RICAM 1.3, RIce growth Calendar Model), this paper simulated the rice development and its yield formation under different climatic conditions at multi-locations of Asia. A three-stage Beta model (3s-Beta) was developed to predict the flowering stage of rice and to describe its three successive phases of photo-thermal response, i.e., basic vegetative phase, photoperiod-sensitive phase, and post photoperiod-sensitive phase. The 1980-1989 multi-location data of Morioka (Japan, 39 degrees 43'N), Nanchang (China, 28 degrees 36'N) and Los Banos (Philippines, 14 degrees 11'N) were used to verify the suitability of the model in studying ecosystem change. Comparisons of simulated results with observed data showed that this model could generally predict the eco-physiological processes of rice, and performed very well over a wide range of environments.

  14. Mechanistic modelling of the drying behaviour of single pharmaceutical granules

    DEFF Research Database (Denmark)

    Thérèse F.C. Mortier, Séverine; Beer, Thomas De; Gernaey, Krist

    2012-01-01

    The trend to move towards continuous production processes in pharmaceutical applications enhances the necessity to develop mechanistic models to understand and control these processes. This work focuses on the drying behaviour of a single wet granule before tabletting, using a six...... of b on the drying behaviour. Experimental data with the six-segmented fluidised bed dryer were collected to calibrate b. An exponential dependence on the drying air temperature was found. Independent experiments were done for the validation of the drying model.......-segmented fluidised bed drying system, which is part of a fully continuous from-powder-to-tablet manufacturing line. The drying model is based on a model described by Mezhericher et al. [1] and consists of two submodels. In the first drying phase (submodel 1), the surface water evaporates, while in the second drying...

  15. Applying math onto mechanisms: mechanistic knowledge is associated with the use of formal mathematical strategies.

    Science.gov (United States)

    Liu, Allison S; Schunn, Christian D

    2017-01-01

    It is notoriously difficult for people to adaptively apply formal mathematical strategies learned in school to real-world contexts, even when they possess the required mathematical skills. The current study explores whether a problem context's mechanism can act as an "embodied analogy" onto which abstract mathematical concepts can be applied, leading to more frequent use of formal mathematical strategies. Participants were asked to program a robot to navigate a maze and to create a navigation strategy that would work for differently sized robots. We compared the strategy complexity of participants with high levels of mechanistic knowledge about the robot against participants with low levels of mechanistic knowledge about the robot. Mechanistic knowledge was significantly associated with the frequency and complexity of the mathematical strategies used by participants, suggesting that learning to recognize a problem context's mechanism may promote independent mathematical problem solving in applied contexts.

  16. Ghana Journal of Development Studies: Editorial Policies

    African Journals Online (AJOL)

    Ghana Journal of Development Studies (GJDS) is a multi-, trans- and an ... on critical research and analysis of development issues with emphasis on, ... Lobnibe is an Associate Professor of Anthropology at Western Oregon University, USA.

  17. Toward a mechanistic understanding of human-induced rapid environmental change: A case study linking energy development, avian nest predation, and predators

    Science.gov (United States)

    Hethcoat, Matthew G.; Chalfoun, Anna D.

    2015-01-01

    Demographic consequences of human-induced rapid environmental change (HIREC) have been widely documented for many populations. The mechanisms underlying such patterns, however, are rarely investigated and yet are critical to understand for effective conservation and management.

  18. Aegle marmelos (L.) Corr. impedes onset of Insulin resistance syndrome in rats provided with drinking fructose from weaning to adulthood stages of development: A mechanistic study.

    Science.gov (United States)

    Mathur, Rajani; Sehgal, Ratika; Rajora, Preeti; Sharma, Shveta; Kumar, Rajesh; Mathur, Sandeep

    2016-12-17

    To explore the effect of aqueous extract of leaves of Aegle marmelos (AM) on hepatic carbohydrate metabolism and insulin downstream signalling in rats provided with drinking fructose (15%) from weaning to adulthood. Wistar albino rats (4week) were randomly divided into Normal Control (NC), Fructose Control (FC) and treatment (AMT) groups and provided over 8 weeks, chow + water, chow + fructose (15%) and chow + fructose (15%) + AM (500 mg/kg/d, p.o.), respectively. Significantly (pInsulin Resistance Syndrome (IRS) is delineated here, along with the potential of Aegle marmelos in impeding the same.

  19. Mechanistic curiosity will not kill the Bayesian cat

    NARCIS (Netherlands)

    Borsboom, Denny; Wagenmakers, Eric-Jan; Romeijn, Jan-Willem

    2011-01-01

    Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer spe

  20. Toward a mechanistic modeling of nitrogen limitation for photosynthesis

    Science.gov (United States)

    Xu, C.; Fisher, R. A.; Travis, B. J.; Wilson, C. J.; McDowell, N. G.

    2011-12-01

    The nitrogen limitation is an important regulator for vegetation growth and global carbon cycle. Most current ecosystem process models simulate nitrogen effects on photosynthesis based on a prescribed relationship between leaf nitrogen and photosynthesis; however, there is a large amount of variability in this relationship with different light, temperature, nitrogen availability and CO2 conditions, which can affect the reliability of photosynthesis prediction under future climate conditions. To account for the variability in nitrogen-photosynthesis relationship under different environmental conditions, in this study, we developed a mechanistic model of nitrogen limitation for photosynthesis based on nitrogen trade-offs among light absorption, electron transport, carboxylization and carbon sink. Our model shows that strategies of nitrogen storage allocation as determined by tradeoff among growth and persistence is a key factor contributing to the variability in relationship between leaf nitrogen and photosynthesis. Nitrogen fertilization substantially increases the proportion of nitrogen in storage for coniferous trees but much less for deciduous trees, suggesting that coniferous trees allocate more nitrogen toward persistence compared to deciduous trees. The CO2 fertilization will cause lower nitrogen allocation for carboxylization but higher nitrogen allocation for storage, which leads to a weaker relationship between leaf nitrogen and maximum photosynthesis rate. Lower radiation will cause higher nitrogen allocation for light absorption and electron transport but less nitrogen allocation for carboxylyzation and storage, which also leads to weaker relationship between leaf nitrogen and maximum photosynthesis rate. At the same time, lower growing temperature will cause higher nitrogen allocation for carboxylyzation but lower allocation for light absorption, electron transport and storage, which leads to a stronger relationship between leaf nitrogen and maximum

  1. Conservative or reactive? Mechanistic chemical perspectives on organic matter stability

    Science.gov (United States)

    Koch, Boris

    2016-04-01

    Carbon fixation by terrestrial and marine primary production has a fundamental seasonal effect on the atmospheric carbon content and it profoundly contributes to long-term carbon storage in form of organic matter (OM) in soils, water, and sediments. The efficacy of this sequestration process strongly depends on the degree of OM persistence. Therefore, one of the key issues in dissolved and particulate OM research is to assess the stability of reservoirs and to quantify their contribution to global carbon fluxes. Incubation experiments are helpful to assess OM stability during the first, early diagenetic turnover induced by sunlight or microbes. However, net carbon fluxes within the global carbon cycle also act on much longer time scales, which are not amenable in experiments. It is therefore critical to improve our mechanistic understanding to be able to assess potential future changes in the organic matter cycle. This session contribution highlights some achievements and open questions in the field. An improved mechanistic understanding of OM turnover particularly depends on the molecular characterization of biogeochemical processes and their kinetics: (i) in soils and sediments, aggregation/disaggregation of OM is primarily controlled by its molecular composition. Hence, the chemical composition determines the transfer of organic carbon from the large particulate to the small dissolved organic matter reservoir - an important substrate for microbial metabolism. (ii) In estuaries, dissolved organic carbon gradients usually suggest conservative behavior, whereas molecular-level studies reveal a substantial chemical modification of terrestrial DOM along the land-ocean interface. (iii) In the ocean, previous studies have shown that the recalcitrance of OM depends on bulk concentration and energy yield. However, ultrahigh resolution mass spectrometry in combination with radiocarbon analyses also emphasized that stability is tightly connected to molecular composition

  2. Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

    Directory of Open Access Journals (Sweden)

    Regina Berg

    2013-12-01

    Full Text Available The copper-catalyzed azide–alkyne cycloaddition (CuAAC is one of the most broadly applicable and easy-to-handle reactions in the arsenal of organic chemistry. However, the mechanistic understanding of this reaction has lagged behind the plethora of its applications for a long time. As reagent mixtures of copper salts and additives are commonly used in CuAAC reactions, the structure of the catalytically active species itself has remained subject to speculation, which can be attributed to the multifaceted aggregation chemistry of copper(I alkyne and acetylide complexes. Following an introductory section on common catalyst systems in CuAAC reactions, this review will highlight experimental and computational studies from early proposals to very recent and more sophisticated investigations, which deliver more detailed insights into the CuAAC’s catalytic cycle and the species involved. As diverging mechanistic views are presented in articles, books and online resources, we intend to present the research efforts in this field during the past decade and finally give an up-to-date picture of the currently accepted dinuclear mechanism of CuAAC. Additionally, we hope to inspire research efforts on the development of molecularly defined copper(I catalysts with defined structural characteristics, whose main advantage in contrast to the regularly used precatalyst reagent mixtures is twofold: on the one hand, the characteristics of molecularly defined, well soluble catalysts can be tuned according to the particular requirements of the experiment; on the other hand, the understanding of the CuAAC reaction mechanism can be further advanced by kinetic studies and the isolation and characterization of key intermediates.

  3. Parameter and uncertainty estimation for mechanistic, spatially explicit epidemiological models

    Science.gov (United States)

    Finger, Flavio; Schaefli, Bettina; Bertuzzo, Enrico; Mari, Lorenzo; Rinaldo, Andrea

    2014-05-01

    Epidemiological models can be a crucially important tool for decision-making during disease outbreaks. The range of possible applications spans from real-time forecasting and allocation of health-care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. Our spatially explicit, mechanistic models for cholera epidemics have been successfully applied to several epidemics including, the one that struck Haiti in late 2010 and is still ongoing. Calibration and parameter estimation of such models represents a major challenge because of properties unusual in traditional geoscientific domains such as hydrology. Firstly, the epidemiological data available might be subject to high uncertainties due to error-prone diagnosis as well as manual (and possibly incomplete) data collection. Secondly, long-term time-series of epidemiological data are often unavailable. Finally, the spatially explicit character of the models requires the comparison of several time-series of model outputs with their real-world counterparts, which calls for an appropriate weighting scheme. It follows that the usual assumption of a homoscedastic Gaussian error distribution, used in combination with classical calibration techniques based on Markov chain Monte Carlo algorithms, is likely to be violated, whereas the construction of an appropriate formal likelihood function seems close to impossible. Alternative calibration methods, which allow for accurate estimation of total model uncertainty, particularly regarding the envisaged use of the models for decision-making, are thus needed. Here we present the most recent developments regarding methods for parameter and uncertainty estimation to be used with our mechanistic, spatially explicit models for cholera epidemics, based on informal measures of goodness of fit.

  4. A new mechanistic framework to predict OCS fluxes in soils

    Science.gov (United States)

    Sauze, Joana; Ogee, Jérôme; Launois, Thomas; Kesselmeier, Jürgen; Van Diest, Heidi; Wingate, Lisa

    2015-04-01

    A better description of the amplitude of photosynthetic and respiratory gross CO2 fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulfide (COS) is the most abundant sulphur gas in the atmosphere and has been proposed as a new tracer of gross photosynthesis, as the uptake of COS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. However, soils also exchange COS with the atmosphere and there is growing evidence that this flux must also be accounted for in atmospheric budgets. In this context a new mechanistic description of soil-atmosphere COS exchange is clearly needed. Soils can take up COS from the atmosphere as the soil biota also contain CA, and COS emissions from soils have also been reported in agricultural fields or anoxic soils. Previous studies have also shown that soil COS fluxes present an optimum soil water content and soil temperature. Here we propose a new mechanistic framework to predict the fluxes of COS between the soils and the atmosphere. We describe the COS soil budget by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of COS by CA is total and irreversible. To describe COS diffusion through the soil matrix, we use different formulations of soil air-filled pore space and temperature, depending on the turbulence level above the soil surface. Using this model we are able to explain the observed presence of an optimum temperature for soil COS uptake and show how this optimum can shift to cooler temperatures in the presence of soil COS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature (e.g. Van Diest & Kesselmeier, 2008) as a result of diffusional constraints on COS hydrolysis. These diffusional constraints are also responsible for the response of COS uptake to soil

  5. Mechanistic failure mode investigation and resolution of parvovirus retentive filters.

    Science.gov (United States)

    LaCasse, Daniel; Lute, Scott; Fiadeiro, Marcus; Basha, Jonida; Stork, Matthew; Brorson, Kurt; Godavarti, Ranga; Gallo, Chris

    2016-07-01

    Virus retentive filters are a key product safety measure for biopharmaceuticals. A simplistic perception is that they function solely based on a size-based particle removal mechanism of mechanical sieving and retention of particles based on their hydrodynamic size. Recent observations have revealed a more nuanced picture, indicating that changes in viral particle retention can result from process pressure and/or flow interruptions. In this study, a mechanistic investigation was performed to help identify a potential mechanism leading to the reported reduced particle retention in small virus filters. Permeate flow rate or permeate driving force were varied and analyzed for their impact on particle retention in three commercially available small virus retentive filters. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:959-970, 2016.

  6. Automaticity: Componential, Causal, and Mechanistic Explanations.

    Science.gov (United States)

    Moors, Agnes

    2016-01-01

    The review first discusses componential explanations of automaticity, which specify non/automaticity features (e.g., un/controlled, un/conscious, non/efficient, fast/slow) and their interrelations. Reframing these features as factors that influence processes (e.g., goals, attention, and time) broadens the range of factors that can be considered (e.g., adding stimulus intensity and representational quality). The evidence reviewed challenges the view of a perfect coherence among goals, attention, and consciousness, and supports the alternative view that (a) these and other factors influence the quality of representations in an additive way (e.g., little time can be compensated by extra attention or extra stimulus intensity) and that (b) a first threshold of this quality is required for unconscious processing and a second threshold for conscious processing. The review closes with a discussion of causal explanations of automaticity, which specify factors involved in automatization such as repetition and complexity, and a discussion of mechanistic explanations, which specify the low-level processes underlying automatization.

  7. Semiconductor photocatalysis--mechanistic and synthetic aspects.

    Science.gov (United States)

    Kisch, Horst

    2013-01-14

    Preceding work on photoelectrochemistry at semiconductor single-crystal electrodes has formed the basis for the tremendous growth in the three last decades in the field of photocatalysis at semiconductor powders. The reason for this is the unique ability of inorganic semiconductor surfaces to photocatalyze concerted reduction and oxidation reactions of a large variety of electron-donor and -acceptor substrates. Whereas great attention was paid to water splitting and the exhaustive aerobic degradation of pollutants, only a small amount of research also explored synthetic aspects. After introducing the basic mechanistic principles, standard experiments for the preparation and characterization of visible light active photocatalysts as well as the investigation of reaction mechanisms are discussed. Novel atom-economic C-C and C-N coupling reactions illustrate the relevance of semiconductor photocatalysis for organic synthesis, and demonstrate that the multidisciplinary field combines classical photochemistry with electrochemistry, solid-state chemistry, and heterogeneous catalysis. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Journal of Development and Communication Studies

    African Journals Online (AJOL)

    The Journal of Development and Communications Studies (JDCS), published online and in print by Development Media Consulting, is a biannual academic, peer ... of social development in Malawi and Africa, foremost, and the world, second. ... Adoption of nutrition and environment-related technologies by women: Case of ...

  9. Rh-Catalyzed Decarbonylation of Conjugated Ynones via Carbon–Alkyne Bond Activation: Reaction Scope and Mechanistic Exploration via DFT Calculations

    Science.gov (United States)

    Dermenci, Alpay; Whittaker, Rachel E.; Gao, Yang; Cruz, Faben A.; Yu, Zhi-Xiang; Dong, Guangbin

    2015-01-01

    In this full article, detailed development of a catalytic decarbonylation of conjugated monoynones to synthesize disubstituted alkynes is described. The reaction scope and limitation has been thoroughly investigated, and a broad range of functional groups including heterocycles were compatible under the catalytic conditions. Mechanistic exploration via DFT calculations has also been executed. Through the computational study, a proposed catalytic mechanism has been carefully evaluated. These efforts are expected to serve as an important exploratory study for developing catalytic alkyne-transfer reactions via carbon−alkyne bond activation. PMID:26229587

  10. New Simulation Methods to Facilitate Achieving a Mechanistic Understanding of Basic Pharmacology Principles in the Classroom

    Science.gov (United States)

    Grover, Anita; Lam, Tai Ning; Hunt, C. Anthony

    2008-01-01

    We present a simulation tool to aid the study of basic pharmacology principles. By taking advantage of the properties of agent-based modeling, the tool facilitates taking a mechanistic approach to learning basic concepts, in contrast to the traditional empirical methods. Pharmacodynamics is a particular aspect of pharmacology that can benefit from…

  11. Evaluation of a mechanistic lactation model using cow, goat and sheep data

    NARCIS (Netherlands)

    Dijkstra, J.; Lopez, S.; Bannink, A.; Dhanoa, M.S.; Kebreab, E.; Odongo, N.E.; Fathi Nasri, M.H.; Behera, U.K.; Hernandez-Ferrer, D.; France, J.

    2010-01-01

    A mechanistic lactation model, based on a theory of mammary cell proliferation and cell death, was studied and compared to the equation of Wood (1967). Lactation curves of British Holstein Friesian cows (176 curves), Spanish Churra sheep (40 curves) and Spanish Murciano–Granadina goats (30 curves)

  12. Evaluation of a mechanistic lactation model using cow, goat and sheep data

    NARCIS (Netherlands)

    Dijkstra, J.; Lopez, S.; Bannink, A.; Dhanoa, M.S.; Kebreab, E.; Odongo, N.E.; Fathi Nasri, M.H.; Behera, U.K.; Hernandez-Ferrer, D.; France, J.

    2010-01-01

    A mechanistic lactation model, based on a theory of mammary cell proliferation and cell death, was studied and compared to the equation of Wood (1967). Lactation curves of British Holstein Friesian cows (176 curves), Spanish Churra sheep (40 curves) and Spanish Murciano–Granadina goats (30 curves) w

  13. Mechanistic, mathematical model to predict the dynamics of tissue genesis in bone defects via mechanical feedback and mediation of biochemical factors.

    Directory of Open Access Journals (Sweden)

    Shannon R Moore

    2014-06-01

    Full Text Available The link between mechanics and biology in the generation and the adaptation of bone has been well studied in context of skeletal development and fracture healing. Yet, the prediction of tissue genesis within - and the spatiotemporal healing of - postnatal defects, necessitates a quantitative evaluation of mechano-biological interactions using experimental and clinical parameters. To address this current gap in knowledge, this study aims to develop a mechanistic mathematical model of tissue genesis using bone morphogenetic protein (BMP to represent of a class of factors that may coordinate bone healing. Specifically, we developed a mechanistic, mathematical model to predict the dynamics of tissue genesis by periosteal progenitor cells within a long bone defect surrounded by periosteum and stabilized via an intramedullary nail. The emergent material properties and mechanical environment associated with nascent tissue genesis influence the strain stimulus sensed by progenitor cells within the periosteum. Using a mechanical finite element model, periosteal surface strains are predicted as a function of emergent, nascent tissue properties. Strains are then input to a mechanistic mathematical model, where mechanical regulation of BMP-2 production mediates rates of cellular proliferation, differentiation and tissue production, to predict healing outcomes. A parametric approach enables the spatial and temporal prediction of endochondral tissue regeneration, assessed as areas of cartilage and mineralized bone, as functions of radial distance from the periosteum and time. Comparing model results to histological outcomes from two previous studies of periosteum-mediated bone regeneration in a common ovine model, it was shown that mechanistic models incorporating mechanical feedback successfully predict patterns (spatial and trends (temporal of bone tissue regeneration. The novel model framework presented here integrates a mechanistic feedback system based

  14. Rational Design of Transcranial Current Stimulation (TCS through Mechanistic Insights into Cortical Network Dynamics

    Directory of Open Access Journals (Sweden)

    Flavio eFrohlich

    2013-11-01

    Full Text Available Transcranial current stimulation (TCS is a promising method of non-invasive brain stimulation to modulate cortical network dynamics. Preliminary studies have demonstrated the ability of TCS to enhance cognition and reduce symptoms in both neurological and psychiatric illnesses. Despite the encouraging results of these studies, the mechanisms by which TCS and endogenous network dynamics interact remain poorly understood. Here, we propose that the development of the next generation of TCS paradigms with increased efficacy requires such mechanistic understanding of how weak electric fields imposed by TCS interact with the nonlinear dynamics of large-scale cortical networks. We highlight key recent advances in the study of the interaction dynamics between TCS and cortical network activity. In particular, we demonstrate the opportunities provided by an interdisciplinary approach that bridges neurobiology and electrical engineering. We discuss the use of (1 hybrid biological-electronic experimental approaches to disentangle feedback interactions, (2 large-scale computer simulations for the study of weak global perturbations imposed by TCS, and (3 optogenetic manipulations informed by dynamics systems theory to probe network dynamics. Together, we here provide the foundation for the use of rational design for the development of the next generation of TCS neurotherapeutics.

  15. Journal of Development and Communication Studies: Editorial ...

    African Journals Online (AJOL)

    “Ideally, [research findings] must be published locally [because] it has been shown that ... Centre for Governance and Diplomatic Studies, Catholic University of Malawi, ... Design and Rural Development, University of Guelph, Guelph, Canada.

  16. DEVELOPMENT AND STUDY OF ANTIMYCOTIC MEDICATION

    Directory of Open Access Journals (Sweden)

    Lokarev A. V.

    2016-09-01

    Full Text Available The article presents the results of development and study of antimycotic gel, containing herbal composition of the medicinal plants extracts. The drug's high fungicidal activity and thixotropic properties are shown

  17. Modelling soil-plant-atmosphere interactions by coupling the regional weather model WRF to mechanistic plant models

    Science.gov (United States)

    Klein, C.; Hoffmann, P.; Priesack, E.

    2012-04-01

    Climate change causes altering distributions of meteorological factors influencing plant growth and its interactions between the land surface and the atmosphere. Recent studies show, that uncertainties in regional and global climate simulations are also caused by lacking descriptions of the soil-plant-atmosphere system. Therefore, we couple a mechanistic soil-plant model to a regional climate and forecast model. The detailed simulation of the water and energy exchanges, especially the transpiration of grassland and forests stands, are the key features of the modelling framework. The Weather Research and Forecasting model (WRF) (Skamarock 2008) is an open source mesoscale numerical weather prediction model. The WRF model was modified in a way, to either choose its native, static land surface model NOAH or the mechanistic eco-system model Expert-N 5.0 individually for every single grid point within the simulation domain. The Expert-N 5.0 modelling framework provides a highly modular structure, enabling the development and use of a large variety of different plant and soil models, including heat transfer, nitrogen uptake/turnover/transport as well as water uptake/transport and crop management. To represent the key landuse types grassland and forest, we selected two mechanistic plant models: The Hurley Pasture model (Thornley 1998) and a modified TREEDYN3 forest simulation model (Bossel 1996). The models simulate plant growth, water, nitrogen and carbon flows for grassland and forest stands. A mosaic approach enables Expert-N to use high resolution land use data e.g. CORINE Land Cover data (CLC, 2006) for the simulation, making it possible to simulate different land use distributions within a single grid cell. The coupling results are analyzed for plausibility and compared with the results of the default land surface model