reaction pathways leading: Topics by WorldWideScience.org

Sample records for reaction pathways leading

A mechanistic study on the reaction pathways leading to benzene and naphthalene in cellulose vapor phase cracking

International Nuclear Information System (INIS)

Norinaga, Koyo; Yang, Huamei; Tanaka, Ryota; Appari, Srinivas; Iwanaga, Keita; Takashima, Yuka; Kudo, Shinji; Shoji, Tetsuya; Hayashi, Jun-ichiro

2014-01-01

The reaction pathways leading to aromatic hydrocarbons such as benzene and naphthalene in gas-phase reactions of multi-component mixtures derived from cellulose fast pyrolysis were studied both experimentally and numerically. A two-stage tubular reactor was used for evaluating the reaction kinetics of secondary vapor phase cracking of the nascent pyrolysates at temperature ranging from 400 to 900 °C, residence time from 0.2 to 4.3 s, and at 241 kPa. The products of alkyne and diene were identified from the primary pyrolysis of cellulose even at low temperature range 500–600 °C. These products include acetylene, propyne, propadiene, vinylacetylene, and cyclopentadiene. Experiments were also numerically validated by a detailed chemical kinetic model consisting of more than 8000 elementary step-like reactions with over 500 chemical species. Acceptable capabilities of the kinetic model in predicting concentration profiles of the products enabled us to assess reaction pathways leading to benzene and naphthalene via the alkyne and diene from primary pyrolysates of cellulose. C 3 alkyne and diene are primary precursors of benzene at 650 °C, while combination of ethylene and vinylacetylene produces benzene dominantly at 850 °C. Cyclopentadiene is a prominent precursor of naphthalene. Combination of acetylene with propyne or allyl radical leads to the formation of cyclopentadiene. Furan and acrolein are likely important alkyne precursors in cellulose pyrolysis at low temperature, whereas dehydrogenations of olefins are major route to alkyne at high temperatures. - Highlights: • Analytical pyrolysis experiments provided data for kinetic modeling. • Detailed chemical kinetic model was used and evaluated. • Alkyne and diene were important intermediates for aromatic hydrocarbon formation. • Reaction pathways leading to aromatic hydrocarbons were proposed
Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

International Nuclear Information System (INIS)

Wang Sufan; Smith, Sean C.

2006-01-01

The 'leading coordinate' approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information
Minimum Energy Pathways for Chemical Reactions

Science.gov (United States)

Walch, S. P.; Langhoff, S. R. (Technical Monitor)

1995-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.
Kynurenine pathway metabolites and enzymes involved in redox reactions.

Science.gov (United States)

González Esquivel, D; Ramírez-Ortega, D; Pineda, B; Castro, N; Ríos, C; Pérez de la Cruz, V

2017-01-01

Oxido-reduction reactions are a fundamental part of the life due to support many vital biological processes as cellular respiration and glucose oxidation. In the redox reactions, one substance transfers one or more electrons to another substance. An important electron carrier is the coenzyme NAD + , which is involved in many metabolic pathways. De novo biosynthesis of NAD + is through the kynurenine pathway, the major route of tryptophan catabolism, which is sensitive to redox environment and produces metabolites with redox capacity, able to alter biological functions that are controlled by redox-responsive signaling pathways. Kynurenine pathway metabolites have been implicated in the physiology process and in the physiopathology of many diseases; processes that also share others factors as dysregulation of calcium homeostasis, mitochondrial dysfunction, oxidative stress, inflammation and cell death, which impact the redox environment. This review examines in detail the available evidence in which kynurenine pathway metabolites participate in redox reactions and their effect on cellular redox homeostasis, since the knowledge of the main factors and mechanisms that lead to cell death in many neurodegenative disorders and other pathologies, such as mitochondrial dysfunction, oxidative stress and kynurenines imbalance, will allow to develop therapies using them as targets. This article is part of the Special Issue entitled 'The Kynurenine Pathway in Health and Disease'. Copyright Â© 2016 Elsevier Ltd. All rights reserved.
Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

Science.gov (United States)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.
Reactivity of Single-Walled Carbon Nanotubes in the Diels-Alder Cycloaddition Reaction: Distortion-Interaction Analysis along the Reaction Pathway.

Science.gov (United States)

Li, Yingzi; Osuna, Sílvia; Garcia-Borràs, Marc; Qi, Xiaotian; Liu, Song; Houk, Kendall N; Lan, Yu

2016-08-26

Diels-Alder cycloaddition is one of the most powerful tools for the functionalization of single-walled carbon nanotubes (SWCNTs). Density functional theory at the B3-LYP level of theory has been used to investigate the reactivity of different-diameter SWCNTs (4-9,5) in Diels-Alder reactions with 1,3-butadiene; the reactivity was found to decrease with increasing SWCNT diameter. Distortion/interaction analysis along the whole reaction pathway was found to be a better way to explore the reactivity of this type of reaction. The difference in interaction energy along the reaction pathway is larger than that of the corresponding distortion energy. However, the distortion energy plots for these reactions show the same trend. Therefore, the formation of the transition state can be determined from the interaction energy. A lower interaction energy leads to an earlier transition state, which indicates a lower activation energy. The computational results also indicate that the original distortion of the SWCNTs leads to an increase in the reactivity of the SWCNTs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

Directory of Open Access Journals (Sweden)

Yiran Huang

Full Text Available Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.
Pathways of the Maillard reaction under physiological conditions.

Science.gov (United States)

Henning, Christian; Glomb, Marcus A

2016-08-01

Initially investigated as a color formation process in thermally treated foods, nowadays, the relevance of the Maillard reaction in vivo is generally accepted. Many chronic and age-related diseases such as diabetes, uremia, atherosclerosis, cataractogenesis and Alzheimer's disease are associated with Maillard derived advanced glycation endproducts (AGEs) and α-dicarbonyl compounds as their most important precursors in terms of reactivity and abundance. However, the situation in vivo is very challenging, because Maillard chemistry is paralleled by enzymatic reactions which can lead to both, increases and decreases in certain AGEs. In addition, mechanistic findings established under the harsh conditions of food processing might not be valid under physiological conditions. The present review critically discusses the relevant α-dicarbonyl compounds as central intermediates of AGE formation in vivo with a special focus on fragmentation pathways leading to formation of amide-AGEs.
Combustion kinetics and reaction pathways

Energy Technology Data Exchange (ETDEWEB)

Klemm, R.B.; Sutherland, J.W. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01

This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.
Permanganate oxidation of α-amino acids: kinetic correlations for the nonautocatalytic and autocatalytic reaction pathways.

Science.gov (United States)

Perez-Benito, Joaquin F

2011-09-08

The reactions of permanganate ion with seven α-amino acids in aqueous KH(2)PO(4)/K(2)HPO(4) buffers have been followed spectrophotometrically at two different wavelengths: 526 nm (decay of MnO(4)(-)) and 418 nm (formation of colloidal MnO(2)). All of the reactions studied were autocatalyzed by colloidal MnO(2), with the contribution of the autocatalytic reaction pathway decreasing in the order glycine > l-threonine > l-alanine > l-glutamic acid > l-leucine > l-isoleucine > l-valine. The rate constants corresponding to the nonautocatalytic and autocatalytic pathways were obtained by means of either a differential rate law or an integrated one, the latter requiring the use of an iterative method for its implementation. The activation parameters for the two pathways were determined and analyzed to obtain statistically significant correlations for the series of reactions studied. The activation enthalpy of the nonautocatalytic pathway showed a strong, positive dependence on the standard Gibbs energy for the dissociation of the protonated amino group of the α-amino acid. Linear enthalpy-entropy correlations were found for both pathways, leading to isokinetic temperatures of 370 ± 21 K (nonautocatalytic) and 364 ± 28 K (autocatalytic). Mechanisms in agreement with the experimental data are proposed for the two reaction pathways.
Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

Science.gov (United States)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.
Explorations into Chemical Reactions and Biochemical Pathways.

Science.gov (United States)

Gasteiger, Johann

2016-12-01

A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

Science.gov (United States)

Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2016-02-01

Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.
DMPD: Multiple signaling pathways leading to the activation of interferon regulatoryfactor 3. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 12213596 Multiple signaling pathways leading to the activation of interferon regula...(.html) (.csml) Show Multiple signaling pathways leading to the activation of interferon regulatoryfactor 3.... PubmedID 12213596 Title Multiple signaling pathways leading to the activation of
A multi-pathway model for photosynthetic reaction center

International Nuclear Information System (INIS)

Qin, M.; Shen, H. Z.; Yi, X. X.

2016-01-01

Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments.
Identifying Reaction Pathways and their Environments

DEFF Research Database (Denmark)

Maronsson, Jon Bergmann

Finding the mechanisms and estimating the rate of chemical reactions is an essential part of modern research of atomic scale systems. In this thesis, the application of well established methods for reaction rates and paths to important systems for hydrogen storage is considered before developing...... extensions to further identify the reaction environment for a more accurate rate. Complex borohydrides are materials of high hydrogen storage capacity and high thermodynamic stability (too high for hydrogen storage). In an effort to gain insight into the structural transitions of two such materials, Ca(BH4......-interstitial defects. In good agreement with the experiments, C3-type rotations activate at lower temperature than C2-type rotations. In order to investigate the environment of reaction pathways, a method for finding the ridge between first order saddle points on a multidimensional surface was developed...
Serpentinization reaction pathways: implications for modeling approach

Energy Technology Data Exchange (ETDEWEB)

Janecky, D.R.

1986-01-01

Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.
Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP.

Science.gov (United States)

Alvarado, Omar; Jaña, Gonzalo; Delgado, Eduardo J

2012-08-01

In this study the formation of the lactyl-thiamin diphosphate intermediate (L-ThDP) is addressed using density functional theory calculations at X3LYP/6-31++G(d,p) level of theory. The study includes potential energy surface scans, transition state search, and intrinsic reaction coordinate calculations. Reactivity is analyzed in terms of Fukui functions. The results allow to conclude that the reaction leading to the formation of L-ThDP occurs via a concerted mechanism, and during the nucleophilic attack on the pyruvate molecule, the ylide is in its AP form. The calculated activation barrier for the reaction is 19.2 kcal/mol, in agreement with the experimental reported value.
Reaction-transport simulations of non-oxidative methane conversion with continuous hydrogen removal: Homogeneous-heterogeneous methane reaction pathways

International Nuclear Information System (INIS)

Li, Lin; Borry, Richard W.; Iglesia, Enrique

2000-01-01

Detailed kinetic-transport models were used to explore thermodynamic and kinetic barriers in the non-oxidative conversion of CH4 via homogeneous and homogeneous-heterogeneous pathways and the effects of continuous hydrogen removal and of catalytic sites on attainable yields of useful C2-C10 products. The homogeneous kinetic model combines separately developed models for low-conversion pyrolysis and for chain growth to form large aromatics and carbon. The H2 formed in the reaction decreases CH4 pyrolysis rates and equilibrium conversions and it favors the formation of lighter products. The removal of H2 along tubular reactors with permeable walls increases reaction rates and equilibrium CH4 conversions. C2-C10 yields reach values greater than 90 percent at intermediate values of dimensionless transport rates (delta=1-10), defined as the ratio hydrogen transport and methane conversion rates. Homogeneous reactions require impractical residence times, even with H2 removal, because of slow initiation and chain transfer rates. The introduction of heterogeneous chain initiation pathways using surface sites that form methyl radicals eliminates the induction period without influencing the homogeneous product distribution. Methane conversion, however, occurs predominately in the chain transfer regime, within which individual transfer steps and the formation of C2 intermediates become limited by thermodynamic constraints. Catalytic sites alone cannot overcome these constraints. Catalytic membrane reactors with continuous H2 removal remove these thermodynamic obstacles and decrease the required residence time. Reaction rates become limited by homogeneous reactions of C2 products to form C6+ aromatics. Higher delta values lead to subsequent conversion of the desired C2-C10 products to larger polynuclear aromatics. We conclude that catalytic methane pyrolysis at the low temperatures required for restricted chain growth and the elimination of thermodynamics constraints via
Multistage reaction pathways in detonating high explosives

International Nuclear Information System (INIS)

Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya

2014-01-01

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N 2 and H 2 O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N 2 and H 2 O productions

Multistage reaction pathways in detonating high explosives

Energy Technology Data Exchange (ETDEWEB)

Li, Ying [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States)

2014-11-17

Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N{sub 2} and H{sub 2}O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N{sub 2} and H{sub 2}O productions.
Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

Energy Technology Data Exchange (ETDEWEB)

Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

2013-09-15

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.
Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

International Nuclear Information System (INIS)

Ovacik, Meric A.; Androulakis, Ioannis P.

2013-01-01

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy
Stepwise radical cation Diels-Alder reaction via multiple pathways.

Science.gov (United States)

Shimizu, Ryo; Okada, Yohei; Chiba, Kazuhiro

2018-01-01

Herein we disclose the radical cation Diels-Alder reaction of aryl vinyl ethers by electrocatalysis, which is triggered by an oxidative SET process. The reaction clearly proceeds in a stepwise fashion, which is a rare mechanism in this class. We also found that two distinctive pathways, including "direct" and "indirect", are possible to construct the Diels-Alder adduct.
Soil is an important pathway of human lead exposure.

OpenAIRE

Mielke, H W; Reagan, P L

1998-01-01

This review shows the equal or greater importance of leaded gasoline-contaminated dust compared to lead-based paint to the child lead problem, and that soil lead, resulting from leaded gasoline and pulverized lead-based paint, is at least or more important than lead-based paint (intact and not pulverized) as a pathway of human lead exposure. Because lead-based paint is a high-dose source, the biologically relevant dosage is similar to lead in soil. Both lead-based paint and soil lead are asso...
MAPK pathway activation by chronic lead-exposure increases vascular reactivity through oxidative stress/cyclooxygenase-2-dependent pathways

Energy Technology Data Exchange (ETDEWEB)

Simões, Maylla Ronacher, E-mail: yllars@hotmail.com [Dept. of Physiological Sciences, Federal University of Espirito Santo, Vitória, ES CEP 29040-091 (Brazil); Department of Pharmacology, Universidad Autonoma de Madrid, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid (Spain); Aguado, Andrea [Department of Pharmacology, Universidad Autonoma de Madrid, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid (Spain); Fiorim, Jonaína; Silveira, Edna Aparecida; Azevedo, Bruna Fernandes; Toscano, Cindy Medice [Dept. of Physiological Sciences, Federal University of Espirito Santo, Vitória, ES CEP 29040-091 (Brazil); Zhenyukh, Olha; Briones, Ana María [Department of Pharmacology, Universidad Autonoma de Madrid, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid (Spain); Alonso, María Jesús [Dept. of Biochemistry, Physiology and Molecular Genetics, Universidad Rey Juan Carlos, Alcorcón (Spain); Vassallo, Dalton Valentim [Dept. of Physiological Sciences, Federal University of Espirito Santo, Vitória, ES CEP 29040-091 (Brazil); Health Science Center of Vitória-EMESCAM, Vitória, ES CEP 29045-402 (Brazil); Salaices, Mercedes, E-mail: mercedes.salaices@uam.es [Department of Pharmacology, Universidad Autonoma de Madrid, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid (Spain)

2015-03-01

Chronic exposure to low lead concentration produces hypertension; however, the underlying mechanisms remain unclear. We analyzed the role of oxidative stress, cyclooxygenase-2-dependent pathways and MAPK in the vascular alterations induced by chronic lead exposure. Aortas from lead-treated Wistar rats (1st dose: 10 μg/100 g; subsequent doses: 0.125 μg/100 g, intramuscular, 30 days) and cultured aortic vascular smooth muscle cells (VSMCs) from Sprague Dawley rats stimulated with lead (20 μg/dL) were used. Lead blood levels of treated rats attained 21.7 ± 2.38 μg/dL. Lead exposure increased systolic blood pressure and aortic ring contractile response to phenylephrine, reduced acetylcholine-induced relaxation and did not affect sodium nitroprusside relaxation. Endothelium removal and L-NAME left-shifted the response to phenylephrine more in untreated than in lead-treated rats. Apocynin and indomethacin decreased more the response to phenylephrine in treated than in untreated rats. Aortic protein expression of gp91(phox), Cu/Zn-SOD, Mn-SOD and COX-2 increased after lead exposure. In cultured VSMCs lead 1) increased superoxide anion production, NADPH oxidase activity and gene and/or protein levels of NOX-1, NOX-4, Mn-SOD, EC-SOD and COX-2 and 2) activated ERK1/2 and p38 MAPK. Both antioxidants and COX-2 inhibitors normalized superoxide anion production, NADPH oxidase activity and mRNA levels of NOX-1, NOX-4 and COX-2. Blockade of the ERK1/2 and p38 signaling pathways abolished lead-induced NOX-1, NOX-4 and COX-2 expression. Results show that lead activation of the MAPK signaling pathways activates inflammatory proteins such as NADPH oxidase and COX-2, suggesting a reciprocal interplay and contribution to vascular dysfunction as an underlying mechanisms for lead-induced hypertension. - Highlights: • Lead-exposure increases oxidative stress, COX-2 expression and vascular reactivity. • Lead exposure activates MAPK signaling pathway. • ROS and COX-2 activation by
Drug metabolism by cytochrome p450 enzymes: what distinguishes the pathways leading to substrate hydroxylation over desaturation?

Science.gov (United States)

Ji, Li; Faponle, Abayomi S; Quesne, Matthew G; Sainna, Mala A; Zhang, Jing; Franke, Alicja; Kumar, Devesh; van Eldik, Rudi; Liu, Weiping; de Visser, Sam P

2015-06-15

Cytochrome P450 enzymes are highly versatile biological catalysts in our body that react with a broad range of substrates. Key functions in the liver include the metabolism of drugs and xenobiotics. One particular metabolic pathway that is poorly understood relates to the P450 activation of aliphatic groups leading to either hydroxylation or desaturation pathways. A DFT and QM/MM study has been carried out on the factors that determine the regioselectivity of aliphatic hydroxylation over desaturation of compounds by P450 isozymes. The calculations establish multistate reactivity patterns, whereby the product distributions differ on each of the spin-state surfaces; hence spin-selective product formation was found. The electronic and thermochemical factors that determine the bifurcation pathways were analysed and a model that predicts the regioselectivity of aliphatic hydroxylation over desaturation pathways was established from valence bond and molecular orbital theories. Thus, the difference in energy of the OH versus the OC bond formed and the π-conjugation energy determines the degree of desaturation products. In addition, environmental effects of the substrate binding pocket that affect the regioselectivities were identified. These studies imply that bioengineering P450 isozymes for desaturation reactions will have to include modifications in the substrate binding pocket to restrict the hydroxylation rebound reaction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
The role of grain boundaries and transient porosity increase as fluid pathways for reaction front propagation

Science.gov (United States)

Jonas, Laura; John, Timm; Geisler, Thorsten; Putnis, Andrew

2013-04-01

The pseudomorphic replacement of Carrara marble by calcium phosphates was studied as a model system to examine the influence of different fluid pathways for reaction front propagation induced by fluid-rock interaction. In this model system, the grain boundaries present in the rock and the transient porosity structures developing throughout the replacement reaction enable the reaction front to progress further into the rock as well as to the center of each single grain until complete transformation. Hydrothermal treatment of the marble using phosphate bearing solutions at temperature levels of 150° C and 200° C for different durations lead to the formation of two product phases which were identified as hydroxyapatite [Ca5(PO4)3OH] as well as β-tricalcium phosphate [β-Ca3(PO4)2] (β-TCP). The formation of β-TCP was probably favored by the presence of ~0.6wt.% of Mg in the parent phase. Completely transformed single grains show a distinctive zoning, both in composition and texture. Whereas areas next to the grain boundary consist of nearly pure hydroxyapatite and show a coarse porosity, areas close to the center of the single grains show a high amount of β-TCP and a very fine porous microstructure. If F was added as an additional solution component, the formation of β-TCP was avoided and up to 3wt.% of F were incorporated into the product apatite. The use of the isotope 18O as a chronometer for the replacement reaction makes it possible to reconstruct the chronological development of the calcium phosphate reaction front. Raman analysis revealed that the incorporation of 18O in the PO4 tetrahedron of hydroxyapatite results in the development of distinct profiles in the calcium phosphate reaction front perpendicular to the grain boundaries of the marble. Through the use of the 18O chronometer, it is possible to estimate and compare the time effectiveness of the different fluid pathways in this model system. The results show that the grain boundaries serve as a
Density Functional Theory Study of Competitive Reaction Pathways of Ti+ with Fluorinated Acetone in the Gas Phase

International Nuclear Information System (INIS)

Hong, Kiryong; Kim, Tae Kyu

2012-01-01

We investigate the doublet and quartet potential energy surfaces associated with the gas-phase reaction between Ti + and CF 3 COCH 3 for two plausible reaction pathways, TiF 2 + and TiO + formation pathways by using the density functional theory (DFT) method. The molecular structures of intermediates and transition states involved in these reaction pathways are optimized at the DFT level by using the PBE0 functional. All transition states are identified by using the intrinsic reaction coordinate (IRC) method, and the resulting reaction coordinates describe how Ti + activates CF 3 COCH 3 and produces TiF 2 + and TiO + as products. On the basis of presented results, we propose the most favorable reaction pathway in the reaction between Ti + and CF 3 COCH 3
RhoA/ROCK Signaling Pathway Mediates Shuanghuanglian Injection-Induced Pseudo-allergic Reactions.

Science.gov (United States)

Han, Jiayin; Zhao, Yong; Zhang, Yushi; Li, Chunying; Yi, Yan; Pan, Chen; Tian, Jingzhuo; Yang, Yifei; Cui, Hongyu; Wang, Lianmei; Liu, Suyan; Liu, Jing; Deng, Nuo; Liang, Aihua

2018-01-01

Background: Shuanghuanglian injection (SHLI) is a famous Chinese medicine used as an intravenous preparation for the treatment of acute respiratory tract infections. In the recent years, the immediate hypersensitivity reactions induced by SHLI have attracted broad attention. However, the mechanism involved in these reactions has not yet been elucidated. The present study aims to explore the characteristics of the immediate hypersensitivity reactions induced by SHLI and deciphers the role of the RhoA/ROCK signaling pathway in these reactions. Methods: SHLI-immunized mice or naive mice were intravenously injected (i.v.) with SHLI (600 mg/kg) once, and vascular leakage in the ears was evaluated. Passive cutaneous anaphylaxis test was conducted using sera collected from SHLI-immunized mice. Naive mice were administered (i.v.) with a single dose of 150, 300, or 600 mg/kg of SHLI, and vascular leakage, histamine release, and histopathological alterations in the ears, lungs, and intestines were tested. In vitro , human umbilical vein endothelial cell (HUVEC) monolayer was incubated with SHLI (0.05, 0.1, or 0.15 mg/mL), and the changes in endothelial permeability and cytoskeleton were observed. Western blot analysis was performed and ROCK inhibitor was employed to investigate the contribution of the RhoA/ROCK signaling pathway in SHLI-induced hypersensitivity reactions, both in HUVECs and in mice. Results: Our results indicate that SHLI was able to cause immediate dose-dependent vascular leakage, edema, and exudates in the ears, lungs, and intestines, and histamine release in mice. These were pseudo-allergic reactions, as SHLI-specific IgE was not elicited during sensitization. In addition, SHLI induced reorganization of actin cytoskeleton and disrupted the endothelial barrier. The administration of SHLI directly activated the RhoA/ROCK signaling pathway both in HUVECs and in the ears, lungs, and intestines of mice. Fasudil hydrochloride, a ROCK inhibitor, ameliorated the
Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

DEFF Research Database (Denmark)

Jin, Biao; Rolle, Massimo

2016-01-01

The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework ...
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

Science.gov (United States)

Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

2013-01-01

Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008
On the deduction of chemical reaction pathways from measurements of time series of concentrations.

Science.gov (United States)

Samoilov, Michael; Arkin, Adam; Ross, John

2001-03-01

We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system. (c) 2001 American Institute of Physics.
Competing retention pathways of uranium upon reaction with Fe(II)

Science.gov (United States)

Massey, Michael S.; Lezama-Pacheco, Juan S.; Jones, Morris E.; Ilton, Eugene S.; Cerrato, José M.; Bargar, John R.; Fendorf, Scott

2014-10-01

Biogeochemical retention processes, including adsorption, reductive precipitation, and incorporation into host minerals, are important in contaminant transport, remediation, and geologic deposition of uranium. Recent work has shown that U can become incorporated into iron (hydr)oxide minerals, with a key pathway arising from Fe(II)-induced transformation of ferrihydrite, (Fe(OH)3·nH2O) to goethite (α-FeO(OH)); this is a possible U retention mechanism in soils and sediments. Several key questions, however, remain unanswered regarding U incorporation into iron (hydr)oxides and this pathway's contribution to U retention, including: (i) the competitiveness of U incorporation versus reduction to U(IV) and subsequent precipitation of UO2; (ii) the oxidation state of incorporated U; (iii) the effects of uranyl aqueous speciation on U incorporation; and, (iv) the mechanism of U incorporation. Here we use a series of batch reactions conducted at pH ∼7, [U(VI)] from 1 to 170 μM, [Fe(II)] from 0 to 3 mM, and [Ca] at 0 or 4 mM coupled with spectroscopic examination of reaction products of Fe(II)-induced ferrihydrite transformation to address these outstanding questions. Uranium retention pathways were identified and quantified using extended X-ray absorption fine structure (EXAFS) spectroscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. Analysis of EXAFS spectra showed that 14-89% of total U was incorporated into goethite, upon reaction with Fe(II) and ferrihydrite. Uranium incorporation was a particularly dominant retention pathway at U concentrations ⩽50 μM when either uranyl-carbonato or calcium-uranyl-carbonato complexes were dominant, accounting for 64-89% of total U. With increasing U(VI) and Fe(II) concentrations, U(VI) reduction to U(IV) became more prevalent, but U incorporation remained a functioning retention pathway. These findings highlight the potential importance of U(V) incorporation within iron
Reaction pathways for reduction of nitrate ions on platinum, rhodium, and platinum-rhodium alloy electrodes

International Nuclear Information System (INIS)

Cunha, M.C.P.M. da; De Souza, J.P.I.; Nart, F.C.

2000-01-01

The reduction of nitrate ions on platinum, rhodium, and platinum-rhodium alloy electrodes has been investigated using differential electrochemical mass spectrometry and in situ FTIR measurements. For 3 M HNO 3 concentration it has been found that nitrate starts the reduction with partial N-O bond dissociation and N-N bond formation generating NO and N 2 O. At potentials lower than 0.2 V the reaction proceeds forming dissolved NH 4 + . For potentials lower than 0 V the reduction continues via a multiple pathway reaction leading to the nonselective production of N 2 , NH 2 OH, and N 2 H 2 . On the alloyed electrodes, the production of NO and N 2 O has been observed in both cathodic and anodic scans, while on pure platinum and rhodium electrodes the reaction has been observed only during the cathodic scan. Contrasting with the pure platinum and rhodium alloys, where the N-O bond break starts forming NO and N 2 O, on the alloys HNO 2 has been observed as the first reaction step. For alloys with higher rhodium composition, like Pt 75 Rh 25 , no N 2 has been detected for potentials lower than 0 V
Exploring the Reaction Pathways of Bioglycerol Hydrodeoxygenation to Propene over Molybdena-Based Catalysts.

Science.gov (United States)

Zacharopoulou, Vasiliki; Vasiliadou, Efterpi S; Lemonidou, Angeliki A

2018-01-10

The one-step reaction of glycerol with hydrogen to form propene selectively is a particularly challenging catalytic pathway that has not yet been explored thoroughly. Molybdena-based catalysts are active and selective to C-O bond scission; propene is the only product in the gas phase under the standard reaction conditions, and further hydrogenation to propane is impeded. Within this context, this work focuses on the exploration of the reaction pathways and the investigation of various parameters that affect the catalytic performance, such as the role of hydrogen on the product distribution and the effect of the catalyst pretreatment step. Under a hydrogen atmosphere, propene is produced primarily via 2-propenol, whereas under an inert atmosphere propanal and glycerol dissociation products are formed mainly. The reaction most likely proceeds through a reverse Mars-van Krevelen mechanism as partially reduced Mo species drive the reaction to the formation of the desired product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Reaction pathways for catalytic gas-phase oxidation of glycerol over mixed metal oxides

Energy Technology Data Exchange (ETDEWEB)

Suprun, W.; Glaeser, R.; Papp, H. [Leipzig Univ. (Germany). Inst. of Chemical Technology

2011-07-01

Glycerol as a main by-product from bio-diesel manufacture is a cheap raw material with large potential for chemical or biochemical transformations to value-added C3-chemicals. One possible way of glycerol utilization involves its catalytic oxidation to acrylic acid as an alternative to petrochemical routes. However, this catalytic conversion exhibits various problems such as harsh reaction conditions, severe catalyst coking and large amounts of undesired by-products. In this study, the reaction pathways for gas-phase conversion of glycerol over transition metal oxides (Mo, V und W) supported on TiO{sub 2} and SiO{sub 2} were investigated by two methods: (i) steady state experiments of glycerol oxidation and possible reactions intermediates, i.e., acrolein, 3-hydroxy propionaldehyde and acetaldehyde, and (ii) temperature-programmed surface reaction (TPSR) studies of glycerol conversion in the presence and in the absence of gas-phase oxygen. It is shown that the supported W-, V and Mo-oxides possess an ability to catalyze the oxidation of glycerol to acrylic acid. These investigations allowed us to gain a deeper insight into the reaction mechanism. Thus, based on the obtained results, three possible reactions pathways for the selective oxidation of glycerol to acrylic acid on the transition metal-containing catalysts are proposed. The major pathways in presence of molecular oxygen are a fast successive destructive oxidation of glycerol to CO{sub x} and the dehydration of glycerol to acrolein which is a rate-limiting step. (orig.)
Proatherogenic pathways leading to vascular calcification

International Nuclear Information System (INIS)

Mazzini, Michael J.; Schulze, P. Christian

2006-01-01

Cardiovascular disease is the leading cause of morbidity and mortality in the western world and atherosclerosis is the major common underlying disease. The pathogenesis of atherosclerosis involves local vascular injury, inflammation and oxidative stress as well as vascular calcification. Vascular calcification has long been regarded as a degenerative process leading to mineral deposition in the vascular wall characteristic for late stages of atherosclerosis. However, recent studies identified vascular calcification in early stages of atherosclerosis and its occurrence has been linked to clinical events in patients with cardiovascular disease. Its degree correlates with local vascular inflammation and with the overall impact and the progression of atherosclerosis. Over the last decade, diverse and highly regulated molecular signaling cascades controlling vascular calcification have been described. Local and circulating molecules such as osteopontin, osteoprogerin, leptin and matrix Gla protein were identified as critical regulators of vascular calcification. We here review the current knowledge on molecular pathways of vascular calcification and their relevance for the progression of cardiovascular disease
Modeling chemical reactions for drug design.

Science.gov (United States)

Gasteiger, Johann

2007-01-01

Chemical reactions are involved at many stages of the drug design process. This starts with the analysis of biochemical pathways that are controlled by enzymes that might be downregulated in certain diseases. In the lead discovery and lead optimization process compounds have to be synthesized in order to test them for their biological activity. And finally, the metabolism of a drug has to be established. A better understanding of chemical reactions could strongly help in making the drug design process more efficient. We have developed methods for quantifying the concepts an organic chemist is using in rationalizing reaction mechanisms. These methods allow a comprehensive modeling of chemical reactivity and thus are applicable to a wide variety of chemical reactions, from gas phase reactions to biochemical pathways. They are empirical in nature and therefore allow the rapid processing of large sets of structures and reactions. We will show here how methods have been developed for the prediction of acidity values and of the regioselectivity in organic reactions, for designing the synthesis of organic molecules and of combinatorial libraries, and for furthering our understanding of enzyme-catalyzed reactions and of the metabolism of drugs.
Reaction pathways of the dissociation of methylal: A DFT study

Energy Technology Data Exchange (ETDEWEB)

Frey, H -M; Beaud, P; Gerber, T; Mischler, B; Radi, P P; Tzannis, A -P [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1999-08-01

Schemata for modelling combustion processes do not yet include reaction rates for oxygenated fuels like methylal (DMM) which is considered as an additive or replacement for diesel due to its low sooting propensity. Density functional theory (DFT) studies of the possible reaction pathways for different dissociation steps of methylal are presented. Cleavage of a hydrogen bond to the methoxy group or the central carbon atom were simulated at the BLYP/6-311++G{sup **} level of theory. The results are compared to the experiment when dissociating and/or ionising DMM with femtosecond pulses. (author) 1 fig., 1 tab., 1 ref.

Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

International Nuclear Information System (INIS)

Jin, Biao; Rolle, Massimo

2016-01-01

The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces the multi-element isotope data observed in previous experimental studies. Furthermore, it precisely captures the dual element isotope trends characteristic of different reaction pathways as well as their range of variation consistent with observed bulk isotope fractionation. It was also possible to directly validate the model capability to predict the evolution of position-specific isotope ratios with available experimental data. Therefore, the approach is useful both for a mechanism-based evaluation of experimental results and as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. - Highlights: • Mechanism-based, position-specific isotope modeling of micropollutants degradation. • Simultaneous description of concentration and primary and secondary isotope effects. • Key features of the model are demonstrated with three illustrative examples. • Model as a tool to explore reaction mechanisms and to design experiments. - We propose a modeling approach incorporating mechanistic information and
Reaction pathways of biomass-derived oxygenates on noble metal surfaces

Science.gov (United States)

McManus, Jesse R.

As the global demand for energy continues to rise, the environmental concerns associated with increased fossil fuel consumption have motivated the use of biomass as an alternative, carbon-renewable energy feedstock. Controlling reactive chemistry of the sugars that comprise biomass through the use of catalysis becomes essential in effectively producing green fuels and value-added chemicals. Recent work on biomass conversion catalysts have demonstrated the efficacy of noble metal catalyst systems for the reforming of biomass to hydrogen fuel, and the hydrodeoxygenation of biomass-derived compounds to value-added chemicals. In particular, Pt and Pd surfaces have shown considerable promise as reforming catalysts in preliminary aqueous phase reforming studies. It becomes important to understand the mechanisms by which these molecules react on the catalyst surfaces in order to determine structure-activity relationships and bond scission energetics as to provide a framework for engineering more active and selective catalysts. Fundamental surface science techniques provide the tools to do this; however, work in this field has been so far limited to simple model molecules like ethanol and ethylene glycol. Herein, temperature programmed desorption and high resolution electron energy loss spectroscopy are utilized in an ultra-high vacuum surface science study of the biomass-derived sugar glucose on Pt and Pd single crystal catalysts. Overall, it was determined that the aldehyde function of a ring-open glucose molecule plays an integral part in the initial bonding and reforming reaction pathway, pointing to the use of aldoses glycolaldehyde and glyceraldehyde as the most appropriate model compounds for future studies. Furthermore, the addition of adatom Zn to a Pt(111) surface was found to significantly decrease the C-H and C-C bond scission activity in aldehyde containing compounds, resulting in a preferred deoxygenation pathway in opposition to the decarbonylation pathway
Reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma

Science.gov (United States)

Zhao, Yuefeng; Wang, Chao; Li, Li; Wang, Lijuan; Pan, Jie

2018-03-01

In this work, a two-dimensional fluid model is built up to numerically investigate the reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma. The calculation results indicate that the electron collisions with CH4 are the key pathways to produce the neutral particles CH2 and CH as well as the charged particles e and CH3+. CH3, H2, H, C2H2, and C2H4 primarily result from the reactions between the neutral particles and CH4. The charge transfer reactions are the significant pathways to produce CH4+, C2H2+, and C2H4+. As to the neutral species CH and H and the charged species CH3+, the reactions between themselves and CH4 contribute to substantial losses of these particles. The ways responsible for losing CH3, H2, C2H2, and C2H4 are CH3 + H → CH4, H2 + CH → CH2 + H, CH4+ + C2H2 → C2H2+ + CH4, and CH4+ + C2H4 → C2H4+ + CH4, respectively. Both electrons and C2H4+ are consumed by the dissociative electron-ion recombination reactions. The essential reaction pathways of losing CH4+ and C2H2+ are the charge transfer reactions.
Relative importance of dissolved and food pathways for lead contamination in shrimp

Energy Technology Data Exchange (ETDEWEB)

Boisson, F.; Cotret, O.; Teyssie, J.-L.; El-Baradeie, M.; Fowler, S.W

2003-12-01

The relative importance of dissolved and food pathways and the influence of food type in the bioaccumulation and retention of lead in the shrimp Palaemonetes varians were examined using a radiotracer method. Shrimp were exposed to {sup 210}Pb-labelled seawater or fed two types of {sup 210}Pb-labelled food, viz. mussels or worms. The amount of radiotracer accumulated by shrimp was examined over a 7-day period, followed by a 1-month and a 7-day depuration period for the dissolved and food source, respectively. Steady state in the uptake was reached after 2 days exposure to dissolved lead, with a resultant estimated concentration factor of 98 {+-} 3. Transfer factors following ingestion of contaminated mussels and worms were lower than unity for both food types, with lead transfer from worms being significantly higher than that from mussels. Accumulation of dissolved Pb by shrimp was found to occur mainly through adsorption on the exoskeleton with a minor accumulation in the internal tissues probably resulting from the intake of seawater for osmoregulation. In contrast, lead taken up from contaminated food was readily absorbed and bound in the internal tissues of P. varians. Although the transfer of lead to P. varians through the ingestion of contaminated food was low (TF < 1%), it still represented 4 to 8% of the lead content in the prey which is a significant additional contribution of lead to the shrimp body burden. Independent of food type, following ingestion of contaminated food, approximately 23-27% of total lead accumulated in shrimp was located in the edible parts (e.g. muscle). Therefore, the food pathway is suggested to be a significant contributor to the lead transfer to humans through ingestion of contaminated shrimp. After exposure to contaminated food, lead loss kinetics were described by a two-component model, whereas Pb loss following direct uptake from seawater was best described by a three-component model. The additional compartment representing 64
Relative importance of dissolved and food pathways for lead contamination in shrimp

International Nuclear Information System (INIS)

Boisson, F.; Cotret, O.; Teyssie, J.-L.; El-Baradeie, M.; Fowler, S.W.

2003-01-01

The relative importance of dissolved and food pathways and the influence of food type in the bioaccumulation and retention of lead in the shrimp Palaemonetes varians were examined using a radiotracer method. Shrimp were exposed to 210 Pb-labelled seawater or fed two types of 210 Pb-labelled food, viz. mussels or worms. The amount of radiotracer accumulated by shrimp was examined over a 7-day period, followed by a 1-month and a 7-day depuration period for the dissolved and food source, respectively. Steady state in the uptake was reached after 2 days exposure to dissolved lead, with a resultant estimated concentration factor of 98 ± 3. Transfer factors following ingestion of contaminated mussels and worms were lower than unity for both food types, with lead transfer from worms being significantly higher than that from mussels. Accumulation of dissolved Pb by shrimp was found to occur mainly through adsorption on the exoskeleton with a minor accumulation in the internal tissues probably resulting from the intake of seawater for osmoregulation. In contrast, lead taken up from contaminated food was readily absorbed and bound in the internal tissues of P. varians. Although the transfer of lead to P. varians through the ingestion of contaminated food was low (TF < 1%), it still represented 4 to 8% of the lead content in the prey which is a significant additional contribution of lead to the shrimp body burden. Independent of food type, following ingestion of contaminated food, approximately 23-27% of total lead accumulated in shrimp was located in the edible parts (e.g. muscle). Therefore, the food pathway is suggested to be a significant contributor to the lead transfer to humans through ingestion of contaminated shrimp. After exposure to contaminated food, lead loss kinetics were described by a two-component model, whereas Pb loss following direct uptake from seawater was best described by a three-component model. The additional compartment representing 64% of total Pb
Kinetic and reaction pathways of methanol oxidation on platinum

International Nuclear Information System (INIS)

McCabe, R.W.; McCready, D.F.

1986-01-01

Methanol oxidation kinetics were measured on Pt wires in a flow reactor at pressures between 30 and 130 Pa. The kinetics were measured as a function of oxygen-to-methanol equivalence ratio phi and wire temperature. In methanol-lean feeds (phi 2 CO, CO 2 , and H 2 O were the only products; in methanol-rich feeds (phi > 1), CO, H 2 , H 2 CO, CO 2 , and H 2 O were observed. Experiments with 18 O 2 showed that the principal methanol oxidation pathway does not involve C-O bond dissociation. However, the 18 O 2 experiments, together with other features of the methanol oxidation data, also provided evidence for a minor oxidation pathway (accounting for less than 1% of the product CO 2 ) which proceeds through a carbon intermediate. A mathematical model is presented which describes the principal CH 3 OH oxidation pathway as a series reaction involving adsorbed H 2 CO and CO intermediates. Consistent with experimental results, the model predicts that inhibition by adsorbed CO should be weaker for CH 3 OH and H 2 CO oxidation than for CO oxidation. 34 references, 10 figures, 2 tables
Hydrogen oxidation mechanisms on Ni/yttria stabilized zirconia anodes: Separation of reaction pathways by geometry variation of pattern electrodes

Science.gov (United States)

Doppler, M. C.; Fleig, J.; Bram, M.; Opitz, A. K.

2018-03-01

Nickel/yttria stabilized zirconia (YSZ) electrodes are affecting the overall performance of solid oxide fuel cells (SOFCs) in general and strongly contribute to the cell resistance in case of novel metal supported SOFCs in particular. The electrochemical fuel conversion mechanisms in these electrodes are, however, still only partly understood. In this study, micro-structured Ni thin film electrodes on YSZ with 15 different geometries are utilized to investigate reaction pathways for the hydrogen electro-oxidation at Ni/YSZ anodes. From electrodes with constant area but varying triple phase boundary (TPB) length a contribution to the electro-catalytic activity is found that does not depend on the TPB length. This additional activity could clearly be attributed to a yet unknown reaction pathway scaling with the electrode area. It is shown that this area related pathway has significantly different electrochemical behavior compared to the TPB pathway regarding its thermal activation, sulfur poisoning behavior, and H2/H2O partial pressure dependence. Moreover, possible reaction mechanisms of this reaction pathway are discussed, identifying either a pathway based on hydrogen diffusion through Ni with water release at the TPB or a path with oxygen diffusion through Ni to be a very likely explanation for the experimental results.
Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions and novel technologies

Directory of Open Access Journals (Sweden)

Frank eSchreiber

2012-10-01

Full Text Available Nitrous oxide (N2O is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH or the reduction of nitrite (NO2- to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO2- to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria. In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO2-, NH2OH and nitroxyl (HNO. Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser based absorption spectroscopy. In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build-up.
Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Science.gov (United States)

Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

2012-01-01

Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build
MAPKs are essential upstream signaling pathways in proteolytic cartilage degradation--divergence in pathways leading to aggrecanase and MMP-mediated articular cartilage degradation

DEFF Research Database (Denmark)

Sondergaard, B-C; Schultz, N; Madsen, S H

2010-01-01

Matrix metalloproteinases (MMPs) and aggrecanases are essential players in cartilage degradation. However, the signaling pathways that results in MMP and/or aggrecanase synthesis and activation are not well understood. We investigated the molecular events leading to MMP- and aggrecanase-mediated ......Matrix metalloproteinases (MMPs) and aggrecanases are essential players in cartilage degradation. However, the signaling pathways that results in MMP and/or aggrecanase synthesis and activation are not well understood. We investigated the molecular events leading to MMP- and aggrecanase......-mediated cartilage degradation....
Quantum chemical investigation of the reaction of O( P2) with certain ...

Indian Academy of Sciences (India)

WINTEC

In the case of methyl radical the minimum energy reaction pathway leads to the products CO + H2 + H. In ... Reactions of atomic oxygen with hydrocarbon radicals play an important role in ..... The reaction between singlet oxygen and propyl ...
Electrode Reaction Pathway in Oxide Anode for Solid Oxide Fuel Cells

Science.gov (United States)

Li, Wenyuan

the electrolyte to change 3PB kinetics. Compared to Ni, Co doping activates the bulk oxygen more significantly, promoting the reaction at 2PB. The active surface reaction zone is found to be enlarged by the electrolyte with high oxygen activity (SSZ vs. YSZ) when charge transfer is one of the RDS. Due to the larger exchange current for charge transfer in 3PB with SSZ electrolyte, the adsorption gradient zone is broadened, leading to enhanced surface reaction kinetics. The potential application of such finding is demonstrated on SSZ/YSZ/SSZ sandwich, showing largely improved electrode performance, opening a wide door for the utilization of electrolytes that are too expensive, fragile or instable to be used before. The bulk path way in 2PB reaction can be affected by overpotential in terms of local vacancy concentration, built-in electrical field and stability. It is proven that an uneven distribution of lattice oxygen is established under operation conditions with overpotential by both qualitative analysis and analytic solution. An electrostatic field force is present besides the concentration gradient in the anode lattice to control the motion of oxygen ions. Compared to the usual estimation based on chemical diffusion mechanism, the real deviation of ionic defects concentration under polarization from the equilibrium state near electrode/electrolyte interface is smaller with the built-in electrical field. The overpotential is demonstrated to be able to open up or shut down the bulk pathway depending on the ionic defects of electrodes. The analysis on the bulk pathway in terms of local charged species and various potentials provides new insight in anion diffusion and electrode stability.
Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

Science.gov (United States)

Dateo, Christopher E.; Walch, Stephen P.

2002-01-01

As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.
Thermal decomposition of a molecular material {N(n-C4H94[FeIIFeIII(C2O43]}∞ leading to ferrite: A reaction kinetics study

Directory of Open Access Journals (Sweden)

Bhattacharjee Ashis

2013-01-01

Full Text Available A multi-step thermal decomposition of a molecular precursor, {N(n-C4H94[FeIIFeIII(C2O43}∞ has been studied using non-isothermal thermogravimetry (TG measurements in the temperature range 300 to ~800 K at multiple heating rates (5, 10 and 20 K min-1. The thermal decomposition of the oxalate-based complex proceeds stepwise through a series of intermediate reactions. Two different isoconversional methods, namely, improved iterative method and model-free method are employed to evaluate the kinetic parameters: activation energy and rate of reaction, and the most probable reaction mechanism of thermal decomposition is also determined. The different reaction pathways leading to different steps in the TG profile have also been explored which are supplemented by earlier experimental observations of the present authors.
Evidence for leading mesons in anti p4He reactions at 0.6 GeV/c incident momentum

International Nuclear Information System (INIS)

Breivik, F.O.; Haatuft, A.; Halsteinslid, A.

1990-05-01

In a previous report, evidence has been shown for leading mesons in anti p Ne - reactions at 0.6 Gev/c incident momentum. In this report evidence is shown for leading mesons in anti p 4 He reactions at the same incident momentum, based on data from the same detector. In anti p Ne - reactions, only kaons are observed as leading mesons in K o s-events, and only pions are observed as leading mesons in Λ o -events. In anti p He - reactions this is not longer true, since also pions behave as leading mesons in K o s-events. 5 refs., 9 figs
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

KAUST Repository

Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin

2016-01-01

To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

KAUST Repository

Kuwahara, Hiroyuki

2016-04-29

To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
Removing antimony from waste lead storage batteries alloy by vacuum displacement reaction technology.

Science.gov (United States)

Liu, Tiantian; Qiu, Keqiang

2018-04-05

With the wide application of lead acid battery, spent lead acid battery has become a serious problem to environmental protection and human health. Though spent battery can be a contaminant if not handled properly, it is also an important resource to obtain refined lead. Nowadays, the Sb-content in lead storage batteries is about 0.5-3 wt%, which is higher than the Sb-content in the crude lead. However, there are few reports about the process of removing antimony from high-antimony lead bullion. In this study, vacuum displacement reaction technology, a new process for removing antimony from high-antimony lead melts, was investigated. During this process, lead oxide was added to the system and antimony from lead melts was converted into antimony trioxide, which easily was evaporated under vacuum so that antimony was removed from lead melts. The experimental results demonstrated that Sb-content in lead melts decreased from 2.5% to 23 ppm under following conditions: mass ratio of PbO/lead bullion of 0.33, residual gas pressure of 30 Pa, melt temperature of 840 °C, reaction time of 60 min. The distillate gotten can be used as by-product to produce antimony white. Moreover, this study is of importance to recycling of waste lead storage batteries alloy. Copyright © 2018 Elsevier B.V. All rights reserved.
Reaction pathways of model compounds of biomass-derived oxygenates on Fe/Ni bimetallic surfaces

Science.gov (United States)

Yu, Weiting; Chen, Jingguang G.

2015-10-01

Controlling the activity and selectivity of converting biomass-derivatives to fuels and valuable chemicals is critical for the utilization of biomass feedstocks. There are primarily three classes of non-food competing biomass, cellulose, hemicellulose and lignin. In the current work, glycolaldehyde, furfural and acetaldehyde are studied as model compounds of the three classes of biomass-derivatives. Monometallic Ni(111) and monolayer (ML) Fe/Ni(111) bimetallic surfaces are studied for the reaction pathways of the three biomass surrogates. The ML Fe/Ni(111) surface is identified as an efficient surface for the conversion of biomass-derivatives from the combined results of density functional theory (DFT) calculations and temperature programmed desorption (TPD) experiments. A correlation is also established between the optimized adsorption geometry and experimental reaction pathways. These results should provide helpful insights in catalyst design for the upgrading and conversion of biomass.
Molecular extinction coefficients of lead sulfide and polymerized diaminobenzidine as final reaction products of histochemical phosphatase reactions

NARCIS (Netherlands)

van Noorden, C. J.; Jonges, G. N.

1992-01-01

Molar extinction coefficients of precipitated lead sulfide (PbS) and polymerized diaminobenzidine (polyDAB) have been determined at wavelengths of 450 nm and 480 nm, respectively, for quantitative histochemical analysis of phosphatase reactions. These values are essential for the conversion of

Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

DEFF Research Database (Denmark)

Nielsen, Jens Bredal

1997-01-01

Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...
Kinetics of the glucose/glycine Maillard reaction pathways: influences of pH and reactant initial concentrations

NARCIS (Netherlands)

Martins, S.I.F.S.; Boekel, van M.A.J.S.

2005-01-01

A previously proposed kinetic model for the glucose/glycine Maillard reaction pathways has been validated by changing the initial pH (4.8, 5.5, 6.0, 6.8 and 7.5) of the reaction and reactant initial concentrations (1:2 and 2:1 molar ratios were compared to the 1:1 ratio). The model consists of 10
Chemical form of selenium differentially influences DNA repair pathways following exposure to lead nitrate.

Science.gov (United States)

McKelvey, Shauna M; Horgan, Karina A; Murphy, Richard A

2015-01-01

Lead, an environmental toxin is known to induce a broad range of physiological and biochemical dysfunctions in humans through a number of mechanisms including the deactivation of antioxidants thus leading to generation of reactive oxygen species (ROS) and subsequent DNA damage. Selenium on the other hand has been proven to play an important role in the protection of cells from free radical damage and oxidative stress, though its effects are thought to be form and dose dependent. As the liver is the primary organ required for metabolite detoxification, HepG2 cells were chosen to assess the protective effects of various selenium compounds following exposure to the genotoxic agent lead nitrate. Initially DNA damage was quantified using a comet assay, gene expression patterns associated with DNA damage and signalling were also examined using PCR arrays and the biological pathways which were most significantly affected by selenium were identified. Interestingly, the organic type selenium compounds (selenium yeast and selenomethionine) conferred protection against lead induced DNA damage in HepG2 cells; this is evident by reduction in the quantity of DNA present in the comet tail of cells cultured in their presence with lead. This trend also followed through the gene expression changes noted in DNA damage pathways analysed. These results were in contrast with those of inorganic sodium selenite which promoted lead induced DNA damage evident in both the comet assay results and the gene expression analysis. Over all this study provided valuable insights into the effects which various selenium compounds had on the DNA damage and signalling pathway indicating the potential for using organic forms of selenium such as selenium enriched yeast to protect against DNA damaging agents. Copyright © 2014 Elsevier GmbH. All rights reserved.
Degradation of ibuprofen by hydrodynamic cavitation: Reaction pathways and effect of operational parameters.

Science.gov (United States)

Musmarra, Dino; Prisciandaro, Marina; Capocelli, Mauro; Karatza, Despina; Iovino, Pasquale; Canzano, Silvana; Lancia, Amedeo

2016-03-01

Ibuprofen (IBP) is an anti-inflammatory drug whose residues can be found worldwide in natural water bodies resulting in harmful effects to aquatic species even at low concentrations. This paper deals with the degradation of IBP in water by hydrodynamic cavitation in a convergent-divergent nozzle. Over 60% of ibuprofen was degraded in 60 min with an electrical energy per order (EEO) of 10.77 kWh m(-3) at an initial concentration of 200 μg L(-1) and a relative inlet pressure pin=0.35 MPa. Five intermediates generated from different hydroxylation reactions were identified; the potential mechanisms of degradation were sketched and discussed. The reaction pathways recognized are in line with the relevant literature, both experimental and theoretical. By varying the pressure upstream the constriction, different degradation rates were observed. This effect was discussed according to a numerical simulation of the hydroxyl radical production identifying a clear correspondence between the maximum kinetic constant kOH and the maximum calculated OH production. Furthermore, in the investigated experimental conditions, the pH parameter was found not to affect the extent of degradation; this peculiar feature agrees with a recently published kinetic insight and has been explained in the light of the intermediates of the different reaction pathways. Copyright © 2015 Elsevier B.V. All rights reserved.
Pathways for the release of polonium from a lead-bismuth spallation target (thermochemical calculation); Verfluechtigungspfade des Poloniums aus einem Pb-Bi-Spallationstarget (Thermochemische Kalkulation)

Energy Technology Data Exchange (ETDEWEB)

Eichler, B.; Neuhausen, J

2004-06-01

An analysis of literature data for the thermochemical constants of polonium reveals considerable discrepancies in the relations of these data among each other as well as in their expected trends within the chalcogen group. This fact hinders a reliable assessment of possible reaction paths for the release of polonium from a liquid lead-bismuth spallation target. In this work an attempt is made to construct a coherent data set for the thermochemical properties of polonium and some of its compounds that are of particular importance with respect to the behaviour of polonium in a liquid Pb-Bi target. This data set is based on extrapolations using general trends throughout the periodic table and, in particular, within the chalcogen group. Consequently, no high accuracy should be attributed to the derived data set. However, the data set derived in this work is consistent with definitely known experimental data. Furthermore, it complies with the general trends of physicochemical properties within the chalcogen group. Finally, well known relations between thermochemical quantities are fulfilled by the data derived in this work. Thus, given the lack of accurate experimental data it can be regarded as best available data. Thermochemical constants of polonium hydride, lead polonide and polonium dioxide are derived based on extrapolative procedures. Furthermore, the possibility of formation of the gaseous intermetallic molecule BiPo, which has been omitted from discussion up to now, is investigated. From the derived thermochemical data the equilibrium constants of formation, release and dissociation reactions are calculated for different polonium containing species. Furthermore equilibrium constants are determined for the reaction of lead polonide and polonium dioxide with hydrogen, water vapour and the target components lead and bismuth. The most probable release pathways are discussed. From thermochemical evaluations polonium is expected to be released from liquid lead
Chemical pathways for the formation of ammonia in Hanford wastes

Energy Technology Data Exchange (ETDEWEB)

Stock, L.M.; Pederson, L.R.

1997-09-01

This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence.
Chemical pathways for the formation of ammonia in Hanford wastes

International Nuclear Information System (INIS)

Stock, L.M.; Pederson, L.R.

1997-09-01

This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence
A facile and expedient one-pot three-component reaction leading to ...

Indian Academy of Sciences (India)

Sci. Vol. 124, No. 5, September 2012, pp. 1007–1012. c Indian Academy of Sciences. A facile and expedient one-pot three-component reaction leading to multifunctionalized stabilized phosphorus ylides. ZAHRA HASSANI. ∗ and ZEINAB ESFANDIARPOUR. Department of New Materials, International Center for Science, ...
Reaction of H2 with O2 in Excited Electronic States: Reaction Pathways and Rate Constants.

Science.gov (United States)

Pelevkin, Alexey V; Loukhovitski, Boris I; Sharipov, Alexander S

2017-12-21

Comprehensive quantum chemical analysis with the use of the multireference state-averaged complete active space self-consistent field approach was carried out to study the reactions of H 2 with O 2 in a 1 Δ g , b 1 Σ g + , c 1 Σ u - , and A' 3 Δ u electronically excited states. The energetically favorable reaction pathways and possible intersystem crossings have been revealed. The energy barriers were refined employing the extended multiconfiguration quasi-degenerate second-order perturbation theory. It has been shown that the interaction of O 2 (a 1 Δ g ) and O 2 (A' 3 Δ u ) with H 2 occurs through the H-abstraction process with relatively low activation barriers that resulted in the formation of the HO 2 molecule in A″ and A' electronic states, respectively. Meanwhile, molecular oxygen in singlet sigma states (b 1 Σ g + and c 1 Σ u - ) was proved to be nonreactive with respect to the molecular hydrogen. Appropriate rate constants for revealed reaction and quenching channels have been estimated using variational transition-state theory including corrections for the tunneling effect, possible nonadiabatic transitions, and anharmonicity of vibrations for transition states and reactants. It was demonstrated that the calculated reaction rate constant for the H 2 + O 2 (a 1 Δ g ) process is in reasonable agreement with known experimental data. The Arrhenius approximations for these processes have been proposed for the temperature range T = 300-3000 K.
Laccase-catalyzed removal of the antimicrobials chlorophene and dichlorophen from water: Reaction kinetics, pathway and toxicity evaluation.

Science.gov (United States)

Shi, Huanhuan; Peng, Jianbiao; Li, Jianhua; Mao, Liang; Wang, Zunyao; Gao, Shixiang

2016-11-05

As active agents in cleaning and disinfecting products, antimicrobials have been widely spread in the environment and have drawn extensive attention as potential threats to the ecological system and human health. In this study, the laccase-catalyzed removal of two emerging antimicrobials, chlorophene (CP) and dichlorophen (DCP), was investigated under simulated environmental conditions. Intrinsic reaction kinetics showed that the removal of CP and DCP followed second-order reaction kinetics, first-order with respect to both the enzyme and the substrate concentration. It was also found that fulvic acid could suppress the transformation of CP and DCP by reversing the oxidation reactions through its action as a scavenger of the free radical intermediates produced from reactions between laccase and the substrates. Several reaction products were identified by a quadrupole time-of-flight mass spectrometer, and detailed reaction pathways were proposed. For both CP and DCP, direct polymerization was the principal pathway, and the coupling patterns were further corroborated based on molecular modeling. The nucleophilic substitution of chlorine by the hydroxyl group was observed, and further oxidation products capable of coupling with each other were also found. Additionally, toxicity evaluation tests using Scenedesmus obliquus confirmed that the toxicity of CP and DCP was effectively eliminated during the reaction processes. Copyright © 2016 Elsevier B.V. All rights reserved.
Diversion of the melanin synthetic pathway by dopamine product scavengers: A quantum chemical modeling of the reaction mechanisms

Directory of Open Access Journals (Sweden)

T. B. Demissie

2017-01-01

Full Text Available We report the stability and reactivity of the oxidation products as well as L-cysteine and N-acetylcysteine adducts of dopamine studied using quantum chemical calculations. The overall reactions studied were subdivided into four reaction channels. The first reaction channel is the oxidation of dopamine to form dopaminoquinone. The second reaction channel leads to melanin formation through subsequent reactions. The third and fourth reaction channels are reactions leading to the formation of dopaminoquinone adducts which are aimed to divert the synthesis of melanin. The results indicate that L-cysteine and N-acetylcysteine undergo chemical reactions mainly at C5 position of dopaminoquinone. The analyses of the thermodynamic energies indicate that L-cysteine and N-acetylcysteine covalently bind to dopaminoquinone by competing with the internal cyclization reaction of dopaminoquinone which leads to the synthesis of melanin. The analysis of the results, based on the reaction free energies, is also supported by the investigation of the natural bond orbitals of the reactants and products.
Study of the optimal reaction conditions for assay of the mouse alternative complement pathway

NARCIS (Netherlands)

Dijk, H. van; Rademaker, P.M.; Klerx, J.P.A.M.; Willers, J.M.M.

1985-01-01

The optimal reaction conditions for hemolytic assay of alternative complement pathway activity in mouse serum were investigated. A microtiter system was used, in which a number of 7.5×106 rabbit erythrocytes per test well appeared to be optimal. Rabbit erythrocytes were superior as target cells over
Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

Science.gov (United States)

Jin, Biao; Rolle, Massimo

2016-04-01

Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M
Chemical pathways for the formation of ammonia in Hanford wastes

International Nuclear Information System (INIS)

Stock, L.M.; Pederson, L.R.

1997-12-01

This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important)
Chemical pathways for the formation of ammonia in Hanford wastes

Energy Technology Data Exchange (ETDEWEB)

Stock, L.M.; Pederson, L.R.

1997-12-01

This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important).
Academic provenance: Investigation of pathways that lead students into the geosciences

Science.gov (United States)

Houlton, Heather R.

Pathways that lead students into the geosciences as a college major have not been fully explored in the current literature, despite the recent studies on the "geoscience pipeline model." Anecdotal evidence suggests low quality geoscience curriculum in K-12 education, lack of visibility of the discipline and lack of knowledge about geoscience careers contribute to low geoscience enrollments at universities. This study investigated the reasons why college students decided to major in the geosciences. Students' interests, experiences, motivations and desired future careers were examined to develop a pathway model. In addition, self-efficacy was used to inform pathway analyses, as it is an influential factor in academic major and career choice. These results and interpretations have strong implications for recruitment and retention in academia and industry. A semi-structured interview protocol was developed, which was informed by John Flanagan's critical incident theory. The responses to this interview were used to identify common experiences that diverse students shared for reasons they became geoscience majors. Researchers used self-efficacy theory by Alfred Bandura to assess students' pathways. Seventeen undergraduate geoscience majors from two U.S. Midwest research universities were sampled for cross-comparison and analysis. Qualitative analyses led to the development of six categorical steps for the geoscience pathway. The six pathway steps are: innate attributes/interest sources, pre-college critical incidents, college critical incidents, current/near future goals, expected career attributes and desired future careers. Although, how students traversed through each step was unique for individuals, similar patterns were identified between different populations in our participants: Natives, Immigrants and Refugees. In addition, critical incidents were found to act on behavior in two different ways: to support and confirm decision-making behavior (supportive critical
Methane coupling reaction in an oxy-steam stream through an OH radical pathway by using supported alkali metal catalysts

KAUST Repository

Liang, Yin

2014-03-24

A universal reaction mechanism involved in the oxidative coupling of methane (OCM) is demonstrated under oxy-steam conditions using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from a H 2O-O2 reaction followed by C-H activation in CH 4 with an OH radical. Thus, the presence of water enhances both the CH4 conversion rate and the C2 selectivity. This OH radical pathway that is selective for the OCM was observed for the catalyst without Mn, which suggests clearly that Mn is not the essential component in a selective OCM catalyst. The experiments with different catalyst compositions revealed that the OH.-mediated pathway proceeded in the presence of catalysts with different alkali metals (Na, K) and different oxo anions (W, Mo). This difference in catalytic activity for OH radical generation accounts for the different OCM selectivities. As a result, a high C2 yield is achievable by using Na2WO4/SiO2, which catalyzes the OH.-mediated pathway selectively. Make it methane: A universal reaction mechanism involved in the oxidative coupling of methane is demonstrated under oxy-stream conditions by using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from an H2O-O2 reaction, followed by C-H activation in CH4 with an OH radical. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions.

Science.gov (United States)

Netto, Luis Eduardo S; de Oliveira, Marcos Antonio; Tairum, Carlos A; da Silva Neto, José Freire

2016-01-01

Thiol-disulfide exchange reactions are highly reversible, displaying nucleophilic substitutions mechanism (S(N)2 type). For aliphatic, low molecular thiols, these reactions are slow, but can attain million times faster rates in enzymatic processes. Thioredoxin (Trx) proteins were the first enzymes described to accelerate thiol-disulfide exchange reactions and their high reactivity is related to the high nucleophilicity of the attacking thiol. Substrate specificity in Trx is achieved by several factors, including polar, hydrophobic, and topological interactions through a groove in the active site. Glutaredoxin (Grx) enzymes also contain the Trx fold, but they do not share amino acid sequence similarity with Trx. A conserved glutathione binding site is a typical feature of Grx that can reduce substrates by two mechanisms (mono and dithiol). The high reactivity of Grx enzymes is related to the very acid pK(a) values of reactive Cys that plays roles as good leaving groups. Therefore, although distinct oxidoreductases catalyze similar thiol–disulfide exchange reactions, their enzymatic mechanisms vary. PDI and DsbA are two other oxidoreductases, but they are involved in disulfide bond formation, instead of disulfide reduction, which is related to the oxidative environment where they are found. PDI enzymes and DsbC are endowed with disulfide isomerase activity, which is related with their tetra-domain architecture. As illustrative description of specificity in thiol-disulfide exchange, redox aspects of transcription activation in bacteria, yeast, and mammals are presented in an evolutionary perspective. Therefore, thiol-disulfide exchange reactions play important roles in conferring specificity to pathways, a required feature for signaling.
Heterogeneous reaction of particulate chlorpyrifos with NO3 radicals: Products, pathways, and kinetics

Science.gov (United States)

Li, Nana; Zhang, Peng; Yang, Bo; Shu, Jinian; Wang, Youfeng; Sun, Wanqi

2014-08-01

Chlorpyrifos is a typical chlorinated organophosphorus pesticide. The heterogeneous reaction of chlorpyrifos particles with NO3 radicals was investigated using a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and a real-time atmospheric gas analysis mass spectrometer. Chlorpyrifos oxon, 3,5,6-trichloro-2-pyridinol, O,O-diethyl O-hydrogen phosphorothioate, O,O-diethyl ester thiophosphoric acid, diethyl hydrogen phosphate and a phosphinyl disulfide compound were identified as the main degradation products. The heterogeneous reaction pathways were proposed and their kinetic processes were investigated via a mixed-phase relative rate method. The observed effective rate constant is 3.4 ± 0.2 × 10-12 cm3 molecule-1 s-1.
Automated pathway and reaction prediction facilitates in silico identification of unknown metabolites in human cohort studies.

Science.gov (United States)

Quell, Jan D; Römisch-Margl, Werner; Colombo, Marco; Krumsiek, Jan; Evans, Anne M; Mohney, Robert; Salomaa, Veikko; de Faire, Ulf; Groop, Leif C; Agakov, Felix; Looker, Helen C; McKeigue, Paul; Colhoun, Helen M; Kastenmüller, Gabi

2017-12-15

Identification of metabolites in non-targeted metabolomics continues to be a bottleneck in metabolomics studies in large human cohorts. Unidentified metabolites frequently emerge in the results of association studies linking metabolite levels to, for example, clinical phenotypes. For further analyses these unknown metabolites must be identified. Current approaches utilize chemical information, such as spectral details and fragmentation characteristics to determine components of unknown metabolites. Here, we propose a systems biology model exploiting the internal correlation structure of metabolite levels in combination with existing biochemical and genetic information to characterize properties of unknown molecules. Levels of 758 metabolites (439 known, 319 unknown) in human blood samples of 2279 subjects were measured using a non-targeted metabolomics platform (LC-MS and GC-MS). We reconstructed the structure of biochemical pathways that are imprinted in these metabolomics data by building an empirical network model based on 1040 significant partial correlations between metabolites. We further added associations of these metabolites to 134 genes from genome-wide association studies as well as reactions and functional relations to genes from the public database Recon 2 to the network model. From the local neighborhood in the network, we were able to predict the pathway annotation of 180 unknown metabolites. Furthermore, we classified 100 pairs of known and unknown and 45 pairs of unknown metabolites to 21 types of reactions based on their mass differences. As a proof of concept, we then looked further into the special case of predicted dehydrogenation reactions leading us to the selection of 39 candidate molecules for 5 unknown metabolites. Finally, we could verify 2 of those candidates by applying LC-MS analyses of commercially available candidate substances. The formerly unknown metabolites X-13891 and X-13069 were shown to be 2-dodecendioic acid and 9

Catalytic Hydrotreatment of Fast Pyrolysis Oil : Model Studies on Reaction Pathways for the Carbohydrate Fraction

NARCIS (Netherlands)

Wildschut, J.; Arentz, J.; Rasrendra, C. B.; Venderbosch, R. H.; Heeres, H. J.

2009-01-01

Fast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250-400 degrees C, 100-200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon-like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions
Products and stability of phosphate reactions with lead under freeze-thaw cycling in simple systems

International Nuclear Information System (INIS)

Hafsteinsdottir, Erla G.; White, Duanne A.; Gore, Damian B.; Stark, Scott C.

2011-01-01

Orthophosphate fixation of metal contaminated soils in environments that undergo freeze-thaw cycles is understudied. Freeze-thaw cycling potentially influences the reaction rate, mineral chemical stability and physical breakdown of particles during fixation. This study determines what products form when phosphate (triple superphosphate [Ca(H 2 PO 4 ) 2 ] or sodium phosphate [Na 3 PO 4 ]) reacts with lead (PbSO 4 or PbCl 2 ) in simple chemical systems in vitro, and assesses potential changes in formation during freeze-thaw cycles. Systems were subjected to multiple freeze-thaw cycles from +10 deg. C to -20 deg. C and then analysed by X-ray diffractometry. Pyromorphite formed in all systems and was stable over multiple freeze-thaw cycles. Low temperature lead orthophosphate reaction efficiency varied according to both phosphate and lead source; the most time-efficient pyromorphite formation was observed when PbSO 4 and Na 3 PO 4 were present together. These findings have implications for the manner in which metal contaminated materials in freezing ground can be treated with phosphate. - Highlights: → Formation of lead phosphate products in cold environments is identified. → Potential change in formation during freeze-thaw cycling is assessed. → Lead phosphate reaction efficiency varies according to phosphate and lead source. → Pyromorphite formation is stable during 240 freeze-thaw cycles. - Pyromorphite, formed from Pb phosphate fixation, is stable during multiple freeze-thaw cycles but the efficiency of the fixation depends on the phosphate source and the type of Pb mineral.
Roles of different initial Maillard intermediates and pathways in meat flavor formation for cysteine-xylose-glycine model reaction systems.

Science.gov (United States)

Hou, Li; Xie, Jianchun; Zhao, Jian; Zhao, Mengyao; Fan, Mengdie; Xiao, Qunfei; Liang, Jingjing; Chen, Feng

2017-10-01

To explore initial Maillard reaction pathways and mechanisms for maximal formation of meaty flavors in heated cysteine-xylose-glycine systems, model reactions with synthesized initial Maillard intermediates, Gly-Amadori, TTCA (2-threityl-thiazolidine-4-carboxylic acids) and Cys-Amadori, were investigated. Relative relativities were characterized by spectrophotometrically monitoring the development of colorless degradation intermediates and browning reaction products. Aroma compounds formed were determined by solid-phase microextraction combined with GC-MS and GC-olfactometry. Gly-Amadori showed the fastest reaction followed by Cys-Amadori then TTCA. Free glycine accelerated reaction of TTCA, whereas cysteine inhibited that of Gly-Amadori due to association forming relatively stable thiazolidines. Cys-Amadori/Gly had the highest reactivity in development of both meaty flavors and brown products. TTCA/Gly favored yielding meaty flavors, whereas Gly-Amadori/Cys favored generation of brown products. Conclusively, initial formation of TTCA and pathway involving TTCA with glycine were more applicable to efficiently produce processed-meat flavorings in a cysteine-xylose-glycine system. Copyright © 2017 Elsevier Ltd. All rights reserved.
Reaction Pathways in Catechol/Primary Amine Mixtures: A Window on Crosslinking Chemistry.

Directory of Open Access Journals (Sweden)

Juan Yang

Full Text Available Catechol chemistry is used as a crosslinking tool abundantly in both natural organisms (e.g. mussels, sandcastle worms and synthetic systems to achieve the desired mechanical properties. Despite this abundance and success, the crosslinking chemistry is still poorly understood. In this study, to simplify the system, yet to capture the essential chemistry, model compounds 4-methyl catechol and propylamine are used. The reaction of 4-methyl catechol (2 mM with propylamine (6 mM is carried out in the presence of NaIO4 (2 mM in 10 mM Na2CO3 aqueous solution. A variety of spectroscopic/spectrometric and chromatographic methods such as 1H NMR, LC-MS, and UV-VIS are used to track the reaction and identify the products/intermediates. It is found that the crosslinking chemistry of a catechol and an amine is both fast and complicated. Within five minutes, more than 60 products are formed. These products encompass 19 different masses ranging from molecular weight of 179 to 704. By combining time-dependent data, it is inferred that the dominant reaction pathways: the majority is formed via aryloxyl-phenol coupling and Michael-type addition, whereas a small fraction of products is formed via Schiff base reactions.
Products and stability of phosphate reactions with lead under freeze-thaw cycling in simple systems

Energy Technology Data Exchange (ETDEWEB)

Hafsteinsdottir, Erla G., E-mail: erla.hafsteinsdottir@gmail.com [Department of Environment and Geography, Macquarie University, NSW 2109 (Australia); White, Duanne A., E-mail: duanne.white@mq.edu.au [Department of Environment and Geography, Macquarie University, NSW 2109 (Australia); Gore, Damian B., E-mail: damian.gore@mq.edu.au [Department of Environment and Geography, Macquarie University, NSW 2109 (Australia); Stark, Scott C., E-mail: scott.stark@aad.gov.au [Environmental Protection and Change, Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and Communities, Tasmania 7050 (Australia)

2011-12-15

Orthophosphate fixation of metal contaminated soils in environments that undergo freeze-thaw cycles is understudied. Freeze-thaw cycling potentially influences the reaction rate, mineral chemical stability and physical breakdown of particles during fixation. This study determines what products form when phosphate (triple superphosphate [Ca(H{sub 2}PO{sub 4}){sub 2}] or sodium phosphate [Na{sub 3}PO{sub 4}]) reacts with lead (PbSO{sub 4} or PbCl{sub 2}) in simple chemical systems in vitro, and assesses potential changes in formation during freeze-thaw cycles. Systems were subjected to multiple freeze-thaw cycles from +10 deg. C to -20 deg. C and then analysed by X-ray diffractometry. Pyromorphite formed in all systems and was stable over multiple freeze-thaw cycles. Low temperature lead orthophosphate reaction efficiency varied according to both phosphate and lead source; the most time-efficient pyromorphite formation was observed when PbSO{sub 4} and Na{sub 3}PO{sub 4} were present together. These findings have implications for the manner in which metal contaminated materials in freezing ground can be treated with phosphate. - Highlights: > Formation of lead phosphate products in cold environments is identified. > Potential change in formation during freeze-thaw cycling is assessed. > Lead phosphate reaction efficiency varies according to phosphate and lead source. > Pyromorphite formation is stable during 240 freeze-thaw cycles. - Pyromorphite, formed from Pb phosphate fixation, is stable during multiple freeze-thaw cycles but the efficiency of the fixation depends on the phosphate source and the type of Pb mineral.
Production of He-, Ne-, Ar-, Kr-, and Xe-isotopes by proton-induced reactions on lead

International Nuclear Information System (INIS)

Leya, I.; Michel, R.

2003-01-01

We measured integral thin target cross sections for the proton-induced production of He-, Ne-, Ar-, Kr-, and Xe-isotopes from lead from the respective reaction thresholds up to 2.6 GeV. The production of noble gas isotopes in lead by proton-induced reactions is of special importance for design studies of accelerator driven systems and energy amplifiers. In order to minimise the influences of secondary particles on the production of residual nuclides a new Mini-Stack approach was used instead of the well-known stacked-foil techniques for all experiments with proton energies above 200 MeV. With some exceptions our database for the proton-induced production of noble gas isotopes from lead is consistent and nearly complete. In contradistinction to the production of He from Al and Fe, where the cross sections obtained by thin-target irradiation experiments are up to a factor of 2 higher than the NESSI data, both datasets agree for the He production from lead. (orig.)
Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

Science.gov (United States)

Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

2007-10-31

Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.
An autonomous organic reaction search engine for chemical reactivity

Science.gov (United States)

Dragone, Vincenza; Sans, Victor; Henson, Alon B.; Granda, Jaroslaw M.; Cronin, Leroy

2017-06-01

The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical reactivity within a network of 64 possible reaction combinations and aims for new reactivity, rather than a predefined set of targets. The robotic system combines chemical handling, in-line spectroscopy and real-time feedback and analysis with an algorithm that is able to distinguish and select the most reactive pathways, generating a reaction selection index (RSI) without need for separate work-up or purification steps. This allows the automatic navigation of a chemical network, leading to previously unreported molecules while needing only to do a fraction of the total possible reactions without any prior knowledge of the chemistry. We show the RSI correlates with reactivity and is able to search chemical space using the most reactive pathways.
Formation pathways of DMSO from DMS-OH in the presence of O(2) and NO(x): A theoretical study.

Science.gov (United States)

Ramírez-Anguita, Juan M; González-Lafont, Angels; Lluch, José M

2009-01-30

The relative importance of the reaction pathways and thus the product yields in the dimethyl sulfide (DMS) degradation scheme initiated by the hydroxyl (OH) radical has been said to be influenced by the content of nitrogen oxides (NO(x)) in chamber experiments. In this study, ab initio and density functional electronic structure calculations of all the possible reaction pathways corresponding to the reaction process initiated by DMS-OH + oxygen (O(2)), leading to the formation of the dimethyl sulfoxide (DMSO) product in the presence of NO(x) (NO and NO(2)), are carried out for the first time. The results for the different pathways are compared with the objective of inferring their kinetic relevance in the laboratory experiments that measure DMSO formation yields. Our theoretical results clearly show the existence of NO(x)-dependent pathways leading to the formation of DMSO in addition to O(2)-dependent channels. So then, NO(x)-containing conditions would have to modify the relative importance of the addition channel in the DMS oxidation process. (c) 2008 Wiley Periodicals, Inc.
Lead (Pb) induced ATM-dependent mitophagy via PINK1/Parkin pathway.

Science.gov (United States)

Gu, Xueyan; Qi, Yongmei; Feng, Zengxiu; Ma, Lin; Gao, Ke; Zhang, Yingmei

2018-07-01

Lead (Pb), a widely distributed environmental pollutant, is known to induce mitochondrial damage as well as autophagy in vitro and in vivo. In this study, we found that Pb could trigger mitophagy in both HEK293 cells and the kidney cortex of male Kunming mice. However, whether ataxia telangiectasis mutated (ATM) which is reported to be linked with PTEN-induced putative kinase 1 (PINK1)/Parkin pathway (a well-characterized mitophagic pathway) participates in the regulation of Pb-induced mitophagy and its exact role remains enigmatic. Our results indicated that Pb activated ATM in vitro and in vivo, and further in vitro studies showed that ATM could co-localize with PINK1 and Parkin in cytosol and interact with PINK1. Knockdown of ATM by siRNA blocked Pb-induced mitophagy even under the circumstance of enhanced accumulation of PINK1 and mitochondrial Parkin. Intriguingly, elevation instead of reduction in phosphorylation level of PINK1 and Parkin was observed in response to ATM knockdown and Pb did not contribute to the further increase of their phosphorylation level, implying that ATM indirectly regulated PINK1/Parkin pathway. These findings reveal a novel mechanism for Pb toxicity and suggest the regulatory importance of ATM in PINK1/Parkin-mediated mitophagy. Copyright © 2018 Elsevier B.V. All rights reserved.
Simulation studies in biochemical signaling and enzyme reactions

Science.gov (United States)

Nelatury, Sudarshan R.; Vagula, Mary C.

2014-06-01

Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.
Combustion modeling and kinetic rate calculations for a stoichiometric cyclohexane flame. 1. Major reaction pathways.

Science.gov (United States)

Zhang, Hongzhi R; Huynh, Lam K; Kungwan, Nawee; Yang, Zhiwei; Zhang, Shaowen

2007-05-17

The Utah Surrogate Mechanism was extended in order to model a stoichiometric premixed cyclohexane flame (P = 30 Torr). Generic rates were assigned to reaction classes of hydrogen abstraction, beta scission, and isomerization, and the resulting mechanism was found to be adequate in describing the combustion chemistry of cyclohexane. Satisfactory results were obtained in comparison with the experimental data of oxygen, major products and important intermediates, which include major soot precursors of C2-C5 unsaturated species. Measured concentrations of immediate products of fuel decomposition were also successfully reproduced. For example, the maximum concentrations of benzene and 1,3-butadiene, two major fuel decomposition products via competing pathways, were predicted within 10% of the measured values. Ring-opening reactions compete with those of cascading dehydrogenation for the decomposition of the conjugate cyclohexyl radical. The major ring-opening pathways produce 1-buten-4-yl radical, molecular ethylene, and 1,3-butadiene. The butadiene species is formed via beta scission after a 1-4 internal hydrogen migration of 1-hexen-6-yl radical. Cascading dehydrogenation also makes an important contribution to the fuel decomposition and provides the exclusive formation pathway of benzene. Benzene formation routes via combination of C2-C4 hydrocarbon fragments were found to be insignificant under current flame conditions, inferred by the later concentration peak of fulvene, in comparison with benzene, because the analogous species series for benzene formation via dehydrogenation was found to be precursors with regard to parent species of fulvene.
An Alternative Reaction Pathway for Iridium Catalyzed Water Oxidation Driven by CAN

KAUST Repository

Bucci, Alberto; Menendez Rodriguez, Gabriel; Bellachioma, Gianfranco; Zuccaccia, Cristiano; Poater, Albert; Cavallo, Luigi; Macchioni, Alceo

2016-01-01

The generation of solar fuels by means of a photosynthetic apparatus strongly relies on the development of an efficient water oxidation catalyst (WOC). Cerium ammonium nitrate (CAN) is the most commonly used sacrificial oxidant to explore the potentiality of WOCs. It is usually assumed that CAN has the unique role to oxidatively energize WOCs, making them capable to offer a low energy reaction pathway to transform H2O to O2. Herein we show that CAN might have a much more relevant and direct role in WO, mainly related to the capture and liberation of O–O containing molecular moieties.
An Alternative Reaction Pathway for Iridium Catalyzed Water Oxidation Driven by CAN

KAUST Repository

Bucci, Alberto

2016-06-10

The generation of solar fuels by means of a photosynthetic apparatus strongly relies on the development of an efficient water oxidation catalyst (WOC). Cerium ammonium nitrate (CAN) is the most commonly used sacrificial oxidant to explore the potentiality of WOCs. It is usually assumed that CAN has the unique role to oxidatively energize WOCs, making them capable to offer a low energy reaction pathway to transform H2O to O2. Herein we show that CAN might have a much more relevant and direct role in WO, mainly related to the capture and liberation of O–O containing molecular moieties.
Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase

NARCIS (Netherlands)

Ridder, L.; Mulholland, A.; Rietjens, I.M.C.M.; Vervoort, J.

1999-01-01

The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the
Conditions for extinction events in chemical reaction networks with discrete state spaces.

Science.gov (United States)

Johnston, Matthew D; Anderson, David F; Craciun, Gheorghe; Brijder, Robert

2018-05-01

We study chemical reaction networks with discrete state spaces and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction event. The conditions we derive involve creating a modified chemical reaction network called a domination-expanded reaction network and then checking properties of this network. Unlike previous results, our analysis allows algorithmic implementation via systems of equalities and inequalities and suggests sequences of reactions which may lead to extinction events. We apply the results to several networks including an EnvZ-OmpR signaling pathway in Escherichia coli.
Food contamination as a pathway for lead exposure in children during the 2010-2013 lead poisoning epidemic in Zamfara, Nigeria.

Science.gov (United States)

Tirima, Simba; Bartrem, Casey; von Lindern, Ian; von Braun, Margrit; Lind, Douglas; Anka, Shehu Mohamed; Abdullahi, Aishat

2018-05-01

In 2010, an estimated 400 to 500 children died of acute lead poisoning associated with artisanal gold mining in Zamfara, Nigeria. Processing of gold ores containing up to 10% lead within residential compounds put residents, especially children, at the highest risk. Principal routes of exposure were incidental ingestion and inhalation of contaminated soil and dusts. Several Nigerian and international health organizations collaborated to reduce lead exposures through environmental remediation and medical treatment. The contribution of contaminated food to total lead exposure was assessed during the environmental health response. Objectives of this investigation were to assess the influence of cultural/dietary habits on lead exposure pathways and estimate the contribution of contaminated food to children's blood lead levels (BLLs). A survey of village dietary practices and staple food lead content was conducted to determine dietary composition, caloric intakes, and lead intake. Potential blood lead increments were estimated using bio-kinetic modeling techniques. Most dietary lead exposure was associated with contamination of staple cereal grains and legumes during post-harvest processing and preparation in contaminated homes. Average post-harvest and processed cereal grain lead levels were 0.32mg/kg and 0.85mg/kg dry weight, respectively. Age-specific food lead intake ranged from 7 to 78μg/day. Lead ingestion and absorption were likely aggravated by the dusty environment, fasting between meals, and nutritional deficiencies. Contamination of staple cereal grains by highly bioavailable pulverized ores could account for as much as 11%-34% of children's BLLs during the epidemic, and were a continuing source after residential soil remediation until stored grain inventories were exhausted. Copyright © 2017. Published by Elsevier B.V.
Solid-state reactions to synthesize nanostructured lead selenide semiconductor powders by high-energy milling

Energy Technology Data Exchange (ETDEWEB)

Rojas-Chavez, H., E-mail: uu_gg_oo@yahoo.com.mx [Centro de Investigacion e Innovacion Tecnologica - IPN, Cerrada de CECATI s/n, Col. Santa Catarina, Del. Azcapotzalco (Mexico) and Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada - IPN, Legaria 694, Col. Irrigacion, Del. Miguel Hidalgo (Mexico); Reyes-Carmona, F. [Facultad de Quimica - UNAM, Circuito de la Investigacion Cientifica s/n, C.U. Del. Coyoacan (Mexico); Jaramillo-Vigueras, D. [Centro de Investigacion e Innovacion Tecnologica - IPN, Cerrada de CECATI s/n, Col. Santa Catarina, Del. Azcapotzalco (Mexico)

2011-10-15

Highlights: {yields} PbSe synthesized from PbO instead of Pb powder do not require an inert atmosphere. {yields} During high-energy milling oxygen has to be chemically reduced from the lead oxide. {yields} Solid-state and solid-gas chemical reactions promote both solid and gaseous products. -- Abstract: Both solid-solid and gas-solid reactions have been traced during high-energy milling of Se and PbO powders under vial (P, T) conditions in order to synthesize the PbSe phase. Chemical and thermodynamic arguments are postulated to discern the high-energy milling mechanism to transform PbO-Se micropowders onto PbSe-nanocrystals. A set of reactions were evaluated at around room temperature. Therefore an experimental campaign was designed to test the nature of reactions in the PbO-Se system during high-energy milling.
Solid-state reactions to synthesize nanostructured lead selenide semiconductor powders by high-energy milling

International Nuclear Information System (INIS)

Rojas-Chavez, H.; Reyes-Carmona, F.; Jaramillo-Vigueras, D.

2011-01-01

Highlights: → PbSe synthesized from PbO instead of Pb powder do not require an inert atmosphere. → During high-energy milling oxygen has to be chemically reduced from the lead oxide. → Solid-state and solid-gas chemical reactions promote both solid and gaseous products. -- Abstract: Both solid-solid and gas-solid reactions have been traced during high-energy milling of Se and PbO powders under vial (P, T) conditions in order to synthesize the PbSe phase. Chemical and thermodynamic arguments are postulated to discern the high-energy milling mechanism to transform PbO-Se micropowders onto PbSe-nanocrystals. A set of reactions were evaluated at around room temperature. Therefore an experimental campaign was designed to test the nature of reactions in the PbO-Se system during high-energy milling.
A mechanochemical study of the effects of compression on a Diels-Alder reaction

Science.gov (United States)

Jha, Sanjiv K.; Brown, Katie; Todde, Guido; Subramanian, Gopinath

2016-08-01

We examine the effects of compressive external forces on the mechanisms of the parent Diels-Alder (DA) reaction between butadiene and ethylene. Reaction pathways and transition states were calculated using the nudged elastic band method within a mechanochemical framework at the CASSCF(6,6)/6-31G**, as well as the B3LYP/6-311++G** levels of theory. Our results suggest that compressive hydrostatic pressure lowers the energy barrier for the parent DA reaction while suppressing the undesirable side reaction, thereby leading to a direct increase in the yield of cyclohexene. Compressive pressure also increases the exothermicity of the parent DA reaction, which would lead to increased temperatures in a reaction vessel and thereby indirectly increase the yield of cyclohexene. Our estimates indicate that the compression used in our study corresponds to a range of 68 MPa-1410 MPa.

Theoretical investigation of the gas-phase reactions of CrO(+) with ethylene.

Science.gov (United States)

Scupp, Thomas M; Dudley, Timothy J

2010-01-21

The potential energy surfaces associated with the reactions of chromium oxide cation (CrO(+)) with ethylene have been characterized using density functional, coupled-cluster, and multireference methods. Our calculations show that the most probable reaction involves the formation of acetaldehyde and Cr(+) via a hydride transfer involving the metal center. Our calculations support previous experimental hypotheses that a four-membered ring intermediate plays an important role in the reactivity of the system. We have also characterized a number of viable reaction pathways that lead to other products, including ethylene oxide. Due to the experimental observation that CrO(+) can activate carbon-carbon bonds, a reaction pathway involving C-C bond cleavage has also been characterized. Since many of the reactions involve a change in the spin state in going from reactants to products, locations of these spin surface crossings are presented and discussed. The applicability of methods based on Hartree-Fock orbitals is also discussed.
Method of determining paper-deposited materials, eg. lead, by their reaction with radioactive krypton

International Nuclear Information System (INIS)

Tolgyessy, J.; Pruzinec, J.

1976-01-01

The invention claims a method of determining substances on a paper carrier based on the substance reaction with 85 Kr gas and the measurement of radioactivity of the kryptonate formed. Lead is shown as an example. Different amounts of lead acetate were deposited on Whatman 2 chromatographic paper as was an unknown sample of Pb salt. The paper was exposed to a 2.5 mCi 85 Kr atmosphere for 48 hours. The activity of the individual spots was then measured, a calibration curve established and the amount of lead in the analyzed sample read-out. (Ha)
Fluid flow pathways through the oceanic crust: reaction permeability and isotopic tracing

Science.gov (United States)

McCaig, Andrew; Castelain, Teddy; Klein, Frieder

2013-04-01

It is generally assumed that the dominant means of creating permeability in ocean floor hydrothermal systems is fracturing, induced either by cooling or by tectonic stress. Here we show textural evidence that metamorphic reactions can create a hierarchy of permeable pathways through gabbroic rocks similar to a fracture hierarchy. Isotopic microsampling shows that just as with fractures, most flow occurs through the larger channelways, and that even at the microscale, flow can be extremely heterogeneous with alteration affecting only certain minerals in the framework, leaving others untouched. Reaction permeability is created in three ways; dissolution creating open porosity, microcracking due to volume increase reactions involving olivine, and expansion of water due to rapid heating in dyke margins, particularly when intruded into brecciated rocks. Our data comes from IODP Hole U1309D, which was drilled to 1400 mbsf in the footwall of the Atlantis Massif detachment fault at the Mid-Atlantic Ridge 30°N. The core is composed of gabbroic rocks interlayered with olivine rich troctolites, with several basalt/diabase sills in the top 130 m. The dominant alteration occurred in the greenschist facies, at depths at least 1 km below seafloor, and decreases in intensity downhole. Whole rock oxygen isotope values range from +5.5 permil to +1.5 permil, indicating variable degrees of interaction with seawater at temperatures generally > 250 °C. Gabbroic rocks and diabases exhibit a range of Sr isotope ratios from MORB values (0.70261) to intermediate ratios (0.70429). Microsampling shows that amphiboles are often more radiogenic than coexisting plagioclase and can sometimes be isotopically altered in the same rock as completely unaltered primary minerals. Large (10 cm) amphibole-filled vugs show values ranging up to 0.708, close to seawater. In some cases however the secondary minerals are virtually unaltered indicating low fluid fluxes in pervasive alteration. SEM textures in
Confining Domains Lead to Reaction Bursts: Reaction Kinetics in the Plasma Membrane

Science.gov (United States)

Kalay, Ziya; Fujiwara, Takahiro K.; Kusumi, Akihiro

2012-01-01

Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity. PMID:22479350
Confining domains lead to reaction bursts: reaction kinetics in the plasma membrane.

Directory of Open Access Journals (Sweden)

Ziya Kalay

Full Text Available Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity.
Probabilistic pathway construction.

Science.gov (United States)

Yousofshahi, Mona; Lee, Kyongbum; Hassoun, Soha

2011-07-01

Expression of novel synthesis pathways in host organisms amenable to genetic manipulations has emerged as an attractive metabolic engineering strategy to overproduce natural products, biofuels, biopolymers and other commercially useful metabolites. We present a pathway construction algorithm for identifying viable synthesis pathways compatible with balanced cell growth. Rather than exhaustive exploration, we investigate probabilistic selection of reactions to construct the pathways. Three different selection schemes are investigated for the selection of reactions: high metabolite connectivity, low connectivity and uniformly random. For all case studies, which involved a diverse set of target metabolites, the uniformly random selection scheme resulted in the highest average maximum yield. When compared to an exhaustive search enumerating all possible reaction routes, our probabilistic algorithm returned nearly identical distributions of yields, while requiring far less computing time (minutes vs. years). The pathways identified by our algorithm have previously been confirmed in the literature as viable, high-yield synthesis routes. Prospectively, our algorithm could facilitate the design of novel, non-native synthesis routes by efficiently exploring the diversity of biochemical transformations in nature. Copyright © 2011 Elsevier Inc. All rights reserved.
A Networks Approach to Modeling Enzymatic Reactions.

Science.gov (United States)

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.
Pathways and Mechanisms Underlying the Photophysics and Photochemistry of Riboflavin induced cornea crosslinking

DEFF Research Database (Denmark)

Breitenbach, Thomas; Ogilby, Peter Remsen

In this talk, we will describe general pathways involved in the photophysics of a photosensitized process, which can lead to crosslinking due to light excitation of Riboflavin in the cornea. Furthermore, we will elucidate different aspects of reactions that can produce crosslinks, with respect...
Reaction pathway and oxidation mechanisms of dibutyl phthalate by persulfate activated with zero-valent iron

Energy Technology Data Exchange (ETDEWEB)

Li, Huanxuan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); Wan, Jinquan, E-mail: ppjqwan@scut.edu.cn [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Ma, Yongwen [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Wang, Yan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China)

2016-08-15

This study investigated reaction pathway and oxidation mechanisms of dibutyl phthalate (DBP) by persulfate (PS) activated with zero-valent iron (ZVI). The DBP degradation was studied at three pH values (acidic, neutral and basic) in the presence of different organic scavengers. Using a chemical probe method, both sulfate radical (SO{sub 4}·{sup −}) and hydroxyl radical (·OH) were found to be primary oxidants at pH 3.0 and pH 7.0, respectively while ·OH was the major specie to oxidize DBP at pH 11.0. A similar result was found in an experiment of Electron Spin Resonance spin-trapping where in addition to ·OH, superoxide radical (O{sub 2}·{sup −}) was detected at pH 11.0. The transformation of degradation products including dimethyl phthalate (DMP), diethyl phthalate (DEP), phthalic anhydride, and acetophenone exhibited diverse variation during the reaction processes. The phthalic anhydride concentration appeared to be maximum at all pHs. Another eleven intermediate products were also found at pH 3.0 by GC–MS and HPLC analysis, and their degradation mechanisms and pathways were proposed. It was suggested that dealkylation, hydroxylation, decarboxylation and hydrogen extraction were the dominant degradation mechanisms of DBP at pH 3.0. - Highlights: • Both SO{sub 4}{sup −}· and ·OH were found to be the major active species at pH 3.0 and pH 7.0. • ·OH and ·O2– were the primary oxidants pH 11.0. • The intermediate products were investigated as well as the degradation pathway. • Dealkylation, hydroxylation, decarboxylation, H-extraction were the major mechanisms.
Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

Science.gov (United States)

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-04-10

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.
Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

Directory of Open Access Journals (Sweden)

Xue Zhang

2015-04-01

Full Text Available As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs and polychlorinated biphenyls (PCBs are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD. Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.
Recyclization reactions leading to benzimidazoles

Science.gov (United States)

Mamedov, Vakhid A.; Murtazina, Anna M.

2011-05-01

The published data on the recyclization reactions that afford benzimidazoles are generalized and systematized. Both classical and new methods of benzimidazole synthesis are considered. Attention is focused on the publications over the recent 10-15 years; of the earlier publications, only those unknown to the wide circle of chemists are analyzed.
Recyclization reactions leading to benzimidazoles

International Nuclear Information System (INIS)

Mamedov, Vakhid A; Murtazina, Anna M

2011-01-01

The published data on the recyclization reactions that afford benzimidazoles are generalized and systematized. Both classical and new methods of benzimidazole synthesis are considered. Attention is focused on the publications over the recent 10-15 years; of the earlier publications, only those unknown to the wide circle of chemists are analyzed.
Anodic Cyclization Reactions and the Mechanistic Strategies That Enable Optimization.

Science.gov (United States)

Feng, Ruozhu; Smith, Jake A; Moeller, Kevin D

2017-09-19

Oxidation reactions are powerful tools for synthesis because they allow us to reverse the polarity of electron-rich functional groups, generate highly reactive intermediates, and increase the functionality of molecules. For this reason, oxidation reactions have been and continue to be the subject of intense study. Central to these efforts is the development of mechanism-based strategies that allow us to think about the reactive intermediates that are frequently central to the success of the reactions and the mechanistic pathways that those intermediates trigger. For example, consider oxidative cyclization reactions that are triggered by the removal of an electron from an electron-rich olefin and lead to cyclic products that are functionalized for further elaboration. For these reactions to be successful, the radical cation intermediate must first be generated using conditions that limit its polymerization and then channeled down a productive desired pathway. Following the cyclization, a second oxidation step is necessary for product formation, after which the resulting cation must be quenched in a controlled fashion to avoid undesired elimination reactions. Problems can arise at any one or all of these steps, a fact that frequently complicates reaction optimization and can discourage the development of new transformations. Fortunately, anodic electrochemistry offers an outstanding opportunity to systematically probe the mechanism of oxidative cyclization reactions. The use of electrochemical methods allows for the generation of radical cations under neutral conditions in an environment that helps prevent polymerization of the intermediate. Once the intermediates have been generated, a series of "telltale indicators" can be used to diagnose which step in an oxidative cyclization is problematic for less successful transformation. A set of potential solutions to address each type of problem encountered has been developed. For example, problems with the initial
Development and implementation of a critical pathway for prevention of adverse reactions to contrast media for computed tomography

International Nuclear Information System (INIS)

Jang, Keun Jo; Kweon, Dae Cheol; Kim, Myeong Goo; Yoo, Beong Gyu

2007-01-01

The purpose of this study is to develop a critical pathway (CP) for the prevention of adverse reactions to contrast media for computed tomography. The CP was developed and implemented by a multidisciplinary group is Seoul National University Hospital. The CP was applied to CT patients. Patients who underwent CT scanning were included in the CP group from March in 2004. The satisfaction of the patients with CP was compared with non-CP groups. We also investigated the degree of satisfaction among the radiological technologists and nurses. The degree of patient satisfaction with the care process increased patient information (24%), prevention of adverse reactions to contrast media (19%), pre-cognitive effect of adverse reactions to contrast media (39%) and information degree of adverse reactions to contrast media (19%). This CP program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings
Development and implementation of a critical pathway for prevention of adverse reactions to contrast media for computed tomography

Energy Technology Data Exchange (ETDEWEB)

Jang, Keun Jo [Presbyterian Medical Center, Seoul (Korea, Republic of); Kweon, Dae Cheol; Kim, Myeong Goo [Seoul National University Hospital, Seoul (Korea, Republic of); Yoo, Beong Gyu [Wonkwang Health Science College, Iksan (Korea, Republic of)

2007-03-15

The purpose of this study is to develop a critical pathway (CP) for the prevention of adverse reactions to contrast media for computed tomography. The CP was developed and implemented by a multidisciplinary group is Seoul National University Hospital. The CP was applied to CT patients. Patients who underwent CT scanning were included in the CP group from March in 2004. The satisfaction of the patients with CP was compared with non-CP groups. We also investigated the degree of satisfaction among the radiological technologists and nurses. The degree of patient satisfaction with the care process increased patient information (24%), prevention of adverse reactions to contrast media (19%), pre-cognitive effect of adverse reactions to contrast media (39%) and information degree of adverse reactions to contrast media (19%). This CP program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings.
Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".

Science.gov (United States)

Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J; Nauta, Arjen; Geurts, Jan M W

2014-01-01

The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the "missing links" between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology.
Catalytic Hydrotreatment of Fast Pyrolysis Oil: Model Studies on Reaction Pathways for the Carbohydrate Fraction

OpenAIRE

Wildschut, J.; Arentz, J.; Rasrendra, C. B.; Venderbosch, R. H.; Heeres, H. J.

2009-01-01

Fast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250-400 degrees C, 100-200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon-like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions during hydrotreatment is desirable to reduce the formation of by-products such as char and gaseous components. This paper deals with the catalytic hydrotreatment of representative model components for t...
Modeling reaction histories to study chemical pathways in condensed phase detonation

International Nuclear Information System (INIS)

Scott Stewart, D.; Hernández, Alberto; Lee, Kibaek

2016-01-01

The estimation of pressure and temperature histories, which are required to understand chemical pathways in condensed phase explosives during detonation, is discussed. We argue that estimates made from continuum models, calibrated by macroscopic experiments, are essential to inform modern, atomistic-based reactive chemistry simulations at detonation pressures and temperatures. We present easy to implement methods for general equation of state and arbitrarily complex chemical reaction schemes that can be used to compute reactive flow histories for the constant volume, the energy process, and the expansion process on the Rayleigh line of a steady Chapman-Jouguet detonation. A brief review of state-of-the-art of two-component reactive flow models is given that highlights the Ignition and Growth model of Lee and Tarver [Phys. Fluids 23, 2362 (1980)] and the Wide-Ranging Equation of State model of Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. We discuss evidence from experiments and reactive molecular dynamic simulations that motivate models that have several components, instead of the two that have traditionally been used to describe the results of macroscopic detonation experiments. We present simplified examples of a formulation for a hypothetical explosive that uses simple (ideal) equation of state forms and detailed comparisons. Then, we estimate pathways computed from two-component models of real explosive materials that have been calibrated with macroscopic experiments.
Centrality in Hadron-Carbon, Hadron-Lead, and Lead-Lead Reactions at 158 GeV/c

International Nuclear Information System (INIS)

Rybicki, A.

2006-08-01

A study of centrality in p + C, π + C, p + Pb, π + Pb, and Pb + Pb reactions is made. The analysis is performed by means of a simple geometrical model. The mean number of elementary collisions, , is estimated in minimum bias p + C reactions. For the specific case of the carbon nucleus, estimates on appear to depend strongly on assumed nuclear densities. Most realistic of the presented assumptions result in a value of 1.71 ± 0.05. Additional quantities, like predictions for the total inelastic cross-section in p + C reactions, or the number of participants in minimum bias C + C collisions, are given. The analysis is subsequently extended to minimum bias π + C, π + Pb, and p + Pb reactions. Estimates are given for the mean number of elementary collisions as well as for the contribution of single collisions P(1). A comparison with experimental data is made. Finally, the impact parameter dependence of p + Pb and Pb + Pb collisions is discussed. In view of future studies, various aspects of the analysis are discussed in detail; a bibliography of used references is included. (author)

Surface-Activated Coupling Reactions Confined on a Surface.

Science.gov (United States)

Dong, Lei; Liu, Pei Nian; Lin, Nian

2015-10-20

-functional theory (DFT) transition-state calculations have been used to shed light on reaction mechanisms and to unravel the trends of different surface materials. In this Account, we discuss recent progress made in two widely studied surface-confined coupling reactions, aryl-aryl (Ullmann-type) coupling and alkyne-alkyne (Glaser-type) coupling, and focus on surface activation effects. Combined experimental and theoretical studies on the same reactions taking place on different metal surfaces have clearly demonstrated that different surfaces not only reduce the reaction barrier differently and render different reaction pathways but also control the morphology of the reaction products and, to some degree, select the reaction products. We end the Account with a list of questions to be addressed in the future. Satisfactorily answering these questions may lead to using the surface-confined coupling reactions to synthesize predefined products with high yield.
Chemical reactions confined within carbon nanotubes.

Science.gov (United States)

Miners, Scott A; Rance, Graham A; Khlobystov, Andrei N

2016-08-22

In this critical review, we survey the wide range of chemical reactions that have been confined within carbon nanotubes, particularly emphasising how the pairwise interactions between the catalysts, reactants, transition states and products of a particular molecular transformation with the host nanotube can be used to control the yields and distributions of products of chemical reactions. We demonstrate that nanoscale confinement within carbon nanotubes enables the control of catalyst activity, morphology and stability, influences the local concentration of reactants and products thus affecting equilibria, rates and selectivity, pre-arranges the reactants for desired reactions and alters the relative stability of isomeric products. We critically evaluate the relative advantages and disadvantages of the confinement of chemical reactions inside carbon nanotubes from a chemical perspective and describe how further developments in the controlled synthesis of carbon nanotubes and the incorporation of multifunctionality are essential for the development of this ever-expanding field, ultimately leading to the effective control of the pathways of chemical reactions through the rational design of multi-functional carbon nanoreactors.
Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction

DEFF Research Database (Denmark)

Solov'yov, Ilia; Domratcheva, Tatiana; Shahi, Abdul Rehaman Moughal

2012-01-01

of cryptochrome must arise from the photoactivation reaction occurring in the protein: exposure to blue light results in electron transfer to a flavin pigment co-factor, leading to formation of an electron spin-entangled pair of radicals. Theoretical and experimental studies established long ago that such radical...... pairs, indeed, can act as a magnetic compass. The photo-reaction pathway in cryptochrome is not fully resolved yet. We employ ab initio quantum chemistry and classical all-atom MD simulations for Arabidopsis thaliana cryptochrome to determine how the radical pair is formed, becomes stabilized through...
Effects of Water Molecule on CO Oxidation by OH: Reaction Pathways, Kinetic Barriers, and Rate Constants.

Science.gov (United States)

Zhang, Linyao; Yang, Li; Zhao, Yijun; Zhang, Jiaxu; Feng, Dongdong; Sun, Shaozeng

2017-07-06

The water dilute oxy-fuel combustion is a clean combustion technology for near-zero emission power; and the presence of water molecule could have both kinetic and dynamic effects on combustion reactions. The reaction OH + CO → CO 2 + H, one of the most important elementary reactions, has been investigated by extensive electronic structure calculations. And the effects of a single water molecule on CO oxidation have been studied by considering the preformed OH(H 2 O) complex reacts with CO. The results show little change in the reaction pathways, but the additional water molecule actually increases the vibrationally adiabatic energy barriers (V a G ). Further thermal rate constant calculations in the temperature range of 200 to 2000 K demonstrate that the total low-pressure limit rate constant for the water assisted OH(H 2 O) + CO → CO 2 + H 2 O + H reaction is 1-2 orders lower than that of the water unassisted one, which is consistent with the change of V a G . Therefore, the hydrated radical OH(H 2 O) would actually slow down the oxidation of CO. Meanwhile, comparisons show that the M06-2X/aug-cc-pVDZ method gives a much better estimation in energy and thus is recommended to be employed for direct dynamics simulations.
Organosulfate Formation through the Heterogeneous Reaction of Sulfur Dioxide with Unsaturated Compounds

Science.gov (United States)

George, C.; Passananti, M.; Kong, L.; Shang, J.; Perrier, S.; Jianmin, C.; Donaldson, D. J.

2016-12-01

The atmospheric formation of organosulfur derivatives through reaction with SO2 is generally mediated by oxidants such as O3, OH; recently we have proposed a direct reaction between SO2 and unsaturated compounds as another possible pathway for organosulfate formation in the troposphere. For the first time it was shown recently that a heterogeneous reaction between SO2 and oleic acid (OA; an unsaturated fatty acid) takes place and leads efficiently to the formation of organosulfur products. Here, we demonstrate that this reaction proceeds on various unsaturated compounds, and may therefore have a general environmental impact. We used different experimental strategies i.e., a coated flow tube (CFT), an aerosol flow tube (AFT) and a DRIFT (diffuse reflectance infrared Fourier transform) cell. The reaction products were analyzed by means of liquid chromatography coupled to a high resolution mass spectrometer (LC-HR-MS). We report indeed that SO2 reacts with large variety of C=C unsaturations and that even in the presence of ozone, SO2 reacts with OA leading to organosulfur products. A strong enhancement in product formation is observed under actinic illumination, increases the atmospheric significance of this chemical pathway. This is probably due to the chromophoric nature of the SO2 adduct with C=C bonds, and means that the contribution of this direct addition of SO2 could be in excess of 5%. The detection in atmospheric aerosols of organosulfur compounds with the same chemical formulae as the products identified here seems to confirm the importance of this reaction in the atmosphere.
One-step simultaneous differential scanning calorimetry-FTIR microspectroscopy to quickly detect continuous pathways in the solid-state glucose/asparagine Maillard reaction.

Science.gov (United States)

Hwang, Deng-Fwu; Hsieh, Tzu-Feng; Lin, Shan-Yang

2013-01-01

The stepwise reaction pathway of the solid-state Maillard reaction between glucose (Glc) and asparagine (Asn) was investigated using simultaneous differential scanning calorimetry (DSC)-FTIR microspectroscopy. The color change and FTIR spectra of Glc-Asn physical mixtures (molar ratio = 1:1) preheated to different temperatures followed by cooling were also examined. The successive reaction products such as Schiff base intermediate, Amadori product, and decarboxylated Amadori product in the solid-state Glc-Asn Maillard reaction were first simultaneously evidenced by this unique DSC-FTIR microspectroscopy. The color changed from white to yellow-brown to dark brown, and appearance of new IR peaks confirmed the formation of Maillard reaction products. The present study clearly indicates that this unique DSC-FTIR technique not only accelerates but also detects precursors and products of the Maillard reaction in real time.
Elementary steps and reaction pathways in the aqueous phase alkylation of phenol with ethanol

Energy Technology Data Exchange (ETDEWEB)

Eckstein, Sebastian; Hintermeier, Peter H.; Olarte, Mariefel V.; Liu, Yue; Baráth, Eszter; Lercher, Johannes A.

2017-08-01

The hydronium ion normalized reaction rate in aqueous phase alkylation of phenol with ethanol on H-MFI zeolites increases with decreasing concentration of acid sites. Higher rates are caused by higher concentrations of phenol in the zeolite pores, as the concentration of hydronium ions generated by zeolite Brønsted acid sites decreases. Considering the different concentrations of reacting species it is shown that the intrinsic rate constant for alkylation is independent of the concentration of hydronium ions in the zeolite pores. Alkylation at the aromatic ring of phenol and of toluene as well as O-alkylation of phenol have the same activation energy, 104 ± 5 kJ/mol. This is energetic barrier to form the ethyl carbenium ion from ethanol associated to the hydronium ion. Thus, in both the reaction pathways the catalyst involves a carbenium ion, which forms a bond to a nucleophilic oxygen (ether formation) or carbon (alkylation).
Reaction between peroxynitrite and boronates: EPR spin-trapping, HPLC analyses, and quantum mechanical study of the free radical pathway

Science.gov (United States)

Sikora, Adam; Zielonka, Jacek; Lopez, Marcos; Dybala-Defratyka, Agnieszka; Joseph, Joy; Marcinek, Andrzej; Kalyanaraman, Balaraman

2013-01-01

Recently we showed that peroxynitrite (ONOO−) reacts directly and rapidly with aromatic and aliphatic boronic acids (k ≈ 106 M−1s−1). Product analyses and substrate consumption data indicated that ONOO− reacts stoichiometrically with boronates, yielding the corresponding phenols as the major product (~85–90%), and the remaining products (10–15%) were proposed to originate from free radical intermediates (phenyl and phenoxyl radicals). Here we investigated in detail the minor, free radical pathway of boronate reaction with ONOO−. The electron paramagnetic resonance (EPR) spin-trapping technique was used to characterize the free radical intermediates formed from the reaction between boronates and ONOO−. Using 2-methyl-2-nitrosopropane (MNP) and 5-diethoxyphosphoryl-5-methyl-1-pyrroline-N-oxide (DEPMPO) spin traps, phenyl radicals were trapped and detected. Although phenoxyl radicals were not detected, the positive effects of molecular oxygen, and inhibitory effects of hydrogen atom donors (acetonitrile, and 2-propanol) and general radical scavengers (GSH, NADH, ascorbic acid and tyrosine) on the formation of phenoxyl radical-derived nitrated product, suggest that phenoxyl radical was formed as the secondary species. We propose that the initial step of the reaction involves the addition of ONOO− to the boron atom in boronates. The anionic intermediate undergoes both heterolytic (major pathway) and homolytic (minor pathway) cleavage of the peroxy (O-O) bond to form phenol and nitrite as a major product (via a non-radical mechanism), or a radical pair PhB(OH)2O•−…•NO2 as a minor product. It is conceivable that phenyl radicals are formed by the fragmentation of PhB(OH)2O•− radical anion. According to the DFT quantum mechanical calculations, the energy barrier for the dissociation of PhB(OH)2O•− radical anion to form phenyl radicals is only a few kcal/mol, suggesting rapid and spontaneous fragmentation of PhB(OH)2O•− radical anion
Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway.

Science.gov (United States)

Ries, Marco I; Ali, Hazrat; Lankhorst, Peter P; Hankemeier, Thomas; Bovenberg, Roel A L; Driessen, Arnold J M; Vreeken, Rob J

2013-12-27

Metabolic profiling and structural elucidation of novel secondary metabolites obtained from derived deletion strains of the filamentous fungus Penicillium chrysogenum were used to reassign various previously ascribed synthetase genes of the roquefortine/meleagrin pathway to their corresponding products. Next to the structural characterization of roquefortine F and neoxaline, which are for the first time reported for P. chrysogenum, we identified the novel metabolite roquefortine L, including its degradation products, harboring remarkable chemical structures. Their biosynthesis is discussed, questioning the exclusive role of glandicoline A as key intermediate in the pathway. The results reveal that further enzymes of this pathway are rather unspecific and catalyze more than one reaction, leading to excessive branching in the pathway with meleagrin and neoxaline as end products of two branches.
Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A: Kinetics, reaction pathways, and formation of brominated by-products

Energy Technology Data Exchange (ETDEWEB)

Ji, Yuefei [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China); Kong, Deyang [Nanjing Institute of Environmental Science, Ministry of Environmental Protection of PRC, Nanjing 210042 (China); Lu, Junhe, E-mail: jhlu@njau.edu.cn [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China); Jin, Hao; Kang, Fuxing; Yin, Xiaoming; Zhou, Quansuo [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China)

2016-08-05

Highlights: • Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A. • Phenolic moiety was the reactive site for sulfate radical attack. • Pathways include β-scission, oxidation, debromination and coupling reactions. • Brominated disinfection by-products were found during TBBPA degradation. • Humic acid inhibited TBBPA degradation but promoted DBPs formation. - Abstract: Degradation of tetrabromobisphenol A (TBBPA), a flame retardant widely spread in the environment, in Co(II) catalyzed peroxymonosulfate (PMS) oxidation process was systematically explored. The second-order-rate constant for reaction of sulfate radical (SO{sub 4}{sup ·−}) with TBBPA was determined to be 5.27 × 10{sup 10} M{sup −1} s{sup −1}. Apparently, degradation of TBBPA showed first-order kinetics to the concentrations of both Co(II) and PMS. The presence of humic acid (HA) and bicarbonate inhibited TBBPA degradation, most likely due to their competition for SO{sub 4}{sup ·−}. Degradation of TBBPA was initiated by an electron abstraction from one of the phenolic rings. Detailed transformation pathways were proposed, including β-scission of isopropyl bridge, phenolic ring oxidation, debromination and coupling reactions. Further oxidative degradation of intermediates in Co(II)/PMS process yielded brominated disinfection by-products (Br-DBPs) such as bromoform and brominated acetic acids. Evolution profile of Br-DBPs showed an initially increasing and then decreasing pattern with maximum concentrations occurring around 6–10 h. The presence of HA enhanced the formation of Br-DBPs significantly. These findings reveal potentially important, but previously unrecognized, formation of Br-DBPs during sulfate radical-based oxidation of bromide-containing organic compounds that may pose toxicological risks to human health.
Palladium-catalyzed three-component reaction of N-tosyl hydrazones, isonitriles and amines leading to amidines.

Science.gov (United States)

Dai, Qiang; Jiang, Yan; Yu, Jin-Tao; Cheng, Jiang

2015-12-04

A palladium-catalyzed three-component reaction between N-tosyl hydrazones, aryl isonitriles and amines was developed, leading to amidines in moderate to good yields. This procedure features the rapid construction of amidine frameworks with high diversity and complexity. Ketenimines serve as intermediates, which encounter nucleophilic attack by amines to produce amidines.
Reaction chemistry in rechargeable Li-O2 batteries.

Science.gov (United States)

Lim, Hee-Dae; Lee, Byungju; Bae, Youngjoon; Park, Hyeokjun; Ko, Youngmin; Kim, Haegyeom; Kim, Jinsoo; Kang, Kisuk

2017-05-22

The seemingly simple reaction of Li-O 2 batteries involving lithium and oxygen makes this chemistry attractive for high-energy-density storage systems; however, achieving this reaction in practical rechargeable Li-O 2 batteries has proven difficult. The reaction paths leading to the final Li 2 O 2 discharge products can be greatly affected by the operating conditions or environment, which often results in major side reactions. Recent research findings have begun to reveal how the reaction paths may be affected by the surrounding conditions and to uncover the factors contributing to the difficulty in achieving the reactions of lithium and oxygen. This progress report describes the current state of understanding of the electrode reaction mechanisms in Li-O 2 batteries; the factors that affect reaction pathways; and the effect of cell components such as solvents, salts, additives, and catalysts on the discharge product and its decomposition during charging. This comprehensive review of the recent progress in understanding the reaction chemistry of the Li-O 2 system will serve as guidelines for future research and aid in the development of reliable high-energy-density rechargeable Li-O 2 batteries.
Prediction of novel synthetic pathways for the production of desired chemicals

Directory of Open Access Journals (Sweden)

Park Jin

2010-03-01

Full Text Available Abstract Background There have been several methods developed for the prediction of synthetic metabolic pathways leading to the production of desired chemicals. In these approaches, novel pathways were predicted based on chemical structure changes, enzymatic information, and/or reaction mechanisms, but the approaches generating a huge number of predicted results are difficult to be applied to real experiments. Also, some of these methods focus on specific pathways, and thus are limited to expansion to the whole metabolism. Results In the present study, we propose a system framework employing a retrosynthesis model with a prioritization scoring algorithm. This new strategy allows deducing the novel promising pathways for the synthesis of a desired chemical together with information on enzymes involved based on structural changes and reaction mechanisms present in the system database. The prioritization scoring algorithm employing Tanimoto coefficient and group contribution method allows examination of structurally qualified pathways to recognize which pathway is more appropriate. In addition, new concepts of binding site covalence, estimation of pathway distance and organism specificity were taken into account to identify the best synthetic pathway. Parameters of these factors can be evolutionarily optimized when a newly proven synthetic pathway is registered. As the proofs of concept, the novel synthetic pathways for the production of isobutanol, 3-hydroxypropionate, and butyryl-CoA were predicted. The prediction shows a high reliability, in which experimentally verified synthetic pathways were listed within the top 0.089% of the identified pathway candidates. Conclusions It is expected that the system framework developed in this study would be useful for the in silico design of novel metabolic pathways to be employed for the efficient production of chemicals, fuels and materials.
Voltammetry coupled to mass spectrometry in the presence of isotope {sup 18}O labeled water for the prediction of oxidative transformation pathways of activated aromatic ethers: Acebutolol

Energy Technology Data Exchange (ETDEWEB)

Bussy, Ugo; Tea, Illa [LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Ferchaud-Roucher, Véronique; Krempf, Michel [Université de Nantes, Plateforme Spectrométrie de Masse, CRNH, SFR Santé F. Bonamy, Institut du Thorax, UMR S1087, IRT-UN, BP 70721, 8 Quai Moncousu, 44007 Nantes cedex 1 (France); Silvestre, Virginie; Galland, Nicolas [LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Jacquemin, Denis [LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Institut Universitaire de France, 103, Boulevard Saint-Michel, 75005 Cedex 5 France (France); Andresen-Bergström, Moa; Jurva, Ulrik [CVGI iMed DMPK, AstraZeneca R and D Mölndal, Mölndal (Sweden); and others

2013-01-31

Highlights: ► Voltammetry coupled to mass spectrometry method as a useful tool for on-line predictions of electrochemical transformations. ► Evidence of the O-dealkoxylation reaction pathway of acebutolol in the presence of labeled water. ► New approach for on line EC-MS applications. -- Abstract: The coupling between an electrochemical cell (EC) and a mass spectrometer (MS) is a useful screening tool (EC-MS) to study the oxidative transformation pathways of various electroactive species. For that purpose, we showed that the EC-MS method, carried out in the presence and absence of isotope {sup 18}O labeled water leads not only to a fast identification of oxidation products but also leads to a fast elucidation of the mechanism pathway reaction. We examined herein the case of the electrochemical hydrolysis of activated aromatic ether. Acebutolol (β-blockers) was selected herein as model of activated aromatic ether, and its electrochemical oxidation was examined in both the presence and absence of isotope {sup 18}O labeled water. To elucidate electrochemical hydrolysis pathway reaction: O-dealkylation or O-dealkoxylation, our approach was used to prove its applicability. The electrochemical oxidation mechanism was then elucidated showing an O-dealkoxylation reaction. In addition, density functional theory (DFT) calculations fully support the experimental conclusions.
Extracting reaction networks from databases-opening Pandora's box.

Science.gov (United States)

Fearnley, Liam G; Davis, Melissa J; Ragan, Mark A; Nielsen, Lars K

2014-11-01

Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge. © The Author 2013. Published by Oxford University Press.
DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

Science.gov (United States)

Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

2017-09-24

We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.
Unconventional exo selectivity in thermal normal-electron-demand Diels-Alder reactions

Science.gov (United States)

Ho, Guo-Ming; Huang, Ci-Jhang; Li, Elise Yu-Tzu; Hsu, Sheng-Kai; Wu, Ti; Zulueta, Medel Manuel L.; Wu, Kevin Binchia; Hung, Shang-Cheng

2016-10-01

The Diels-Alder reaction is a useful tool for generating functionalized chiral molecules through the concerted cycloaddition of dienes and dienophiles leading to six-membered rings. Traditionally, the selective predictions of the products rely heavily on consideration of the secondary orbital interactions that stabilize the endo pathway. However, there remain some basic examples defying this notion and produce the exo-isomer as major product. Here we systematically evaluated of the structural features driving exo selectivity in thermal normal-electron-demand Diels-Alder reactions. Substitution at the Cβ position and the size and electronegativity of the electron-withdrawing group of the dienophile are contributing factors. Experimental and computational studies both point toward the steric and electrostatic forces between the substituents in both the diene and the dienophile that increase the likelihood of the exo pathway. For these substrates, the dominance of the endo pathway is reduced by transition state distortions and poor structural alignments of the reacting partners. We also noted the tilt of the dienophile with respect to the diene causing steric strain on the functionalities at the more advanced bond forming carbon-carbon position of the endo transition state. Insights into such factors may benefit synthetic planning and asserting control over this important named reaction.
Theoretical study of the oxidation mechanisms of naphthalene initiated by hydroxyl radicals: the OH-addition pathway.

Science.gov (United States)

Shiroudi, Abolfazl; Deleuze, Michael S; Canneaux, Sébastien

2014-07-03

The oxidation mechanisms of naphthalene by OH radicals under inert (He) conditions have been studied using density functional theory along with various exchange-correlation functionals. Comparison has been made with benchmark CBS-QB3 theoretical results. Kinetic rate constants were correspondingly estimated by means of transition state theory and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Comparison with experiment confirms that, on the OH-addition reaction pathway leading to 1-naphthol, the first bimolecular reaction step has an effective negative activation energy around -1.5 kcal mol(-1), whereas this step is characterized by an activation energy around 1 kcal mol(-1) on the OH-addition reaction pathway leading to 2-naphthol. Effective rate constants have been calculated according to a steady state analysis upon a two-step model reaction mechanism. In line with experiment, the correspondingly obtained branching ratios indicate that, at temperatures lower than 410 K, the most abundant product resulting from the oxidation of naphthalene by OH radicals must be 1-naphthol. The regioselectivity of the OH(•)-addition onto naphthalene decreases with increasing temperatures and decreasing pressures. Because of slightly positive or even negative activation energies, the RRKM calculations demonstrate that the transition state approximation breaks down at ambient pressure (1 bar) for the first bimolecular reaction steps. Overwhelmingly high pressures, larger than 10(5) bar, would be required for restoring to some extent (within ∼5% accuracy) the validity of this approximation for all the reaction channels that are involved in the OH-addition pathway. Analysis of the computed structures, bond orders, and free energy profiles demonstrate that all reaction steps involved in the oxidation of naphthalene by OH radicals satisfy Leffler-Hammond's principle. Nucleus independent chemical shift indices and natural bond orbital analysis also show that the computed
Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

Science.gov (United States)

Zhang, Hong; Zuo, Ran; Zhang, Guoyi

2017-11-01

In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.
Pyrite formation and mineral transformation pathways upon sulfidation of ferric hydroxides depend on mineral type and sulfide concentration

NARCIS (Netherlands)

Peiffer, Stefan; Behrends, Thilo; Hellige, Katrin; Larese-Casanova, Philip; Wan, Moli; Pollok, Kilian

2015-01-01

The reaction of ferric (hydr)oxides with dissolved sulfide does not lead to the instantaneous production of thermodynamically stable products but can induce a variety of mineral transformations including the formation of metastable intermediates. The importance of the various transformation pathways

Evaluation of potential reaction mechanisms leading to the formation of coniferyl alcohol α-linkages in lignin: a density functional theory study.

Science.gov (United States)

Watts, Heath D; Mohamed, Mohamed Naseer Ali; Kubicki, James D

2011-12-21

Five potential reaction mechanisms, each leading to the formation of an α-O-4-linked coniferyl alcohol dimer, and one scheme leading to the formation of a recently proposed free-radical coniferyl alcohol trimer were assessed using density functional theory (DFT) calculations. These potential reaction mechanisms were evaluated using both the calculated Gibbs free energies, to predict the spontaneity of the constituent reactions, and the electron-density mapped Fukui function, to determine the most reactive sites of each intermediate species. The results indicate that each reaction in one of the six mechanisms is thermodynamically favorable to those in the other mechanisms; what is more, the Fukui function for each free radical intermediate corroborates with the thermochemical results for this mechanism. This mechanism proceeds via the formation of two distinct free-radical intermediates, which then react to produce the four α-O-4 stereoisomers.
Mechanisms for the inversion of chirality: Global reaction route mapping of stereochemical pathways in a probable chiral extraterrestrial molecule, 2-aminopropionitrile

International Nuclear Information System (INIS)

Kaur, Ramanpreet; Vikas

2015-01-01

2-Aminopropionitrile (APN), a probable candidate as a chiral astrophysical molecule, is a precursor to amino-acid alanine. Stereochemical pathways in 2-APN are explored using Global Reaction Route Mapping (GRRM) method employing high-level quantum-mechanical computations. Besides predicting the conventional mechanism for chiral inversion that proceeds through an achiral intermediate, a counterintuitive flipping mechanism is revealed for 2-APN through chiral intermediates explored using the GRRM. The feasibility of the proposed stereochemical pathways, in terms of the Gibbs free-energy change, is analyzed at the temperature conditions akin to the interstellar medium. Notably, the stereoinversion in 2-APN is observed to be more feasible than the dissociation of 2-APN and intermediates involved along the stereochemical pathways, and the flipping barrier is observed to be as low as 3.68 kJ/mol along one of the pathways. The pathways proposed for the inversion of chirality in 2-APN may provide significant insight into the extraterrestrial origin of life
Mutations in the HECT domain of NEDD4L lead to AKT-mTOR pathway deregulation and cause periventricular nodular heterotopia.

Science.gov (United States)

Broix, Loïc; Jagline, Hélène; Ivanova, Ekaterina; Schmucker, Stéphane; Drouot, Nathalie; Clayton-Smith, Jill; Pagnamenta, Alistair T; Metcalfe, Kay A; Isidor, Bertrand; Louvier, Ulrike Walther; Poduri, Annapurna; Taylor, Jenny C; Tilly, Peggy; Poirier, Karine; Saillour, Yoann; Lebrun, Nicolas; Stemmelen, Tristan; Rudolf, Gabrielle; Muraca, Giuseppe; Saintpierre, Benjamin; Elmorjani, Adrienne; Moïse, Martin; Weirauch, Nathalie Bednarek; Guerrini, Renzo; Boland, Anne; Olaso, Robert; Masson, Cecile; Tripathy, Ratna; Keays, David; Beldjord, Cherif; Nguyen, Laurent; Godin, Juliette; Kini, Usha; Nischké, Patrick; Deleuze, Jean-François; Bahi-Buisson, Nadia; Sumara, Izabela; Hinckelmann, Maria-Victoria; Chelly, Jamel

2016-11-01

Neurodevelopmental disorders with periventricular nodular heterotopia (PNH) are etiologically heterogeneous, and their genetic causes remain in many cases unknown. Here we show that missense mutations in NEDD4L mapping to the HECT domain of the encoded E3 ubiquitin ligase lead to PNH associated with toe syndactyly, cleft palate and neurodevelopmental delay. Cellular and expression data showed sensitivity of PNH-associated mutants to proteasome degradation. Moreover, an in utero electroporation approach showed that PNH-related mutants and excess wild-type NEDD4L affect neurogenesis, neuronal positioning and terminal translocation. Further investigations, including rapamycin-based experiments, found differential deregulation of pathways involved. Excess wild-type NEDD4L leads to disruption of Dab1 and mTORC1 pathways, while PNH-related mutations are associated with deregulation of mTORC1 and AKT activities. Altogether, these data provide insights into the critical role of NEDD4L in the regulation of mTOR pathways and their contributions in cortical development.
CO2 Reduction Catalyzed by Nitrogenase: Pathways to Formate, Carbon Monoxide, and Methane.

Science.gov (United States)

Khadka, Nimesh; Dean, Dennis R; Smith, Dayle; Hoffman, Brian M; Raugei, Simone; Seefeldt, Lance C

2016-09-06

The reduction of N2 to NH3 by Mo-dependent nitrogenase at its active-site metal cluster FeMo-cofactor utilizes reductive elimination of Fe-bound hydrides with obligatory loss of H2 to activate the enzyme for binding/reduction of N2. Earlier work showed that wild-type nitrogenase and a nitrogenase with amino acid substitutions in the MoFe protein near FeMo-cofactor can catalytically reduce CO2 by two or eight electrons/protons to carbon monoxide (CO) and methane (CH4) at low rates. Here, it is demonstrated that nitrogenase preferentially reduces CO2 by two electrons/protons to formate (HCOO(-)) at rates >10 times higher than rates of CO2 reduction to CO and CH4. Quantum mechanical calculations on the doubly reduced FeMo-cofactor with a Fe-bound hydride and S-bound proton (E2(2H) state) favor a direct reaction of CO2 with the hydride ("direct hydride transfer" reaction pathway), with facile hydride transfer to CO2 yielding formate. In contrast, a significant barrier is observed for reaction of Fe-bound CO2 with the hydride ("associative" reaction pathway), which leads to CO and CH4. Remarkably, in the direct hydride transfer pathway, the Fe-H behaves as a hydridic hydrogen, whereas in the associative pathway it acts as a protic hydrogen. MoFe proteins with amino acid substitutions near FeMo-cofactor (α-70(Val→Ala), α-195(His→Gln)) are found to significantly alter the distribution of products between formate and CO/CH4.
Rapid Synthesis of Lead Oxide Nanorods by One-step Solid-state Chemical Reaction at Room Temperature

Institute of Scientific and Technical Information of China (English)

CAO, Ya-Li(曹亚丽); JIA, Dian-Zeng(贾殿赠); LIU, Lang(刘浪); LUO, Jian-Min(骆建敏)

2004-01-01

A simple and facile method was reported to synthesize lead oxide nanorods. Nanorods of lead oxide were obtained directly from grinding solid metal salt and sodium hydroxide in agate mortar with the assistance of a suitable nonionic surfactant in only one step, which is different from the result of hydroxide in solution. The product has been characterized by XRD, TEM and SEM. The formation mechanism of rod-like morphology is discussed and the surfactant plays an important soft-template role in modifying the interface of solid-state reaction and according process of rod-formation.
Pacing Lead-Induced Granuloma in the Atrium: A Foreign Body Reaction to Polyurethane

Directory of Open Access Journals (Sweden)

Shinagawa Yoko

2013-01-01

Full Text Available We described a case of an 82-year-old male who presented with a granuloma entrapping the polyurethane-coated pacing lead at the site of contact on the atrium. He had been paced for 8 years without symptoms or signs suggestive of an allergic reaction to the pacemaker system and died from thrombosis of the superior mesenteric artery and heart failure. A histological examination of the nodule showed an incidental granuloma with multinucleated giant cells. No granuloma was found in the heart or the lung.
Stochasticity in the yeast mating pathway

International Nuclear Information System (INIS)

Hong-Li, Wang; Zheng-Ping, Fu; Xin-Hang, Xu; Qi, Ouyang

2009-01-01

We report stochastic simulations of the yeast mating signal transduction pathway. The effects of intrinsic and external noise, the influence of cell-to-cell difference in the pathway capacity, and noise propagation in the pathway have been examined. The stochastic temporal behaviour of the pathway is found to be robust to the influence of inherent fluctuations, and intrinsic noise propagates in the pathway in a uniform pattern when the yeasts are treated with pheromones of different stimulus strengths and of varied fluctuations. In agreement with recent experimental findings, extrinsic noise is found to play a more prominent role than intrinsic noise in the variability of proteins. The occurrence frequency for the reactions in the pathway are also examined and a more compact network is obtained by dropping most of the reactions of least occurrence
Dexmedetomidine Inhibits Inflammatory Reaction in Lung Tissues of Septic Rats by Suppressing TLR4/NF-κB Pathway

Directory of Open Access Journals (Sweden)

Yuqing Wu

2013-01-01

and 20 μg/kg significantly decreased mortality and pulmonary inflammation of septic rats, as well as suppressed CLP-induced elevation of TNF-α and IL-6 and inhibited TLR4/MyD88 expression and NF-κB activation. These results suggest that dexmedetomidine may decrease mortality and inhibit inflammatory reaction in lung tissues of septic rats by suppressing TLR4/MyD88/NF-κB pathway.
Primary Metabolic Pathways and Metabolic Flux Analysis

DEFF Research Database (Denmark)

Villadsen, John

2015-01-01

his chapter introduces the metabolic flux analysis (MFA) or stoichiometry-based MFA, and describes the quantitative basis for MFA. It discusses the catabolic pathways in which free energy is produced to drive the cell-building anabolic pathways. An overview of these primary pathways provides...... the reader who is primarily trained in the engineering sciences with atleast a preliminary introduction to biochemistry and also shows how carbon is drained off the catabolic pathways to provide precursors for cell mass building and sometimes for important industrial products. The primary pathways...... to be examined in the following are: glycolysis, primarily by the EMP pathway, but other glycolytic pathways is also mentioned; fermentative pathways in which the redox generated in the glycolytic reactions are consumed; reactions in the tricarboxylic acid (TCA) cycle, which produce biomass precursors and redox...
Analyzing atmospheric kinetic pathways using PumpKin

Science.gov (United States)

Markosyan, A. H.; Luque, A.; Gordillo-Vázquez, F. J.; Ebert, U.

2013-09-01

In the present work we show the application of our software tool called PumpKin (pathway reduction method for plasma kinetic models) to find all principal pathways of atmospheric kinetic system, i.e. the dominant reaction sequences, in chemical reaction systems. The goal was to reduce a complex plasma chemistry model. Recent kinetic models of atmospheric chemistry, or any industrial application, contain thousands of chemical reactions and species. The main difficulty is that these reduced chemical pathways depend on timescales, electric field, temperature, pressure etc. PumpKin is a universal tool, which only requires from user the temporal profile of the densities of species and the reaction rates, as well the stoichiometric matrix of the system. Also, the user should specify the timescale of interest.
ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

Science.gov (United States)

Kayala, Matthew A; Baldi, Pierre

2012-10-22

Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction
Electrophilic properties of patulin. Adduct structures and reaction pathways with 4-bromothiophenol and other model nucleophiles.

Science.gov (United States)

Fliege, R; Metzler, M

2000-05-01

The mycotoxin patulin (PAT) is believed to exert its cytotoxic and chromosome-damaging effects by forming covalent adducts with essential cellular thiols. Since the chemical structures of such adducts are unknown to date, we have studied the reaction of PAT and its O-acetylated derivative with the monofunctional thiol model compound 4-bromothiophenol (BTP), which was chosen due to analytical advantages. By means of analytical and preparative high-performance liquid chromatography, 16 adducts of PAT and 3 adducts of acetyl-PAT were isolated and their chemical structures elucidated by (1)H and (13)C NMR, IR, and UV spectroscopy. Time course studies and analysis of daughter product formation from isolated intermediate adducts led to a detailed scheme for the reaction of PAT with BTP. The structures of adducts of PAT formed with other model nucleophiles, e. g., the aliphatic thiol 2-mercaptoethanol and the aromatic amine 4-bromoaniline, were also elucidated and found to corroborate the reaction scheme. In addition, one further reaction pathway was observed with 2-mercaptoethanol, which appears to be independent from those found for BTP. Our study with model nucleophiles provides insights into the electrophilic reactivity of PAT and proved to be useful for the structure elucidation of PAT adducts with biological nucleophiles of toxicological relevance, as will be reported by Fliege and Metzler [(2000) Chem. Res. Toxicol. 13, 373-381].
Study on the properties of leading protons and antiprotons from exclusive anti pp reactions at 32 GeV/c

International Nuclear Information System (INIS)

Bogolyubskij, M.Yu.; Borovikov, A.A.; Boos, Eh.G.

1986-01-01

The leading properties of protons and antiprotons from the nondiffractive events are studied for p-barp-exclusive reactions at 32 GeV/c. It is found that the relative leading effect of protons and antiprotons does not depend on the final-state multiplicity and that the longitudinal moments of the leading hadrons are uncorrelated, but a significant part of the transverse momentum of a leading hadron is compensated by the transverse momentum of another leading hadron. It is shown that these experimental facts are described well by a statistical jet-independent model but contradict the Lund string-fragmentation model
Degradation of γ-HCH spiked soil using stabilized Pd/Fe0 bimetallic nanoparticles: Pathways, kinetics and effect of reaction conditions

International Nuclear Information System (INIS)

Singh, Ritu; Misra, Virendra; Mudiam, Mohana Krishna Reddy; Chauhan, Lalit Kumar Singh; Singh, Rana Pratap

2012-01-01

Highlights: ► This study explores the potential of CMC-Pd/nFe 0 to degrade γ-HCH in spiked soil. ► Sorption–desorption characteristics and partitioning of γ-HCH is investigated. ► Three degradation pathways has been proposed and discussed. ► γ-HCH degradation mechanism and kinetics is elucidated. ► Activation energy reveals that γ-HCH degradation is a surface mediated reaction. - Abstract: This study investigates the degradation pathway of gamma-hexachlorocyclohexane (γ-HCH) in spiked soil using carboxymethyl cellulose stabilized Pd/Fe 0 bimetallic nanoparticles (CMC-Pd/nFe 0 ). GC–MS analysis of γ-HCH degradation products showed the formation of pentachlorocyclohexene, tri- and di-chlorobenzene as intermediate products while benzene was formed as the most stable end product. On the basis of identified intermediates and final products, degradation pathway of γ-HCH has been proposed. Batch studies showed complete γ-HCH degradation at a loading of 0.20 g/L CMC-Pd/nFe 0 within 6 h of incubation. The surface area normalized rate constant (k SA ) was found to be 7.6 × 10 −2 L min −1 m −2 . CMC-Pd/nFe 0 displayed ∼7-fold greater efficiency for γ-HCH degradation in comparison to Fe 0 nanoparticles (nFe 0 ), synthesized without CMC and Pd. Further studies showed that increase in CMC-Pd/nFe 0 loading and reaction temperature facilitates γ-HCH degradation, whereas a declining trend in degradation was noticed with the increase in pH, initial γ-HCH concentration and in the presence of cations. The data on activation energy (33.7 kJ/mol) suggests that γ-HCH degradation is a surface mediated reaction. The significance of the study with respect to remediation of γ-HCH contaminated soil using CMC-Pd/nFe 0 has been discussed.
The chemical basis of DNA damage by the direct pathway of ionizing radiation

International Nuclear Information System (INIS)

Sharma, Kiran Kumar K.

2013-01-01

Free radicals in living system has been implicated as playing a major role in the etiology of variety of diseases. The mechanism of free radicals in vivo involves predominantly the reaction with the DNA, producing different types of damage to the DNA. These lesions induced to the DNA could lead to mutation and even cell death. Radiolysis techniques, which uses ionizing radiation has proven to be one of the most advanced and excellent tool for studying the free radical reaction mechanisms as it can produce a host of well characterized free radicals. The effects of ionizing radiation on DNA have been studied for many years. Ionizing radiation interacts with DNA in vivo by two pathways, direct and indirect. The indirect accounts for 50-60% while the direct effect accounts for 40-50%. The chemical mechanism of the former reaction arising mainly from the reactive species produced by radiolysis of water has been extensively studied, however with respect to the later pathway, which creates holes and electrons to the DNA molecule using DNA films and crystals is an active area of research as both the pathways plays important roles in DNA damage in vivo particularly in chromosomal DNA which are tightly bound with histones and compartmentalized
Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

KAUST Repository

Mohamed, Samah; Cai, Liming; Khaled, Fathi; Banyon, Colin; Wang, Zhandong; Rachidi, Mariam El; Pitsch, Heinz; Curran, Henry J.; Farooq, Aamir; Sarathy, Mani

2016-01-01

Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.
Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

KAUST Repository

Mohamed, Samah

2016-03-21

Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.
Bonding pathways of high-pressure chemical transformations

International Nuclear Information System (INIS)

Hu Anguang; Zhang Fan

2013-01-01

A three-stage bonding pathway towards high-pressure chemical transformations from molecular precursors or intermediate states has been identified by first-principles simulations. With the evolution of principal stress tensor components in the response of chemical bonding to compressive loading, the three stages can be defined as the van der Waals bonding destruction, a bond breaking and forming reaction, and equilibrium of new bonds. The three-stage bonding pathway leads to the establishment of a fundamental principle of chemical bonding under compression. It reveals that during high-pressure chemical transformation, electrons moving away from functional groups follow anti-addition, collision-free paths to form new bonds in counteracting the local stress confinement. In applying this principle, a large number of molecular precursors were identified for high-pressure chemical transformations, resulting in new materials. (fast track communication)
Benzene destruction in claus process by sulfur dioxide: A reaction kinetics study

KAUST Repository

Sinha, Sourab

2014-07-02

Benzene, toluene and xylene (BTX) are present as contaminants in the H 2S gas stream entering a Claus furnace. The exhaust gases from the furnace enter catalytic units, where BTX form soot particles. These particles clog and deactivate the catalysts. A solution to this problem is BTX oxidation before the gases enter catalyst beds. This work presents a theoretical investigation on benzene oxidation by SO2. Density functional theory is used to develop a detailed mechanism for phenyl radical -SO2 interactions. The mechanism begins with SO2 addition to phenyl radical after overcoming an energy barrier of 6.4 kJ/mol. This addition reaction is highly exothermic, where a reaction energy of 182 kJ/mol is released. The most favorable pathway involves O-S bond breakage, leading to the release of SO. A remarkable similarity between the pathways for phenyl radical oxidation by O2 and its oxidation by SO2 is observed. The reaction rate constants are also evaluated to facilitate process simulations. © 2014 American Chemical Society.
Pathways for the reaction of the butadiene radical cation, [C{sub 4}H{sub 6}]{sup {sm{underscore}bullet}+}, with ethylene

Energy Technology Data Exchange (ETDEWEB)

Hofmann, M.; Schaefer, H.F. III

1999-11-04

The Diels-Alder (DA) reaction, a [4+2] cycloaddition used to build six membered rings, is one of the most valuable cycloadditions in organic chemistry. In cases where the ene does not add to the diene (even with the help of Lewis acids which may reduce the electron density of one reactant by complexation) one electron oxidation (by an oxidizing agent or by photoinduced electron transfer (PET)) may accelerate the reaction. Reaction pathways for the addition of ethylene, 1, to butadiene radical cation, 2, involving H-shifts have been investigated at the coupled cluster UCCSD(T)/DZP//UMP2(fc)/DZP + ZPE level of theory. Activation energies are relatively low for [1,2]- (10.0 kcal mol{sup {minus}1}, TS-4/20) and [1,5]-hydrogen shifts (7.7 kcal mol{sup {minus}1}, TS-4/26) but are relatively high for [1,4]-(33.8 kcal mol{sup {minus}1}, TS-4/14) and [1,3]-H shifts (e.g., 42.2 kcal mol{sup {minus}1}, TS-12/13; 57.2 kcal mol{sup {minus}1}, TS-16/21). Several rearrangement reactions have been found to occur below the energy limit of separated 1 + 2. The cyclopentenyl cation, [C{sub 5}{sub 7}]{sup +}, 18, experimentally observed as reaction product of the butadiene radical cation, 2, and ethylene, 1, in the gas phase may origin from various reaction pathways. The following reaction sequence has been identified as the lowest in energy path from 1 + 2 to 18 with all relative energies ({Delta}E{degree}) of transition structures below that of 1 + 2: (a) ethylene adds to the butadiene radical cation to form an open-chain distonic intermediate, that undergoes a [1,5]-H shift to the 1,4-hexadiene radical cation; (b) intramolecular [2+1] cycloaddition to methyl-cyclopenta-1,3-diyl intermediates, which can interconvert through a bicyclo[2.1.0]pentane radical cation; (c) [1,2]-H shift to the 3-methyl cyclopentene radical cation; (d) methyl radical loss to give cyclopenten-3-yl cation. Along this reaction pathway, {Delta}H{sup 298} is below that of 1 + 2; max. ({Delta}G{sup 298} by

Thermochemistry of the reactions between CN+ and H2O in the gas phase

Science.gov (United States)

Ijjaali, Fatima; Alcami, Manuel; Mo, Otilia; Yanez, Manuel

The [H2, C, N, O]+ potential energy surface (PES) has been explored by means of high-level ab initio calculations, carried out in the framework of the G2 theory. From this survey we concluded that the predominant products of the CN+ +H2O reaction are the result of the dissociation of HNCOH+ species and to a much lesser extent of the CNHOH+ cation to yield CNH+ +OH. According to our results HCN+ should not be a product of this reaction because all pathways leading to its formation are unfavourable with regards to other competitive processes. Other reactive channels lead to the formation of the H2ONC+ structure which dissociates into CN + H2O+. The loss of NH(3Σ) and O(3P) seems to take place following spin-forbidden reaction paths through an intersystem crossing between the singlet and the triplet PESs. The global minimum of the PES, H2NCO+ is easily accessible and should lead to the loss of carbon monoxide which has not been experimentally observed in CN+ + H2O reactions. We cannot oOEer a clear explanation for this disagreement between theory and experiment.
Mechano-chemical pathways to H2O and CO2 splitting

Science.gov (United States)

Vedadi, Mohammad H.; Haas, Stephan

2011-10-01

The shock-induced collapse of CO2-filled nanobubbles is investigated using molecular dynamics simulations based on a reactive force field. The energetic nanojet and high-pressure water hammer shock formed during and after collapse of the nanobubble trigger mechano-chemical H2O-CO2 reactions, some of which lead to splitting of water and formation of O2 molecules. The dominant pathways through which splitting of water molecules occur are identified.
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

Science.gov (United States)

Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

2014-01-01

In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating
NMR studies of stock process water and reaction pathways in hydrothermal carbonization of furfural residue

Directory of Open Access Journals (Sweden)

Fen Yue

2018-04-01

Full Text Available Hydrothermal carbonization (HTC is a valuable approach to convert furfural residue (FR into carbon material. The prepared biochars are usually characterized comprehensively, while the stock process water still remains to be studied in detail. Herein, a NMR study of the main components in stock process water generated at different HTC reaction conditions was reported. Various qualitative and quantitative NMR techniques (1H and 13C NMR, 1H–1H COSY and 1H13C HSQC etc. especially 1D selective gradient total correlation spectroscopy (TOCSY NMR were strategically applied in the analysis of HTC stock process water. Without separation and purification, it was demonstrated that the main detectable compounds are 5-hydroxymethylfurfural, formic acid, methanol, acetic acid, levulinic acid, glycerol, hydroxyacetone and acetaldehyde in this complicate mixture. Furthermore, the relationship between the concentration of major products and the reaction conditions (180–240 °C at 8 h, and 1–24 h at 240 °C was established. Finally, reasonable reaction pathways for hydrothermal conversion of FR were proposed based on this result and our previously obtained characteristics of biochars. The routine and challenging NMR methods utilized here would be an alternative other than HPLC or GC for biomass conversion research and can be extended to more studies. Keywords: NMR, Hydrothermal carbonization, Furfural residue, Stock process water
[Effects and mechanisms of the inflammatory reaction related to NASH and induced by activation of the cholinergic anti-inflammatory pathway].

Science.gov (United States)

Zhou, Zhou; Chen, Xiaomei; Li, Fuqiang; Tang, Cuilan

2015-01-01

To investigate the effects and mechanisms of the inflammatory reaction related to nonalcoholic steatohepatitis (NASH) and induced by activation of the cholinergic anti-inflammatory pathway. A mouse model of NASH was established by feeding a high-fat and high-sugar diet.Activation of the cholinergic anti-inflammatory pathway was achieved by nicotine administration to the NASH modeled mice and normal controls. Liver biopsies were taken and the concentrations of cytokines were measured. Isolated liver primary Kupffer cells and RAw264.7 cells were cultured, pre-treated or not with lipopolysaccharide (LPS) and exposed to nicotine, after which the supernatant concentrations of IL-6 and TNFa were determined by ELISA. The protein expression levels of phosphorylated (p)-NF-kB and I k B were detected in primary cultured Kupffer cells by western blotting. The mouse model of NASH was successfully established, as evidenced by findings from liver biopsy and serum liver function tests. The degree of liver inflammation in the NASH mice decreased after nicotine administration, and the level of serum TNFa also significantly decreased. The levels of serum TNFa were 21.95+/-0.8 pg/mL in nicotine-treated mice and 38.07+/-1.7 pg/mL in the non-nicotine-treated NASH mice (P less than 0.05). The nicotine treatment also significantly reduced the concentration of TNFa in the culture supernatants of Kupffer cells after LPS stimulation; moreover, the supernatant level of TNFa decreased significantly after the nicotine treatment (Pless than 0.05). LPS stimulation of the RAw264.7 cells led to an increased level ofp-NF-kB and a reduced level ofI-kB, suggesting that the NF-kB pathway had been activated; different doses of nicotine pre-treatment led to down-regulation of the p-NF-kB level and up-regulation of the I-kB level, both in dose-dependent manners. Activating the cholinergic anti-inflammatory pathway inhibits the NASH-related inflammatory reaction, and the mechanism for this inhibition
SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis

Science.gov (United States)

Ohashi, Masao; Liu, Fang; Hai, Yang; Chen, Mengbin; Tang, Man-Cheng; Yang, Zhongyue; Sato, Michio; Watanabe, Kenji; Houk, K. N.; Tang, Yi

2017-09-01

Pericyclic reactions—which proceed in a concerted fashion through a cyclic transition state—are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon-carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels-Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-L-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels-Alder and hetero-Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme ‘toolboxes’. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.
Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Science.gov (United States)

Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

2016-07-01

Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.
Blaming for a better future: future orientation and associated intolerance of personal uncertainty lead to harsher reactions toward innocent victims.

Science.gov (United States)

Bal, Michèlle; van den Bos, Kees

2012-07-01

People are often encouraged to focus on the future and strive for long-term goals. This noted, the authors argue that this future orientation is associated with intolerance of personal uncertainty, as people usually cannot be certain that their efforts will pay off. To be able to tolerate personal uncertainty, people adhere strongly to the belief in a just world, paradoxically resulting in harsher reactions toward innocent victims. In three experiments, the authors show that a future orientation indeed leads to more negative evaluations of an innocent victim (Study 1), enhances intolerance of personal uncertainty (Study 2), and that experiencing personal uncertainty leads to more negative evaluations of a victim (Study 3). So, while a future orientation enables people to strive for long-term goals, it also leads them to be harsher toward innocent victims. One underlying mechanism causing these reactions is intolerance of personal uncertainty, associated with a future orientation.
PHYSIOLOGICAL REACTION OF COMMON OSIER (SALIX VIMINIALIS L. VAR. JORR TO THE PRESENCE OF LEAD IN THE SUBSOIL

Directory of Open Access Journals (Sweden)

Katarzyna Malinowska

2015-02-01

Full Text Available The effect of lead ions of the concentrations within the range of 15–1000 mg∙dm-3 on the physiological reaction of common osier var. Jorr was examined. The content of assimilation pigments, the rate the CO2 assimilation, transpiration, the indices of relative water content and the deficit of water saturation and the content of lead in the nutrient solution. The studied physiological parameters in common osier var. Jorr were differentiated by the rate of lead ions in the nutrient solution. The Jorr variety of common osier was characterised by good values of the determined physiological parameters under stressful conditions at a large accumulation of lead. This suggests that it shows quite a high tolerance to the stress caused by contamination of the subsoil with lead.
Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes

NARCIS (Netherlands)

Barman, Prasenjit; Faponle, Abayomi S; Vardhaman, Anil Kumar; Angelone, Davide; Löhr, Anna-Maria; Browne, Wesley R; Comba, Peter; Sastri, Chivukula V; de Visser, Sam P

2016-01-01

Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes,
Predicting metabolic pathways by sub-network extraction.

Science.gov (United States)

Faust, Karoline; van Helden, Jacques

2012-01-01

Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( http://rsat.ulb.ac.be/neat/ ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.
Application of Enzyme Coupling Reactions to Shift Thermodynamically Limited Biocatalytic Reactions

DEFF Research Database (Denmark)

Abu, Rohana; Woodley, John M.

2015-01-01

, it can be challenging to combine several engineered enzymes in vitro for the conversion of non-natural substrates. In this mini-review we focus on enzyme coupling reactions as a tool to alleviate thermodynamic constraints in synthetically useful biocatalytic reactions. The implications of thermodynamic...... shift the equilibrium of otherwise thermodynamically unfavourable reactions to give a higher conversion of the target product. By coupling an energetically unfavourable reaction with a more favourable one, the multi-enzyme cascade mimics the approach taken in nature in metabolic pathways. Nevertheless...
Skin: Major target organ of allergic reactions to small molecular weight compounds

International Nuclear Information System (INIS)

Merk, Hans F.; Baron, Jens M.; Neis, Mark M.; Obrigkeit, Daniela Hoeller; Karlberg, Ann-Therese

2007-01-01

Skin is a major target organ for allergic reactions to small molecular weight compounds. Drug allergic reactions may be life-threatening such as in the case of anaphylactic reactions or bullous drug reactions and occur in about 5% of all hospitalized patients. Allergic contact dermatitis has an enormous influence on the social life of the patient because it is the most frequent reason for occupational skin diseases and the treatment and prevention of this disease cost approximately Euro 3 billion per year in Germany. The different proposed pathophysiological pathways leading to a drug eruption are discussed in this paper. All major enzymes which are involved in the metabolism of xenobiotica were shown to be present in skin. Evidence supporting the role of metabolism in the development of drug allergy and allergic contact dermatitis is demonstrated in the example of sulphonamides and fragrances
Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway.

Directory of Open Access Journals (Sweden)

Manpreet Randhawa

Full Text Available Skin chronically exposed to sun results in phenotypic changes referred as photoaging. This aspect of aging has been studied extensively through genomic and proteomic tools. Metabolites, the end product are generated as a result of biochemical reactions are often studied as a culmination of complex interplay of gene and protein expression. In this study, we focused exclusively on the metabolome to study effects from sun-exposed and sun-protected skin sites from 25 human subjects. We generated a highly accurate metabolomic signature for the skin that is exposed to sun. Biochemical pathway analysis from this data set showed that sun-exposed skin resides under high oxidative stress and the chains of reactions to produce these metabolites are inclined toward catabolism rather than anabolism. These catabolic activities persuade the skin cells to generate metabolites through the salvage pathway instead of de novo synthesis pathways. Metabolomic profile suggests catabolic pathways and reactive oxygen species operate in a feed forward fashion to alter the biology of sun exposed skin.
Radiation therapy and late reactions in normal tissues

International Nuclear Information System (INIS)

Aoyama, Takashi; Kuroda, Yasumasa

1998-01-01

Recent developments in cancer therapy have made us increasingly aware that the quality of life of a patient is as valuable as other benefits received from therapy. This awareness leads to an emphasis on organ and/or function preservation in the course of therapy. In line with this new thinking, greater consideration is placed on radiation therapy as an appropriate modality of cancer therapy. Possible complications in normal tissues, especially those of late reaction type after the therapy must be overcome. This review, therefore, focuses on recent progress of studies on mechanisms of the complications of the late reaction type. An observation of a clinical case concerning a late reaction of spinal cord (radiation myelopathy) and surveys of experimental studies on the mechanisms of late reactions (including radiation pneumonitis and lung fibrosis, and radiation response of vascular endothelial cells) provide a hypothesis that apoptosis through the pathway starting with radiation-induced sphingomyelin hydrolysis may play an important role in causing a variety of late reactions. This insight is based on the fact that radiation also activates protein kinase C which appears to block apoptosis. The mechanisms of late reactions, therefore, may involve a balance between radiation-induced apoptotic death and its down regulation by suppressor mechanisms through protein kinase C. (author)
Synthetic Control of Kinetic Reaction Pathway and Cationic Ordering in High-Ni Layered Oxide Cathodes

Energy Technology Data Exchange (ETDEWEB)

Wang, Dawei [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA; Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory Physical Chemistry Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen Fujian 361005 China; Kou, Ronghui [X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Ren, Yang [X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Sun, Cheng-Jun [X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Zhao, Hu [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA; Zhang, Ming-Jian [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA; School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen Guangdong 518055 P. R. China; Li, Yan [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Huq, Ashifia [Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge TN 37831 USA; Ko, J. Y. Peter [The Cornell High Energy Synchrotron Source, Cornell University, Ithaca NY 14853 USA; Pan, Feng [School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen Guangdong 518055 P. R. China; Sun, Yang-Kook [Department of Energy Engineering, Hanyang University, Seoul 133-791 South Korea; Yang, Yong [Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory Physical Chemistry Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen Fujian 361005 China; Amine, Khalil [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Bai, Jianming [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton NY 11973 USA; Chen, Zonghai [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Wang, Feng [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA

2017-08-25

Nickel-rich layered transition metal oxides, LiNi1-x(MnCo)(x)O-2 (1-x >= 0.5), are appealing candidates for cathodes in next-generation lithium-ion batteries (LIBs) for electric vehicles and other large-scale applications, due to their high capacity and low cost. However, synthetic control of the structural ordering in such a complex quaternary system has been a great challenge, especially in the presence of high Ni content. Herein, synthesis reactions for preparing layered LiNi0.7Mn0.15Co0.15O2 (NMC71515) by solid-state methods are investigated through a combination of time-resolved in situ high-energy X-ray diffraction and absorption spectroscopy measurements. The real-time observation reveals a strong temperature dependence of the kinetics of cationic ordering in NMC71515 as a result of thermal-driven oxidation of transition metals and lithium/oxygen loss that concomitantly occur during heat treatment. Through synthetic control of the kinetic reaction pathway, a layered NMC71515 with low cationic disordering and a high reversible capacity is prepared in air. The findings may help to pave the way for designing high-Ni layered oxide cathodes for LIBs.
Interfacial reactions in intermetallic matrix composites

International Nuclear Information System (INIS)

Cantrell, L.B.; Clevenger, E.M.; Perepezko, J.H.

1993-01-01

The thermal stability of advanced composites is dominated by the behavior of internal interfaces. Analysis of these internal interfaces often involves consideration of at least ternary order phase equilibria. Limited thermodynamic data exists for ternary and higher order systems. However, a combined approach based upon the use of binary data to estimate ternary phase equilibria and experimentally determined reaction pathways is effective in the analysis of interface reactions in composite systems. In blended powder samples, thermal analysis was used to find possible reaction temperatures, while X-ray analysis, EDS, and EPMA of diffusion couples were used to assess interdiffusion reaction pathways. The approach is illustrated by compatibility studies between TiAl and TiSi 2 at 1,100 C, and in-situ reactions between B 4 C and TiAl at 1300 C where multiple reaction sequences have been analyzed to provide guidance for the design of in-situ reaction processing of composites
Reactions of ferrate(VI) with iodide and hypoiodous acid: kinetics, pathways, and implications for the fate of iodine during water treatment.

Science.gov (United States)

Shin, Jaedon; von Gunten, Urs; Reckhow, David A; Allard, Sebastien; Lee, Yunho

2018-06-01

Oxidative treatment of iodide-containing waters can form iodinated disinfection by-products (I-DBPs) that are more toxic than the regulated DBPs. To better understand the fate of iodine during water treatment with ferrate(VI), kinetics, products, and stoichiometries for the reactions of ferrate(VI) with iodide (I - ) and hypoiodous acid (HOI) were determined. Ferrate(VI) showed considerable reactivities to both I - and HOI with higher reactivities at lower pH. Interestingly, the reaction of ferrate(VI) with HOI ( k = 6.0×10 3 M -1 s -1 at pH 9) was much faster than with I - ( k = 5.6×10 M -1 s -1 at pH 9). The main reaction pathway during treatment of I - -containing waters was the oxidation of I - to HOI and its further oxidation to IO 3 - by ferrate(VI). However, for pH > 9, the HOI disproportionation catalyzed by ferrate(VI) became an additional transformation pathway forming I - and IO 3 - . The reduction of HOI by hydrogen peroxide ( k = 2.0×10 8 M -1 s -1 for the reaction, HOI + HO 2 - → I - + O 2 + 2H + ), the latter being produced from ferrate(VI) decomposition, also contributes to the I - regeneration in the pH range 9 - 11. A kinetic model was developed that could well simulate the fate of iodine in the ferrate(VI)-I - system. Overall, due to a rapid oxidation of I - to IO 3 - with short-lifetimes of HOI, ferrate(VI) oxidation appears to be a promising option for I-DBP mitigation during treatment of I - -containing waters.
Investigations on organolead compounds V. Lead---lead bond cleavage reactions of hexaphenyldilead

NARCIS (Netherlands)

Willemsens, L.C.; Kerk, G.J.M. van der

1968-01-01

It has been shown that a number of nucleophilic and weakly electrophilic reagents (organolithium and organomagnesium compounds, metallic lithium, potassium permanganate, sodium ethoxide, diaryl disulphides, sulphur, ozone, hypochlorous acid and iodine/iodide) selectively cleave the lead---lead bond
Reaction pathways of furfural, furfuryl alcohol and 2-methylfuran on Cu(111) and NiCu bimetallic surfaces

Science.gov (United States)

Xiong, Ke; Wan, Weiming; Chen, Jingguang G.

2016-10-01

Hydrodeoxygenation (HDO) is an important reaction for converting biomass-derived furfural to value-added 2-methylfuran, which is a promising fuel additive. In this work, the HDO of furfural to produce 2-methylfuran occurred on the NiCu bimetallic surfaces prepared on either Ni(111) or Cu(111). The reaction pathways of furfural were investigated on Cu(111) and Ni/Cu(111) surfaces using density functional theory (DFT) calculations, temperature-programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) experiments. These studies provided mechanistic insights into the effects of bimetallic formation on enhancing the HDO activity. Specifically, furfural weakly adsorbed on Cu(111), while it strongly adsorbed on Ni/Cu(111) through an η2(C,O) configuration, which led to the HDO of furfural on Ni/Cu(111). The ability to dissociate H2 on Ni/Cu(111) is also an important factor for enhancing the HDO activity over Cu(111).

Study of the properties of leading protons and antiprotons produced in p-barp exclusive reactions at 32 GeV/c

International Nuclear Information System (INIS)

Bogolyubskii, M.Y.; Boos, E.G.; Borovikov, A.A.

1986-01-01

We study the properties of leading protons and antiprotons from nondiffractive events in p-barp exclusive reactions at 32 GeV/c. It is found that the relative leading of protons and antiprotons does not depend on the final-state multiplicity and that the longitudinal momenta of leading hadrons are not correlated, but a significant part of the transverse momentum of a leading hadron is compensated by the transverse momentum of another hadron. It is shown that these experimental data are well described by the statistical model of independent particle emission but contradict the Lund string-fragmentation model
Reaction pathway of the degradation of the p-hydroxybenzoic acid by sulfate radical generated by ionizing radiations

International Nuclear Information System (INIS)

Criquet, Justine; Leitner, Nathalie Karpel Vel

2015-01-01

The degradation of p-hydroxybenzoic acid (HBA) in aqueous solutions by ionizing radiation was studied. The phenolic pollutant was easily removed by the electron beam irradiation, as more than 80% of the initial 100 µM introduced was degraded for a dose of 600 Gy. It was shown that the addition of persulfate, producing the sulfate radical as additional reactive species, induced a change in the reaction pathway. LC–MS analyses were performed in order to identify the different by-products formed. In the absence of persulfate, the main by-product formed was 3,4-dihydroxybenzoic acid, while in presence of persulfate, 1,4-benzoquinone was detected and the hydroxylated by-products were not present. A reaction pathway of HBA degradation by hydroxyl and sulfate radicals was proposed from the identification of the chemical structure of the different by-products detected. The influences of pH and dissolved oxygen were also studied. A high decline of HBA degradation was observed at pH 11 compared to pH 4.5, this decrease was minimized in the presence of persulfate. The dissolved oxygen concentration was found to be a limiting parameter of HBA degradation, however an excess of dissolved oxygen in solution did not improve the degradation to a large extent. - Highlights: • p-Hydroxybenzoic acid (HBA) is easily removed by e-beam irradiation. • The sulfate radicals formed from persulfate induce loss of the benzoic acid skeleton. • The dissolved oxygen concentration is a limiting parameter of the HBA degradation. • The effect of pH is minimized in presence of persulfate
Reaction paths based on mean first-passage times

International Nuclear Information System (INIS)

Park, Sanghyun; Sener, Melih K.; Lu Deyu; Schulten, Klaus

2003-01-01

Finding representative reaction pathways is important for understanding the mechanism of molecular processes. We propose a new approach for constructing reaction paths based on mean first-passage times. This approach incorporates information about all possible reaction events as well as the effect of temperature. As an application of this method, we study representative pathways of excitation migration in a photosynthetic light-harvesting complex, photosystem I. The paths thus computed provide a complete, yet distilled, representation of the kinetic flow of excitation toward the reaction center, thereby succinctly characterizing the function of the system
High-pressure vapor-phase hydrodeoxygenation of lignin-derived oxygenates to hydrocarbons by a PtMo bimetallic catalyst: Product selectivity, reaction pathway, and structural characterization

Energy Technology Data Exchange (ETDEWEB)

Yohe, Sara L.; Choudhari, Harshavardhan J.; Mehta, Dhairya D.; Dietrich, Paul J.; Detwiler, Michael D.; Akatay, Cem M.; Stach, Eric A.; Miller, Jeffrey T.; Delgass, W. Nicholas; Agrawal, Rakesh; Ribeiro, Fabio H.

2016-12-01

High-pressure, vapor-phase, hydrodeoxygenation (HDO) reactions of dihydroeugenol (2-methoxy-4-propylphenol), as well as other phenolic, lignin-derived compounds, were investigated over a bimetallic platinum and molybdenum catalyst supported on multi-walled carbon nanotubes (5%Pt2.5%Mo/MWCNT). Hydrocarbons were obtained in 100% yield from dihydroeugenol, including 98% yield of the hydrocarbon propylcyclohexane. The final hydrocarbon distribution was shown to be a strong function of hydrogen partial pressure. Kinetic analysis showed three main dihydroeugenol reaction pathways: HDO, hydrogenation, and alkylation. The major pathway occurred via Pt catalyzed hydrogenation of the aromatic ring and methoxy group cleavage to form 4-propylcyclohexanol, then Mo catalyzed removal of the hydroxyl group by dehydration to form propylcyclohexene, followed by hydrogenation of propylcyclohexene on either the Pt or Mo to form the propylcyclohexane. Transalkylation by the methoxy group occurred as a minor side reaction. Catalyst characterization techniques including chemisorption, scanning transmission electron microscopy, X-ray absorption spectroscopy, and X-ray photoelectron spectroscopy were employed to characterize the catalyst structure. Catalyst components identified were Pt particles, bimetallic PtMo particles, a Mo carbide-like phase, and Mo oxide phases.
Measurement of activation reaction rate distributions in a lead assembly bombarded with 500-MeV protons

CERN Document Server

Takada, H; Sasa, T; Tsujimoto, K; Yasuda, H

2000-01-01

Reaction rate distributions of various activation detectors such as the /sup nat/Ni(n, x)/sup 58/Co, /sup 197/Au(n,2n)/sup 196/Au, and /sup 197/Au(n,4n)/sup 194/Au reactions were measured to study the production and the transport of spallation neutrons in a lead assembly bombarded with protons of 500 MeV. The measured data were analyzed with the nucleon-meson transport code NMTC/JAERI combined with the MCNP4A code using the nuclide production cross sections based on the JENDL Dosimetry File and those calculated with the ALICE-F code. It was found that the NMTC/JAERI-MCNP4A calculations agreed well with the experiments for the low-energy-threshold reaction of /sup nat/Ni(n, x)/sup 58/Co. With the increase of threshold energy, however, the calculation underestimated the experiments, especially above 20 MeV. The reason for the disagreement can be attributed to the underestimation of the neutron yield in the tens of mega-electron-volt regions by the NMTC/JAERI code. (32 refs).
Study on interfacial reaction between lead-free solders and alternative surface finishes

International Nuclear Information System (INIS)

Siti Rabiatul Aisha; Ourdjini, A.; Saliza Osman

2007-01-01

This study investigates the interfacial reactions occurring during reflow soldering between Sn-Ag-Cu lead-free solder and two surface finishes: electroless nickel/ immersion gold (ENIG) and immersion silver (IAg). The study focuses on interfacial reactions evolution and growth kinetics of intermetallic compounds (IMC) formed during soldering and isothermal ageing at 150 degree Celsius for up to 2000 hours. Optical and scanning electron microscopy were used to measure IMC thickness and examine the morphology of IMC respectively, whereas the IMC phases were identified by energy dispersive X-ray analysis (EDX). The results showed that the IMC formed on ENIG finish is thinner compared to that formed on IAg finish. For IAg surface finish, Cu 6 Sn 5 IMCs with scallop morphology are formed at the solder/ surface finish interface after reflow while a second IMC, Cu 3 Sn was formed between the copper and Cu 6 Sn 5 IMC after the isothermal ageing treatment. For ENIG surface finish both (Cu,Ni) 6 Sn 5 and (Ni,Cu) 3 Sn 4 are formed after soldering. Isothermal aging of the solder joints formed on ENIG finish was found to have a significant effect on the morphology of the intermetallics by transforming to more spherical and denser morphology in addition to increase i their thickness with increased ageing time. (author)
Hi-Jack: a novel computational framework for pathway-based inference of host–pathogen interactions

KAUST Repository

Kleftogiannis, Dimitrios A.

2015-03-09

Motivation: Pathogens infect their host and hijack the host machinery to produce more progeny pathogens. Obligate intracellular pathogens, in particular, require resources of the host to replicate. Therefore, infections by these pathogens lead to alterations in the metabolism of the host, shifting in favor of pathogen protein production. Some computational identification of mechanisms of host-pathogen interactions have been proposed, but it seems the problem has yet to be approached from the metabolite-hijacking angle. Results: We propose a novel computational framework, Hi-Jack, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking. Hi-Jack searches metabolic network data from hosts and pathogens, and identifies candidate reactions where hijacking occurs. A novel scoring function ranks candidate hijacked reactions and identifies pathways in the host that interact with pathways in the pathogen, as well as the associated frequent hijacked metabolites. We also describe host-pathogen interaction principles that can be used in the future for subsequent studies. Our case study on Mycobacterium tuberculosis (Mtb) revealed pathways in human-e.g. carbohydrate metabolism, lipids metabolism and pathways related to amino acids metabolism-that are likely to be hijacked by the pathogen. In addition, we report interesting potential pathway interconnections between human and Mtb such as linkage of human fatty acid biosynthesis with Mtb biosynthesis of unsaturated fatty acids, or linkage of human pentose phosphate pathway with lipopolysaccharide biosynthesis in Mtb. © The Author 2015. Published by Oxford University Press. All rights reserved.
Insulin regulates multiple signaling pathways leading to monocyte/macrophage chemotaxis into the wound tissue

Directory of Open Access Journals (Sweden)

Yan Liu

2018-01-01

Full Text Available Wound healing is a complex process that involves sequential phases that overlap in time and space and affect each other dynamically at the gene and protein levels. We previously showed that insulin accelerates wound healing by stimulating faster and regenerative healing. One of the processes that insulin stimulates is an increase in monocyte/macrophage chemotaxis. In this study, we performed experiments in vivo and in vitro to elucidate the signaling transduction pathways that are involved in insulin-induced monocyte/macrophage chemotaxis. We found that insulin stimulates THP-1 cell chemotaxis in a dose-dependent and insulin receptor-dependent manner. We also show that the kinases PI3K-Akt, SPAK/JNK, and p38 MAPK are key molecules in the insulin-induced signaling pathways that lead to chemoattraction of the THP-1 cell. Furthermore, both PI3K-Akt and SPAK/JNK signaling involve Rac1 activation, an important molecule in regulating cell motility. Indeed, topical application of Rac1 inhibitor at an early stage during the healing process caused delayed and impaired healing even in the presence of insulin. These results delineate cell and molecular mechanisms involved in insulin-induced chemotaxis of monocyte/macrophage, cells that are critical for proper healing.
Reconstructing biochemical pathways from time course data.

Science.gov (United States)

Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

2007-03-01

Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.
Computational Investigation of the Competition between the Concerted Diels-Alder Reaction and Formation of Diradicals in Reactions of Acrylonitrile with Non-Polar Dienes

Science.gov (United States)

James, Natalie C.; Um, Joann M.; Padias, Anne B.; Hall, H. K.; Houk, K. N.

2013-01-01

The energetics of the Diels-Alder cycloaddition reactions of several 1,3-dienes with acrylonitrile, and the energetics of formation of diradicals, were investigated with density functional theory (B3LYP and M06-2X) and compared to experimental data. For the reaction of 2,3-dimethyl-1,3-butadiene with acrylonitrile, the concerted reaction is favored over the diradical pathway by 2.5 kcal/mol using B3LYP/6-31G(d); experimentally this reaction gives both cycloadduct and copolymer. The concerted cycloaddition of cyclopentadiene with acrylonitrile is preferred computationally over the stepwise pathway by 5.9 kcal/mol; experimentally, only the Diels-Alder adduct is formed. For the reactions of (E)-1,3-pentadiene and acrylonitrile, both cycloaddition and copolymerization were observed experimentally; these trends were mimicked by the computational results, which showed only a 1.2 kcal/mol preference for the concerted pathway. For the reactions of (Z)-1,3-pentadiene and acrylonitrile, the stepwise pathway is preferred by 3.9 kcal/mol, in agreement with previous experimental findings that only polymerization occurs. M06-2X is known to give more accurate activation and reaction energetics but the energies of diradicals are too high. PMID:23758325
Removal of lead from crude antimony by using NaPo3 as lead elimination reagent

Directory of Open Access Journals (Sweden)

Ye L.G.

2015-01-01

Full Text Available In order to solve the shortcomings when removing lead from crude antimony in the traditional antimony smelting, a new process was provided using NaPO3 as lead elimination reagent to yield phosphate slag, and it was removed by floating on the surface of the liquid antimony. Reaction mechanism was clarified by using the TG-DTA and XRD techniques and single factor experiments of removal lead from crude antimony were engaged. The results show that PbO and NaPO3 begin endothermic reaction at 863K (590°C, and the reaction mainly form NaPb4(PO43 and NaPbPO4 below 1123K (850°C and above 1123K (850°C, respectively. Sb2O3 and NaPO3 start the reaction at 773K (500°C and generate an antimonic salt compound. The reaction product of the mixture of PbO, Sb2O3 and NaPO3 show that NaPO3 reacted with PbO prior when NaPO3 was insufficient, amorphous antimony glass will be generated only when NaPO3 was adequate. Single factor experiments were taken with NaNO3 as oxidizing agent under argon, effect of reaction time, reaction temperature and dosage of NaPO3 and NaNO3 on smelting results. The average content of lead in refined antimony was 0.05340% and 98.85% of lead were removed under optimal conditions; the content of lead in antimony have meet the requirements of commercial antimony.
The concern of emergence of multi-station reaction pathways that might make stepwise the mechanism of the 1,3-dipolar cycloadditions of azides and alkynes

Science.gov (United States)

Mohtat, Bita; Siadati, Seyyed Amir; Khalilzadeh, Mohammad Ali; Zareyee, Daryoush

2018-03-01

After hot debates on the concerted or stepwise nature of the mechanism of the catalyst-free 1,3-dipolar cycloadditions (DC)s, nowadays, it is being believed that for the reaction of each dipole and dipolarophile, there is a possibility that the reaction mechanism becomes stepwise, intermediates emerge, and the reaction becomes non-stereospecific. Yield of even minimal amounts of unwanted side products or stereoisomers as impurities could bring many troubles like difficult purification steps. In this project, we have made attempts to study all probable reaction channels of the azide cycloadditions with two functionalized alkynes, in order to answer this question: "is there any possibility that intermediates evolve in the catalyst-free click 1,3-DC reaction of azide-alkynes?". During the calculations, several multi-station reaction pathways supporting the stepwise and concerted mechanisms were detected. Also, the born-oppenheimer molecular dynamic (BOMD) simulation was used to find trustable geometries which could be emerged during the reaction coordinate.
Addition reaction of adamantylideneadamantane with Br2 and 2Br2: a computational study.

Science.gov (United States)

Islam, Shahidul M; Poirier, Raymond A

2008-01-10

Ab initio calculations were carried out for the reaction of adamantylideneadamantane (Ad=Ad) with Br2 and 2Br2. Geometries of the reactants, transition states, intermediates, and products were optimized at HF and B3LYP levels of theory using the 6-31G(d) basis set. Energies were also obtained using single point calculations at the MP2/6-31G(d)//HF/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31+G(d)//B3LYP/6-31G(d) levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Only one pathway was found for the reaction of Ad=Ad with one Br2 producing a bromonium/bromide ion pair. Three mechanisms for the reaction of Ad=Ad with 2Br2 were found, leading to three different structural forms of the bromonium/Br3- ion pair. Activation energies, free energies, and enthalpies of activation along with the relative stability of products for each reaction pathway were calculated. The reaction of Ad=Ad with 2Br2 was strongly favored over the reaction with only one Br2. According to B3LYP/6-31G(d) and single point calculations at MP2, the most stable bromonium/Br3- ion pair would form spontaneously. The most stable of the three bromonium/Br3- ion pairs has a structure very similar to the observed X-ray structure. Free energies of activation and relative stabilities of reactants and products in CCl4 and CH2ClCH2Cl were also calculated with PCM using the united atom (UA0) cavity model and, in general, results similar to the gas phase were obtained. An optimized structure for the trans-1,2-dibromo product was also found at all levels of theory both in gas phase and in solution, but no transition state leading to the trans-1,2-dibromo product was obtained.
Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment.

Directory of Open Access Journals (Sweden)

Ruijuan Qu

Full Text Available Tetrabromobisphenol A (TBBPA is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters.
Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment

Science.gov (United States)

Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

2015-01-01

Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733
Cellular and Molecular Pathways Leading to External Root Resorption

Science.gov (United States)

Iglesias-Linares, A.; Hartsfield, J.K.

2016-01-01

External apical root resorption during orthodontic treatment implicates specific molecular pathways that orchestrate nonphysiologic cellular activation. To date, a substantial number of in vitro and in vivo molecular, genomic, and proteomic studies have supplied data that provide new insights into root resorption. Recent mechanisms and developments reviewed here include the role of the cellular component—specifically, the balance of CD68+, iNOS+ M1- and CD68+, CD163+ M2-like macrophages associated with root resorption and root surface repair processes linked to the expression of the M1-associated proinflammatory cytokine tumor necrosis factor, inducible nitric oxide synthase, the M1 activator interferon γ, the M2 activator interleukin 4, and M2-associated anti-inflammatory interleukin 10 and arginase I. Insights into the role of mesenchymal dental pulp cells in attenuating dentin resorption in homeostasis are also reviewed. Data on recently deciphered molecular pathways are reviewed at the level of (1) clastic cell adhesion in the external apical root resorption process and the specific role of α/β integrins, osteopontin, and related extracellular matrix proteins; (2) clastic cell fusion and activation by the RANKL/RANK/OPG and ATP-P2RX7-IL1 pathways; and (3) regulatory mechanisms of root resorption repair by cementum at the proteomic and transcriptomic levels. PMID:27811065
Radical Rearrangement Chemistry in Ultraviolet Photodissociation of Iodotyrosine Systems: Insights from Metastable Dissociation, Infrared Ion Spectroscopy, and Reaction Pathway Calculations.

Science.gov (United States)

Ranka, Karnamohit; Zhao, Ning; Yu, Long; Stanton, John F; Polfer, Nicolas C

2018-05-29

We report on the ultraviolet photodissociation (UVPD) chemistry of protonated tyrosine, iodotyrosine, and diiodotyrosine. Distonic loss of the iodine creates a high-energy radical at the aromatic ring that engages in hydrogen/proton rearrangement chemistry. Based on UVPD kinetics measurements, the appearance of this radical is coincident with the UV irradiation pulse (8 ns). Conversely, sequential UVPD product ions exhibit metastable decay on ca. 100 ns timescales. Infrared ion spectroscopy is capable of confirming putative structures of the rearrangement products as proton transfers from the imine and β-carbon hydrogens. Potential energy surfaces for the various reaction pathways indicate that the rearrangement chemistry is highly complex, compatible with a cascade of rearrangements, and that there is no preferred rearrangement pathway even in small molecular systems like these. Graphical Abstract.
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Science.gov (United States)

Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

2010-01-01

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718
Confirmation of the reaction pathway for obtaining 1-(stearamidoethyl-2-hepta-decyl-2-i midazoline

Directory of Open Access Journals (Sweden)

Ružić Nenad Lj.

2002-01-01

Full Text Available 2-lmidazolines are components of many products, used in industry and households. 1-(Stearamidoethyl-2-heptadecyl-2-imidazoline is a surface active compound, which after quaternization with dimethyl sulfate, is used in lubricants, detergents, shampoos, softeners and cosmetics products. Due to its importance, it was essential to establish the exact reaction pathway for obtaining this compound. Diethylene triamine and stearic acid were used as the starting components. Using titrimetric analysis, and IR and 1H NMR spectros-copic analysis, as well as UV-Vis spectrophotometry it was established that the main intermediate was the 1,3-diamide bis(stearamidoethylamine. Earlier investigations conducted by some authors, using exclusively titrimetric analysis, showed that the main intermediate was the 1,2-diamide. In this paper it was proved that the assumption of these authors that salicylaldehiyde would react only with the primary and not the secondary amine groups was wrong. 1,2-Diamide is the main product of the hydrolysis of 1-(stearamido-ethyl-2-heptadecyl-2-imidazoline. It was shown, in this paper that the reaction of diethylene triamine with stearic acid in xylene at the reflux temperature, yields the salt of 1-(stearamidoethyl-2-heptadecyl-2-imidazoline and stearic acid.
Quantitative evaluation of the biosynthetic pathways leading to δ-aminolevulinic acid from the Shemin precursor glycine via the C5 pathway in Arthrobacter hyalinus by analysis of 13C-labeled coproporphyrinogen III biosynthesized from [2-13C]glycine, [1-13C]acetate, and [2-13C]acetate using 13C NMR spectroscopy

International Nuclear Information System (INIS)

Katsumi Iida

2013-01-01

The biosynthetic pathways leading to δ-aminolevulinic acid (ALA) from the Shemin precursor glycine via the C5 pathway in Arthrobacter hyalinus were quantitatively evaluated by means of feeding experiments with [2- 13 C]glycine, sodium [1- 13 C]acetate, and sodium [2- 13 C]acetate, followed by analysis of the labeling patterns of coproporphyrinogen III (Copro'gen III) (biosynthesized from ALA) using 13 C NMR spectroscopy. Two biosynthetic pathways leading to ALA from glycine via the C5 pathway were identified: i.e., transformation of glycine to l-serine catalyzed by glycine hydroxymethyltransferase, and glycine synthase-catalyzed catabolism of glycine to N 5 , N 10 -methylene-tetrahydrofolic acid (THF), which reacts with another molecule of glycine to afford l-serine. l-Serine is transformed to acetyl-CoA via pyruvic acid. Acetyl-CoA enters the tricarboxylic acid cycle, affording 2-oxoglutaric acid, which in turn is transformed to l-glutamic acid. The l-glutamic acid enters the C5 pathway, affording ALA in A. hyalinus. A 13 C NMR spectroscopic comparison of the labeling patterns of Copro'gen III obtained after feeding of [2- 13 C]glycine, sodium [1- 13 C]acetate, and sodium [2- 13 C]acetate showed that [2- 13 C]glycine transformation and [2- 13 C]glycine catabolism in A. hyalinus proceed in the ratio of 52 and 48 %. The reaction of [2- 13 C]glycine and N 5 , N 10 -methylene-THF, that of glycine and N 5 , N 10 -[methylene- 13 C]methylene-THF generated from the [2- 13 C]glycine catabolism, and that of [2- 13 C]glycine and N 5 , N 10 -[methylene- 13 C]methylene-THF transformed the fed [2- 13 C]glycine to [1- 13 C]acetyl-CoA, [2- 13 C]acetyl-CoA, and [1,2- 13 C 2 ]acetyl-CoA in the ratios of 42, 37, and 21 %, respectively. These labeled acetyl-CoAs were then incorporated into ALA. Our results provide a quantitative picture of the pathways of biosynthetic transformation to ALA from glycine in A. hyalinus. (author)

Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

International Nuclear Information System (INIS)

Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan, Richard; Hazen, Terry C.; Keasling, Jay D.

2007-01-01

Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both GC-MS and Fourier Transform-Ion Cyclotron Resonance mass spectrometry (FT-ICR MS) indicate the lack of oxidatively functional TCA cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80 percent of the lactate was converted to acetate and the reactions involved are the primary route of energy production (NAD(P)H and ATP production). Independent of the TCA cycle, direct cleavage of acetyl-CoA to CO and 5,10-methyl-THF also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports (the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase). These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris, and also demonstrate FT-ICR MS as a powerful tool for isotopomer analysis, overcoming problems in both GC-MS and NMR spectroscopy
An unexpected reaction pathway in the synthesis of the ABCE framework of strychnine-type alkaloids - A multidisciplinary study

Science.gov (United States)

Šoral, Michal; Markus, Jozef; Doháňošová, Jana; Šoralová, Stanislava; Dvoranová, Dana; Chyba, Andrej; Moncol, Ján; Berkeš, Dušan; Liptaj, Tibor

2017-01-01

Acid-catalyzed cyclization of spirocyclic 1‧-benzyl-2‧-(prop-2-en-1-yl)spiro[indole-3,3‧-pyrrolidine]-5‧-one (1) was performed. The pentacyclic product of Povarov-like imino-Diels-Alder reaction was isolated in high yield instead of expected tetracyclic aza-Prins intermediate. The unusual exotic alkaloid-type structure of the resulting molecule 2 was unambiguously confirmed by a detailed NMR analysis using a set of 2D NMR spectra including an INADEQUATE experiment. The relative configuration of 2 was predicted from the synthesis mechanism and DFT geometry calculations and independently confirmed using NOESY and residual dipolar coupling (RDC) assisted NMR analysis in stretched crosslinked polystyrene gels. The reversibility of the cycloaddition in aprotic solvents was observed. A new reaction pathway yielding a rare 6-5-5-5 tetracyclic spiroindoline 3 was suggested. The relative configuration within the tetracyclic framework was ultimately proved using Single-crystal X-ray diffraction analysis of compound 4.
An experimental and theoretical study of reaction mechanisms between nitriles and hydroxylamine.

Science.gov (United States)

Vörös, Attila; Mucsi, Zoltán; Baán, Zoltán; Timári, Géza; Hermecz, István; Mizsey, Péter; Finta, Zoltán

2014-10-28

The industrially relevant reaction between nitriles and hydroxylamine yielding amidoximes was studied in different molecular solvents and in ionic liquids. In industry, this procedure is carried out on the ton scale in alcohol solutions and the above transformation produces a significant amount of unexpected amide by-product, depending on the nature of the nitrile, which can cause further analytical and purification issues. Although there were earlier attempts to propose mechanisms for this transformation, the real reaction pathway is still under discussion. A new detailed reaction mechanistic explanation, based on theoretical and experimental proof, is given to augment the former mechanisms, which allowed us to find a more efficient, side-product free procedure. Interpreting the theoretical results obtained, it was shown that the application of specific imidazolium, phosphonium and quaternary ammonium based ionic liquids could decrease simultaneously the reaction time while eliminating the amide side-product, leading to the targeted product selectively. This robust and economic procedure now affords a fast, selective amide free synthesis of amidoximes.
Hydronium-Induced Switching between CO2 Electroreduction Pathways.

Science.gov (United States)

Seifitokaldani, Ali; Gabardo, Christine M; Burdyny, Thomas; Dinh, Cao-Thang; Edwards, Jonathan P; Kibria, Md Golam; Bushuyev, Oleksandr S; Kelley, Shana O; Sinton, David; Sargent, Edward H

2018-03-21

Over a broad range of operating conditions, many CO 2 electroreduction catalysts can maintain selectivity toward certain reduction products, leading to materials and surfaces being categorized according to their products; here we ask, is product selectivity truly a property of the catalyst? Silver is among the best electrocatalysts for CO in aqueous electrolytes, where it reaches near-unity selectivity. We consider the hydrogenations of the oxygen and carbon atoms via the two proton-coupled-electron-transfer processes as chief determinants of product selectivity; and find using density functional theory (DFT) that the hydronium (H 3 O + ) intermediate plays a key role in the first oxygen hydrogenation step and lowers the activation energy barrier for CO formation. When this hydronium influence is removed, the activation energy barrier for oxygen hydrogenation increases significantly, and the barrier for carbon hydrogenation is reduced. These effects make the formate reaction pathway more favorable than CO. Experimentally, we then carry out CO 2 reduction in highly concentrated potassium hydroxide (KOH), limiting the hydronium concentration in the aqueous electrolyte. The product selectivity of a silver catalyst switches from entirely CO under neutral conditions to over 50% formate in the alkaline environment. The simulated and experimentally observed selectivity shift provides new insights into the role of hydronium on CO 2 electroreduction processes and the ability for electrolyte manipulation to directly influence transition state (TS) kinetics, altering favored CO 2 reaction pathways. We argue that selectivity should be considered less of an intrinsic catalyst property, and rather a combined product of the catalyst and reaction environment.
Progranulin protects vascular endothelium against atherosclerotic inflammatory reaction via Akt/eNOS and nuclear factor-κB pathways.

Science.gov (United States)

Hwang, Hwan-Jin; Jung, Tae Woo; Hong, Ho Cheol; Choi, Hae Yoon; Seo, Ji-A; Kim, Sin Gon; Kim, Nan Hee; Choi, Kyung Mook; Choi, Dong Seop; Baik, Sei Hyun; Yoo, Hye Jin

2013-01-01

Atherosclerosis is considered a chronic inflammatory disease, initiated by activation and dysfunction of the endothelium. Recently, progranulin has been regarded as an important modulator of inflammatory processes; however, the role for prgranulin in regulating inflammation in vascular endothelial cells has not been described. Signaling pathways mediated by progranulin were analyzed in human umbilical vein endothelial cells (HUVECs) treated with progranulin. Progranulin significantly induced Akt and endothelial nitric oxide synthase (eNOS) phosphorylation in HUVECs, an effect that was blocked with Akt inhibitor. Furthermore, nitric oxide (NO) level, the end product of Akt/eNOS pathway, was significantly upregulated after progranulin treatment. Next, we showed that progranulin efficiently inhibited lipopolysaccharide (LPS)-mediated pro-inflammatory signaling. LPS-induced phosphorylation of IκB and nuclear factor-κB (NF-κB) levels decreased after progranulin treatment. Also, progranulin blocked translocation of NF-κB from the cytosol to the nucleus. In addition, progranulin significantly reduced the expression of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1) by inhibiting binding of NF- κB to their promoter regions and blocked attachment of monocytes to HUVECs. Progranulin also significantly reduced the expression of tumor necrosis factor receptor-α (TNF-α) and monocyte chemo-attractant protein-1 (MCP-1), the crucial inflammatory molecules known to aggravate atherosclerosis. Progranulin efficiently inhibited LPS-mediated pro-inflammatory signaling in endothelial cells through activation of the Akt/eNOS pathway and attenuation of the NF-κB pathway, suggesting its protective roles in vascular endothelium against inflammatory reaction underlying atherosclerosis.
Health risk assessment of various metal(loid)s via multiple exposure pathways on children living near a typical lead-acid battery plant, China

International Nuclear Information System (INIS)

Cao, Suzhen; Duan, Xiaoli; Zhao, Xiuge; Wang, Beibei; Ma, Jin; Fan, Delong; Sun, Chengye; He, Bin; Wei, Fusheng; Jiang, Guibin

2015-01-01

Manufacture of lead-acid batteries is of widespread interest because of its emissions of heavy metals and metalloids into environment, harming environmental quality and consequently causing detrimental effects on human health. In this study, exposure pathways and health risks of children to heavy metal(loid)s (Pb, Cd, As, etc) were investigated based on field sampling and questionnaire. Pb was one of the most abundant elements in children's blood, with an elevated blood lead level of 12.45 μg dL −1 . Soil/dust and food were heavily polluted by targeted metal(loid)s. Food ingestion accounted for more than 80% of the total exposure for most metal(loid)s. The non-cancer risks to children were 3–10 times higher than the acceptable level of 1, while the cancer risks were 5–200 times higher than the maximum acceptable level of 1.0 × 10 −4 . The study emphasized the significance of effective environmental management, particularly to ensure food security near battery facilities. - Highlights: • The health risks of children living around a typical lead-acid battery was analyzed. • The exposure pathways of children to 12 heavy metal(loid)s were assessed. • Courtyard soil and indoor dust and duplicate food were contaminated by metal(loid)s. • Food ingestion was the major pathway for children's exposure to most metal(loid)s. • Higher potentially non-cancer and cancer risks happened to the local children. - The children living around a typical lead-acid battery plant suffered from serious health risks, which mainly attributed to food ingestion and air inhalation exposure
Evaluation of a setting reaction pathway in the novel composite TiHA-CSD bone cement by FT-Raman and FT-IR spectroscopy

Science.gov (United States)

Paluszkiewicz, Czesława; Czechowska, Joanna; Ślósarczyk, Anna; Paszkiewicz, Zofia

2013-02-01

The aim of this study was to determine a setting reaction pathway in a novel, surgically handy implant material, based on calcium sulfate hemihydrate (CSH) and titanium doped hydroxyapatite (TiHA). The previous studies confirmed superior biological properties of TiHA in comparison to the undoped hydroxyapatite (HA) what makes it highly attractive for future medical applications. In this study the three types of titanium modified HA powders: untreated, calcined at 800 °C, sintered at 1250 °C and CSH were used to produce bone cements. The Fourier Transform-InfraRed (FT-IR) spectroscopy and Raman spectroscopy were applied to evaluate processes taking place during the setting of the studied materials. Our results undoubtedly confirmed that the reaction pathways and the phase compositions differed significantly for set cements and were dependent on the initial heat treatment of TiHA powder. Final materials were multiphase composites consisting of calcium sulfate dihydrate, bassanite, tricalcium phosphate, hydroxyapatite and calcium titanate (perovskite). The FT-IR and Scanning Electron Microscopy (SEM) measurements performed after the incubation of the cement samples in the simulated body fluid (SBF), indicate on high bioactive potential of the obtained bone cements.
Murine gammaherpesvirus M2 protein induction of IRF4 via the NFAT pathway leads to IL-10 expression in B cells.

Directory of Open Access Journals (Sweden)

Udaya S Rangaswamy

2014-01-01

Full Text Available Reactivation of the gammaherpesviruses Epstein-Barr virus (EBV, Kaposi's sarcoma-associated herpesvirus (KSHV and murine gammaherpesvirus 68 (MHV68 from latently infected B cells has been linked to plasma cell differentiation. We have previously shown that the MHV68 M2 protein is important for virus reactivation from B cells and, when expressed alone in primary murine B cells, can drive B cell differentiation towards a pre-plasma cell phenotype. In addition, expression of M2 in primary murine B cells leads to secretion of high levels of IL-10 along with enhanced proliferation and survival. Furthermore, the absence of M2 in vivo leads to a defect in the appearance of MHV68 infected plasma cells in the spleen at the peak of MHV68 latency. Here, employing an inducible B cell expression system, we have determined that M2 activates the NFAT pathway in a Src kinase-dependent manner--leading to induction of the plasma cell-associated transcription factor, Interferon Regulatory Factor-4 (IRF4. Furthermore, we show that expression of IRF4 alone in a B cell line up-regulates IL-10 expression in culture supernatants, revealing a novel role for IRF4 in B cell induced IL-10. Consistent with the latter observation, we show that IRF4 can regulate the IL-10 promoter in B cells. In primary murine B cells, addition of cyclosporine (CsA resulted in a significant decrease in M2-induced IL-10 levels as well as IRF4 expression, emphasizing the importance of the NFAT pathway in M2- -mediated induction of IL-10. Together, these studies argue in favor of a model wherein M2 activation of the NFAT pathway initiates events leading to increased levels of IRF4--a key player in plasma cell differentiation--which in turn triggers IL-10 expression. In the context of previous findings, the data presented here provides insights into how M2 facilitates plasma cell differentiation and subsequent virus reactivation.
Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

International Nuclear Information System (INIS)

Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas; Goulding, Celia W.

2014-01-01

The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully
Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

Energy Technology Data Exchange (ETDEWEB)

Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas [UC Irvine, 2212 Natural Sciences I, Irvine, CA 92697 (United States); Goulding, Celia W., E-mail: celia.goulding@uci.edu [UC Irvine, 2212 Natural Sciences I, Irvine, CA 92697 (United States); UC Irvine, 2302 Natural Sciences I, Irvine, CA 92697 (United States)

2014-04-01

The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully
DEOP: a database on osmoprotectants and associated pathways

KAUST Repository

Bougouffa, S.

2014-10-17

Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at.
DEOP: a database on osmoprotectants and associated pathways

KAUST Repository

Bougouffa, S.; Radovanovic, A.; Essack, M.; Bajic, Vladimir B.

2014-01-01

Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at.
A Tox21 Approach to Altered Epigenetic Landscapes: Assessing Epigenetic Toxicity Pathways Leading to Altered Gene Expression and Oncogenic Transformation In Vitro

Directory of Open Access Journals (Sweden)

Craig L. Parfett

2017-06-01

Full Text Available An emerging vision for toxicity testing in the 21st century foresees in vitro assays assuming the leading role in testing for chemical hazards, including testing for carcinogenicity. Toxicity will be determined by monitoring key steps in functionally validated molecular pathways, using tests designed to reveal chemically-induced perturbations that lead to adverse phenotypic endpoints in cultured human cells. Risk assessments would subsequently be derived from the causal in vitro endpoints and concentration vs. effect data extrapolated to human in vivo concentrations. Much direct experimental evidence now shows that disruption of epigenetic processes by chemicals is a carcinogenic mode of action that leads to altered gene functions playing causal roles in cancer initiation and progression. In assessing chemical safety, it would therefore be advantageous to consider an emerging class of carcinogens, the epigenotoxicants, with the ability to change chromatin and/or DNA marks by direct or indirect effects on the activities of enzymes (writers, erasers/editors, remodelers and readers that convey the epigenetic information. Evidence is reviewed supporting a strategy for in vitro hazard identification of carcinogens that induce toxicity through disturbance of functional epigenetic pathways in human somatic cells, leading to inactivated tumour suppressor genes and carcinogenesis. In the context of human cell transformation models, these in vitro pathway measurements ensure high biological relevance to the apical endpoint of cancer. Four causal mechanisms participating in pathways to persistent epigenetic gene silencing were considered: covalent histone modification, nucleosome remodeling, non-coding RNA interaction and DNA methylation. Within these four interacting mechanisms, 25 epigenetic toxicity pathway components (SET1, MLL1, KDM5, G9A, SUV39H1, SETDB1, EZH2, JMJD3, CBX7, CBX8, BMI, SUZ12, HP1, MPP8, DNMT1, DNMT3A, DNMT3B, TET1, MeCP2, SETDB2, BAZ2
Bacterial variations on the methionine salvage pathway

Directory of Open Access Journals (Sweden)

Haas Dieter

2004-03-01

Full Text Available Abstract Background The thiomethyl group of S-adenosylmethionine is often recycled as methionine from methylthioadenosine. The corresponding pathway has been unravelled in Bacillus subtilis. However methylthioadenosine is subjected to alternative degradative pathways depending on the organism. Results This work uses genome in silico analysis to propose methionine salvage pathways for Klebsiella pneumoniae, Leptospira interrogans, Thermoanaerobacter tengcongensis and Xylella fastidiosa. Experiments performed with mutants of B. subtilis and Pseudomonas aeruginosa substantiate the hypotheses proposed. The enzymes that catalyze the reactions are recruited from a variety of origins. The first, ubiquitous, enzyme of the pathway, MtnA (methylthioribose-1-phosphate isomerase, belongs to a family of proteins related to eukaryotic intiation factor 2B alpha. mtnB codes for a methylthioribulose-1-phosphate dehydratase. Two reactions follow, that of an enolase and that of a phosphatase. While in B. subtilis this is performed by two distinct polypeptides, in the other organisms analyzed here an enolase-phosphatase yields 1,2-dihydroxy-3-keto-5-methylthiopentene. In the presence of dioxygen an aci-reductone dioxygenase yields the immediate precursor of methionine, ketomethylthiobutyrate. Under some conditions this enzyme produces carbon monoxide in B. subtilis, suggesting a route for a new gaseous mediator in bacteria. Ketomethylthiobutyrate is finally transaminated by an aminotransferase that exists usually as a broad specificity enzyme (often able to transaminate aromatic aminoacid keto-acid precursors or histidinol-phosphate. Conclusion A functional methionine salvage pathway was experimentally demonstrated, for the first time, in P. aeruginosa. Apparently, methionine salvage pathways are frequent in Bacteria (and in Eukarya, with recruitment of different polypeptides to perform the needed reactions (an ancestor of a translation initiation factor and Ru
Pathways leading to self-perceived general health and overall quality of life in burned adults.

Science.gov (United States)

Moi, Asgjerd L; Nilsen, Roy M

2012-12-01

The aim of the study was to explore pathways leading to self-perceived general health and overall quality of life in burn patients. Data on burn-specific health, generic health, overall quality of life, injury characteristics and socio-demographics were obtained from 95 adult burn patients 47.0 (23.8) [mean (SD)] months after injury. A theoretical path model was established based on the concepts of Wilson and Cleary's model on health-related quality of life [1], and the proposed model was examined by structural equation modelling. Two main paths were identified, one leading to general health perception and the other leading to overall quality of life. Together, direct and indirect paths explained 63% of the variance of perceived general health and 43% of the variance in overall quality of life. The total effects of the SF-36 domain Vitality on perceived general health and overall quality of life were 0.62 and 0.66, respectively. No statistically significant path could be revealed between general health perception and overall quality of life. The results indicate that self-perceived general health and overall quality of life are related but distinct constructs. Moreover, vitality seems to be an important factor for the perception of both general health and overall quality of life in burned adults. Copyright © 2012 Elsevier Ltd and ISBI. All rights reserved.
Bioactive lysophospholipids generated by hepatic lipase degradation of lipoproteins lead to complement activation via the classical pathway.

Science.gov (United States)

Ma, Wanchao; Paik, David C; Barile, Gaetano R

2014-09-09

We determined bioactivity of lysophospholipids generated by degradation of the low-density (LDL), very low-density (VLDL), and high-density (HDL) lipoproteins with hepatic lipase (HL), cholesterol esterase (CE), and lipoprotein-associated phospholipase A2 (Lp-PLA2). The LDL, VLDL, and HDL were treated with HL, CE, and Lp-PLA2 after immobilization on plates, and complement activation studies were performed with diluted human serum. Complement component 3 (C3) fixation, a marker for complement activation, was determined with a monoclonal anti-human C3d antibody. Enzymatic properties of HL and CE were assayed with triglyceride and phosphatidylcholine substrates for triglyceride hydrolase and phospholipase A activities. The ARPE-19 cells were used for viability studies. The HL degradation of human lipoproteins LDL, VLDL, or HDL results in the formation of modified lipoproteins that can activate the complement pathway. Complement activation is dose- and time-dependent upon HL and occurs via the classical pathway. Enzymatic studies suggest that the phospholipase A1 activity of HL generates complement-activating lysophospholipids. C-reactive protein (CRP), known to simultaneously interact with complement C1 and complement factor H (CFH), further enhances HL-induced complement activation. The lysophospholipids, 1-Palmitoyl-sn-glycero-3-phosphocholine and 1-Oleoyl-sn-glycero-3-phosphocholine, can be directly cytotoxic to ARPE-19 cells. The HL degradation of lipoproteins, known to accumulate in the outer retina and in drusen, can lead to the formation of bioactive lysophospholipids that can trigger complement activation and induce RPE cellular dysfunction. Given the known risk associations for age-related macular degeneration (AMD) with HL, CRP, and CFH, this study elucidates a possible damage pathway for age-related macular degeneration (AMD) in genetically predisposed individuals, that HL activity may lead to accumulation of lysophospholipids to initiate complement
Synergistic reaction between SO2 and NO2 on mineral oxides: a potential formation pathway of sulfate aerosol.

Science.gov (United States)

Liu, Chang; Ma, Qingxin; Liu, Yongchun; Ma, Jinzhu; He, Hong

2012-02-07

Sulfate is one of the most important aerosols in the atmosphere. A new sulfate formation pathway via synergistic reactions between SO(2) and NO(2) on mineral oxides was proposed. The heterogeneous reactions of SO(2) and NO(2) on CaO, α-Fe(2)O(3), ZnO, MgO, α-Al(2)O(3), TiO(2), and SiO(2) were investigated by in situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy (in situ DRIFTS) at ambient temperature. Formation of sulfate from adsorbed SO(2) was promoted by the coexisting NO(2), while surface N(2)O(4) was observed as the crucial oxidant for the oxidation of surface sulfite. This process was significantly promoted by the presence of O(2). The synergistic effect between SO(2) and NO(2) was not observed on other mineral particles (such as CaCO(3) and CaSO(4)) probably due to the lack of the surface reactive oxygen sites. The synergistic reaction between SO(2) and NO(2) on mineral oxides resulted in the formation of internal mixtures of sulfate, nitrate, and mineral oxides. The change of mixture state will affect the physicochemical properties of atmospheric particles and therefore further influence their environmental and climate effects.
Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity.

Science.gov (United States)

Fan, Pengxiang; Miller, Abigail M; Liu, Xiaoxiao; Jones, A Daniel; Last, Robert L

2017-12-12

Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty.
MicroRNA-124-3p expression and its prospective functional pathways in hepatocellular carcinoma: A quantitative polymerase chain reaction, gene expression omnibus and bioinformatics study.

Science.gov (United States)

He, Rong-Quan; Yang, Xia; Liang, Liang; Chen, Gang; Ma, Jie

2018-04-01

The present study aimed to explore the potential clinical significance of microRNA (miR)-124-3p expression in the hepatocarcinogenesis and development of hepatocellular carcinoma (HCC), as well as the potential target genes of functional HCC pathways. Reverse transcription-quantitative polymerase chain reaction was performed to evaluate the expression of miR-124-3p in 101 HCC and adjacent non-cancerous tissue samples. Additionally, the association between miR-124-3p expression and clinical parameters was also analyzed. Differentially expressed genes identified following miR-124-3p transfection, the prospective target genes predicted in silico and the key genes of HCC obtained from Natural Language Processing (NLP) were integrated to obtain potential target genes of miR-124-3p in HCC. Relevant signaling pathways were assessed with protein-protein interaction (PPI) networks, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Protein Annotation Through Evolutionary Relationships (PANTHER) pathway enrichment analysis. miR-124-3p expression was significantly reduced in HCC tissues compared with expression in adjacent non-cancerous liver tissues. In HCC, miR-124-3p was demonstrated to be associated with clinical stage. The mean survival time of the low miR-124-3p expression group was reduced compared with that of the high expression group. A total of 132 genes overlapped from differentially expressed genes, miR-124-3p predicted target genes and NLP identified genes. PPI network construction revealed a total of 109 nodes and 386 edges, and 20 key genes were identified. The major enriched terms of three GO categories included regulation of cell proliferation, positive regulation of cellular biosynthetic processes, cell leading edge, cytosol and cell projection, protein kinase activity, transcription activator activity and enzyme binding. KEGG analysis revealed pancreatic cancer, prostate cancer and non-small cell lung cancer as the
Fragmentation Pathways of Lithiated Hexose Monosaccharides

Science.gov (United States)

Abutokaikah, Maha T.; Frye, Joseph W.; Tschampel, John; Rabus, Jordan M.; Bythell, Benjamin J.

2018-05-01

We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2A1 and 0,3A1). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B1 ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B1 ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B1 ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed. [Figure not available: see fulltext.

Structure Sensitivity in Pt Nanoparticle Catalysts for Hydrogenation of 1,3-Butadiene: In Situ Study of Reaction Intermediates Using SFG Vibrational Spectroscopy

KAUST Repository

Michalak, William D.

2013-01-31

The product selectivity during 1,3-butadiene hydrogenation on monodisperse, colloidally synthesized, Pt nanoparticles was studied under reaction conditions with kinetic measurements and in situ sum frequency generation (SFG) vibrational spectroscopy. SFG was performed with the capping ligands intact in order to maintain nanoparticle size by reduced sintering. Four products are formed at 75 C: 1-butene, cis-2-butene, trans-2-butene, and n-butane. Ensembles of Pt nanoparticles with average diameters of 0.9 and 1.8 nm exhibit a ∼30% and ∼20% increase in the full hydrogenation products, respectively, as compared to Pt nanoparticles with average diameters of 4.6 and 6.7 nm. Methyl and methylene vibrational stretches of reaction intermediates observed under working conditions using SFG were used to correlate the stable reaction intermediates with the product distribution. Kinetic and SFG results correlate with previous DFT predictions for two parallel reaction pathways of 1,3-butadiene hydrogenation. Hydrogenation of 1,3-butadiene can initiate with H-addition at internal or terminal carbons leading to the formation of 1-buten-4-yl radical (metallocycle) and 2-buten-1-yl radical intermediates, respectively. Small (0.9 and 1.8 nm) nanoparticles exhibited vibrational resonances originating from both intermediates, while the large (4.6 and 6.7 nm) particles exhibited vibrational resonances originating predominately from the 2-buten-1-yl radical. This suggests each reaction pathway competes for partial and full hydrogenation and the nanoparticle size affects the kinetic preference for the two pathways. The reaction pathway through the metallocycle intermediate on the small nanoparticles is likely due to the presence of low-coordinated sites. © 2012 American Chemical Society.
Kinetics of thermal decomposition of some biomasses in an inert environment. An investigation of the effect of lead loaded by biosorption.

Science.gov (United States)

Martín-Lara, María Ángeles; Iáñez-Rodríguez, Irene; Blázquez, Gabriel; Quesada, Lucía; Pérez, Antonio; Calero, Mónica

2017-12-01

The thermal behavior of some types of raw and lead-polluted biomasses typical in south Spain was studied by non-isothermal thermogravimetry. Experiments were carried out in nitrogen atmosphere at three heating rates (5, 10 and 20°C/min). The results of thermogravimetric tests carried out proved that the presence of lead did not change the main degradation pathways of selected biomass (almond shell (AS) and olive pomace (OP)). However, from a point of view of mass loss, lead-polluted samples showed higher decomposition temperatures and decomposition at higher rate. The determination of activation energies was performed by isoconversional methods of Flynn-Wall-Ozawa (FWO), Kissinger-Akahira-Sunose (KAS) and Friedman (FR). In general, lead-polluted samples showed lower activation energies than raw ones. Then, Coast-Redfern method was applied to determine kinetic function. The kinetic function that seems to determine the mechanism of thermal degradation of main components of all samples was nth order reaction. Finally, a model based on three parallel reactions (for three pseudocomponents) that fit to nth order reactions was evaluated. This model was appropriate to predict the pyrolysis behavior of the raw and lead-polluted samples in all pyrolysis conditions studied. Copyright © 2017 Elsevier Ltd. All rights reserved.
Effects of reaction conditions on the emission behaviors of arsenic, cadmium and lead during sewage sludge pyrolysis.

Science.gov (United States)

Han, Hengda; Hu, Song; Syed-Hassan, Syed Shatir A; Xiao, Yiming; Wang, Yi; Xu, Jun; Jiang, Long; Su, Sheng; Xiang, Jun

2017-07-01

Sewage sludge is an important class of bioresources whose energy content could be exploited using pyrolysis technology. However, some harmful trace elements in sewage sludge can escape easily to the gas phase during pyrolysis, increasing the potential of carcinogenic material emissions to the atmosphere. This study investigates emission characteristics of arsenic, cadmium and lead under different pyrolysis conditions for three different sewage sludge samples. The increased temperature (within 723-1123K) significantly promoted the cadmium and lead emissions, but its influence on arsenic emission was not pronounced. The releasing rate order of the three trace elements is volatile arsenic compounds>cadmium>lead in the beginning of pyrolysis. Fast heating rates promoted the emission of trace elements for the sludge containing the highest amount of ash, but exhibited an opposite effect for other studied samples. Overall, the high ash sludge released the least trace elements almost under all reaction conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.
Progranulin protects vascular endothelium against atherosclerotic inflammatory reaction via Akt/eNOS and nuclear factor-κB pathways.

Directory of Open Access Journals (Sweden)

Hwan-Jin Hwang

Full Text Available OBJECTIVE: Atherosclerosis is considered a chronic inflammatory disease, initiated by activation and dysfunction of the endothelium. Recently, progranulin has been regarded as an important modulator of inflammatory processes; however, the role for prgranulin in regulating inflammation in vascular endothelial cells has not been described. METHOD AND RESULTS: Signaling pathways mediated by progranulin were analyzed in human umbilical vein endothelial cells (HUVECs treated with progranulin. Progranulin significantly induced Akt and endothelial nitric oxide synthase (eNOS phosphorylation in HUVECs, an effect that was blocked with Akt inhibitor. Furthermore, nitric oxide (NO level, the end product of Akt/eNOS pathway, was significantly upregulated after progranulin treatment. Next, we showed that progranulin efficiently inhibited lipopolysaccharide (LPS-mediated pro-inflammatory signaling. LPS-induced phosphorylation of IκB and nuclear factor-κB (NF-κB levels decreased after progranulin treatment. Also, progranulin blocked translocation of NF-κB from the cytosol to the nucleus. In addition, progranulin significantly reduced the expression of vascular cell adhesion molecule-1 (VCAM-1 and intercellular adhesion molecule-1 (ICAM-1 by inhibiting binding of NF- κB to their promoter regions and blocked attachment of monocytes to HUVECs. Progranulin also significantly reduced the expression of tumor necrosis factor receptor-α (TNF-α and monocyte chemo-attractant protein-1 (MCP-1, the crucial inflammatory molecules known to aggravate atherosclerosis. CONCLUSION: Progranulin efficiently inhibited LPS-mediated pro-inflammatory signaling in endothelial cells through activation of the Akt/eNOS pathway and attenuation of the NF-κB pathway, suggesting its protective roles in vascular endothelium against inflammatory reaction underlying atherosclerosis.
Allowed energetic pathways for the three-body recombination reaction of nitrogen monoxide with the hydroxyl radical and their potential atmospheric implications

Directory of Open Access Journals (Sweden)

Luca D´Ottone

2010-12-01

Full Text Available The OH initiated oxidation of nitric oxide (NO is an important atmospheric reaction being, during the day time, the main channel that leads to the formation of HONO a reservoir species for both OH and odd nitrogen. This work reports ab initio study of the Potential Energy Surface (PES of NO + OH using density functional theory calculations conducted at the B3LYP level of theory with a 6-311g (d,p basis set. We confirmed experimental observations pointing out that the main channel for this reaction is the formation the HONO. From the addition of OH to NO both cis and trans isomers of HONO were found to be the formed as stable intermediate, both having a negative enthalpy of formation relative to the reactants, the cis isomer being more stable than the trans one. The ab initio calculations were extended to include the hydrogen extraction mechanism with its respective transition state to investigate the potential existence of a reaction channel leading to the formation of NO2 + H, that was found not to be of significant interest.
Theoretical study of the decomposition pathways and products of C5- perfluorinated ketone (C5 PFK)

Energy Technology Data Exchange (ETDEWEB)

Fu, Yuwei; Wang, Xiaohua, E-mail: xhw@mail.xjtu.edu.cn, E-mail: mzrong@mail.xjtu.edu.cn; Li, Xi; Yang, Aijun; Wu, Yi; Rong, Mingzhe, E-mail: xhw@mail.xjtu.edu.cn, E-mail: mzrong@mail.xjtu.edu.cn [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 XianNing West Road, Xi’an, Shaanxi Province 710049 (China); Han, Guohui; Lu, Yanhui [Pinggao Group Co. Ltd., Pingdingshan, Henan Province 467001 (China)

2016-08-15

Due to the high global warming potential (GWP) and increasing environmental concerns, efforts on searching the alternative gases to SF{sub 6}, which is predominantly used as insulating and interrupting medium in high-voltage equipment, have become a hot topic in recent decades. Overcoming the drawbacks of the existing candidate gases, C5- perfluorinated ketone (C5 PFK) was reported as a promising gas with remarkable insulation capacity and the low GWP of approximately 1. Experimental measurements of the dielectric strength of this novel gas and its mixtures have been carried out, but the chemical decomposition pathways and products of C5 PFK during breakdown are still unknown, which are the essential factors in evaluating the electric strength of this gas in high-voltage equipment. Therefore, this paper is devoted to exploring all the possible decomposition pathways and species of C5 PFK by density functional theory (DFT). The structural optimizations, vibrational frequency calculations and energy calculations of the species involved in a considered pathway were carried out with DFT-(U)B3LYP/6-311G(d,p) method. Detailed potential energy surface was then investigated thoroughly by the same method. Lastly, six decomposition pathways of C5 PFK decomposition involving fission reactions and the reactions with a transition states were obtained. Important intermediate products were also determined. Among all the pathways studied, the favorable decomposition reactions of C5 PFK were found, involving C-C bond ruptures producing Ia and Ib in pathway I, followed by subsequent C-C bond ruptures and internal F atom transfers in the decomposition of Ia and Ib presented in pathways II + III and IV + V, respectively. Possible routes were pointed out in pathway III and lead to the decomposition of IIa, which is the main intermediate product found in pathway II of Ia decomposition. We also investigated the decomposition of Ib, which can undergo unimolecular reactions to give the
The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

Science.gov (United States)

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.
Proanthocyanidins Attenuation of Chronic Lead-Induced Liver Oxidative Damage in Kunming Mice via the Nrf2/ARE Pathway

Directory of Open Access Journals (Sweden)

Miao Long

2016-10-01

Full Text Available Lead is harmful for human health and animals. Proanthocyanidins (PCs, a natural antioxidant, possess a broad spectrum of pharmacological and medicinal properties. However, its protective effects against lead-induced liver damage have not been clarified. This study was aimed to evaluate the protective effect of PCs on the hepatotoxicity of male Kunming mice induced by chronic lead exposure. A total of 70 healthy male Kunming mice were averagely divided into four groups: control group, i.e., the group exposed to lead, the group treated with PCs, and the group co-treated with lead and PCs. The mice exposed to lead were given water containing 0.2% lead acetate. Mice treated in the PCs and PCs lead co-treated groups were given PC (100 mg/kg in 0.9% saline by oral gavage. Lead exposure caused a significant elevation in the liver function parameters, lead level, lipid peroxidation, and inhibition of antioxidant enzyme activities. The induction of oxidative stress and histological alterations in the liver were minimized by co-treatment with PCs. Meanwhile, the number of Transferase-Mediated Deoxyuridine Triphosphate-Biotin Nick End Labeling (TUNEL-positive cells was significantly reduced in the PCs/lead co-treated group compared to the lead group. In addition, the lead group showed an increase in the expression level of Bax, while the expression of Bcl-2 was decreased. Furthermore, the lead group showed an increase in the expression level of endoplasmic reticulum (ER stress-related genes and protein (GRP78 and CHOP. Co-treated with PCs significantly reversed these expressions in the liver. PCs were, therefore, demonstrated to have protective, antioxidant, and anti-ER stress and anti-apoptotic activities in liver damage caused by chronic lead exposure in the Kunming mouse. This may be due to the ability of PCs to enhance the ability of liver tissue to protect against oxidative stress via the Nrf2/ARE signaling pathway, resulting in decreasing ER stress
An optimization model for metabolic pathways.

Science.gov (United States)

Planes, F J; Beasley, J E

2009-10-15

Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner.
Method for determining heterologous biosynthesis pathways

KAUST Repository

Gao, Xin

2017-08-10

The present invention relates to a method and system for dynamically analyzing, determining, predicting and displaying ranked suitable heterologous biosynthesis pathways for a specified host. The present invention addresses the problem of finding suitable pathways for the endogenous metabolism of a host organism because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. The present invention is called MRE (Metabolic Route Explorer), and it was conceived and developed to systematically and dynamically search for, determine, analyze, and display promising heterologous pathways while considering competing endogenous reactions in a given host organism.
Reactions of electronically excited molecular nitrogen with H2 and H2O molecules: theoretical study

Science.gov (United States)

Pelevkin, Alexey V.; Sharipov, Alexander S.

2018-05-01

Comprehensive quantum chemical analysis with the usage of the second-order perturbation multireference XMCQDPT2 approach was carried out to study the processes in the + H2 and + H2O systems. The energetically favorable reaction pathways have been revealed based on the exploration of potential energy surfaces. It has been shown that the reactions + H2 and + H2O occur with small activation barriers and, primarily, lead to the formation of N2H + H and N2H + OH products, respectively. Further, the interaction of these species could give rise to the ground state and H2 (or H2O) products, however, the estimations, based on RRKM theory and dynamic reaction coordinate calculations, exhibited that the + H2 and + H2O reactions lead to the dissociative quenching predominately. Appropriate rate constants for revealed reaction channels have been estimated by using a canonical variational theory and capture approximation. Corresponding three-parameter Arrhenius expressions for the temperature range T = 300 ‑ 3000 K were reported.
Physician scientist research pathway leading to certification by the American Board of Pathology.

Science.gov (United States)

Weiss, Sharon W; Johnson, Rebecca L

2016-06-01

In 2014, the American Board of Pathology, in response to the pathology community, approved a physician scientist research pathway (PSRP). This brief report summarizes the history of and objectives for creating the physician scientist research pathway and the requirements of the American Board of Pathology for the certification of physician scientist research pathway trainees. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Degradation of sulfadimethoxine catalyzed by laccase with soybean meal extract as natural mediator: Mechanism and reaction pathway.

Science.gov (United States)

Liang, Shangtao; Luo, Qi; Huang, Qingguo

2017-08-01

Natural laccase-mediator systems have been well recognized as an eco-friendly and energy-saving approach in environmental remediation, whose further application is however limited by the high cost of natural mediators and relatively long treatment time span. This study evaluated the water extract of soybean meal, a low-cost compound system, in mediating the laccase catalyzed degradation of a model contaminant of emerging concern, sulfadimethoxine (SDM), and demonstrated it as a promising alternative mediator for soil and water remediation. Removal of 73.3% and 65.6% was achieved in 9 h using soybean meal extract (SBE) as the mediating system for laccase-catalyzed degradation of sulfadimethoxine at the concentration of 1 ppm and 10 ppm, respectively. Further degradation of sulfadimethoxine was observed with multiple SBE additions. Using SBE as mediator increased the 9-h removal of SDM at 1 ppm initial concentration by 52.9%, 49.4%, and 36.3% in comparison to the system mediated by 1-Hydroxybenzotriazole (HBT), p-Coumaric acid (COU) and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS), respectively. With the detection of stable coupling products formed with radical scavenger (5,5-Dimethyl-1-pyrroline N-oxide, DMPO), three phenolic compounds (vanillin, apocynin, and daidzein) in SBE were confirmed to serve as mediators for Trametes versicolor laccase. Reaction pathways were proposed based on the results of High Resolution Mass Spectrometry. SO 2 excursion happened during SDM transformation, leading to elimination of antimicrobial activity. Therefore, as a natural, phenol rich, and affordable compound system, the future application of SBE in wastewater and soil remediation is worth exploring. Copyright © 2017 Elsevier Ltd. All rights reserved.
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

Directory of Open Access Journals (Sweden)

de Ridder Dick

2008-12-01

Full Text Available Abstract Background Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the variations between them. Results We present an efficient framework, Metabolic Pathway Alignment and Scoring (M-PAS, for identifying and ranking conserved metabolic pathways. M-PAS aligns all reactions in entire metabolic networks of two species and assembles them into pathways, taking mismatches, gaps and crossovers into account. It uses a comprehensive scoring function, which quantifies pathway similarity such that we can focus on different pathways given different biological motivations. Using M-PAS, we detected 1198 length-four pathways fully conserved between Saccharomyces cerevisiae and Escherichia coli, and also revealed 1399 cases of a species using a unique route in otherwise highly conserved pathways. Conclusion Our method efficiently automates the process of exploring reaction arrangement possibilities, both between species and within species, to find conserved pathways. We not only reconstruct conventional pathways such as those found in KEGG, but also discover new pathway possibilities. Our results can help to generate hypotheses on missing reactions and manifest differences in highly conserved pathways, which is useful for biology and life science applications.
Protective Effects of Maillard Reaction Products of Whey Protein Concentrate against Oxidative Stress through an Nrf2-Dependent Pathway in HepG2 Cells.

Science.gov (United States)

Pyo, Min Cheol; Yang, Sung-Yong; Chun, Su-Hyun; Oh, Nam Su; Lee, Kwang-Won

2016-09-01

Whey protein concentrate (WPC), which contains α-lactalbumin and β-lactoglobulin, is utilized widely in the food industry. The Maillard reaction is a complex reaction that produces Maillard reaction products (MRPs), which are associated with the formation of antioxidant compounds. In this study, the hepatoprotection activity of MRPs of WPC against oxidative stress through the nuclear factor-E2-related factor 2 (Nrf2)-dependent antioxidant pathway in HepG2 cells was examined. Glucose-whey protein concentrate conjugate (Glc-WPC) was obtained from Maillard reaction between WPC and glucose. The fluorescence intensity of Glc-WPC increased after 7 d compared to native WPC, and resulted in loss of 48% of the free amino groups of WPC. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of Glc-WPC showed the presence of a high-molecular-weight portion. Treatment of HepG2 cells with Glc-WPC increased cell viability in the presence of oxidative stress, inhibited the generation of intracellular reactive oxygen species by tert-butyl hydroperoxide (t-BHP), and increased the glutathione level. Nrf2 translocation and Nrf2, reduced nicotinamide adenine dinucleotide phosphate (NAD(P)H)-quinone oxidoreductase 1 (NOQ1), heme oxygenase-1 (HO-1), glutamate-L-cysteine ligase (GCL)M and GCLC mRNA levels were increased by Glc-WPC. Also, Glc-WPC increased the phosphorylation of extracellular signal-regulated kinase (ERK) 1/2 and c-Jun N-terminal kinase (JNK). The results of this study demonstrate that Glc-WPC activates the Nrf2-dependent pathway through the phosphorylation of ERK1/2 and JNK in HepG2 cells, and induces production of antioxidant enzymes and phase II enzymes.
A Light-Induced Reaction with Oxygen Leads to Chromophore Decomposition and Irreversible Photobleaching in GFP-Type Proteins.

Science.gov (United States)

Grigorenko, Bella L; Nemukhin, Alexander V; Polyakov, Igor V; Khrenova, Maria G; Krylov, Anna I

2015-04-30

Photobleaching and photostability of proteins of the green fluorescent protein (GFP) family are crucially important for practical applications of these widely used biomarkers. On the basis of simulations, we propose a mechanism for irreversible bleaching in GFP-type proteins under intense light illumination. The key feature of the mechanism is a photoinduced reaction of the chromophore with molecular oxygen (O2) inside the protein barrel leading to the chromophore's decomposition. Using quantum mechanics/molecular mechanics (QM/MM) modeling we show that a model system comprising the protein-bound Chro(-) and O2 can be excited to an electronic state of the intermolecular charge-transfer (CT) character (Chro(•)···O2(-•)). Once in the CT state, the system undergoes a series of chemical reactions with low activation barriers resulting in the cleavage of the bridging bond between the phenolic and imidazolinone rings and disintegration of the chromophore.
Formation of trihalomethanes from the halogenation of 1,3-dihydroxybenzenes in dilute aqueous solution: synthesis of 2-13C-resorcinol and its reaction with chlorine and bromine

International Nuclear Information System (INIS)

Boyce, S.D.; Barefoot, A.C.; Britton, D.R.; Hornig, J.F.

1983-01-01

As part of this study, the reaction of bromine with resorcinol and structurally related substrates to produce bromoform was examined. Preliminary results suggest that the chlorination and bromination of dihydroxybenzenes proceeded by similar reaction pathways. This chapter describes the successful synthesis of 2- 13 C-1, 3-dihydroxybenzene. Treatment of the isotopically labelled substrate with chlorine and bromine in dilute aqueous solution has elucidated many important details of the sequence of reactions leading to the production of chloroform (CHCl 3 ) and bromoform (CHBr 3 ). The 13 C-enriched products and intermediates formed during these reactions were identified by gas chromatography/mass spectrometry
Novel bioassay for the discovery of inhibitors of the 2-C-methyl-D-erythritol 4-phosphate (MEP and terpenoid pathways leading to carotenoid biosynthesis.

Directory of Open Access Journals (Sweden)

Natália Corniani

Full Text Available The 2-C-methyl-D-erythritol 4-phosphate (MEP pathway leads to the synthesis of isopentenyl diphosphate in plastids. It is a major branch point providing precursors for the synthesis of carotenoids, tocopherols, plastoquinone and the phytyl chain of chlorophylls, as well as the hormones abscisic acid and gibberellins. Consequently, disruption of this pathway is harmful to plants. We developed an in vivo bioassay that can measure the carbon flow through the carotenoid pathway. Leaf cuttings are incubated in the presence of a phytoene desaturase inhibitor to induce phytoene accumulation. Any compound reducing the level of phytoene accumulation is likely to interfere with either one of the steps in the MEP pathway or the synthesis of geranylgeranyl diphosphate. This concept was tested with known inhibitors of steps of the MEP pathway. The specificity of this in vivo bioassay was also verified by testing representative herbicides known to target processes outside of the MEP and carotenoid pathways. This assay enables the rapid screen of new inhibitors of enzymes preceding the synthesis of phytoene, though there are some limitations related to the non-specific effect of some inhibitors on this assay.
Density functional computational studies on the glucose and glycine Maillard reaction: Formation of the Amadori rearrangement products

Science.gov (United States)

Jalbout, Abraham F.; Roy, Amlan K.; Shipar, Abul Haider; Ahmed, M. Samsuddin

Theoretical energy changes of various intermediates leading to the formation of the Amadori rearrangement products (ARPs) under different mechanistic assumptions have been calculated, by using open chain glucose (O-Glu)/closed chain glucose (A-Glu and B-Glu) and glycine (Gly) as a model for the Maillard reaction. Density functional theory (DFT) computations have been applied on the proposed mechanisms under different pH conditions. Thus, the possibility of the formation of different compounds and electronic energy changes for different steps in the proposed mechanisms has been evaluated. B-Glu has been found to be more efficient than A-Glu, and A-Glu has been found more efficient than O-Glu in the reaction. The reaction under basic condition is the most favorable for the formation of ARPs. Other reaction pathways have been computed and discussed in this work.0
Metabolic pathways leading to detoxification of triptolide, a major active component of the herbal medicine Tripterygium wilfordii.

Science.gov (United States)

Du, Fuying; Liu, Zhaohua; Li, Xinxiu; Xing, Jie

2014-08-01

Triptolide (TP) shows promising anti-inflammatory and antitumor activity but with severe toxicity. TP is a natural reactive electrophile containing three epoxide groups, which are usually linked to hepatotoxicity via their ability to covalently bind to cellular macromolecules. In this study, metabolic pathways leading to detoxification of TP were evaluated in glutathione (GSH)-depleted (treated with L-buthionine-S,R-sulfoxinine, BSO) and aminobenzotriazole (ABT; a non-specific inhibitor for P450s)-treated mice. The toxicity of TP in mice was evaluated in terms of mortality and levels of serum alanine transaminase (ALT). In incubates with NADPH- and GSH-supplemented liver microsomes, seven GSH conjugates derived from TP were detected. In mice, these hydrolytically unstable GSH conjugates underwent γ-glutamyltranspeptidase/dipeptidases-mediated hydrolysis leading to two major cysteinylglycine conjugates, which underwent further hydrolysis by dipeptidases to form two cysteine conjugates of TP. In ABT-treated mice, the hydroxylated metabolites of TP were found at a lower level than normal mice, and their subsequent conjugated metabolites were not found. The level of cysteinylglycine and cysteine conjugates derived from NADPH-independent metabolism increased in mice treated with both TP and BSO (or ABT), which could be the stress response to toxicity of TP. Compared with normal mice, mortality and ALT levels were significantly higher in TP-treated mice, indicating the toxicity of TP. Pretreatment of ABT increased the toxicity caused by TP, whereas the mortality decreased in GSH-depleted mice. Metabolism by cytochrome P450 enzymes to less reactive metabolites implied a high potential for detoxification of TP. The GSH conjugation pathway also contributed to TP's detoxification in mice. Copyright © 2013 John Wiley & Sons, Ltd.

Precise generation of systems biology models from KEGG pathways.

Science.gov (United States)

Wrzodek, Clemens; Büchel, Finja; Ruff, Manuel; Dräger, Andreas; Zell, Andreas

2013-02-21

The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models. Here, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more.Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages. Building correct BioPAX and SBML signaling models from the KEGG database is a unique characteristic of the proposed method. Further, there is no other approach that is able to appropriately construct metabolic models from KEGG pathways, including correct reactions with stoichiometry. The resulting initial models, which contain valid and comprehensive SBML or BioPAX code and a multitude of cross-references, lay the foundation to facilitate further modeling steps.
Determination of the shapes and sizes of the regions in which in hadron-nucleus collisions reactions leading to the nucleon emission, particle production, and fragment evaporation occur

International Nuclear Information System (INIS)

Strugalski, Z.

1985-01-01

Shapes and sizes of the regions in target-nuclei in which reactions leading to the nucleon emission, particle production and fragment evaporation occur are determined. The region of nucleon emission is of cylindrical shape, with the diameter as large as two nucleon diameters, centered on the incident hadron course. The reactions leading to the particle production happen predominantly along the incident hadron course in nuclear matter. The fragment evaporation goes from the surface layer of the part of the target-nucleus damaged in nucleon emission process
High-level theoretical characterization of the vinoxy radical (•CH2CHO) + O2 reaction

Science.gov (United States)

Weidman, Jared D.; Allen, Ryan T.; Moore, Kevin B.; Schaefer, Henry F.

2018-05-01

Numerous processes in atmospheric and combustion chemistry produce the vinoxy radical (•CH2CHO). To understand the fate of this radical and to provide reliable energies needed for kinetic modeling of such processes, we have examined its reaction with O2 using highly reliable theoretical methods. Utilizing the focal point approach, the energetics of this reaction and subsequent reactions were obtained using coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] extrapolated to the complete basis set limit. These extrapolated energies were appended with several corrections including a treatment of full triples and connected quadruple excitations, i.e., CCSDT(Q). In addition, this study models the initial vinoxy radical + O2 reaction for the first time with multireference methods. We predict a barrier for this reaction of approximately 0.4 kcal mol-1. This result agrees with experimental findings but is in disagreement with previous theoretical studies. The vinoxy radical + O2 reaction produces a 2-oxoethylperoxy radical which can undergo a number of unimolecular reactions. Abstraction of a β-hydrogen (a 1,4-hydrogen shift) and dissociation back to reactants are predicted to be competitive to each other due to their similar barriers of 21.2 and 22.3 kcal mol-1, respectively. The minimum-energy β-hydrogen abstraction pathway produces a hydroperoxy radical (QOOH) that eventually decomposes to formaldehyde, CO, and •OH. Two other unimolecular reactions of the peroxy radical are α-hydrogen abstraction (38.7 kcal mol-1 barrier) and HO2• elimination (43.5 kcal mol-1 barrier). These pathways lead to glyoxal + •OH and ketene + HO2• formation, respectively, but they are expected to be uncompetitive due to their high barriers.
Concise Synthesis of Macrocycles by Multicomponent Reactions

NARCIS (Netherlands)

Abdelraheem, Eman M. M.; Khaksar, Samad; Dömling, Alexander

2018-01-01

A short reaction pathway was devised to synthesize a library of artificial 18-27-membered macrocycles. The five-step reaction sequence involves ring opening of a cyclic anhydride with a diamine, esterification, coupling with an amino acid isocyanide, saponification, and, finally, macro-ring closure
A Pathway to Psychological Difficulty: Perceived Chronic Social Adversity and Its Symptomatic Reactions.

Science.gov (United States)

Ding, Cody; Zhang, Jingqiu; Yang, Dong

2018-01-01

In this paper, we attempt to predict and explain psychological maladjustment or difficulty. Specifically, we discuss the concept of perceived chronic social adversity, and we expect that such perceived chronic social adversity may potentially lead to chronic stress responses. Accordingly, we propose the symptomatic reactions of perceived chronic social adversity. We put forward a set of hypotheses regarding the relationships between perceived chronic social adversity and those chronic stress responses, and we further hypothesize a mediating role of individualized negative essentialism brought by perceived chronical social adversity. Resilience and individual differences in the ability to cope with perceived adversity are discussed. Future research and prevention need to pay more attention to effects of subjective personal experiences on psychological difficulty, focusing on the importance of exploring daily social experiences in improving cognitive construction processes and developing appropriate preventions.
A Pathway to Psychological Difficulty: Perceived Chronic Social Adversity and Its Symptomatic Reactions

Directory of Open Access Journals (Sweden)

Cody Ding

2018-04-01

Full Text Available In this paper, we attempt to predict and explain psychological maladjustment or difficulty. Specifically, we discuss the concept of perceived chronic social adversity, and we expect that such perceived chronic social adversity may potentially lead to chronic stress responses. Accordingly, we propose the symptomatic reactions of perceived chronic social adversity. We put forward a set of hypotheses regarding the relationships between perceived chronic social adversity and those chronic stress responses, and we further hypothesize a mediating role of individualized negative essentialism brought by perceived chronical social adversity. Resilience and individual differences in the ability to cope with perceived adversity are discussed. Future research and prevention need to pay more attention to effects of subjective personal experiences on psychological difficulty, focusing on the importance of exploring daily social experiences in improving cognitive construction processes and developing appropriate preventions.
Evidence for leading mesons in anti p sup 4 He reactions at 0. 6 GeV c sup -1 incident momentum

Energy Technology Data Exchange (ETDEWEB)

Balestra, F.; Bossolasco, S.; Bussa, M.P.; Busso, L.; Fava, L.; Ferrero, L.; Grasso, A.; Maggiora, A.; Panzieri, D.; Piragino, G.; Piragino, R.; Tosello, F. (Ist. di Fisica Generale ' A. Avogadro' , Univ. of Turin (Italy) INFN, Sezione di Torino (Italy)); Bendiscioli, G.; Filippini, V.; Rotondi, A.; Salvini, P.; Venaglioni, A.; Zenoni, A. (Dipt. di Fisica Nucleare e Teoria, Univ. of Pavia (Italy) INFN, Sezione di Pavia (Italy)); Batusov, Yu.; Bunyatov, S.A.; Falomkin, I.V.; Nichitiu, F.; Pontecorvo, G.B.; Rozhdestvensky, A.M.; Sapozhnikov, M.G.; Tretyak, V.I. (Joint Inst. of Nuclear Research, Dubna (USSR)); Guaraldo, C. (Lab. Nazionali di Frascati dell' INFN (Italy)); Lodi Rizzini, E. (Dipt. di Automazione Industriale, Univ. of Brescia (Italy) INFN, Sezione di Pavia (Italy)); Haatuft, A.; Halsteinslid, A.; Myklebost, K.; Olsen, J.M. (Physics Dept., Univ. of Bergen (Norway)); Breivik, F.O.; Danielsen, K.M.; Jacobsen, T.; Soerensen, S.O. (Inst. of Physics, Univ. of Oslo (Norway))

1991-01-01

Leading mesons are seen in anti p {sup 4}He {yields} neutral strange particles at 0.6 GeV c{sup -1} incident momentum. These results differ somewhat from our previous results from anti p Ne-reactions. The concept of an ''effective target'' is useless. (orig.).
Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.

Science.gov (United States)

Beltrame, Luca; Bianco, Luca; Fontana, Paolo; Cavalieri, Duccio

2013-07-15

Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher's test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway expression, leading to the identification of differentially regulated pathways in a dataset of choice. Pathway Processor 2.0 is available as a web service at http://compbiotoolbox.fmach.it/pathwayProcessor/. Sample datasets to test the functionality can be used directly from the application. duccio.cavalieri@fmach.it Supplementary data are available at Bioinformatics online.
The Paterno-Buchi reaction

DEFF Research Database (Denmark)

Brogaard, Rasmus Yding; Schalk, Oliver; Boguslavskiy, Andrey E.

2012-01-01

The Paternò-Büchi (PB) reaction between an excited carbonyl compound and an alkene has been widely studied, but so far little is known about the excited-state dynamics of the reaction. In this investigation, we used a compound in which a formyl and a vinyl group are attached to a [2.......2]paracyclophane in order to obtain a model system in pre-reactive conformation for the PB reaction. We studied the excited-state dynamics of the isolated molecule in a molecular beam using femtosecond time-resolved photoelectron spectroscopy and ab initio calculations. The results show that inter-system crossing...... within two picoseconds competes efficiently with the reaction in the singlet manifold. Thus, the PB reaction in this model system takes place in the triplet state on a time scale of nanoseconds. This result stresses the importance of triplet states in the excited-state pathway of the PB reaction...
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

Directory of Open Access Journals (Sweden)

Karp Peter D

2004-06-01

Full Text Available Abstract Background The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to assign function to 40–60% of sequences. In addition, large numbers of sequences may have non-specific annotations (e.g., thiolase family protein. Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. Results We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. Our algorithm emulates the manual sequence annotation process, considering not only evidence from homology searches, but also considering evidence from genomic context (i.e., is the gene part of an operon? and functional context (e.g., are there functionally-related genes nearby in the genome? to determine the posterior belief that a candidate has the required function. The method can be applied across an entire metabolic pathway network and is generally applicable to any pathway database. The program uses a set of sequences encoding the required activity in other genomes to identify candidate proteins in the genome of interest, and then evaluates each candidate by using a simple Bayes classifier to determine the probability that the candidate has the desired function. We achieved 71% precision at a
Use of ESI-MS to determine reaction pathway for hydrogen sulphide scavenging with 1,3,5-tri-(2-hydroxyethyl)-hexahydro-s-triazine.

Science.gov (United States)

Madsen, Henrik T; Søgaard, Erik G

2012-01-01

To study the reaction between hydrogen sulphide and 1,3,5-tri-(2-hydroxyethyl)-hexahydro-s-triazine, which is an often used hydrogen sulphide scavenger, electro spray ionisation mass spectrometry (ESI-MS) was used. The investigation was carried out in positive mode, and tandem mass spectrometry was used to investigate the nature of unknown peaks in the mass spectra. The reaction was found to proceed as expected from theory with the triazine reacting with hydrogen sulphide to form the corresponding thiadiazine. This species subsequently reacted with a second hydrogen sulphide molecule to form the dithiazine species, hereby confirming previously obtained results and showing the ability of the ESI-MS method for studying the scavenging reaction. The final theoretical product s-trithiane was not detected. Furthermore, fragmentation products of thiadiazine and dithiazine were detected in the solution, and possible pathways and structures were suggested to describe the observed fragments. In these, thiadiazine fragmented to 2-(methylidene amino)-ethanol and 2-(1,3-thiazetidin-3-yl)-ethanol and N-(2-hydroxyethyl)-N-(sulfanylmethyl)-ethaniminium, which underwent a further fragmentation to N-methyl-N-(2-oxoethyl)-methaniminium. Dithiazine fragmented to N-methyl-N-(2-oxoethyl)-methaniminium as well. The by-product from this reaction is methanedithiol, which was not detected due to its low polarity.
Interfacial Reaction of Sn-Ag-Cu Lead-Free Solder Alloy on Cu: A Review

Directory of Open Access Journals (Sweden)

Liu Mei Lee

2013-01-01

Full Text Available This paper reviews the function and importance of Sn-Ag-Cu solder alloys in electronics industry and the interfacial reaction of Sn-Ag-Cu/Cu solder joint at various solder forms and solder reflow conditions. The Sn-Ag-Cu solder alloys are examined in bulk and in thin film. It then examines the effect of soldering conditions to the formation of intermetallic compounds such as Cu substrate selection, structural phases, morphology evolution, the growth kinetics, temperature and time is also discussed. Sn-Ag-Cu lead-free solder alloys are the most promising candidate for the replacement of Sn-Pb solders in modern microelectronic technology. Sn-Ag-Cu solders could possibly be considered and adapted in miniaturization technologies. Therefore, this paper should be of great interest to a large selection of electronics interconnect materials, reliability, processes, and assembly community.
Rate coefficients for hydrogen abstraction reaction of pinonaldehyde

Indian Academy of Sciences (India)

The H abstraction reaction from the –CHO group was found to be the most dominant reaction channelamong all the possible reaction pathways and its corresponding rate coefficient at 300 K is kEckart's unsymmetrical= 3.86 ×10-10 cm3 molecule-1 s-1. Whereas the channel with immediate lower activation energy is the ...
Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

DEFF Research Database (Denmark)

Do, Duy Ngoc; Ostersen, Tage; Strathe, Anders Bjerring

2013-01-01

Genome wide association studies (GWAS) are being extensively used in revealing genetic architecture of complex traits. However, GWAS offer limited understanding of the biological role of significant single nucleotide polymorphisms (SNPs) affecting complex traits. Pathway analysis using GWAS results...... is an important step where we firstly detect genes located near GWAS-detected SNPs and subsequently we detect enrichment of these genes in various biological processes and pathways. The objective of this study was to apply these steps to identify relevant pathways involved in residual feed intake (RFI) in pigs....... Residual feed intake is a feed efficiency measure and is highly economically important in animal production. In our study, a total of 596 Yorkshire boars had phenotypic and genotypic records. After quality control, 37,915 SNPs were available for GWAS which was implemented in the DMU software package...
High-precision Pb isotopic measurements of teeth and environmental samples from Sofia (Bulgaria): insights for regional lead sources and possible pathways to the human body

Science.gov (United States)

Kamenov, George D.

2008-08-01

High-precision Pb isotopic measurements on teeth and possible sources in a given area can provide important insights for the lead (Pb) sources and pathways in the human body. Pb isotopic analyses on soils from the area of Sofia, Bulgaria show that Pb is contributed by three end-members represented by two natural sources and leaded gasoline. Sequential leaching experiments reveal that the alumosilicate fraction of the soils is mainly controlled by natural Pb derived from two mountain massifs bordering the city. Around 1/3 to a half of the Pb in the soil leachates, however, can be explained by contamination from leaded gasoline. Contemporary teeth from Sofia residents show very similar Pb isotopic compositions to the soil leachates, also indicating that around 1/3 to a half of the Pb can be explained by derivation from leaded gasoline. The remarkable isotopic similarities between the teeth and the most labile fractions of the local soils suggest that the lead can be derived from the latter. Pb incorporation in the human body via soil-plant-human or soil-plant-animal-human chains is unlikely due to the fact that no significant farming occurs in the city area. The isotopic compositions of the local soil labile fractions can be used as approximation of the bioaccessible lead for humans. Considering all possible scenarios it appears that soil and/or soil-born dust inhalation and/or ingestion is the most probable pathway for incorporation of local soil lead in the local population. The high-precision Pb isotope data presented in this work indicate that apparently the local soil is what plays major role in the human Pb exposure.
Reaction Hamiltonian and state-to-state description of chemical reactions

International Nuclear Information System (INIS)

Ruf, B.A.; Kresin, V.Z.; Lester, W.A. Jr.

1985-08-01

A chemical reaction is treated as a quantum transition from reactants to products. A specific reaction Hamiltonian (in second quantization formalism) is introduced. The approach leads to Franck-Condon-like factor, and adiabatic method in the framework of the nuclear motion problems. The influence of reagent vibrational state on the product energy distribution has been studied following the reaction Hamiltonian method. Two different cases (fixed available energy and fixed translational energy) are distinguished. Results for several biomolecular reactions are presented. 40 refs., 5 figs
Developmentally programmed DNA deletion in Tetrahymena thermophila by a transposition-like reaction pathway.

Science.gov (United States)

Saveliev, S V; Cox, M M

1996-01-01

We provide a molecular description of key intermediates in the deletion of two internal eliminated sequences (IES elements), the M and R regions, during macronuclear development in Tetrahymena thermophila. Using a variety of PCR-based methods in vivo, double-strand breaks are detected that are generated by hydrolytic cleavage and correspond closely to the observed chromosomal junctions left behind in the macronuclei. The breaks exhibit a temporal and structural relationship to the deletion reaction that provides strong evidence that they are intermediates in the deletion pathway. Breaks in the individual strands are staggered by 4 bp, producing a four nucleotide 5' extension. Evidence is presented that breaks do not occur simultaneously at both ends. The results are most consistent with a deletion mechanism featuring initiation by double-strand cleavage at one end of the deleted element, followed by transesterification to generate the macronuclear junction on one DNA strand. An adenosine residue is found at all the nucleophilic 3' ends used in the postulated transesterification step. Evidence for the transesterification step is provided by detection of a 3' hydroxyl that would be liberated by such a step at a deletion boundary where no other DNA strand ends are detected. Images PMID:8654384
Replisome-mediated Translesion Synthesis and Leading Strand Template Lesion Skipping Are Competing Bypass Mechanisms*

Science.gov (United States)

Gabbai, Carolina B.; Yeeles, Joseph T. P.; Marians, Kenneth J.

2014-01-01

A number of different enzymatic pathways have evolved to ensure that DNA replication can proceed past template base damage. These pathways include lesion skipping by the replisome, replication fork regression followed by either correction of the damage and origin-independent replication restart or homologous recombination-mediated restart of replication downstream of the lesion, and bypass of the damage by a translesion synthesis DNA polymerase. We report here that of two translesion synthesis polymerases tested, only DNA polymerase IV, not DNA polymerase II, could engage productively with the Escherichia coli replisome to bypass leading strand template damage, despite the fact that both enzymes are shown to be interacting with the replicase. Inactivation of the 3′ → 5′ proofreading exonuclease of DNA polymerase II did not enable bypass. Bypass by DNA polymerase IV required its ability to interact with the β clamp and act as a translesion polymerase but did not require its “little finger” domain, a secondary region of interaction with the β clamp. Bypass by DNA polymerase IV came at the expense of the inherent leading strand lesion skipping activity of the replisome, indicating that they are competing reactions. PMID:25301949
Insights into the photochemical transformation pathways of triclosan and 2′-HO-BDE-28

Energy Technology Data Exchange (ETDEWEB)

Zhang, Ya-nan; Xie, Qing; Chen, Jingwen, E-mail: jwchen@dlut.edu.cn; Li, Yingjie; Fu, Zhiqiang

2015-12-30

Highlights: • Direct photolysis of anionic HO-PXDEs occurs through excited singlet states. • Dioxin products are formed from excited singlet states of HO-PXDEs. • Self-sensitized photolysis is involved in the phototransformation of HO-PXDEs. • {sup 1} O{sub 2} and ·OH can be generated in energy or electron transfer reactions between excited HO-PXDEs and dissolved O{sub 2}. - Abstract: Hydroxylated polyhalogenated diphenyl ethers (HO-PXDEs) have been recognized as a group of widely detected emerging contaminants in natural waters. Photolysis was proved to be an important transformation pathway for these compounds and their direct phototransformation results in highly toxic dioxins. However, the roles of excited states and reactive oxygen species in the photochemical transformation of these compounds are still unclear. In this study, 2′-HO-2,4,4′-trichlorodiphenyl ether (triclosan) and 2′-HO-2,4,4′-tribromodiphenyl ether (2′-HO-BDE-28) were selected as model compounds to investigate their phototransformation processes. Results showed that the direct photolysis reactions of both triclosan and 2′-HO-BDE-28 occurred via their respective excited singlet states, leading to the generation of dioxins. In addition, the energy and electron transfer reactions between excited states of model compounds and molecular O{sub 2} can lead to the generation of {sup 1}O{sub 2} and ·OH, which results in self-sensitized photolysis. We also found that both the k, Φ dioxin yield for anionic triclosan were higher than those of anionic 2′-HO-BDE-28. This study revealed the roles of the excited states in direct photolysis and the generation pathway of reactive oxygen species in self-sensitized photolysis of HO-PXDEs, which is important for understanding the phototransformation mechanisms of HO-PXDEs.
The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers.

Science.gov (United States)

Allen, J P; Williams, J C

2011-01-01

In photosynthetic organisms, such as purple bacteria, cyanobacteria, and plants, light is captured and converted into energy to create energy-rich compounds. The primary process of energy conversion involves the transfer of electrons from an excited donor molecule to a series of electron acceptors in pigment-protein complexes. Two of these complexes, the bacterial reaction center and photosystem II, are evolutionarily related and structurally similar. However, only photosystem II is capable of performing the unique reaction of water oxidation. An understanding of the evolutionary process that lead to the development of oxygenic photosynthesis can be found by comparison of these two complexes. In this review, we summarize how insight is being gained by examination of the differences in critical functional properties of these complexes and by experimental efforts to alter pigment-protein interactions of the bacterial reaction center in order to enable it to perform reactions, such as amino acid and metal oxidation, observable in photosystem II.

Synergy and interactions among biological pathways leading to preterm premature rupture of membranes.

Science.gov (United States)

Lannon, Sophia M R; Vanderhoeven, Jeroen P; Eschenbach, David A; Gravett, Michael G; Adams Waldorf, Kristina M

2014-10-01

Preterm premature rupture of membranes (PPROM) occurs in 1% to 2% of births. Impact of PPROM is greatest in low- and middle-income countries where prematurity-related deaths are most common. Recent investigations identify cytokine and matrix metalloproteinase activation, oxidative stress, and apoptosis as primary pathways to PPROM. These biological processes are initiated by heterogeneous etiologies including infection/inflammation, placental bleeding, uterine overdistention, and genetic polymorphisms. We hypothesize that pathways to PPROM overlap and act synergistically to weaken membranes. We focus our discussion on membrane composition and strength, pathways linking risk factors to membrane weakening, and future research directions to reduce the global burden of PPROM. © The Author(s) 2014.
Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows

DEFF Research Database (Denmark)

Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel

2018-01-01

analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimised. We then use a model of sugar...... chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest....
Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.

Science.gov (United States)

Singh, Raman K; Tsuneda, Takao

2013-02-15

The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.
Analysis of Chlorogenic Acid Oxidation Pathway in Simulated ...

African Journals Online (AJOL)

Purpose: To investigate the pathways involved in the oxidation of chlorogenic acid (CA) and phenol metabolism in honeysuckle buds. Methods: A model that mimics CA oxidation by honeysuckle polyphenol oxidase (PPO) by controlling the reaction temperature or reaction duration was employed, and the resulting products ...
New MCRs: The first 4-component reaction leading to 2,4-disubstituted thiazoles

NARCIS (Netherlands)

Kolb, Jürgen; Beck, Barbara; Almstetter, Michael; Heck, Stefan; Herdtweck, Eberhardt; Dömling, Alexander

2003-01-01

New organic reactions allow chemical transformations which were previously not possible. Therefore, new reactions are important contributions to the progress in the field of organic synthesis. In this series we describe the design, scope, and limitations of newly-discovered multi-component reactions
Hydrogen-Etched TiO2−x as Efficient Support of Gold Catalysts for Water–Gas Shift Reaction

Directory of Open Access Journals (Sweden)

Li Song

2018-01-01

Full Text Available Hydrogen-etching technology was used to prepare TiO2−x nanoribbons with abundant stable surface oxygen vacancies. Compared with traditional Au-TiO2, gold supported on hydrogen-etched TiO2−x nanoribbons had been proven to be efficient and stable water–gas shift (WGS catalysts. The disorder layer and abundant stable surface oxygen vacancies of hydrogen-etched TiO2−x nanoribbons lead to higher microstrain and more metallic Au0 species, respectively, which all facilitate the improvement of WGS catalytic activities. Furthermore, we successfully correlated the WGS thermocatalytic activities with their optoelectronic properties, and then tried to understand WGS pathways from the view of electron flow process. Hereinto, the narrowed forbidden band gap leads to the decreased Ohmic barrier, which enhances the transmission efficiency of “hot-electron flow”. Meanwhile, the abundant surface oxygen vacancies are considered as electron traps, thus promoting the flow of “hot-electron” and reduction reaction of H2O. As a result, the WGS catalytic activity was enhanced. The concept involved hydrogen-etching technology leading to abundant surface oxygen vacancies can be attempted on other supported catalysts for WGS reaction or other thermocatalytic reactions.
Tin-Containing Silicates: Identification of a Glycolytic Pathway via 3-Deoxyglucosone

DEFF Research Database (Denmark)

Tolborg, Søren; Meier, Sebastian; Sádaba, I.

2016-01-01

a cascade of four to five sequential steps. Currently, there is a limited understanding of the competing glycolytic pathways within these systems. Here we identify dehydration of glucose to 3-deoxyglucosone as an important pathway that occurs in addition to retro-aldol reaction of hexoses when using tin......-containing silicates. It is possible to influence the relative carbon flux through these pathways by controlling the amount of alkali metal salts present in the reaction mixture. In the absence of added potassium carbonate, at least 15–30% carbon flux via 3-deoxyglucosone is observed. Addition of just a few ppm...
Formation pathways of DMSO(2) in the addition channel of the OH-initiated DMS oxidation: A theoretical study.

Science.gov (United States)

Ramírez-Anguita, Juan M; González-Lafont, Angels; Lluch, José M

2009-07-15

The production of dimethyl sulfoxide (DMSO) and dimethyl sulfone (DMSO(2)) in the dimethyl sulfide (DMS) degradation scheme initiated by the hydroxyl (OH) radical has been shown to be very sensitive to nitrogen oxides (NO(x)) levels. In the present work we have explored the potential energy surfaces corresponding to several reaction pathways which yield DMSO(2) from the CH(3)S(O)(OH)CH(3) adduct [including the formation of CH(3)S(O)(OH)CH(3) from the reaction of DMSO with OH] and the reaction channels that yield DMSO or/and DMSO(2) from the CH(3)S(O(2))(OH)CH(3) adduct are also studied. The formation of the CH(3)S(O(2))(OH)CH(3) adduct from CH(3)S(OH)CH(3) (DMS-OH) and O(2) was analyzed in our previous work. All these pathways due to the presence of NO(x) (NO and NO(2)) and also due to the reactions with O(2), OH and HO(2) are compared with the objective of inferring their kinetic relevance in the laboratory experiments that measure DMSO(2) (and DMSO) formation yields. In particular, our theoretical results clearly show the existence of NO(x)-dependent pathways leading to the formation of DMSO(2), which could explain some of these experimental results in comparison with experimental measurements carried out in NO(x)-free conditions. Our results indicate that the relative importance of the addition channel in the DMS oxidation process can be dependent on the NO(x) content of chamber experiments and of atmospheric conditions. (c) 2008 Wiley Periodicals, Inc.
The Reactome pathway knowledgebase.

Science.gov (United States)

Croft, David; Mundo, Antonio Fabregat; Haw, Robin; Milacic, Marija; Weiser, Joel; Wu, Guanming; Caudy, Michael; Garapati, Phani; Gillespie, Marc; Kamdar, Maulik R; Jassal, Bijay; Jupe, Steven; Matthews, Lisa; May, Bruce; Palatnik, Stanislav; Rothfels, Karen; Shamovsky, Veronica; Song, Heeyeon; Williams, Mark; Birney, Ewan; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter

2014-01-01

Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.
Pyrrolizidine Alkaloids: Metabolic Activation Pathways Leading to Liver Tumor Initiation.

Science.gov (United States)

Fu, Peter P

2017-01-17

Pyrrolizidine alkaloids (PAs) and PA N-oxides are a class of phytochemical carcinogens contained in over 6000 plant species spread around the world. It has been estimated that approximately half of the 660 PAs and PA N-oxides that have been characterized are cytotoxic, genotoxic, and tumorigenic. It was recently determined that a genotoxic mechanism of liver tumor initiation mediated by PA-derived DNA adducts is a common metabolic activation pathway of a number of PAs. We proposed this set of PA-derived DNA adducts could be a common biological biomarker of PA exposure and a potential biomarker of PA-induced liver tumor formation. We have also found that several reactive secondary pyrrolic metabolites can dissociate and interconvert to other secondary pyrrolic metabolites, resulting in the formation of the same exogenous DNA adducts. This present perspective reports the current progress on these new findings and proposes future research needed for obtaining a greater understanding of the role of this activation pathway and validating the use of this set of PA-derived DNA adducts as a biological biomarker of PA-induced liver tumor initiation.
Connecting localized DNA strand displacement reactions

Science.gov (United States)

Mullor Ruiz, Ismael; Arbona, Jean-Michel; Lad, Amitkumar; Mendoza, Oscar; Aimé, Jean-Pierre; Elezgaray, Juan

2015-07-01

Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR02434J
Flavin-catalyzed redox tailoring reactions in natural product biosynthesis.

Science.gov (United States)

Teufel, Robin

2017-10-15

Natural products are distinct and often highly complex organic molecules that constitute not only an important drug source, but have also pushed the field of organic chemistry by providing intricate targets for total synthesis. How the astonishing structural diversity of natural products is enzymatically generated in biosynthetic pathways remains a challenging research area, which requires detailed and sophisticated approaches to elucidate the underlying catalytic mechanisms. Commonly, the diversification of precursor molecules into distinct natural products relies on the action of pathway-specific tailoring enzymes that catalyze, e.g., acylations, glycosylations, or redox reactions. This review highlights a selection of tailoring enzymes that employ riboflavin (vitamin B2)-derived cofactors (FAD and FMN) to facilitate unusual redox catalysis and steer the formation of complex natural product pharmacophores. Remarkably, several such recently reported flavin-dependent tailoring enzymes expand the classical paradigms of flavin biochemistry leading, e.g., to the discovery of the flavin-N5-oxide - a novel flavin redox state and oxygenating species. Copyright © 2017 Elsevier Inc. All rights reserved.
DNA damage and radical reactions: Mechanistic aspects, formation in cells and repair studies

International Nuclear Information System (INIS)

Cadet, J.; Ravanat, J.L.; Carell, T.; Cellai, L.; Chatgilialoglu, Ch.; Gimisis, Th.; Miranda, M.; O'Neill, P.; Robert, M.

2008-01-01

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) · 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)
THE ADVERSE OUTCOME PATHWAY (AOP) FRAMEWORK: A FRAMEWORK FOR ORGANIZING BIOLOGICAL KNOWLEDGE LEADING TO HEALTH RISKS.

Science.gov (United States)

An Adverse Outcome Pathway (AOP) represents the organization of current and newly acquired knowledge of biological pathways. These pathways contain a series of nodes (Key Events, KEs) that when sufficiently altered influence the next node on the pathway, beginning from an Molecul...
Subcritical hydrothermal conversion of organic wastes and biomass. Reaction pathways

Directory of Open Access Journals (Sweden)

Alejandro Amadeus Castro Vega

2007-01-01

Full Text Available Hydrothermal conversion is a procedure which emulates organic matter’s natural conversion into bio-crude having physical and chemical properties analogous to petroleum. The artificial transformation of biomass requi- res previous knowledge of the main reaction routes and product availability. The main component of biomass (depolymerisation by hydrolysis is presented in hydrothermal cellulose conversion, producing oligosaccharides which exhibit dehydration and retro-aldol condensation reactions for transforming into furfurals and carboxylic acids. Other biomass components (such as lignin, proteins, and fat esters present both hydrolysis and pyrolysis reaction routes. As long as biomass mainly contains carbohydrates, subcritical hydrothermal conversion products and their wastes will be fundamentally analogous to those displaying cellulose. These substances have added- value by far surpassing raw material’s acquisition cost. When the main hydrothermal conversion products’ O/C, H/C molar ratios as reported in literature are plotted, an evolutionary tralectory for conversion products appears to be closely or even overlapped with fossil fuels’ geological evolution.
Inactivation of Laccase by the Attack of As (III) Reaction in Water.

Science.gov (United States)

Hu, Jinyuan; Lu, Kun; Dong, Shipeng; Huang, Qingguo; Mao, Liang

2018-03-06

Laccase is a multicopper oxidase containing four coppers as reaction sites, including one type 1, one type 2, and two type 3. We here provide the first experimental data showing that As (III) can be effectively removed from water and transformed to As (V) through reactions mediated by laccase with the presence of oxygen. To this end, the As (III) removal, As (V) yields, total protein, active laccase, and copper concentrations in the aqueous phase were determined, respectively. Additionally, electron paramagnetic resonance spectra and UV-vis spectra were applied to probe possible structural changes of the laccase during the reaction. The data offer the first evidence that laccase can be inactivated by As (III) attack thus leading to the release of type 2 copper. The released copper has no reactivity with the As (III). These findings provide new ideas into a significant pathway likely to master the environmental transformation of arsenite, and advance the understanding of laccase inactivation mechanisms, thus providing a foundation for optimization of enzyme-based processes and potential development for removal and remediation of arsenite contamination in the environment.
Thermal decomposition pathways of hydroxylamine: theoretical investigation on the initial steps.

Science.gov (United States)

Wang, Qingsheng; Wei, Chunyang; Pérez, Lisa M; Rogers, William J; Hall, Michael B; Mannan, M Sam

2010-09-02

Hydroxylamine (NH(2)OH) is an unstable compound at room temperature, and it has been involved in two tragic industrial incidents. Although experimental studies have been carried out to study the thermal stability of hydroxylamine, the detailed decomposition mechanism is still in debate. In this work, several density functional and ab initio methods were used in conjunction with several basis sets to investigate the initial thermal decomposition steps of hydroxylamine, including both unimolecular and bimolecular reaction pathways. The theoretical investigation shows that simple bond dissociations and unimolecular reactions are unlikely to occur. The energetically favorable initial step of decomposition pathways was determined as a bimolecular isomerization of hydroxylamine into ammonia oxide with an activation barrier of approximately 25 kcal/mol at the MPW1K level of theory. Because hydroxylamine is available only in aqueous solutions, solvent effects on the initial decomposition pathways were also studied using water cluster methods and the polarizable continuum model (PCM). In water, the activation barrier of the bimolecular isomerization reaction decreases to approximately 16 kcal/mol. The results indicate that the bimolecular isomerization pathway of hydroxylamine is more favorable in aqueous solutions. However, the bimolecular nature of this reaction means that more dilute aqueous solution will be more stable.
Reaction of Aldehydes/Ketones with Electron-Deficient 1,3,5-Triazines Leading to Functionalized Pyrimidines as Diels-Alder/Retro-Diels-Alder Reaction Products: Reaction Development and Mechanistic Studies.

Science.gov (United States)

Yang, Kai; Dang, Qun; Cai, Pei-Jun; Gao, Yang; Yu, Zhi-Xiang; Bai, Xu

2017-03-03

Catalytic inverse electron demand Diels-Alder (IEDDA) reactions of heterocyclic aza-dienes are rarely reported since highly reactive and electron-rich dienophiles are often found not compatible with strong acids such as Lewis acids. Herein, we disclose that TFA-catalyzed reactions of electron-deficient 1,3,5-triazines and electron-deficient aldehydes/ketones can take place. These reactions led to highly functionalized pyrimidines as products in fair to good yields. The reaction mechanism was carefully studied by the combination of experimental and computational studies. The reactions involve a cascade of stepwise inverse electron demand hetero-Diels-Alder (ihDA) reactions, followed by retro-Diels-Alder (rDA) reactions and elimination of water. An acid was required for both ihDA and rDA reactions. This mechanism was further verified by comparing the relative reactivity of aldehydes/ketones and their corresponding vinyl ethers in the current reaction system.
Theoretical studies of the reactions of HCN with atomic hydrogen

International Nuclear Information System (INIS)

Bair, R.A.; Dunning, T.H. Jr.

1985-01-01

A comprehensive theoretical study has been made of the energetics of the important pathways involved in the reaction of hydrogen atoms with hydrogen cyanide. For each reaction ab initio GVB-CI calculations were carried out to determine the structures and vibrational frequencies of the reactants, transition states, and products; then POL-CI calculations were carried out to more accurately estimate the electronic contribution to the energetics of the reactions. The hydrogen abstraction reaction is calculated to be endoergic by 24 kcal/mol [expt. ΔH (0 K) = 16--19 kcal/mol] with a barrier of 31 kcal/mol in the forward direction and 6 kcal/mol in the reverse direction. For the hydrogen addition reactions, addition to the carbon atom is calculated to be exoergic by 19 kcal/mol with a barrier of 11 kcal/mol, while addition to the nitrogen center is essentially thermoneutral with a barrier of 17 kcal/mol. Calculations were also carried out on the isomerization reactions of the addition products. The cis→trans isomerization of HCNH has a barrier of only 10 kcal/mol with the trans isomer being more stable by 5 kcal/mol. The (1,2)-hydrogen migration reaction, converting H 2 CN to trans-HCNH, is endoergic by only 14 kcal/mol, but the calculated barrier for the transfer is 52 kcal/mol. The energy of the migration pathway thus lies above that of the dissociation--recombination pathway
Reaction progress pathways for glass and spent fuel under unsaturated conditions

International Nuclear Information System (INIS)

Bates, J.; Finn, P.; Bourcier, W.; Stout, R.

1994-10-01

The source term for the release of radionuclides from a nuclear waste repository is the waste form. In order to assess the performance of the repository and the engineered barrier system (EBS) compared to regulations established by the Nuclear Regulatory Commission and the Environmental Protection Agency it is necessary (1) to use available data to place bounding limits on release rates from the EBS, and (2) to develop a mechanistic predictive model of the radionuclide release and validate the model against tests done under a variety of different potential reaction conditions. The problem with (1) is that there is little experience to use when evaluating waste form reaction under unsaturated conditions such that errors in applying expert judgment to the problem may be significant. The second approach, to test and model the waste form reaction, is a more defensible means of providing input to the prediction of radionuclide release. In this approach, information related to the source term has a technical basis and provides a starting point to make reasonable assumptions for long-term behavior. Key aspects of this approach are an understanding of the reaction progress mechanism and the ability to model the tests using a geochemical code such as EQ3/6. Current knowledge of glass, UO 2 , and spent fuel reactions under different conditions are described below

Kinetics and mechanism of the gas-phase reaction of Cl atoms and OH radicals with fluorobenzene at 296 K

DEFF Research Database (Denmark)

Andersen, Mads Peter Sulbæk; Nielsen, Ole John; Hurley, MD

2002-01-01

Smog chamber/FTIR techniques were used to study the kinetics and mechanism of the reaction of Cl atoms and OH radicals with fluorobenzene, C6H5F, in 700 Torr of N-2 or air diluent at 296 K. Reaction of Cl atoms with C6H5F proceeds via two pathways: H-atom abstraction to give HCl and the C6H4F...... with Cl atoms via a mechanism which, at least in part, leads neither to production of C6H5Cl nor to reformation of C6H5F. As the steady-state Cl atom concentration is increased, the fraction of the C6H5F-Cl adduct undergoing reaction with Cl atoms increases causing an increase in the effective rate...
PumpKin: A tool to find principal pathways in plasma chemical models

Science.gov (United States)

Markosyan, A. H.; Luque, A.; Gordillo-Vázquez, F. J.; Ebert, U.

2014-10-01

PumpKin is a software package to find all principal pathways, i.e. the dominant reaction sequences, in chemical reaction systems. Although many tools are available to integrate numerically arbitrarily complex chemical reaction systems, few tools exist in order to analyze the results and interpret them in relatively simple terms. In particular, due to the large disparity in the lifetimes of the interacting components, it is often useful to group reactions into pathways that recycle the fastest species. This allows a researcher to focus on the slow chemical dynamics, eliminating the shortest timescales. Based on the algorithm described by Lehmann (2004), PumpKin automates the process of finding such pathways, allowing the user to analyze complex kinetics and to understand the consumption and production of a certain species of interest. We designed PumpKin with an emphasis on plasma chemical systems but it can also be applied to atmospheric modeling and to industrial applications such as plasma medicine and plasma-assisted combustion.
Discrete event simulations for glycolysis pathway and energy balance

NARCIS (Netherlands)

Zwieten, van D.A.J.; Rooda, J.E.; Armbruster, H.D.; Nagy, J.D.

2010-01-01

In this report, the biological network of the glycolysis pathway has been modeled using discrete event models (DEMs). The most important feature of this pathway is that energy is released. To create a stable steady-state system an energy molecule equilibrating enzyme and metabolic reactions have
An oxidative cross-coupling reaction of 4-hydroxydithiocoumarin and amines/thiols using a combination of I2 and TBHP: access to lead molecules for biomedical applications.

Science.gov (United States)

Mahato, Karuna; Arora, Neha; Ray Bagdi, Prasanta; Gattu, Radhakrishna; Ghosh, Siddhartha Sankar; Khan, Abu T

2018-02-06

A metal-free I 2 /TBHP induced highly atom economic and operationally simple oxidative cross-coupling reaction has been developed for the direct synthesis of sulfenamides/sulfanes/disulfides from the reaction of 4-hydroxydithiocoumarin and amines/thiols. The novelties of the present protocol are unprecedented S-C bond formation in addition to S-N and S-S bonds, shorter reaction time, mild and environmentally benign reaction conditions, functional group tolerance and moderate to excellent yields. Moreover, the four newly synthesized compounds namely 4q, 6d, 6e and 7a exhibit anti-proliferative activity against the breast cancer cell line MCF7, and may be lead molecules for future drug development.
Survivability and Fusibility in Reactions Leading to Heavy Nuclei in the Vicinity of the N=126 Closed Shell

International Nuclear Information System (INIS)

Sagaidak, R. N.

2009-01-01

Nuclear fission is well suited to study the dynamic properties and dissipative processes in cold and moderately excited nuclei. It is also a unique tool to explore level density and shell effects at an extreme deformation. Despite the significant progress in the fission studies, the isospin dependence of fission properties and, in particular, of fission barrier heights still remains an open problem. Theoretical fission model parameters are tuned by using the experimental nuclear and fission data close to stability [1]. The models provide a reasonable description of the fission barriers close to the stability line. However, large deviations are observed between predictions of different models for the fission barriers of very neutron-deficient and neutron-rich nuclei. These discrepancies (by as much as 20-30 MeV, see, e.g. [2]) become especially important in the r-process calculations for extremely neutron-rich nuclei, whose fission barriers determine the termination of the r-process by fission [3]. Unfortunately, such neutron-rich nuclei will probably not become accessible in the nearest experiments. Therefore, fission properties of exotic nuclei and especially their isospin dependence can be investigated in alternative regions of the Nuclide Chart, which are accessible for such studies now. Fusion-evaporation cross sections for heavy fissile nuclei obtained in heavy ion induced reactions as well as their fission cross sections are mainly determined by statistical properties of decaying compound nuclei (CN) and first of all by the fission-barrier heights of nuclei involved in the de-excitation chains leading to observable evaporation residues (ER). At the same time, the ER production and fission in nearly symmetric projectile-target fusion reactions leading to the most neutron-deficient CN could be strongly suppressed due to the quasi-fission (QF) effect [4], as observed recently in the 4 8C a induced reactions leading to Ra [5] and Pb [6] CN. The production of
Human health risk assessment of lead from mining activities at semi-arid locations in the context of total lead exposure.

Science.gov (United States)

Zheng, Jiajia; Huynh, Trang; Gasparon, Massimo; Ng, Jack; Noller, Barry

2013-12-01

Lead from historical mining and mineral processing activities may pose potential human health risks if materials with high concentrations of bioavailable lead minerals are released to the environment. Since the Joint Expert Committee on Food Additives of Food and Agriculture Organization/World Health Organization withdrew the Provisional Tolerable Weekly Intake of lead in 2011, an alternative method was required for lead exposure assessment. This study evaluated the potential lead hazard to young children (0-7 years) from a historical mining location at a semi-arid area using the U.S. EPA Integrated Exposure Uptake Biokinetic (IEUBK) Model, with selected site-specific input data. This study assessed lead exposure via the inhalation pathway for children living in a location affected by lead mining activities and with specific reference to semi-arid conditions and made comparison with the ingestion pathway by using the physiologically based extraction test for gastro-intestinal simulation. Sensitivity analysis for major IEUBK input parameters was conducted. Three groups of input parameters were classified according to the results of predicted blood concentrations. The modelled lead absorption attributed to the inhalation route was lower than 2 % (mean ± SE, 0.9 % ± 0.1 %) of all lead intake routes and was demonstrated as a less significant exposure pathway to children's blood, compared with ingestion. Whilst dermal exposure was negligible, diet and ingestion of soil and dust were the dominant parameters in terms of children's blood lead prediction. The exposure assessment identified the changing role of dietary intake when house lead loadings varied. Recommendations were also made to conduct comprehensive site-specific human health risk assessment in future studies of lead exposure under a semi-arid climate.
Textile Inspired Lithium-Oxygen Battery Cathode with Decoupled Oxygen and Electrolyte Pathways.

Science.gov (United States)

Xu, Shaomao; Yao, Yonggang; Guo, Yuanyuan; Zeng, Xiaoqiao; Lacey, Steven D; Song, Huiyu; Chen, Chaoji; Li, Yiju; Dai, Jiaqi; Wang, Yanbin; Chen, Yanan; Liu, Boyang; Fu, Kun; Amine, Khalil; Lu, Jun; Hu, Liangbing

2018-01-01

The lithium-air (Li-O 2 ) battery has been deemed one of the most promising next-generation energy-storage devices due to its ultrahigh energy density. However, in conventional porous carbon-air cathodes, the oxygen gas and electrolyte often compete for transport pathways, which limit battery performance. Here, a novel textile-based air cathode is developed with a triple-phase structure to improve overall battery performance. The hierarchical structure of the conductive textile network leads to decoupled pathways for oxygen gas and electrolyte: oxygen flows through the woven mesh while the electrolyte diffuses along the textile fibers. Due to noncompetitive transport, the textile-based Li-O 2 cathode exhibits a high discharge capacity of 8.6 mAh cm -2 , a low overpotential of 1.15 V, and stable operation exceeding 50 cycles. The textile-based structure can be applied to a range of applications (fuel cells, water splitting, and redox flow batteries) that involve multiple phase reactions. The reported decoupled transport pathway design also spurs potential toward flexible/wearable Li-O 2 batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
New challenges for text mining: mapping between text and manually curated pathways

Science.gov (United States)

Oda, Kanae; Kim, Jin-Dong; Ohta, Tomoko; Okanohara, Daisuke; Matsuzaki, Takuya; Tateisi, Yuka; Tsujii, Jun'ichi

2008-01-01

Background Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge. Results To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, ‘bio-inference,’ as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of ‘bio-inference’ schemes observed in the pathway corpus. Conclusions We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text. PMID:18426550
Electrocatalysis of anodic oxygen-transfer reactions at modified lead dioxide electrodes

Energy Technology Data Exchange (ETDEWEB)

Hsiao, Yun-Lin.

1990-09-21

The electrocatalytic activities were compared for pure and chloride-doped beta-PbO{sub 2} (Cl-PbO{sub 2}) films on gold and platinum substrates. Rate constants were increased significantly for oxidations of Mn{sup 2+}, toluene, benzyl alcohol, dimethylsulphoxide (DMSO) and benzaldehyde in acidic media by the incorporation of Cl{sup {minus}} into the oxide films. These reactions are concluded to occur by the electrocatalytic transfer of oxygen from H{sub 2}O to the reaction products. Results of x-ray diffraction studies indicate the Cl-PbO{sub 2} film continues to have the slightly distorted rutile structure of pure beta-PbO{sub 2}. The observed electrocatalytic phenomena are concluded to be the beneficial consequence of surface defects generated when Cl{sup {minus}} serves for charge compensation within the surface matrix and, thereby, increases the number of surface sites capable of adsorbing hydroxyl radicals which are transferred in the electrocatalytic O-transfer reactions. 91 refs., 44 figs., 10 tabs.
Dealkylation of alkylbenzenes: a significant pathway in the toluene, o-, m-, p-xylene + OH reaction.

Science.gov (United States)

Noda, Jun; Volkamer, Rainer; Molina, Mario J

2009-09-03

The OH-radical initiated oxidation of a series of monocyclic aromatic hydrocarbons (benzene, toluene, o-, m-, and p-xylene) in the presence of oxygen and NO(x) was investigated in a flowtube coupled with a chemical ionization mass spectrometer (CIMS). OH-radical addition to the aromatic ring--the major reaction pathway--has previously been shown to have a particular sensitivity to experimental conditions. This is the first flowtube study that demonstrates the atmospheric relevance of product yields from the OH-addition channel on the millisecond time scale (35-75 ms); the phenol yield from benzene and cresol yields from toluene are found to be 51.0 +/- 4.3% and 17.7 +/- 2.1%, in excellent agreement with previous studies under close to atmospheric conditions. We further report unambiguous experimental evidence that dealkylation is a novel and significant pathway for toluene and o-, m-, and p-xylene oxidation. At 150 Torr of O2 partial pressure, toluene is found to dealkylate with a yield of 5.4 +/- 1.2% phenol; similarly, m-, o-, and p-xylene dealkylate with yields of 11.2 +/- 3.8%, 4.5 +/- 3.2%, and 4.3 +/- 3.1% cresol, respectively. A dealkylation mechanism via OH-addition in the ipso position is feasible (DeltaH = -9 kcal/mol for phenol formation from toluene) but does not lend itself easily to explain the significant isomer effect observed among xylenes; instead an alternative mechanism is presented that can explain this isomer effect and forms phenol and likely epoxide type products with identical m/z (indistinguishable in our CIMS analysis) via a carbene-type intermediate. Dealkylation adds to the atmospheric production of phenol- and likely epoxide-type products, with aldehydes as expected co-products, and helps improve the carbon balance in the initial stages of aromatic oxidation.
Branching points for transition pathways: assessing responses of actors to challenges on pathways to a low carbon future

International Nuclear Information System (INIS)

Foxon, Timothy J.; Pearson, Peter J.G.; Arapostathis, Stathis; Carlsson-Hyslop, Anna; Thornton, Judith

2013-01-01

This paper describes initial analysis of branching points on a set of transition pathways to a UK low carbon electricity future by 2050. As described in other papers in this special issue, we are exploring and analysing a set of core transition pathways, based on alternative governance patterns in which the ‘logics’ of market actors, government actors and civil society actors, respectively dominate. This core pathway analysis is enhanced by analyses of branching points within and across the pathways, which informs how competition between different logics plays out at key decision points. Branching points are defined as key decision points at which choices made by actors, in response to internal or external stresses or triggers, determine whether and in what ways the pathway is followed. A set of initial branching points for our three core transition pathways is identified through project and stakeholder workshops, and drawing on analysis of actors’ choices and responses at past branching points in energy system transitions. The potential responses of the actors are identified at these branching points, and risk mitigation strategies are formulated for the dominant actors to reinforce that pathway, as well as opportunities for actors to move away from the pathway. - Highlights: Transition Pathways is analysing three potential pathways to a low carbon future. ► Stresses lead to branching points, where actors make choices, creating pathways. ► These choices may lead to path-dependency. ► Differences in governance logics within transition pathways are also analysed. ► Studying branching points adds theoretical understanding and policy relevance to TP.
Chemical burn or reaction

Science.gov (United States)

Chemicals that touch skin can lead to a reaction on the skin, throughout the body, or both. ... leave the person alone and watch carefully for reactions affecting the entire body. Note: If a chemical gets into the eyes, the eyes should be ...
Clustering mechanism of oxocarboxylic acids involving hydration reaction: Implications for the atmospheric models

Science.gov (United States)

Liu, Ling; Kupiainen-Määttä, Oona; Zhang, Haijie; Li, Hao; Zhong, Jie; Kurtén, Theo; Vehkamäki, Hanna; Zhang, Shaowen; Zhang, Yunhong; Ge, Maofa; Zhang, Xiuhui; Li, Zesheng

2018-06-01

The formation of atmospheric aerosol particles from condensable gases is a dominant source of particulate matter in the boundary layer, but the mechanism is still ambiguous. During the clustering process, precursors with different reactivities can induce various chemical reactions in addition to the formation of hydrogen bonds. However, the clustering mechanism involving chemical reactions is rarely considered in most of the nucleation process models. Oxocarboxylic acids are common compositions of secondary organic aerosol, but the role of oxocarboxylic acids in secondary organic aerosol formation is still not fully understood. In this paper, glyoxylic acid, the simplest and the most abundant atmospheric oxocarboxylic acid, has been selected as a representative example of oxocarboxylic acids in order to study the clustering mechanism involving hydration reactions using density functional theory combined with the Atmospheric Clusters Dynamic Code. The hydration reaction of glyoxylic acid can occur either in the gas phase or during the clustering process. Under atmospheric conditions, the total conversion ratio of glyoxylic acid to its hydration reaction product (2,2-dihydroxyacetic acid) in both gas phase and clusters can be up to 85%, and the product can further participate in the clustering process. The differences in cluster structures and properties induced by the hydration reaction lead to significant differences in cluster formation rates and pathways at relatively low temperatures.
Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

NARCIS (Netherlands)

De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

2015-01-01

The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

Science.gov (United States)

Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

2011-08-15

The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.
Molecular weight growth in Titan's atmosphere: branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes.

Science.gov (United States)

Kirk, Benjamin B; Savee, John D; Trevitt, Adam J; Osborn, David L; Wilson, Kevin R

2015-08-28

The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.
Adsorption and reaction of propanal, 2-propenol and 1-propanol on Ni/Pt(111) bimetallic surfaces

Science.gov (United States)

Murillo, Luis E.; Chen, Jingguang G.

2008-07-01

The hydrogenation of acrolein (CH 2dbnd CH sbnd CH dbnd O) can lead to the formation of three hydrogenation products, 2-propenol (CH 2dbnd CH sbnd CH 2sbnd OH), propanal (CH 3sbnd CH 2sbnd CH dbnd O), and 1-propanol (CH 3sbnd CH 2sbnd CH 2sbnd OH). In the current study the adsorption and reaction of these three molecules were investigated on Ni/Pt(111) surfaces to understand the different hydrogenation pathways of acrolein, using temperature programmed desorption (TPD) and high resolution electron energy loss spectroscopy (HREELS). TPD experiments showed that 2-propenol underwent isomerization toward propanal on Pt(111) and the Pt sbnd Ni sbnd Pt(111) bimetallic surface, with a dominant decarbonylation pathway on the Pt(111) surface. A self-hydrogenation (disproportionation) pathway toward 1-propanol was observed on the Ni(111) film, however, the decarbonylation pathway was found to be the most dominant on this surface. Unlike 2-propenol, propanal did not undergo isomerization or self-hydrogenation pathways on any of the surfaces, with the dominant pathway being primarily the decarbonylation on Pt(111) and Ni(111). In contrast, 1-propanol underwent mainly molecular desorption from all three surfaces. These results provided additional understanding of previous studies of hydrogenation pathways of acrolein on the Ni/Pt(111) surfaces.
The root hair assay facilitates the use of genetic and pharmacological tools in order to dissect multiple signalling pathways that lead to programmed cell death.

Directory of Open Access Journals (Sweden)

Joanna Kacprzyk

Full Text Available The activation of programmed cell death (PCD is often a result of complex signalling pathways whose relationship and intersection are not well understood. We recently described a PCD root hair assay and proposed that it could be used to rapidly screen genetic or pharmacological modulators of PCD. To further assess the applicability of the root hair assay for studying multiple signalling pathways leading to PCD activation we have investigated the crosstalk between salicylic acid, autophagy and apoptosis-like PCD (AL-PCD in Arabidopsis thaliana. The root hair assay was used to determine rates of AL-PCD induced by a panel of cell death inducing treatments in wild type plants treated with chemical modulators of salicylic acid synthesis or autophagy, and in genetic lines defective in autophagy or salicylic acid signalling. The assay demonstrated that PCD induced by exogenous salicylic acid or fumonisin B1 displayed a requirement for salicylic acid signalling and was partially dependent on the salicylic acid signal transducer NPR1. Autophagy deficiency resulted in an increase in the rates of AL-PCD induced by salicylic acid and fumonisin B1, but not by gibberellic acid or abiotic stress. The phenylalanine ammonia lyase-dependent salicylic acid synthesis pathway contributed only to death induced by salicylic acid and fumonisin B1. 3-Methyladenine, which is commonly used as an inhibitor of autophagy, appeared to influence PCD induction in all treatments suggesting a possible secondary, non-autophagic, effect on a core component of the plant PCD pathway. The results suggest that salicylic acid signalling is negatively regulated by autophagy during salicylic acid and mycotoxin-induced AL-PCD. However, this crosstalk does not appear to be directly involved in PCD induced by gibberellic acid or abiotic stress. This study demonstrates that the root hair assay is an effective tool for relatively rapid investigation of complex signalling pathways leading to
Biochemical Plant Responses to Ozone (IV. Cross-Induction of Defensive Pathways in Parsley (Petroselinum crispum L.) Plants).

Science.gov (United States)

Eckey-Kaltenbach, H.; Ernst, D.; Heller, W.; Sandermann, H.

1994-01-01

Parsley (Petroselinum crispum L.) is known to respond to ultraviolet irradiation by the synthesis of flavone glycosides, whereas fungal or elicitor stress leads to the synthesis of furanocoumarin phytoalexins. We tested how these defensive pathways are affected by a single ozone treatment (200 nL L-1; 10 h). Assays were performed at the levels of transcripts, for enzyme activities, and for secondary products. The most rapid transcript accumulation was maximal at 3 h, whereas flavone glycosides and furanocoumarins were maximally induced at 12 and 24 h, respectively, after the start of ozone treatment. Ozone acted as a cross-inducer because the two distinct pathways were simultaneously induced. These results are consistent with the previously observed ozone induction of fungal and viral defense reactions in tobacco, spruce, and pine. PMID:12232062
Does lead use the intestinal absorptive pathways of iron? Impact of iron status on murine 210Pb and 59Fe absorption in duodenum and ileum in vivo

International Nuclear Information System (INIS)

Elsenhans, Bernd; Janser, Heinz; Windisch, Wilhelm; Schuemann, Klaus

2011-01-01

Highlights: → Absorption of 210 Pb increases much less than that of 59 Fe in murine duodena. → 210 Pb-absorption is almost equally high in murine duodenal and ileal segments. → 59 Fe absorption is much lower in ileal than in duodenal segments. → There must be an additional DMT1-independet pathway for intestinal Pb absorption. -- Abstract: Background: Human isotope studies and epidemiological trials are controversial as to whether lead absorption shares the absorptive pathways of iron and whether body lead content can be reduced by iron supplementation. Aim: To compare the impact of iron-deficiency on 59 Fe- and 210 Pb-absorption rates in duodenal and ileal segments. Methods: 59 Fe- and 210 Pb-absorption was determined in ligated duodenal and ileal segments from juvenile and adult iron-deficient and iron-adequate C57Bl6 wild-type mice (n = 6) in vivo at luminal concentrations corresponding to human exposure (Fe: 1 and 100 μmol/L; Pb: 1 μmol/L). Results and discussion: 59 Fe-absorption increased 10-15-fold in iron-deficient duodena from adult and adolescent mice. Ileal 59 Fe-absorption was 4-6 times lower than in iron-adequate duodena showing no adaptation to iron-deficiency. This in accordance to expectation as the divalent metal transport 1 (DMT1) shows low ileal expression levels. Juvenile 59 Fe-absorption was about twice as high as in adult mice. In contrast, duodenal 210 Pb-absorption was increased only 1.5-1.8-fold in iron-deficiency in juvenile and adult mice and, again in contrast to 59 Fe, ileal 210 Pb-absorption was as high as in iron-adequate duodena. Conclusions: The findings suggest a DMT1-independent pathway to mediate lead absorption along the entire small intestine in addition to DMT1-mediated duodenal uptake. Ileal lead absorption appears substantial, due the much longer residence of ingesta in the distal small intestine. Differences in lead-solubility and -binding to luminal ligands can, thus, explain the conflicting findings regarding the

In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

Science.gov (United States)

Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

2016-10-24

The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Small scale lithium-lead/water-interaction studies

International Nuclear Information System (INIS)

Kranert, O.; Kottowski, H.

1991-01-01

One current concept in fusion blanket design is to utilize water as the coolant and liquid lithium-lead as the breeding/neutron multiplier material. Considering the complex design of the blanket module, it is likely that a water leakage into the liquid alloy may occur due to a tube rupture provoking an intolerable pressure increase in the blanket module. The pressure increase is caused by the combined chemical and thermohydraulic reaction of lithium-lead with water. Experiments which simulate such a transient event are necessary to obtain information which is important for the blanket module design. The interaction has been investigated by conducting small-scale experiments at various injection pressures, alloy- and coolant temperatures. Besides using eutectic Li 17 Pb 83 , Li 7 Pb 2 , lithium and lead have been used. Among other results, the experiments indicate increasing chemical reaction with increasing lithium concentration. At the same time, the chemical reaction inhibits violent thermohydaulic reactions due to the attenuating effect of the hydrogen produced. The preliminary epxerimental results from Li 17 Pb 83 and Li 7 Pb 2 reveal that the pressure- and temperature transients caused by the chemical and thermohydraulic reactions lie within technically manageable limits. (orig.)
[Polyketone Reaction in Biosynthetic Pathways of 2, 3, 5, 4'-Tetrahydroxy Stilhene-2-O-β-D-glucoside in Polygonum multiflorum by Biocatalysis].

Science.gov (United States)

Lei, Lei; Xia, Wan-xia; Shao, Li; Zhao, Shu-jin

2015-10-01

2, 3, 5, 4'-Tetrahydroxy stilbene-2-O-β-D-glucoside (THSG), the active ingredient of Polygonum multiflorum, its polyketone reaction in the biosynthesis pathways was studied by biocatalysis method. The substrates 4-coumaroyl-CoA and malonyl-CoA were catalyzed in vitro by the crude enzyme extracted from Polygonum multiflorum callus, then the products were verified by HPLC and LC-MS methods. And the crude enzyme was analyzed by ammonium sulfate precipitation method and SDS-PAGE. HPLC chromatogram showed the same retention time of both the product and resveratrol standards; LC-MS spectra showed that the m/z of product was 227, which was consistent with resveratrol standards under the mode of negative ion; Ammonium sulfate (AS) precipitation method showed AS of 40% - 70% had catalytic activity,and 50% - 60% was the optimum; SDS-PAGE showed protein bands were obviously different among different AS concentration between 20% - 80%, the protein band of 42 kDa was found in AS of 50% - 60%, which had the same molecular weight with stilbene synthase. The product of polyketone reaction in the biosynthesis of THSG is resveratrol rather than THSG, so it is speculated that THSG is the conversion product of resveratrol instead of the direct product of the polyketone reaction.
Comments on leading mesons in anti p Ne - reactions at 607 MeV/c incident momentum in terms of four-momentum transfers in two-vertex diagrams

International Nuclear Information System (INIS)

Breivik, F.O.; Haatuft, A.; Halsteinslid, A.

1990-02-01

Based on previous observations of anti p Ne - reactions the author discuss, in terms of four-momentum transfers, why only leading pions are seen in events detected by their Λ-decays, and only leading kaons in the events detected by their neutral K-decays. The experimental results are consistent with a two-vertex model with strange or non-strange baryon exchange. 3 refs.; 4 figs.; 1 tab
Parallel proton transfer pathways in aqueous acid-base reactions

NARCIS (Netherlands)

Cox, M.J.; Bakker, H.J.

2008-01-01

We study the mechanism of proton transfer (PT) between the photoacid 8-hydroxy-1,3, 6-pyrenetrisulfonic acid (HPTS) and the base chloroacetate in aqueous solution. We investigate both proton and deuteron transfer reactions in solutions with base concentrations ranging from 0.25M to 4M. Using
Quantitative trait loci and metabolic pathways

Science.gov (United States)

McMullen, M. D.; Byrne, P. F.; Snook, M. E.; Wiseman, B. R.; Lee, E. A.; Widstrom, N. W.; Coe, E. H.

1998-01-01

The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for “channeling” of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits. PMID:9482823
Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.

Science.gov (United States)

Dailey, Harry A; Dailey, Tamara A; Gerdes, Svetlana; Jahn, Dieter; Jahn, Martina; O'Brian, Mark R; Warren, Martin J

2017-03-01

The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized. Copyright © 2017 American Society for Microbiology.
Alternative reaction routes during coal hydrogenation and coal derived oil upgrading

Energy Technology Data Exchange (ETDEWEB)

Schulz, H.; Kordokuzis, G.; Langner, M. (University of Karlsruhe, Karlsruhe (Germany, F.R.). Engler-Bunte-Institute)

1989-10-01

Alternative reaction routes have been traced for the hydrodenitrogenation and hydrodeoxygenation of coal structure related model compounds. Reaction pathways are very structure specific. It is shown how reaction mechanisms switch from one route to another with changes in reaction conditions and catalyst features. Optimization of coal liquefaction processes can make use of this detailed understanding of selectivity. 5 refs., 7 figs.
Vapor-Phase Hydrodeoxygenation of Guaiacol to Aromatics over Pt/HBeta: Identification of the Role of Acid Sites and Metal Sites on the Reaction Pathway

Energy Technology Data Exchange (ETDEWEB)

Nie, Lei [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Peng, Bo [Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Zhu, Xinli [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China

2018-02-05

Hydrodeoxygenation of guaiacol, a phenolic compound derived from lignin fraction of biomass, over a Pt/HBeta catalyst at 350 °C and atmospheric pressure produces benzene, toluene, xylenes, and C9+ aromatics with yield of 42%, 29%, 12%, and 5%, respectively. Reaction pathways for conversion of two functional groups (hydroxyl and methoxyl) over the bifunctional catalyst were studied. Both guaiacol and intermediate products (catechol and cyclopentanone) were fed onto zeolite HBeta and Pt/SiO2 to identify the individual role of acid site and metal site. Acid sites (mainly Brønsted acid site, BAS) catalyze transalkylation and dehydroxylation reactions in sequence, producing phenol, cresols and xylenols as the major products at high conversion. Pt sites catalyze demethylation reaction resulting in catechol as the primary product, which can either be deoxygenated to phenol followed by phenol to benzene, or decarbonylated to cyclopentanone and further to butane. The close proximity of Pt and BAS in bifunctional Pt/HBeta enables both transalkylation and deoxygenation reactions with inhibited demethylation and decarbonylation reactions, producing aromatics as major final products with a total yield > 85%. Both activity and stability of bifunctional Pt/HBeta during hydrodeoxygenation of guaiacol is improved compared to HBeta and Pt/SiO2. The addition of water to the feed further improves the activity and stability via hydrolysis of O-CH3 bond of guaiacol on BAS and removing coke around Pt.
Kinetics of oil saponification by lead salts in ancient preparations of pharmaceutical lead plasters and painting lead mediums.

Science.gov (United States)

Cotte, M; Checroun, E; Susini, J; Dumas, P; Tchoreloff, P; Besnard, M; Walter, Ph

2006-12-15

Lead soaps can be found in archaeological cosmetics as well as in oil paintings, as product of interactions of lead salts with oil. In this context, a better understanding of the formation of lead soaps allows a follow-up of the historical evolution of preparation recipes and provides new insights into conservation conditions. First, ancient recipes of both pharmaceutical lead plasters and painting lead mediums, mixtures of oil and lead salts, were reconstructed. The ester saponification by lead salts is determined by the preparation parameters which were quantified by FT-IR spectrometry. In particular, ATR/FT-IR spectrometer was calibrated by the standard addition method to quantitatively follow the kinetics of this reaction. The influence of different parameters such as temperature, presence of water and choice of lead salts was assessed: the saponification is clearly accelerated by water and heating. This analysis provides chemical explanations to the historical evolution of cosmetic and painting preparation recipes.
Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus

DEFF Research Database (Denmark)

Thykær, Jette; Andersen, Mikael Rørdam; Baker, S. E.

2009-01-01

with the reactions, we identified orthologous candidate essential genes in Aspergillus fumigatus. Our predictions are validated in part by the modes of action for some antifungal drugs and by molecular genetic studies of essential genes in A. fumigatus and other fungi. The use of metabolic models to predict...... of 1190 biochemically unique reactions that are associated with 871 open reading frames. Through a systematic in silico deletion of single metabolic reactions using this model, several essential metabolic pathways were identified for A. niger. A total of 138 reactions were identified as being essential...... biochemical reactions during growth on a minimal glucose medium. The majority of the reactions grouped into essential biochemical pathways covering cell wall biosynthesis, amino acid biosynthesis, energy metabolism and purine and pyrimidine metabolism. Based on the A. niger open reading frames associated...
Crystallization Pathways in Biomineralization

Science.gov (United States)

Weiner, Steve; Addadi, Lia

2011-08-01

A crystallization pathway describes the movement of ions from their source to the final product. Cells are intimately involved in biological crystallization pathways. In many pathways the cells utilize a unique strategy: They temporarily concentrate ions in intracellular membrane-bound vesicles in the form of a highly disordered solid phase. This phase is then transported to the final mineralization site, where it is destabilized and crystallizes. We present four case studies, each of which demonstrates specific aspects of biological crystallization pathways: seawater uptake by foraminifera, calcite spicule formation by sea urchin larvae, goethite formation in the teeth of limpets, and guanine crystal formation in fish skin and spider cuticles. Three representative crystallization pathways are described, and aspects of the different stages of crystallization are discussed. An in-depth understanding of these complex processes can lead to new ideas for synthetic crystallization processes of interest to materials science.
Investigation of reaction mechanisms during electroreduction of carbon dioxide on lead electrode for the production of organic compounds

International Nuclear Information System (INIS)

Innocent, B.

2008-09-01

The aim of this work was to promote the reduction of CO 2 through its electrochemical conversion (electro-synthesis) on a lead electrode into high added value products. Depending on the nature of electrolyte, the electro-reduction of carbon dioxide leads to different products. Various electrolytes (aqueous or organic, protic or aprotic) were used to study two mechanisms: hydrogenation (formation of formate) and electro-dimerization (synthesis of oxalate). Cyclic voltammetry studies have been carried out for electrochemically characterizing CO 2 reduction on Pb. The electrochemical investigation of the electrode electrolyte interface has shown that the process of CO 2 electro-reduction is a mass transfer control both in the organic and aqueous media. Electrochemical experiments (cyclic voltammetry, chrono-amperometry) coupled with in situ infrared reflectance spectroscopic techniques (SPAIRS, SNIFTIRS) have also shown that in aqueous medium (7 ≤pH≤9) hydrogeno-carbonate ions were reduced to formate. The modification of solvent (propylene carbonate) leads selectively to oxalate as the main reaction product. Long-term electrolyses were performed in a filter-press cell to deal large volumes. In aqueous medium, the reduction of HCO 3 - to HCOO - (R F = 89% at -2.5 mA cm -2 and 4 C) is always accompanied by the production of H 2 . (author)
Back-reactions, short-circuits, leaks and other energy wasteful reactions in biological electron transfer: redox tuning to survive life in O(2).

Science.gov (United States)

Rutherford, A William; Osyczka, Artur; Rappaport, Fabrice

2012-03-09

The energy-converting redox enzymes perform productive reactions efficiently despite the involvement of high energy intermediates in their catalytic cycles. This is achieved by kinetic control: with forward reactions being faster than competing, energy-wasteful reactions. This requires appropriate cofactor spacing, driving forces and reorganizational energies. These features evolved in ancestral enzymes in a low O(2) environment. When O(2) appeared, energy-converting enzymes had to deal with its troublesome chemistry. Various protective mechanisms duly evolved that are not directly related to the enzymes' principal redox roles. These protective mechanisms involve fine-tuning of reduction potentials, switching of pathways and the use of short circuits, back-reactions and side-paths, all of which compromise efficiency. This energetic loss is worth it since it minimises damage from reactive derivatives of O(2) and thus gives the organism a better chance of survival. We examine photosynthetic reaction centres, bc(1) and b(6)f complexes from this view point. In particular, the evolution of the heterodimeric PSI from its homodimeric ancestors is explained as providing a protective back-reaction pathway. This "sacrifice-of-efficiency-for-protection" concept should be generally applicable to bioenergetic enzymes in aerobic environments. Copyright Â© 2012 Federation of European Biochemical Societies. All rights reserved.
Dissipative effects in fission investigated with proton-on-lead reactions

Directory of Open Access Journals (Sweden)

Rodríguez-Sánchez J. L.

2016-01-01

Full Text Available The complete kinematic measurement of the two fission fragments permitted us to investigate dissipative effects at large deformations, between the saddle-point and the corresponding scission configurations. Up to now, this kind of study has only been performed with fusionfission reactions using a limited number of observables, such as the mass distribution of the fission fragments or the neutron multiplicities. However, the large angular momenta gained by the compound nucleus could affect the conclusions drawn from such experiments. In this work, the use of spallation reactions, where the fissioning systems are produced with low angular momentum, small deformations and high excitation energies, favors the study of dissipation, and allowed us to define new observables, such as postscission neutron multiplicities and the neutron excess of the final fission fragments as a function of the atomic number of the fissioning system. These new observables are used to investigate the dissipation at large deformations.
Reaction of Titanocene Alkyls with Pyridines; A Novel Type of Cyclometallation Reaction

NARCIS (Netherlands)

Klei, E.; Teuben, J.H.

1981-01-01

Reaction of Cp2TiR (R = alkyl) with 2-substituted-pyridines and with quinolines leads to α-metallation of these ligands with formation of triangular titanocycles containing TiIII. Proof of the metallation at the α-position comes from reactions of the complexes formed with I2 and D2O/DCl which yield
Pion-transfer (n,d) and (d, 3He) reactions leading to deeply bound pionic atoms

International Nuclear Information System (INIS)

Toki, H.; Hirenzaki, S.; Yamazaki, T.

1990-11-01

Theoretical studies are given on the (n,d) and (d, 3 He) reactions leading to deeply bound pionic atoms in heavy nuclei of configuration [(nl) π ·j n -1 ]J. The cross sections for various pionic and neutron-hole configurations in the case of a 208 Pb target are calculated at incident energies 300-1000 MeV/u by using the effective number approach and the eikonal approximation for distortion. The effective number with a pion in the 1s or 2p state and a neutron hole in the i 13/2 orbit peaks around the same incident energy (T n =600 MeV) as the elementary cross section n+n→d+π - , where the momentum transfer matches the angular-momentum transfer of L=5∼7. The DWIA cross section for (n,d) producing a pion in the 1s or 2p orbit at T n =600 MeV is found to be around 42 or 75 μb/sr, respectively. At T n =350 MeV, where the momentum transfer is small, quasi-substitutional states of configurations [(2p) π (3p 1/2 ) n -1 ]L=0 and [(2p) π (3p 3/2 ) n -1 ]L=0 are preferentially populated with cross sections of 190 and 380 μb/sr, respectively. The (d, 3 He) cross sections are estimated to be an order of magnitude smaller than the (n,d) cross sections. Thus, the (n,d) and (d, 3 He) reactions are found to be suited for the production of deeply bound pionic atoms. (author)
Activation of the TREM-1 pathway in human monocytes by periodontal pathogens and oral commensal bacteria.

Science.gov (United States)

Varanat, M; Haase, E M; Kay, J G; Scannapieco, F A

2017-08-01

Periodontitis is a highly prevalent disease caused in part by an aberrant host response to the oral multi-species biofilm. A balance between the oral bacteria and host immunity is essential for oral health. Imbalances in the oral microbiome lead to an uncontrolled host inflammatory response and subsequent periodontal disease (i.e. gingivitis and periodontitis). TREM-1 is a signaling receptor present on myeloid cells capable of acting synergistically with other pattern recognition receptors leading to amplification of inflammatory responses. The aim of this study was to investigate the activation of the TREM-1 pathway in the human monocyte-like cell line THP-1 exposed to both oral pathogens and commensals. The relative expression of the genes encoding TREM-1 and its adapter protein DAP12 were determined by quantitative real-time polymerase chain reaction. The surface expression of TREM-1 was determined by flow cytometry. Soluble TREM-1 and cytokines were measured by enzyme-linked immunosorbent assay. The results demonstrate that both commensal and pathogenic oral bacteria activate the TREM-1 pathway, resulting in a proinflammatory TREM-1 activity-dependent increase in proinflammatory cytokine production. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Persistent ER stress induces the spliced leader RNA silencing pathway (SLS, leading to programmed cell death in Trypanosoma brucei.

Directory of Open Access Journals (Sweden)

Hanoch Goldshmidt

2010-01-01

Full Text Available Trypanosomes are parasites that cycle between the insect host (procyclic form and mammalian host (bloodstream form. These parasites lack conventional transcription regulation, including factors that induce the unfolded protein response (UPR. However, they possess a stress response mechanism, the spliced leader RNA silencing (SLS pathway. SLS elicits shut-off of spliced leader RNA (SL RNA transcription by perturbing the binding of the transcription factor tSNAP42 to its cognate promoter, thus eliminating trans-splicing of all mRNAs. Induction of endoplasmic reticulum (ER stress in procyclic trypanosomes elicits changes in the transcriptome similar to those induced by conventional UPR found in other eukaryotes. The mechanism of up-regulation under ER stress is dependent on differential stabilization of mRNAs. The transcriptome changes are accompanied by ER dilation and elevation in the ER chaperone, BiP. Prolonged ER stress induces SLS pathway. RNAi silencing of SEC63, a factor that participates in protein translocation across the ER membrane, or SEC61, the translocation channel, also induces SLS. Silencing of these genes or prolonged ER stress led to programmed cell death (PCD, evident by exposure of phosphatidyl serine, DNA laddering, increase in reactive oxygen species (ROS production, increase in cytoplasmic Ca(2+, and decrease in mitochondrial membrane potential, as well as typical morphological changes observed by transmission electron microscopy (TEM. ER stress response is also induced in the bloodstream form and if the stress persists it leads to SLS. We propose that prolonged ER stress induces SLS, which serves as a unique death pathway, replacing the conventional caspase-mediated PCD observed in higher eukaryotes.
Electrical properties of a novel lead alkoxide precursor: Lead glycolate

International Nuclear Information System (INIS)

Tangboriboon, Nuchnapa; Pakdeewanishsukho, Kittikhun; Jamieson, Alexander; Sirivat, Anuvat; Wongkasemjit, Sujitra

2006-01-01

The reaction of lead acetate trihydrate Pb(CH 3 COO) 2 .3H 2 O and ethylene glycol, using triethylenetetramine (TETA) as a catalyst, provides in one step access to a polymer-like precursor of lead glycolate [-PbOCH 2 CH 2 O-]. On the basis of high-resolution mass spectroscopy, chemical analysis composition, FTIR, 13 C-solid state NMR and TGA, the lead glycolate precursor can be identified as a trimer structure. The FTIR spectrum demonstrates the characteristics of lead glycolate; the peaks at 1086 and 1042 cm -1 can be assigned to the C-O-Pb stretchings. The 13 C-solid state NMR spectrum gives notably only one peak at 68.639 ppm belonging to the ethylene glycol ligand. The phase transformations of lead glycolate and lead acetate trihydrate to lead oxide, their microstructures, and electrical properties were found to vary with increasing temperature. The lead glycolate precursor has superior electrical properties relative to those of lead acetate trihydrate, suggesting that the lead glycolate precursor can possibly be used as a starting material for producing electrical and semiconducting ceramics, viz. ferroelectric, anti-ferroelectric, and piezoelectric materials

Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

Science.gov (United States)

Minakata, Daisuke; Mezyk, Stephen P; Jones, Jace W; Daws, Brittany R; Crittenden, John C

2014-12-02

Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.
Leading survey and research report for fiscal 1999. Survey and research on chemical reaction simulator technology; 1999 nendo kagaku hanno simulator gijutsu no chosa kenkyu hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

Although various chemical reactions are made use of at scenes of chemical industry for the acquisition of desired chemicals, the control of reaction process governing factors, such as temperature, pressure, catalysts, solutions, etc., is found to be carried out only on the empirical basis. At the present time, rational or optimum reaction designs are not to be prepared in a short period of time in the presence of the widespread shortage of knowledge about chemical reactions and of the shortage of understanding of chemical reactions at the micro level. Leading survey and research are conducted for the development of a 'chemical reaction simulator' technology to enable the acquisition of optimum reaction designing guidelines in a short period of time. Using the simulator, a chemical of his choice is inputted by a researcher engaged in the study of an real chemical reaction and then various techniques of computer science are mobilized for the preparation of a huge number of feasible reaction routes, and high-precision simulations are conducted for the feasible reaction routes. The results achieved this fiscal year are reported. The purpose of this research and its ripple effect on new product industry creation are stated. Then the positioning, mission, and concept of such a chemical reaction simulator are described. Finally, the result of research and survey of knowledge databases and the result of research and survey of computational chemistry are stated. (NEDO)
Leading survey and research report for fiscal 1999. Survey and research on chemical reaction simulator technology; 1999 nendo kagaku hanno simulator gijutsu no chosa kenkyu hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

Although various chemical reactions are made use of at scenes of chemical industry for the acquisition of desired chemicals, the control of reaction process governing factors, such as temperature, pressure, catalysts, solutions, etc., is found to be carried out only on the empirical basis. At the present time, rational or optimum reaction designs are not to be prepared in a short period of time in the presence of the widespread shortage of knowledge about chemical reactions and of the shortage of understanding of chemical reactions at the micro level. Leading survey and research are conducted for the development of a 'chemical reaction simulator' technology to enable the acquisition of optimum reaction designing guidelines in a short period of time. Using the simulator, a chemical of his choice is inputted by a researcher engaged in the study of an real chemical reaction and then various techniques of computer science are mobilized for the preparation of a huge number of feasible reaction routes, and high-precision simulations are conducted for the feasible reaction routes. The results achieved this fiscal year are reported. The purpose of this research and its ripple effect on new product industry creation are stated. Then the positioning, mission, and concept of such a chemical reaction simulator are described. Finally, the result of research and survey of knowledge databases and the result of research and survey of computational chemistry are stated. (NEDO)
Long-term human exposure to lead from different media and intake pathways.

Science.gov (United States)

Pizzol, Massimo; Thomsen, Marianne; Andersen, Mikael Skou

2010-10-15

Lead (Pb) is well known as an environmental pollutant: it can accumulate in various media, so actual lead exposure reflects both historical and present contaminations. Two main challenges then emerge: obtaining updated information to gain an overall picture of the sources of exposure, and predicting the resulting internal body exposure levels and effects that occur under long-term exposure conditions. In this paper, a modeling approach is used to meet these challenges with reference to Danish exposure conditions. Levels of lead content in various media have been coupled with data for lead intake and absorption in the human body, for both children and adults. An age-dependent biokinetic model allows then for determination of the blood lead levels resulting from chronic exposure. The study shows that the actual intake of lead is up to 27% of the Provisional Tolerable Daily Intake (PTDI) for children and around 8% for adults. It is confirmed that the critical route of exposure is via ingestion, accounting for 99% of total lead intake, while inhalation contributes only to 1% of total lead intake. The resulting lead levels in the blood after 2 years of exposure to actual contamination conditions have been estimated as up to 2.2μg/dl in children and almost 1μg/dl in adults. Impacts from lead can occur even at such levels. The role of historical and present sources to lead in the environment is discussed, and, for specific child and adult exposure scenarios, external-internal concentration relationships for the direct linkage between lead in environmental media and resulting concentrations of lead in blood are then presented. Copyright © 2010 Elsevier B.V. All rights reserved.
The functionalities of Pt/{gamma}-Al{sub 2}O{sub 3} catalysts in simultaneous HDS and HDA reactions

Energy Technology Data Exchange (ETDEWEB)

V.G. Baldovino-Medrano; Sonia A. Giraldo; Aristobulo Centeno [Universidad Industrial de Santander (UIS), Bucaramanga (Colombia). Centro de Investigaciones en Catalisis (CICAT)

2008-08-15

A Pt/{gamma}-Al{sub 2}O{sub 3} catalyst was tested in simultaneous hydrodesulfurization (HDS) of dibenzothiophene and hydrodearomatization (HDA) of naphthalene reactions. Samples of it were subjected to different pretreatments: reduction, reduction-sulfidation, sulfidation with pure H{sub 2}S and non-activation. The reduced catalyst presented the best performance, even comparable to that of Co(Ni)Mo catalysts. All catalyst samples were selective to the HDS reaction over HDA, and to the direct desulfurization pathway of dibenzothiophene HDS over the hydrogenation reaction pathway of HDS. The effect of H{sub 2}S partial pressure on the functionalities of the reduced Pt/{gamma}-Al{sub 2}O{sub 3} catalyst was studied. The results showed that an increase in H{sub 2}S partial pressure does not cause poisoning, but an inhibition effect, without changing the catalyst selectivity. Accordingly, the activity trends were ascribed to adsorption differences between the different reactive molecules over the same catalytic active site. TPR characterization along with a thermodynamics analysis showed that the active phase of reduced Pt/{gamma}-Al{sub 2}O{sub 3} is constituted by Pt{sup 0} particles. However, presulfidation of the catalyst leads to a mixture of PtS and Pt{sup 0}which has a negative effect on the catalytic performance without changing catalyst functionalities. 61 refs., 4 figs., 1 tab.
A thermodynamic solution model for calcium carbonate: Towards an understanding of multi-equilibria precipitation pathways.

Science.gov (United States)

Donnet, Marcel; Bowen, Paul; Lemaître, Jacques

2009-12-15

Thermodynamic solubility calculations are normally only related to thermodynamic equilibria in solution. In this paper, we extend the use of such solubility calculations to help elucidate possible precipitation reaction pathways during the entire reaction. We also estimate the interfacial energy of particles using only solubility data by a modification of Mersmann's approach. We have carried this out by considering precipitation reactions as a succession of small quasi-equilibrium states. Thus possible equilibrium precipitation pathways can be evaluated by calculating the evolution of surface charge, particle size and/or interfacial energy during the ongoing reaction. The approach includes the use of the Kelvin's law to express the influence of particle size on the solubility constant of precipitates, the use of Nernst's law to calculate surface potentials from solubility calculations and relate this to experimentally measured zeta potentials. Calcium carbonate precipitation and zeta potential measurements of well characterised high purity calcite have been used as a model system to validate the calculated values. The clarification of the change in zeta potential on titration illustrates the power of this approach as a tool for reaction pathway prediction and hence knowledge based tailoring of precipitation reactions.
Comprehensive Theoretical Studies on the Reaction of 1-Bromo-3,3,3-trifluoropropene with OH Free Radicals

Directory of Open Access Journals (Sweden)

Yan Tian

2013-07-01

Full Text Available The potential energy surfaces (PES for the reaction of 1-bromo-3,3,3-trifluoropropene (CF3CHCBrH with hydroxyl (OH free radicals is probed theoretically at the CCSD/aug-cc-pVDZ//B3LYP/6-311++G(d,p level of theory. All the possible stationary and first-order saddle points along the reaction paths were verified by the vibrational analysis. The calculations account for all the product channels. Based on the calculated CCSD/aug-cc-pVDZ potential energy surface, the possible reaction mechanism is discussed. Six distinct reaction pathways of 1-bromo-3,3,3-trifluoropropene (BTP with OH are investigated. The geometries, reaction enthalpies and energy barriers are determined. Canonical transition-state theory with Wigner tunneling correction was used to predict the rate constants for the temperature range of 290–3,000 K without any artificial adjustment, and the computed rate constants for elementary channels can be accurately fitted with three-parameter Arrhenius expressions. OH addition reaction channel and the H atom abstraction channels related to the carbon-carbon double bond are found to be the main reaction channels for the reaction of 1-bromo-3,3,3-trifluoropropene (CF3CHCBrH with hydroxyl (OH free radicals while the products leading to CF3CHCH + BrOH and COHF2CHCBrH + F play a negligible role.
Accurate atom-mapping computation for biochemical reactions.

Science.gov (United States)

Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

2012-11-26

The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.
Nonclassical nucleation pathways in protein crystallization.

Science.gov (United States)

Zhang, Fajun

2017-11-08

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
Nonclassical nucleation pathways in protein crystallization

Science.gov (United States)

Zhang, Fajun

2017-11-01

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
Modeled aerosol nitrate formation pathways during wintertime in the Great Lakes region of North America

Science.gov (United States)

Kim, Yoo Jung; Spak, Scott N.; Carmichael, Gregory R.; Riemer, Nicole; Stanier, Charles O.

2014-11-01

Episodic wintertime particle pollution by ammonium nitrate is an important air quality concern across the Midwest U.S. Understanding and accurately forecasting PM2.5 episodes are complicated by multiple pathways for aerosol nitrate formation, each with uncertain rate parameters. Here, the Community Multiscale Air Quality model (CMAQ) simulated regional atmospheric nitrate budgets during the 2009 LADCO Winter Nitrate Study, using integrated process rate (IPR) and integrated reaction rate (IRR) tools to quantify relevant processes. Total nitrate production contributing to PM2.5 episodes is a regional phenomenon, with peak production over the Ohio River Valley and southern Great Lakes. Total nitrate production in the lower troposphere is attributed to three pathways, with 57% from heterogeneous conversion of N2O5, 28% from the reaction of OH and NO2, and 15% from homogeneous conversion of N2O5. TNO3 formation rates varied day-to-day and on synoptic timescales. Rate-limited production does not follow urban-rural gradients and NOx emissions due, to counterbalancing of urban enhancement in daytime HNO3 production with nocturnal reductions. Concentrations of HNO3 and N2O5 and nighttime TNO3 formation rates have maxima aloft (100-500 m), leading to net total nitrate vertical flux during episodes, with substantial vertical gradients in nitrate partitioning. Uncertainties in all three pathways are relevant to wintertime aerosol modeling and highlight the importance of interacting transport and chemistry processes during ammonium nitrate episodes, as well as the need for additional constraint on the system through field and laboratory experiments.
Development of the adverse outcome pathway "alkylation of DNA in male premeiotic germ cells leading to heritable mutations" using the OECD's users' handbook supplement.

Science.gov (United States)

Yauk, Carole L; Lambert, Iain B; Meek, M E Bette; Douglas, George R; Marchetti, Francesco

2015-12-01

The Organisation for Economic Cooperation and Development's (OECD) Adverse Outcome Pathway (AOP) programme aims to develop a knowledgebase of all known pathways of toxicity that lead to adverse effects in humans and ecosystems. A Users' Handbook was recently released to provide supplementary guidance on AOP development. This article describes one AOP-alkylation of DNA in male premeiotic germ cells leading to heritable mutations. This outcome is an important regulatory endpoint. The AOP describes the biological plausibility and empirical evidence supporting that compounds capable of alkylating DNA cause germ cell mutations and subsequent mutations in the offspring of exposed males. Alkyl adducts are subject to DNA repair; however, at high doses the repair machinery becomes saturated. Lack of repair leads to replication of alkylated DNA and ensuing mutations in male premeiotic germ cells. Mutations that do not impair spermatogenesis persist and eventually are present in mature sperm. Thus, the mutations are transmitted to the offspring. Although there are some gaps in empirical support and evidence for essentiality of the key events for certain aspects of this AOP, the overall AOP is generally accepted as dogma and applies broadly to any species that produces sperm. The AOP was developed and used in an iterative process to test and refine the Users' Handbook, and is one of the first publicly available AOPs. It is our hope that this AOP will be leveraged to develop other AOPs in this field to advance method development, computational models to predict germ cell effects, and integrated testing strategies. © 2015 Her Majesty the Queen in Right of Canada.
Chemically activated formation of organic acids in reactions of the Criegee intermediate with aldehydes and ketones.

Science.gov (United States)

Jalan, Amrit; Allen, Joshua W; Green, William H

2013-10-21

Reactions of the Criegee intermediate (CI, ˙CH2OO˙) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between ˙CH2OO˙ and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48-51 kcal mol(-1) lower in energy, formed via 1,3-cycloaddition of ˙CH2OO˙ across the C=O bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O-O bond to form hydroxyalkyl esters. These hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.
Clinical Implications of Hedgehog Pathway Signaling in Prostate Cancer

Directory of Open Access Journals (Sweden)

Daniel L. Suzman

2015-09-01

Full Text Available Activity in the Hedgehog pathway, which regulates GLI-mediated transcription, is important in organogenesis and stem cell regulation in self-renewing organs, but is pathologically elevated in many human malignancies. Mutations leading to constitutive activation of the pathway have been implicated in medulloblastoma and basal cell carcinoma, and inhibition of the pathway has demonstrated clinical responses leading to the approval of the Smoothened inhibitor, vismodegib, for the treatment of advanced basal cell carcinoma. Aberrant Hedgehog pathway signaling has also been noted in prostate cancer with evidence suggesting that it may render prostate epithelial cells tumorigenic, drive the epithelial-to-mesenchymal transition, and contribute towards the development of castration-resistance through autocrine and paracrine signaling within the tumor microenvironment and cross-talk with the androgen pathway. In addition, there are emerging clinical data suggesting that inhibition of the Hedgehog pathway may be effective in the treatment of recurrent and metastatic prostate cancer. Here we will review these data and highlight areas of active clinical research as they relate to Hedgehog pathway inhibition in prostate cancer.
Quantum state-resolved gas/surface reaction dynamics probed by reflection absorption infrared spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen Li [Department of Dynamics at Surfaces, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen (Germany); Ueta, Hirokazu; Beck, Rainer D. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Federale de Lausanne (Switzerland); Bisson, Regis [Aix-Marseille Universite, PIIM, CNRS, UMR 7345, 13397 Marseille (France)

2013-05-15

We report the design and characterization of a new molecular-beam/surface-science apparatus for quantum state-resolved studies of gas/surface reaction dynamics combining optical state-specific reactant preparation in a molecular beam by rapid adiabatic passage with detection of surface-bound reaction products by reflection absorption infrared spectroscopy (RAIRS). RAIRS is a non-invasive infrared spectroscopic detection technique that enables online monitoring of the buildup of reaction products on the target surface during reactant deposition by a molecular beam. The product uptake rate obtained by calibrated RAIRS detection yields the coverage dependent state-resolved reaction probability S({theta}). Furthermore, the infrared absorption spectra of the adsorbed products obtained by the RAIRS technique provide structural information, which help to identify nascent reaction products, investigate reaction pathways, and determine branching ratios for different pathways of a chemisorption reaction. Measurements of the dissociative chemisorption of methane on Pt(111) with this new apparatus are presented to illustrate the utility of RAIRS detection for highly detailed studies of chemical reactions at the gas/surface interface.
Transformation kinetics and pathways of tetracycline antibiotics with manganese oxide

Energy Technology Data Exchange (ETDEWEB)

Wanru, Chen [School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332 (United States); Huang, Ching-Hua [School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332 (United States)

2011-05-15

Tetracycline antibiotics including tetracycline (TTC), oxytetracycline (OTC) and chlorotetracycline (CTC) undergo rapid transformation to yield various products in the presence of MnO{sub 2} at mild conditions (pH 4-9 and 22 {sup o}C). Reaction rates follow the trend of CTC > TTC > OTC, and are affected by pH and complexation of TCs with Mg{sup 2+} or Ca{sup 2+}. Experimental results of TTC indicate that MnO{sub 2} promotes isomerization at the C ring to form iso-TTC and oxidizes the phenolic-diketone and tricarbonylamide groups, leading to insertion of up to 2 O most likely at the C9 and C2 positions. In contrast, reactions of OTC with MnO{sub 2} generate little iso-OTC, but occur mainly at the A ring's dimethylamine group to yield N-demethylated products. CTC yields the most complicated products upon reactions with MnO{sub 2}, encompassing transformation patterns observed with both TTC and OTC. The identified product structures suggest lower antibacterial activity than that of the parent tetracyclines. - Highlights: > Tetracyclines transform rapidly by MnO{sub 2} to yield complicated products. > Isomerized, (hydr)oxygenated and N-demethylated products are formed. > Transformation product structures may suggest lowered antibacterial activity. - The complex transformation pathways of three popular tetracycline antibiotics (tetracycline, oxytetracycline and chlorotetracycline) with MnO{sub 2} under environmental conditions are systematically evaluated and elucidated.
Transformation kinetics and pathways of tetracycline antibiotics with manganese oxide

International Nuclear Information System (INIS)

Chen Wanru; Huang, Ching-Hua

2011-01-01

Tetracycline antibiotics including tetracycline (TTC), oxytetracycline (OTC) and chlorotetracycline (CTC) undergo rapid transformation to yield various products in the presence of MnO 2 at mild conditions (pH 4-9 and 22 o C). Reaction rates follow the trend of CTC > TTC > OTC, and are affected by pH and complexation of TCs with Mg 2+ or Ca 2+ . Experimental results of TTC indicate that MnO 2 promotes isomerization at the C ring to form iso-TTC and oxidizes the phenolic-diketone and tricarbonylamide groups, leading to insertion of up to 2 O most likely at the C9 and C2 positions. In contrast, reactions of OTC with MnO 2 generate little iso-OTC, but occur mainly at the A ring's dimethylamine group to yield N-demethylated products. CTC yields the most complicated products upon reactions with MnO 2 , encompassing transformation patterns observed with both TTC and OTC. The identified product structures suggest lower antibacterial activity than that of the parent tetracyclines. - Highlights: → Tetracyclines transform rapidly by MnO 2 to yield complicated products. → Isomerized, (hydr)oxygenated and N-demethylated products are formed. → Transformation product structures may suggest lowered antibacterial activity. - The complex transformation pathways of three popular tetracycline antibiotics (tetracycline, oxytetracycline and chlorotetracycline) with MnO 2 under environmental conditions are systematically evaluated and elucidated.
Peripheral blood signatures of lead exposure.

Directory of Open Access Journals (Sweden)

Heather G LaBreche

Full Text Available BACKGROUND: Current evidence indicates that even low-level lead (Pb exposure can have detrimental effects, especially in children. We tested the hypothesis that Pb exposure alters gene expression patterns in peripheral blood cells and that these changes reflect dose-specific alterations in the activity of particular pathways. METHODOLOGY/PRINCIPAL FINDING: Using Affymetrix Mouse Genome 430 2.0 arrays, we examined gene expression changes in the peripheral blood of female Balb/c mice following exposure to per os lead acetate trihydrate or plain drinking water for two weeks and after a two-week recovery period. Data sets were RMA-normalized and dose-specific signatures were generated using established methods of supervised classification and binary regression. Pathway activity was analyzed using the ScoreSignatures module from GenePattern. CONCLUSIONS/SIGNIFICANCE: The low-level Pb signature was 93% sensitive and 100% specific in classifying samples a leave-one-out crossvalidation. The high-level Pb signature demonstrated 100% sensitivity and specificity in the leave-one-out crossvalidation. These two signatures exhibited dose-specificity in their ability to predict Pb exposure and had little overlap in terms of constituent genes. The signatures also seemed to reflect current levels of Pb exposure rather than past exposure. Finally, the two doses showed differential activation of cellular pathways. Low-level Pb exposure increased activity of the interferon-gamma pathway, whereas high-level Pb exposure increased activity of the E2F1 pathway.
Lithium-lead/water interaction. Large break experiments

International Nuclear Information System (INIS)

Savatteri, C.; Gemelli, A.

1991-01-01

One current concept in fusion blanket module design is to utilize water as coolant and liquid lithium-lead as breeding/neutron-multiplier material. Considering the possibility of certain off-normal events, it is possible that water leakage into the liquid metal may occur due to a tube rupture. The lithium-lead/water contact can lead to a thermal and chemical reaction which should provoke an intolerable pressure increase in the blanket module. For realistic simulation of such in-blanket events, the Blanket Safety Test (BLAST) facility has been built. It simulates the transient event by injecting subcooled water under high pressure into a stagnant pool of about 500 kg liquid Pb-17Li. Eight fully instrumented large break tests were carried out under different conditions. The aim of the experiments is to study the chemical and thermal process and particularly: The pressurization history of the reaction vessel, the formation and deposition of the reaction products, the identification and propagation of the reaction zones and the temperature transient in the liquid metal. In this paper the results of all tests performed are presented and discussed. (orig.)
Uranium fluoride chemistry. Part 1. The gas phase reaction of uranium hexafluoride with alcohols

International Nuclear Information System (INIS)

Schnautz, N.G.; Venter, P.J.

1992-01-01

The reaction between uranium hexafluoride (UF 6 ) and simple alcohols in the gas phase was observed to proceed by way of three possible reaction pathways involving dehydration, deoxygenative fluorination, and ether formation. These reactions can best be explained by assuming that alcohols first react with UF 6 to afford the alkoxy uranium pentafluoride intermediate ROUF 5 , which reacts further to give the dehydration, deoxygenative fluorination, and ether products. In each of the above three reaction pathways, UF 6 is transformed to UOF 4 , which being as reactive toward alcohols as UF 6 , reacts further with the alcohol in question to finally afford the unreactive uranyl fluoride (UO 2 F 2 ). 6 refs., 2 tabs

Long-term human exposure to lead from different media and intake pathways

DEFF Research Database (Denmark)

Pizzol, Massimo; Thomsen, Marianne; Andersen, Mikael Skou

2010-01-01

, and predicting the resulting internal body exposure levels and effects that occur under long-term exposure conditions. In this paper, a modeling approach is used to meet these challenges with reference to Danish exposure conditions. Levels of lead content in various media have been coupled with data for lead......Lead (Pb) is well known as an environmental pollutant: it can accumulate in various media, so actual lead exposure reflects both historical and present contaminations. Two main challenges then emerge: obtaining updated information to gain an overall picture of the sources of exposure......–internalconcentration relationships for the direct linkage between lead in environmental media and resultingconcentrations of lead in blood are then presented....
Correcting ligands, metabolites, and pathways

Directory of Open Access Journals (Sweden)

Vriend Gert

2006-11-01

Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and
Redox reactions in food fermentations

DEFF Research Database (Denmark)

Hansen, Egon Bech

2018-01-01

involves oxidative steps in the early part of the pathways whereas a multitude of different reactions are used as compensating reductions. Much of the diversity seen between food fermentations arise from the different routes and the different electron acceptors used by microorganisms to counterbalance...... and this contributes to the diversity in flavor, color, texture, and shelf life. The review concludes that these reactions are still only incompletely understood and that they represent an interesting area for fundamental research and also represent a fertile field for product development through a more conscious use...... of the redox properties of strains used to compose food cultures....
Shock wave and modeling study of the thermal decomposition reactions of pentafluoroethane and 2-H-heptafluoropropane.

Science.gov (United States)

Cobos, C J; Sölter, L; Tellbach, E; Troe, J

2014-06-07

The thermal decomposition reactions of CF3CF2H and CF3CFHCF3 have been studied in shock waves by monitoring the appearance of CF2 radicals. Temperatures in the range 1400-2000 K and Ar bath gas concentrations in the range (2-10) × 10(-5) mol cm(-3) were employed. It is shown that the reactions are initiated by C-C bond fission and not by HF elimination. Differing conclusions in the literature about the primary decomposition products, such as deduced from experiments at very low pressures, are attributed to unimolecular falloff effects. By increasing the initial reactant concentrations in Ar from 60 to 1000 ppm, a retardation of CF2 formation was observed while the final CF2 yields remained close to two CF2 per C2F5H or three CF2 per C3F7H decomposed. This is explained by secondary bimolecular reactions which lead to comparably stable transient species like CF3H, releasing CF2 at a slower rate. Quantum-chemical calculations and kinetic modeling help to identify the reaction pathways and provide estimates of rate constants for a series of primary and secondary reactions in the decomposition mechanism.
Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1.

Science.gov (United States)

Juarez, Antonio; Villa, Juan A; Lanza, Val F; Lázaro, Beatriz; de la Cruz, Fernando; Alvarez, Héctor M; Moncalián, Gabriel

2017-02-27

Rhodococcus jostii RHA1 and other actinobacteria accumulate triglycerides (TAG) under nutrient starvation. This property has an important biotechnological potential in the production of sustainable oils. To gain insight into the metabolic pathways involved in TAG accumulation, we analysed the transcriptome of R jostii RHA1 under nutrient-limiting conditions. We correlate these physiological conditions with significant changes in cell physiology. The main consequence was a global switch from catabolic to anabolic pathways. Interestingly, the Entner-Doudoroff (ED) pathway was upregulated in detriment of the glycolysis or pentose phosphate pathways. ED induction was independent of the carbon source (either gluconate or glucose). Some of the diacylglycerol acyltransferase genes involved in the last step of the Kennedy pathway were also upregulated. A common feature of the promoter region of most upregulated genes was the presence of a consensus binding sequence for the cAMP-dependent CRP regulator. This is the first experimental observation of an ED shift under nutrient starvation conditions. Knowledge of this switch could help in the design of metabolomic approaches to optimize carbon derivation for single cell oil production.
Enzymatic description of the anhydrofructose pathway of glycogen degradation. I

DEFF Research Database (Denmark)

Yu, Shukun; Refdahl, Charlotte; Lundt, Inge

2004-01-01

The anhydrofructose pathway describes the degradation of glycogen and starch to metabolites via 1,5-anhydro-D-fructose (1,5AnFru). The enzyme catalyzing the first reaction step of this pathway, i.e., a-1,4-glucan lyase (EC 4.2.1.13), has been purified, cloned and characterized from fungi and red...... possessed all enzymes needed for conversion of glycogen to APP, an a-1,4-glucan lyase from this fungus was isolated and partially sequenced. Based on this work, a scheme of the enzymatic description of the anhydrofructose pathway in A. melaloma was proposed. Keywords: Anhydrofructose pathway; Anthracobia...
Mechanism for the reaction of 2-naphthol with N-methyl-N-phenyl-hydrazine suggested by the density functional theory investigations.

Science.gov (United States)

Gao, Jie Ying; Zhang, Cheng Hua; Luo, Mei Ming; Kim, Chan Kyung; Chu, Wei; Xue, Ying

2012-01-15

For the first time the computed mechanisms for the novel reaction of 2-naphthol with N-methyl-N-phenylhydrazine, leading to 1-amino-2-naphthol (Tang et al., J Am Chem Soc 2008, 130, 5840), have been investigated using the density functional theory. Four distinct possible pathways were evaluated: two amination mechanisms with the attack of NH(2) group respectively at the α-position C1 and β-position C3 atoms of 2-naphthol (pathways 1 and 2) as well as two rearrangement processes with displacement of the phenolic hydroxyl group followed by the benzidine-like rearrangement at the α-position C1 and β-position C3 atoms of 2-naphthol, respectively (pathways 3 and 4). Solvent effect has been tested based on the optimized geometries of the stationary points in solution at the B3LYP/PCM/6-31+G(d,p) level of theory with an averaged dielectric constant of binary solvent. Single-point energies of the optimized structures have been calculated using three hybrid density functionals, B3LYP, MPW3LYP, and B3PW91 with the 6-311++G(3df,2p) basis set. Our computed results clearly manifest that pathway 1 (α-amination) has the highest possibility to occur, with the Gibbs free energies being lower by 6 to 20 kcal/mol compared with the other three pathways, which leads to 1-amino-2-naphthol and N-methylaniline as products. It is in excellent agreement with the experimental observation. Copyright © 2011 Wiley Periodicals, Inc.
The evolution of plant virus transmission pathways

Science.gov (United States)

Frédéric M. Hamelin; Linda J.S. Allen; Holly R. Prendeville; M. Reza Hajimorad; Michael J. Jeger

2016-01-01

The evolution of plant virus transmission pathways is studied through transmission via seed, pollen, oravector. We address the questions: under what circumstances does vector transmission make pollen transmission redundant? Can evolution lead to the coexistence of multiple virus transmission pathways? We restrict the analysis to an annual plant population in which...
A kinetic model for the glucose/glycine Maillard reaction pathways

NARCIS (Netherlands)

Martins, S.I.F.S.; Boekel, van M.A.J.S.

2005-01-01

A comprehensive kinetic model for the glucose/glycine Maillard reaction is proposed based on an approach called multiresponse kinetic modelling. Special attention was paid to reactants, intermediates and end products: -fructose, N-(1-deoxy--fructos-1-yl)-glycine (DFG), 1-deoxy-2,3-hexodiulose and
Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

International Nuclear Information System (INIS)

Osborn, David L.

2017-01-01

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low temperature combustion and the oxidation of volatile organic compounds in earth’s atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization make characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, while master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.
Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

Science.gov (United States)

Osborn, David L.

2017-05-01

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low-temperature combustion and in the oxidation of volatile organic compounds in Earth's atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization makes characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, and master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.
Covalent bonding of chloroanilines to humic constituents: Pathways, kinetics, and stability

International Nuclear Information System (INIS)

Kong, Deyang; Xia, Qing; Liu, Guoqiang; Huang, Qingguo; Lu, Junhe

2013-01-01

Covalent coupling to natural humic constituents comprises an important transformation pathway for anilinic pollutants in the environment. We systematically investigated the reactions of chlorine substituted anilines with catechol and syringic acid in horseradish peroxidase (HRP) catalyzed systems. It was demonstrated that although nucleophilic addition was the mechanism of covalent bonding to both catechol and syringic acid, chloroanilines coupled to the 2 humic constituents via slightly different pathways. 1,4-addition and 1,2-addition are involved to catechol and syringic acid, respectively. 1,4-addition showed empirical 2nd order kinetics and this pathway seemed to be more permanent than 1,2-addition. Stability experiments demonstrated that cross-coupling products with syringic acid could be easily released in acidic conditions. However, cross-coupling with catechol was relatively stable at similar conditions. Thus, the environmental behavior and bioavailability of the coupling products should be carefully assessed. -- Highlights: •Chloroanilines covalently coupled to humic constituents in HRP catalyzed processes, which facilitated their transformation. •MS technique was employed to analyze the coupling products and therefore elucidate the reaction pathways. •Chloroanilines couple to catechol and syringic acid via 1,4- and 1,2-nucleophilic addition pathways, respectively. •Cross-coupling products formed via 1,4-nucleophilic addition pathway were more stable than those via 1,2-addition pathway. -- Bound residues of chloroanilines formed via 1,2- and 1,4-nucleophilic addition pathways showed different stability
Temperature dependence of muonium reaction rates in the gas phase

International Nuclear Information System (INIS)

Fleming, D.G.; Garner, D.M.; Mikula, R.J.; British Columbia Univ., Vancouver

1981-01-01

A study of the temperature dependence of reaction rates has long been an important tool in establishing reaction pathways in chemical reactions. This is particularly true for the reactions of muonium (in comparison with those of hydrogen) since a measurement of the activation energy for chemical reaction is sensitive to both the height and the position of the potential barrier in the reaction plane. For collision controlled reactions, on the other hand, the reaction rate is expected to exhibit a weak T 1 sup(/) 2 dependence characteristic of the mean collision velocity. These concepts are discussed and their effects illustrated in a comparison of the chemical and spin exchange reaction rates of muonium and hydrogen in the temperature range approx.300-approx.500 K. (orig.)
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

Directory of Open Access Journals (Sweden)

Goutsias John

2010-11-01

Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for
Vanillin biosynthetic pathways in plants.

Science.gov (United States)

Kundu, Anish

2017-06-01

The present review compiles the up-to-date knowledge on vanillin biosynthesis in plant systems to focus principally on the enzymatic reactions of in planta vanillin biosynthetic pathway and to find out its impact and prospect in future research in this field. Vanillin, a very popular flavouring compound, is widely used throughout the world. The principal natural resource of vanillin is the cured vanilla pods. Due to the high demand of vanillin as a flavouring agent, it is necessary to explore its biosynthetic enzymes and genes, so that improvement in its commercial production can be achieved through metabolic engineering. In spite of significant advancement in elucidating vanillin biosynthetic pathway in the last two decades, no conclusive demonstration had been reported yet for plant system. Several biosynthetic enzymes have been worked upon but divergences in published reports, particularly in characterizing the crucial biochemical steps of vanillin biosynthesis, such as side-chain shortening, methylation, and glucoside formation and have created a space for discussion. Recently, published reviews on vanillin biosynthesis have focused mainly on the biotechnological approaches and bioconversion in microbial systems. This review, however, aims to compile in brief the overall vanillin biosynthetic route and present a comparative as well as comprehensive description of enzymes involved in the pathway in Vanilla planifolia and other plants. Special emphasis has been given on the key enzymatic biochemical reactions that have been investigated extensively. Finally, the present standpoint and future prospects have been highlighted.
Directing reaction pathways by catalyst active-site selection using self-assembled monolayers.

Science.gov (United States)

Pang, Simon H; Schoenbaum, Carolyn A; Schwartz, Daniel K; Medlin, J Will

2013-01-01

One key route for controlling reaction selectivity in heterogeneous catalysis is to prepare catalysts that exhibit only specific types of sites required for desired product formation. Here we show that alkanethiolate self-assembled monolayers with varying surface densities can be used to tune selectivity to desired hydrogenation and hydrodeoxygenation products during the reaction of furfural on supported palladium catalysts. Vibrational spectroscopic studies demonstrate that the selectivity improvement is achieved by controlling the availability of specific sites for the hydrogenation of furfural on supported palladium catalysts through the selection of an appropriate alkanethiolate. Increasing self-assembled monolayer density by controlling the steric bulk of the organic tail ligand restricts adsorption on terrace sites and dramatically increases selectivity to desired products furfuryl alcohol and methylfuran. This technique of active-site selection simultaneously serves both to enhance selectivity and provide insight into the reaction mechanism.
Degradation of Nicotine in Chlorinated Water: Pathways and ...

Science.gov (United States)

Report The objective of the study is to illustrate how drinking water would affect alkaloid pesticides, and to address the issue by (a) investigating the fate of nicotine in chlorinated drinking water and deionized water, (b) determining the reaction rate and pathway of the reaction between nicotine and aqueous chlorine, (c) identifying nicotine’s degradation products, and (d) providing data that can be used to assess the potential threat from nicotine in drinking water.
Enhancing NAD+ Salvage Pathway Reverts the Toxicity of Primary Astrocytes Expressing Amyotrophic Lateral Sclerosis-linked Mutant Superoxide Dismutase 1 (SOD1)*

Science.gov (United States)

Harlan, Benjamin A.; Pehar, Mariana; Sharma, Deep R.; Beeson, Gyda; Beeson, Craig C.; Vargas, Marcelo R.

2016-01-01

Nicotinamide adenine dinucleotide (NAD+) participates in redox reactions and NAD+-dependent signaling pathways. Although the redox reactions are critical for efficient mitochondrial metabolism, they are not accompanied by any net consumption of the nucleotide. On the contrary, NAD+-dependent signaling processes lead to its degradation. Three distinct families of enzymes consume NAD+ as substrate: poly(ADP-ribose) polymerases, ADP-ribosyl cyclases (CD38 and CD157), and sirtuins (SIRT1–7). Because all of the above enzymes generate nicotinamide as a byproduct, mammalian cells have evolved an NAD+ salvage pathway capable of resynthesizing NAD+ from nicotinamide. Overexpression of the rate-limiting enzyme in this pathway, nicotinamide phosphoribosyltransferase, increases total and mitochondrial NAD+ levels in astrocytes. Moreover, targeting nicotinamide phosphoribosyltransferase to the mitochondria also enhances NAD+ salvage pathway in astrocytes. Supplementation with the NAD+ precursors nicotinamide mononucleotide and nicotinamide riboside also increases NAD+ levels in astrocytes. Amyotrophic lateral sclerosis (ALS) is caused by the progressive degeneration of motor neurons in the spinal cord, brain stem, and motor cortex. Superoxide dismutase 1 (SOD1) mutations account for up to 20% of familial ALS and 1–2% of apparently sporadic ALS cases. Primary astrocytes isolated from mutant human superoxide dismutase 1-overexpressing mice as well as human post-mortem ALS spinal cord-derived astrocytes induce motor neuron death in co-culture. Increasing total and mitochondrial NAD+ content in ALS astrocytes increases oxidative stress resistance and reverts their toxicity toward co-cultured motor neurons. Taken together, our results suggest that enhancing the NAD+ salvage pathway in astrocytes could be a potential therapeutic target to prevent astrocyte-mediated motor neuron death in ALS. PMID:27002158
A SNARE-protein has opposing functions in penetration resistance and defence signalling pathways

DEFF Research Database (Denmark)

Zhang, Ziguo; Feechan, Angela; Pedersen, Carsten

2007-01-01

Penetration resistance is often the first line of defence against fungal pathogens. Subsequently induced defences are mediated by the programmed cell death (PCD) reaction pathway and the salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) signalling pathways. We previously demonstrated...
Reaction 12C(16O,α)24Mg leading to nuclear molecular resonances

International Nuclear Information System (INIS)

Nagatani, K.; Shimoda, T.; Tanner, D.; Tribble, R.; Yamaya, T.

1979-01-01

The reactions 12 C( 16 O,α) 24 Mg and 13 C( 16 O,α) 25 Mg were investigated at an incident energy of 145 MeV. In the reaction with the 12 C target, broad peaks are observed at forward angles which correspond to the molecular resonance states of the 12 C+ 12 C system, while the spectra with 13 C target show only a smooth continuum

Investigation of corrosion, water reaction, polonium evaporation and bismuth resource in liquid metal lead-bismuth technology

Energy Technology Data Exchange (ETDEWEB)

Takano, Hideki; Takizuka, Takakazu [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Kitano, Teruaki [Mitsui Shipbuilding and Engineering Co. Ltd., Tokyo (Japan)

2000-10-01

Lead-bismuth is the first candidate material for liquid metal target find coolant of fueled blanket system in accelerator-driven system (ADS) studied at JAERI. Advantages of the lead-bismuth utilization are non-active material, very low capture cross section, low melting point of 125degC and high boiling point of 1670degC, and beside coolant void reactivity become negative. But problems are due to the high corrosivity to most of the structural materials and the corrosive data are scarcity. In this report, corrosivity, reaction with water, thermal-hydraulics, chemical toxicity etc. are studied by investigating some facilities utilized and researched really for lead or lead-bismuth. And, furthermore, polonium evaporation rate and bismuth resource are investigated. Main results obtained are as follows: (1) In a refinery, there are enough employment experience for liquid Pb-Bi in period of about 17 years and not corrosion for the thermal conductive materials (1Cr-0.5Mo steel) used under the condition of natural convection with temperature around 400degC. (2) In Russia, extensive experience in the use as Russian submarines and in R and D during about 50 years are available. And as a result, it will be able to lead approximately zero corrosion for Cr-Si materials by adjusting oxygen film with oxygen concentration control between 10{sup -7} to 10{sup -5}% mass. However, the corrosion data are not enough systematically collected involving them in radiation dose field. (3) In liquid-dropping experiment, it is shown that interaction between water and high temperature liquid Pb-Bi is reduced steeply with rising of atmosphere pressure. But, in order to design the second circuit removal model of ADS, the interaction should be evaluated by water continuous injection experiment. (4) Polonium forms PbPo in Pb-Bi, and the evaporation rate become less three factor than that of Po, and furthermore, the rate decreases in the atmosphere. The effects of Po on employee and environment
Lessons learned from mice deficient in lectin complement pathway molecules

DEFF Research Database (Denmark)

Genster, Ninette; Takahashi, Minoru; Sekine, Hideharu

2014-01-01

in turn activate downstream complement components, ultimately leading to elimination of the pathogen. Mice deficient in the key molecules of lectin pathway of complement have been generated in order to build knowledge of the molecular mechanisms of the lectin pathway in health and disease. Despite......The lectin pathway of the complement system is initiated when the pattern-recognition molecules, mannose-binding lectin (MBL), ficolins or collectin-11, bind to invading pathogens or damaged host cells. This leads to activation of MBL/ficolin/collectin-11 associated serine proteases (MASPs), which...... differences in the genetic arrangements of murine and human orthologues of lectin pathway molecules, the knockout mice have proven to be valuable models to explore the effect of deficiency states in humans. In addition, new insight and unexpected findings on the diverse roles of lectin pathway molecules...
A B Cell-Driven Autoimmune Pathway Leading to Pathological Hallmarks of Progressive Multiple Sclerosis in the Marmoset Experimental Autoimmune Encephalomyelitis Model

Directory of Open Access Journals (Sweden)

Bert A. ’t Hart

2017-07-01

Full Text Available The absence of pathological hallmarks of progressive multiple sclerosis (MS in commonly used rodent models of experimental autoimmune encephalomyelitis (EAE hinders the development of adequate treatments for progressive disease. Work reviewed here shows that such hallmarks are present in the EAE model in marmoset monkeys (Callithrix jacchus. The minimal requirement for induction of progressive MS pathology is immunization with a synthetic peptide representing residues 34–56 from human myelin oligodendrocyte glycoprotein (MOG formulated with a mineral oil [incomplete Freund’s adjuvant (IFA]. Pathological aspects include demyelination of cortical gray matter with microglia activation, oxidative stress, and redistribution of iron. When the peptide is formulated in complete Freund’s adjuvant, which contains mycobacteria that relay strong activation signals to myeloid cells, oxidative damage pathways are strongly boosted leading to more intensive pathology. The proven absence of immune potentiating danger signals in the MOG34–56/IFA formulation implies that a narrow population of antigen-experienced T cells present in the monkey’s immune repertoire is activated. This novel pathway involves the interplay of lymphocryptovirus-infected B cells with MHC class Ib/Caja-E restricted CD8+ CD56+ cytotoxic T lymphocytes.
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling.

Science.gov (United States)

Zhong, Jun; Sharma, Jyoti; Raju, Rajesh; Palapetta, Shyam Mohan; Prasad, T S Keshava; Huang, Tai-Chung; Yoda, Akinori; Tyner, Jeffrey W; van Bodegom, Diederik; Weinstock, David M; Ziegler, Steven F; Pandey, Akhilesh

2014-01-01

Thymic stromal lymphopoietin (TSLP) is a four-helix bundle cytokine that plays a critical role in the regulation of immune responses and in the differentiation of hematopoietic cells. TSLP signals through a heterodimeric receptor complex consisting of an interleukin-7 receptor α chain and a unique TSLP receptor (TSLPR) [also known as cytokine receptor-like factor 2 (CRLF2)]. Cellular targets of TSLP include dendritic cells, B cells, mast cells, regulatory T (Treg) cells and CD4+ and CD8+ T cells. The TSLP/TSLPR axis can activate multiple signaling transduction pathways including the JAK/STAT pathway and the PI-3 kinase pathway. Aberrant TSLP/TSLPR signaling has been associated with a variety of human diseases including asthma, atopic dermatitis, nasal polyposis, inflammatory bowel disease, eosinophilic eosophagitis and, most recently, acute lymphoblastic leukemia. A centralized resource of the TSLP signaling pathway cataloging signaling events is not yet available. In this study, we present a literature-annotated resource of reactions in the TSLP signaling pathway. This pathway map is publicly available through NetPath (http://www.netpath.org/), an open access signal transduction pathway resource developed previously by our group. This map includes 236 molecules and 252 reactions that are involved in TSLP/TSLPR signaling pathway. We expect that the TSLP signaling pathway map will provide a rich resource to study the biology of this important cytokine as well as to identify novel therapeutic targets for diseases associated with dysregulated TSLP/TSLPR signaling. Database URL: http://www.netpath.org/pathways?path_id=NetPath_24.
Intermolecula transfer and elimination of molecular hydrogen in thermal reactions of unsaturated organic compounds

Energy Technology Data Exchange (ETDEWEB)

Suria, Sabartanty [Iowa State Univ., Ames, IA (United States)

1995-02-10

Two reactions which are important to coal liquefaction include intermolecular transfer and the elimination of two hydrogen atoms. We have designed several model reactions to probe the viability of several hydrogen transfer and elimination pathways. This report described studies on these reactions using organic model compounds.
Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network

International Nuclear Information System (INIS)

Pal, Krishnendu; Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

2015-01-01

We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction. (paper)
Photonuclear reactions in the GNASH code: Benchmarking model calculations for reactions on lead up to 140 MeV

International Nuclear Information System (INIS)

Chadwick, M.B.; Young, P.G.

1994-08-01

The authors have developed the GNASH code to include photonuclear reactions for incident energies up to 140 MeV. Photoabsorption is modeled through the giant resonance at the lower energies, and the quasideuteron mechanism at the higher energies, and the angular momentum coupling of the incident photon to the target is properly accounted for. After the initial interaction, primary and multiple preequilibrium emission of fast particles can occur before compound nucleus decay from the equilibrated compound nucleus. The angular distributions from compound nucleus decay are taken as isotropic, and those from preequilibrium emission (which they obtain from a phase-space model which conserves momentum) are forward-peaked. To test the new modeling they apply the code to calculate photonuclear reactions on 208 Pb for incident energies up to 140 MeV
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

Science.gov (United States)

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.
Boson states in the reaction π-p → π-π-π+p with leading π+ meson at 25 GeV/c

International Nuclear Information System (INIS)

Antipov, Yu.M.; Baud, R.

1975-01-01

The reaction π - + p → p + π - + π - + π + at 25 GeV/c was studied in the mass region M sub(3π) >>= 1.8 GeV with leading π + in the final state. The mass spectrum of π 1 π - -system evidently shows peaks rho deg, f, g deg resonances and an enhancement in S'-region. It is shown that the g deg and π - mesons are mainly in A4 state J sub(P) = 3 + S-wave g degπ - like A1(sup(rhoπ)) and A3(sup(fπ))
The Protective Effect of Gangliosides on Lead (Pb)-Induced Neurotoxicity Is Mediated by Autophagic Pathways.

Science.gov (United States)

Meng, Hongtao; Wang, Lan; He, Junhong; Wang, Zhufeng

2016-03-25

Lead (Pb) is a ubiquitous environmental and industrial pollutant and can affect intelligence development and the learning ability and memory of children. Therefore, necessary measures should be taken to protect the central nervous system (CNS) from Pb toxicity. Gangliosides are sialic acid-containing glycosphingolipids that are constituents of mammalian cell membranes and are more abundantly expressed in the CNS. Studies have shown that gangliosides constitute a useful tool in the attempt to promote functional recovery of CNS and can reverse Pb-induced impairments of synaptic plasticity in rats. However, the detailed mechanisms have yet to be fully understood. In our present study, we tried to investigate the role of gangliosides in Pb-induced injury in hippocampus neurons and to further confirm the detailed mechanism. Our results show that Pb-induced injuries in the spatial reference memory were associated with a reduction of cell viability and cell apoptosis, and treatment with gangliosides markedly ameliorated the Pb-induced injury by inhibition of apoptosis action. Gangliosides further attenuated Pb-induced the abnormal autophagic process by regulation of mTOR pathways. In summary, our study establishes the efficacy of gangliosides as neuroprotective agents and provides a strong rationale for further studies on the underlying mechanisms of their neuroprotective functions.
The Protective Effect of Gangliosides on Lead (Pb-Induced Neurotoxicity Is Mediated by Autophagic Pathways

Directory of Open Access Journals (Sweden)

Hongtao Meng

2016-03-01

Full Text Available Lead (Pb is a ubiquitous environmental and industrial pollutant and can affect intelligence development and the learning ability and memory of children. Therefore, necessary measures should be taken to protect the central nervous system (CNS from Pb toxicity. Gangliosides are sialic acid-containing glycosphingolipids that are constituents of mammalian cell membranes and are more abundantly expressed in the CNS. Studies have shown that gangliosides constitute a useful tool in the attempt to promote functional recovery of CNS and can reverse Pb-induced impairments of synaptic plasticity in rats. However, the detailed mechanisms have yet to be fully understood. In our present study, we tried to investigate the role of gangliosides in Pb-induced injury in hippocampus neurons and to further confirm the detailed mechanism. Our results show that Pb-induced injuries in the spatial reference memory were associated with a reduction of cell viability and cell apoptosis, and treatment with gangliosides markedly ameliorated the Pb-induced injury by inhibition of apoptosis action. Gangliosides further attenuated Pb-induced the abnormal autophagic process by regulation of mTOR pathways. In summary, our study establishes the efficacy of gangliosides as neuroprotective agents and provides a strong rationale for further studies on the underlying mechanisms of their neuroprotective functions.
Maternal Chromium Restriction Leads to Glucose Metabolism Imbalance in Mice Offspring through Insulin Signaling and Wnt Signaling Pathways

Science.gov (United States)

Zhang, Qian; Sun, Xiaofang; Xiao, Xinhua; Zheng, Jia; Li, Ming; Yu, Miao; Ping, Fan; Wang, Zhixin; Qi, Cuijuan; Wang, Tong; Wang, Xiaojing

2016-01-01

An adverse intrauterine environment, induced by a chromium-restricted diet, is a potential cause of metabolic disease in adult life. Up to now, the relative mechanism has not been clear. C57BL female mice were time-mated and fed either a control diet (CD), or a chromium-restricted diet (CR) throughout pregnancy and the lactation period. After weaning, some offspring continued the diet diagram (CD-CD or CR-CR), while other offspring were transferred to another diet diagram (CD-CR or CR-CD). At 32 weeks of age, glucose metabolism parameters were measured, and the liver from CR-CD group and CD-CD group was analyzed using a gene array. Quantitative real-time polymerase chain reaction (qPCR) and Western blot were used to verify the result of the gene array. A maternal chromium-restricted diet resulted in obesity, hyperglycemia, hyperinsulinemia, increased area under the curve (AUC) of glucose in oral glucose tolerance testing and homeostasis model assessment of insulin resistance (HOMA-IR). There were 463 genes that differed significantly (>1.5-fold change, p chromium deficiency influences glucose metabolism in pups through the regulation of insulin signaling and Wnt signaling pathways. PMID:27782077
Bioelectrocatalytic dechlorination of trichloroacetic acid at gel-immobilized hemoglobin on multiwalled carbon nanotubes modified graphite electrode: Kinetic modeling and reaction pathways

International Nuclear Information System (INIS)

Liu, Qi; Yu, Jianming; Xu, Yinghua; Wang, Jiade; Ying, Le; Song, Xinxin; Zhou, Gendi; Chen, Jianmeng

2013-01-01

Highlights: ► The electrons transfer from enzyme in the electrode to COCs was the key step. ► The average current efficiency was influenced by pH and temperature of the systems. ► The most favourable degradation conditions for TCA were found to be pH 3 and 310 K. ► The activation energy of 26.2 kJ mol −1 was also calculated by the Arrhenius equation. ► Bioelectrocatalytic mechanism of TCA was verified by kinetic expressions. -- Abstract: In bioelectrochemically reductive dechlorination of chlorinated organic compounds (COCs), the electrons transfer from enzyme in the electrode to COCs was the key step, which determined the average current efficiency (CE) and was influenced by the pH and temperature of the systems. In this work, the effect of temperature (288–318 K) and pH (2–11) of the electrolyte on decholrination of trichloroacetic acid (TCA) was investigated in the sodium alginate/hemoglobin-multiwalled carbon nanotubes-graphite composite electrode (Hb/SA–MWCNT–GE). The results showed that the most favourable degradation conditions for TCA by Hb/SA–MWCNT–GE were found to be pH 3 and 310 K. By varying the pH of the systems, it was found that a proton accompanied with an electron transfer between the electrode and heme Fe(III)/Fe(II) of Hb during the reaction. Additionally, the activation energy of 26.2 kJ mol −1 was also calculated by the Arrhenius equation for the reaction. The total mass balance of the reactant and the products was in the range of 97–105% during the bioelectrochemically reductive reaction. The CE only decreased from 87% to 83% when the Hb/SA–MWCNT–GE was used 5 times. Based on the intermediates detected, a pathway was proposed for TCA degradation in which it underwent dechlorination process. The main degradation mechanism described by a parallel reaction rather than by a sequential reaction for dechlorination of TCA in Hb/SA–MWCNT–GE system was proposed. These data provided relevant information about the
The Role of Psychological Stress Reactions in the Longitudinal Relation Between Workplace Bullying and Turnover.

Science.gov (United States)

Nabe-Nielsen, Kirsten; Grynderup, Matias Brødsgaard; Conway, Paul Maurice; Clausen, Thomas; Bonde, Jens Peter; Garde, Anne Helene; Hogh, Annie; Kaerlev, Linda; Török, Eszter; Hansen, Åse Marie

2017-07-01

To investigate the association between workplace bullying and change of job/unemployment, and to investigate whether psychological stress reactions constitute a potential pathway linking workplace bullying and change of job/unemployment. We used questionnaire data on workplace bullying and psychological stress reactions and register data on change of job/unemployment. We applied a multiple pathway approach to estimate the proportion of the association between workplace bullying and subsequent change of job/unemployment that was potentially mediated by psychological stress reactions. Workplace bullying was associated with risk of change of job (odds ratio [OR] = 1.35; 95% confidence interval [CI]: 1.06-1.72; 24% potentially mediated by psychological stress reactions) and unemployment (OR = 4.90; 95% CI: 3.18-7.55; 19% potentially mediated by psychological stress reactions). Workplace bullying has important consequences for labor market outcomes. Psychological stress reactions may play a vital role in this process.
Pathways for Learning from 3D Technology

Science.gov (United States)

Carrier, L. Mark; Rab, Saira S.; Rosen, Larry D.; Vasquez, Ludivina; Cheever, Nancy A.

2016-01-01

The purpose of this study was to find out if 3D stereoscopic presentation of information in a movie format changes a viewer's experience of the movie content. Four possible pathways from 3D presentation to memory and learning were considered: a direct connection based on cognitive neuroscience research; a connection through "immersion" in that 3D presentations could provide additional sensorial cues (e.g., depth cues) that lead to a higher sense of being surrounded by the stimulus; a connection through general interest such that 3D presentation increases a viewer’s interest that leads to greater attention paid to the stimulus (e.g., "involvement"); and a connection through discomfort, with the 3D goggles causing discomfort that interferes with involvement and thus with memory. The memories of 396 participants who viewed two-dimensional (2D) or 3D movies at movie theaters in Southern California were tested. Within three days of viewing a movie, participants filled out an online anonymous questionnaire that queried them about their movie content memories, subjective movie-going experiences (including emotional reactions and "presence") and demographic backgrounds. The responses to the questionnaire were subjected to path analyses in which several different links between 3D presentation to memory (and other variables) were explored. The results showed there were no effects of 3D presentation, either directly or indirectly, upon memory. However, the largest effects of 3D presentation were on emotions and immersion, with 3D presentation leading to reduced positive emotions, increased negative emotions and lowered immersion, compared to 2D presentations. PMID:28078331
A facile and expedient one-pot three-component reaction leading to ...

Indian Academy of Sciences (India)

A three-component reaction between triphenylphosphine, a dialkyl acetylenedicarboxylate and phthalazin-1(2H)-ones that affords novel organic phosphorane derivatives in good to excellent yields is reported. FTIR, 1H, 13C and 31P NMR and elemental analyses have been utilized to characterize the synthesized ...
Ozonation of norfloxacin and levofloxacin in water: Specific reaction rate constants and defluorination reaction.

Science.gov (United States)

Ling, Wencui; Ben, Weiwei; Xu, Ke; Zhang, Yu; Yang, Min; Qiang, Zhimin

2018-03-01

The degradation kinetics and mechanism of two typical fluoroquinolones (FQs), norfloxacin (NF) and levofloxacin (LOF), by ozone in water were investigated. Semi-continuous mode and competition kinetics mode experiments were conducted to determine the reaction rate constants of target FQs with ozone and OH, separately. Results indicate that both NF and LOF were highly reactive toward ozone, and the reactivity was strongly impacted by the solution pH. The specific reaction rate constants of the diprotonated, monoprotonated and deprotonated species were determined to be 7.20 × 10 2 , 8.59 × 10 3 , 4.54 × 10 5  M -1  s -1 respectively for NF and 1.30 × 10 3 , 1.40 × 10 4 , 1.33 × 10 6  M -1  s -1 respectively for LOF. The reaction rate constants of target FQs toward OH were measured to be (4.81-7.41) × 10 9  M -1  s -1 in the pH range of 6.3-8.3. Furthermore, NF was selected as a model compound to clarify the degradation pathways, with a particular focus on the defluorination reaction. The significant release of F - ions and the formation of three F-free organic byproducts indicated that defluorination was a prevalent pathway in ozonation of FQs, while six F-containing organic byproducts indicated that ozone also attacked the piperazinyl and quinolone moieties. Escherichia coli growth inhibition tests revealed that ozonation could effectively eliminate the antibacterial activity of target FQ solutions, and the residual antibacterial activity had a negative linear correlation with the released F - concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.
Oxidation of fluoroquinolone antibiotics and structurally related amines by chlorine dioxide: Reaction kinetics, product and pathway evaluation.

Science.gov (United States)

Wang, Pei; He, Yi-Liang; Huang, Ching-Hua

2010-12-01

Fluoroquinolones (FQs) are a group of widely prescribed antibiotics and have been frequently detected in the aquatic environment. The reaction kinetics and transformation of seven FQs (ciprofloxacin (CIP), enrofloxacin (ENR), norfloxacin (NOR), ofloxacin (OFL), lomefloxacin (LOM), pipemidic acid (PIP) and flumequine (FLU)) and three structurally related amines (1-phenylpiperazine (PP), N-phenylmorpholine (PM) and 4-phenylpiperidine (PD)) toward chlorine dioxide (ClO(2)) were investigated to elucidate the behavior of FQs during ClO(2) disinfection processes. The reaction kinetics are highly pH-dependent, can be well described by a second-order kinetic model incorporating speciation of FQs, and follow the trend of OFL > ENR > CIP ∼ NOR ∼ LOM > > PIP in reactivity. Comparison among FQs and related amines and product characterization indicate that FQs' piperazine ring is the primary reactive center toward ClO(2). ClO(2) likely attacks FQ's piperazinyl N4 atom followed by concerted fragmentation involving piperazinyl N1 atom, leading to dealkylation, hydroxylation and intramolecular ring closure at the piperazine moiety. While FQs with tertiary N4 react faster with ClO(2) than FQs with secondary N4, the overall reactivity of the piperazine moiety also depends strongly on the quinolone ring through electronic effects. The reaction rate constants obtained in clean water matrix can be used to model the decay of CIP by ClO(2) in surface water samples, but overestimate the decay in wastewater samples. Overall, transformation of FQs, particularly for those with tertiary N4 amines, could be expected under typical ClO(2) disinfection conditions. However, the transformation may not eliminate antibacterial activity because of little destruction at the quinolone ring. Copyright © 2010 Elsevier Ltd. All rights reserved.
Tandem Wittig-ene reaction approach to kainic acid

Digital Repository Service at National Institute of Oceanography (India)

Majik, M.S.; Parameswaran, P.S.; Tilve, S.G.

The first example of a tandem Wittig-intramolecular ene reaction approach and its application toward the synthesis of kainic acid is reported. The synthetic pathway involves conversion of prenyl bromide into phosphorane 3, followed by one-pot Wittig...
Targeting Wnt Pathways in Disease

Science.gov (United States)

Zimmerman, Zachary F.; Moon, Randall T.

2012-01-01

Wnt-mediated signal transduction pathways have long been recognized for their roles in regulating embryonic development, and have more recently been linked to cancer, neurologic diseases, inflammatory diseases, and disorders of endocrine function and bone metabolism in adults. Although therapies targeting Wnt signaling are attractive in theory, in practice it has been difficult to obtain specific therapeutics because many components of Wnt signaling pathways are also involved in other cellular processes, thereby reducing the specificity of candidate therapeutics. New technologies, and advances in understanding the mechanisms of Wnt signaling, have improved our understanding of the nuances of Wnt signaling and are leading to promising new strategies to target Wnt signaling pathways. PMID:23001988

Pericyclic reactions in an aqueous molecular flask.

Science.gov (United States)

Murase, Takashi; Fujita, Makoto

2010-10-01

A self-assembled molecular flask with a nanometer-sized restricted cavity offers a new reaction environment that is quite different from the bulk solution. The self-assembled cage accommodates a pair of hydrophobic molecules to perform unusual Diels-Alder reactions and [2+2] photoadditions of otherwise unreactive aromatic molecules. In this cage, for example, the Diels-Alder reaction of naphthalene proceeds smoothly under mild conditions, and aceanthrylene shows reactivity for both [2+2] and [2+4] cycloadditions via the identical ternary host-guest complex. The observed greatly enhanced reactivity stems from the increased local concentration and pre-organization of the substrate pair within the cage, which reduces the entropic cost and switches the reaction profile from a bimolecular to a pseudo-intramolecular reaction pathway. The reinforced orientation and arrangement of substrate pairs specify regio- and stereo-selectivities of the subsequent reactions in the cavity. Chiral auxiliaries outside the cage create the inner chiral environment and induce asymmetric reactions inside the cage (up to 50% ee). © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.
Capture reactions on C-14 in nonstandard big bang nucleosynthesis

Science.gov (United States)

Wiescher, Michael; Gorres, Joachim; Thielemann, Friedrich-Karl

1990-01-01

Nonstandard big bang nucleosynthesis leads to the production of C-14. The further reaction path depends on the depletion of C-14 by either photon, alpha, or neutron capture reactions. The nucleus C-14 is of particular importance in these scenarios because it forms a bottleneck for the production of heavier nuclei A greater than 14. The reaction rates of all three capture reactions at big bang conditions are discussed, and it is shown that the resulting reaction path, leading to the production of heavier elements, is dominated by the (p, gamma) and (n, gamma) rates, contrary to earlier suggestions.
A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version

Energy Technology Data Exchange (ETDEWEB)

Price, M.; Raju, M.; Taylor, R.

1993-01-01

This report summarizes the reactions that occur in some of the principal metabolic pathways of E. coli. These pathways have been encoded as objects in GenoBase, an integrated database under development at Argonne National Laboratory in collaboration with researchers at the National Institutes of Health and at Harvard University. The report lists the substrates, products, enzymes, and cofactors for each pathway as a whole, followed by a detailed description of each reaction in the pathway. In addition, for each enzyme, the report displays a description and activity as listed in the Enzyme Data Bank, followed by the corresponding Swiss Protein Data Bank entries. Separate summary lines are included for each of the E. coli genes associated with each enzyme.
Targeting Apoptosis Signaling Pathways for Anticancer Therapy

Energy Technology Data Exchange (ETDEWEB)

Fulda, Simone, E-mail: simone.fulda@kgu.de [Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt (Germany)

2011-08-29

Treatment approaches for cancer, for example chemotherapy, radiotherapy, or immunotherapy, primarily act by inducing cell death in cancer cells. Consequently, the inability to trigger cell death pathways or alternatively, evasion of cancer cells to the induction of cell death pathways can result in resistance of cancers to current treatment protocols. Therefore, in order to overcome treatment resistance a better understanding of the underlying mechanisms that regulate cell death and survival pathways in cancers and in response to cancer therapy is necessary to develop molecular-targeted therapies. This strategy should lead to more effective and individualized treatment strategies that selectively target deregulated signaling pathways in a tumor type- and patient-specific manner.
Targeting Apoptosis Signaling Pathways for Anticancer Therapy

International Nuclear Information System (INIS)

Fulda, Simone

2011-01-01

Treatment approaches for cancer, for example chemotherapy, radiotherapy, or immunotherapy, primarily act by inducing cell death in cancer cells. Consequently, the inability to trigger cell death pathways or alternatively, evasion of cancer cells to the induction of cell death pathways can result in resistance of cancers to current treatment protocols. Therefore, in order to overcome treatment resistance a better understanding of the underlying mechanisms that regulate cell death and survival pathways in cancers and in response to cancer therapy is necessary to develop molecular-targeted therapies. This strategy should lead to more effective and individualized treatment strategies that selectively target deregulated signaling pathways in a tumor type- and patient-specific manner.
Low energy ion-molecule reactions

Energy Technology Data Exchange (ETDEWEB)

Farrar, J.M. [Univ. of Rochester, NY (United States)

1993-12-01

This project is concerned with elucidating the dynamics of elementary ion-molecule reactions at collision energies near and below 1 eV. From measurements of the angular and energy distributions of the reaction products, one can infer intimathe details about the nature of collisions leading to chemical reaction, the geometries and lifetimes of intermediate complexes that govern the reaction dynamics, and the collision energy dependence of these dynamical features. The author employs crossed-beam low energy mass spectrometry technology developed over the last several years, with the focus of current research on proton transfer and hydrogen atom transfer reactions of te O{sup {minus}} ion with species such as HF, H{sub 2}O, and NH{sub 3}.
Benzene destruction in claus process by sulfur dioxide: A reaction kinetics study

KAUST Repository

Sinha, Sourab; Raj, Abhijeet Dhayal; Alshoaibi, Ahmed S.; Alhassan, Saeed M.; Chung, Suk-Ho

2014-01-01

interactions. The mechanism begins with SO2 addition to phenyl radical after overcoming an energy barrier of 6.4 kJ/mol. This addition reaction is highly exothermic, where a reaction energy of 182 kJ/mol is released. The most favorable pathway involves O-S bond
Solution growth of single crystal methylammonium lead halide perovskite nanostructures for optoelectronic and photovoltaic applications.

Science.gov (United States)

Fu, Yongping; Meng, Fei; Rowley, Matthew B; Thompson, Blaise J; Shearer, Melinda J; Ma, Dewei; Hamers, Robert J; Wright, John C; Jin, Song

2015-05-06

Understanding crystal growth and improving material quality is important for improving semiconductors for electronic, optoelectronic, and photovoltaic applications. Amidst the surging interest in solar cells based on hybrid organic-inorganic lead halide perovskites and the exciting progress in device performance, improved understanding and better control of the crystal growth of these perovskites could further boost their optoelectronic and photovoltaic performance. Here, we report new insights on the crystal growth of the perovskite materials, especially crystalline nanostructures. Specifically, single crystal nanowires, nanorods, and nanoplates of methylammonium lead halide perovskites (CH3NH3PbI3 and CH3NH3PbBr3) are successfully grown via a dissolution-recrystallization pathway in a solution synthesis from lead iodide (or lead acetate) films coated on substrates. These single crystal nanostructures display strong room-temperature photoluminescence and long carrier lifetime. We also report that a solid-liquid interfacial conversion reaction can create a highly crystalline, nanostructured MAPbI3 film with micrometer grain size and high surface coverage that enables photovoltaic devices with a power conversion efficiency of 10.6%. These results suggest that single-crystal perovskite nanostructures provide improved photophysical properties that are important for fundamental studies and future applications in nanoscale optoelectronic and photonic devices.
Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

Directory of Open Access Journals (Sweden)

Shinichi Yamabe

2014-01-01

Full Text Available Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p SCRF=(PCM, solvent = 1,2-ethanediol optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H2N–NH2 and (H2O8. A ready reaction channel of acetone → acetone hydrazine (Me2C=N–NH2 was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N2 extrusion step from the isopropyl diimine intermediate (Me2C(H–N=N–H. Two base-catalyzed reactions were investigated by models of the ketone, H2N–NH2 and OH−(H2O7. Here, ketones are acetone and acetophenone. While routes of the ketone → hydrazone → diimine are similar, those from the diimines are different. From the isopropyl diimine, the N2 extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenylethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.
Formation of iodo-trihalomethanes, iodo-acetic acids, and iodo-acetamides during chloramination of iodide-containing waters: Factors influencing formation and reaction pathways

Energy Technology Data Exchange (ETDEWEB)

Liu, Shaogang [Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085 (China); Guangxi Colleges and Universities Key Laboratory of Food Safety and Pharmaceutical Analytical Chemistry, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, 530006, Guangxi (China); Li, Zhenlin [Guangxi Colleges and Universities Key Laboratory of Food Safety and Pharmaceutical Analytical Chemistry, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, 530006, Guangxi (China); Dong, Huiyu [Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085 (China); Goodman, Bernard A. [College of Physical Science and Engineering, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 520004, Guangxi (China); Qiang, Zhimin, E-mail: qiangz@rcees.ac.cn [Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085 (China)

2017-01-05

This study investigated systematically the factors influencing the formation of iodinated disinfection by-products (I-DBPs) during chloramination of I{sup −}-containing waters, including reaction time, NH{sub 2}Cl dose, I{sup −} concentration, pH, natural organic matter (NOM) concentration, Br{sup −}/I{sup −} molar ratio, and water matrix. Among the I-DBPs detected, iodoform (CHI{sub 3}), iodoacetic acid (IAA), diiodoacetic acid (DIAA), triiodoacetic acid (TIAA), and diiodoacetamide (DIAcAm) were the major species produced from reactions between reactive iodine species (HOI/I{sub 2}) and NOM. A kinetic model involving the reactions of NH{sub 2}Cl auto-decomposition, iodine species transformation and NOM consumption was developed, which could well describe NH{sub 2}Cl decay and HOI/I{sub 2} evolution. Higher concentrations of CHI{sub 3}, IAA, DIAA, TIAA, and DIAcAm were observed in chloramination than in chlorination, whereas IO{sub 3}{sup −} was only formed significantly in chlorination. Maximum formation of I-DBPs occurred at pH 8.0, but acidic conditions favored the formation of iodinated haloacetic acids and DIAcAm. Increasing Br{sup −}/I{sup −} molar ratio from 1 to 10 did not increase the total amount of I-DBPs, but produced more bromine-substituting species. In addition, chloramination of 18 model compounds indicated that low-SUVA{sub 254} (specific ultraviolet absorbance at 254 nm) NOM generally favored the formation of I-DBPs compared to high-SUVA{sub 254} NOM. Finally, potential pathways for I-DBPs formation from chloramination of NOM were proposed.
Investigation of lead workers for subclinical effects of lead using three performance tests

Energy Technology Data Exchange (ETDEWEB)

Milburn, H; Mitran, E; Crockford, G W

1976-12-01

Using three performance tests, lead exposed workers were studied for signs of subclinical neurological effects. The three tests were: two flash fusion threshold, a test considered to indicate the level of arousal; reaction time to a touch stimulus and the rate at which hand grip pressure is developed, both influenced by the conduction velocity of the peripheral nerves and impulse transmission across the motor end plates. Sixteen male lead workers were tested and compared with a non-exposed matched control group of fifteen. The occupational history, neurological symptoms and blood lead levels were recorded. The three performance tests revealed no differences between the exposed and the non-exposed groups.
Nucleolus-derived mediators in oncogenic stress response and activation of p53-dependent pathways.

Science.gov (United States)

Stępiński, Dariusz

2016-08-01

Rapid growth and division of cells, including tumor ones, is correlated with intensive protein biosynthesis. The output of nucleoli, organelles where translational machineries are formed, depends on a rate of particular stages of ribosome production and on accessibility of elements crucial for their effective functioning, including substrates, enzymes as well as energy resources. Different factors that induce cellular stress also often lead to nucleolar dysfunction which results in ribosome biogenesis impairment. Such nucleolar disorders, called nucleolar or ribosomal stress, usually affect cellular functioning which in fact is a result of p53-dependent pathway activation, elicited as a response to stress. These pathways direct cells to new destinations such as cell cycle arrest, damage repair, differentiation, autophagy, programmed cell death or aging. In the case of impaired nucleolar functioning, nucleolar and ribosomal proteins mediate activation of the p53 pathways. They are also triggered as a response to oncogenic factor overexpression to protect tissues and organs against extensive proliferation of abnormal cells. Intentional impairment of any step of ribosome biosynthesis which would direct the cells to these destinations could be a strategy used in anticancer therapy. This review presents current knowledge on a nucleolus, mainly in relation to cancer biology, which is an important and extremely sensitive element of the mechanism participating in cellular stress reaction mediating activation of the p53 pathways in order to counteract stress effects, especially cancer development.
Reciprocal subsidies and food web pathways leading to chum salmon fry in a temperate marine-terrestrial ecotone.

Science.gov (United States)

Romanuk, Tamara N; Levings, Colin D

2010-04-08

Stable isotope analysis was used to determine the relative proportions of terrestrial and marine subsidies of carbon to invertebrates along a tidal gradient (low-intertidal, mid-intertidal, high-intertidal, supralittoral) and to determine the relative importance of terrestrial carbon in food web pathways leading to chum salmon fry Oncorhynchus keta (Walbaum) in Howe Sound, British Columbia. We found a clear gradient in the proportion of terrestrially derived carbon along the tidal gradient ranging from 68% across all invertebrate taxa in the supralittoral to 25% in the high-intertidal, 20% in the mid-intertidal, and 12% in the low-intertidal. Stable isotope values of chum salmon fry indicated carbon contributions from both terrestrial and marine sources, with terrestrially derived carbon ranging from 12.8 to 61.5% in the muscle tissue of chum salmon fry (mean 30%). Our results provide evidence for reciprocal subsidies of marine and terrestrially derived carbon on beaches in the estuary and suggest that the vegetated supralittoral is an important trophic link in supplying terrestrial carbon to nearshore food webs.
Histopathology and immune histochemistry of red tattoo reactions. Interface dermatitis is the lead pathology, with increase in T-lymphocytes and Langerhans cells suggesting an allergic pathomechanism.

Science.gov (United States)

Høgsberg, T; Thomsen, B M; Serup, J

2015-11-01

The majority of tattoo reactions are affiliated to red pigmented areas and often suspected to be allergic in nature. A sizeable series of biopsies of such reactions has not previously been performed. The aim of this study was to type and grade epidermal and dermal changes in tattoo reactions to red/red nuances by microscopy and immunochemistry relevant for the assessment of a possible allergic pathomechanism. Skin biopsies were taken from red tattoo reactions, graded by conventional microscopy and stained for T and B-lymphocytes, Langerhans cells, macrophages and tumour necrosis factor (TNF)-α. The study included 19 biopsies from 19 patients. The culprit colours were red/pink (n = 15) and purple/bordeaux (n = 4). Interface dermatitis was clearly the lead pathology found in 78% of samples, overlapped with granulomatous (in 32%) and pseudolymphomatous reaction patterns (in 32%). Epidermal hyperkeratosis (in 89%) was common as was leakage of red pigment across the dermo-epidermal junction, with transepidermal elimination (in 28%). The dermal cellular infiltration was dominated by T-lymphocytes (in 100%), Langerhans cells (in 95%) and macrophages (in 100%). TNF-α was common. The predominant histological pattern of chronic tattoo reactions in red/red nuances is interface dermatitis. T-lymphocytes and Langerhans cells are increased suggesting an allergic pathomechanism. TNF-α may contribute to reactions. In many cases, overlapping reactive patterns were identified. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Oxidation of nonylphenol and octylphenol by manganese dioxide: Kinetics and pathways

International Nuclear Information System (INIS)

Lu, Zhijiang; Gan, Jay

2013-01-01

Due to their potent estrogenicity and ubiquitous occurrence, non-ionic surfactant metabolites nonylphenol (NP) and octylphenol (OP) are of significant concern. Abiotic chemical oxidation by naturally abundant metal oxides may be an important route of their environmental attenuation, but is poorly understood. We investigated the reaction kinetics and pathways of NP and OP with MnO 2 . At pH 5.5 and 100 mg/L δ-MnO 2 , 92, 84 and 76% of 4-n-NP, 4-tert-OP and technical nonylphenol (tNP) was transformed in 90 min, respectively. A further experiment using a Mn-containing soil and Mn-removed soil confirmed that soil MnO 2 caused NP removal. Multiple reaction products, including hydroquinone, hydroxylated products, dimers and trimers were identified through fragmentation analysis by GC–MS/MS and UPLC–MS/MS, allowing the construction of tentative pathways. This study suggested that abiotic oxidation by MnO 2 may contribute to the dissipation of tNP, 4-n-NP, 4-tert-OP and their analogues in the natural environment. Highlights: •The oxidation of nonylphenol and octylphenol by manganese dioxide was efficient and pH dependent. •The importance of soil MnO 2 was further confirmed by experiment using Mn-containing soil. •The reaction in environment is substantially slower than with synthetic MnO 2 . •The oxidation was inhibited by metal ions and enhanced by humic acids. •Reaction pathway is proposed based on reaction intermediates identified. -- Naturally occurring MnO 2 may contribute significantly to the attenuation of nonylphenol and octylphenol in soil, water and sediment
Enhancing NAD+ Salvage Pathway Reverts the Toxicity of Primary Astrocytes Expressing Amyotrophic Lateral Sclerosis-linked Mutant Superoxide Dismutase 1 (SOD1).

Science.gov (United States)

Harlan, Benjamin A; Pehar, Mariana; Sharma, Deep R; Beeson, Gyda; Beeson, Craig C; Vargas, Marcelo R

2016-05-13

Nicotinamide adenine dinucleotide (NAD(+)) participates in redox reactions and NAD(+)-dependent signaling pathways. Although the redox reactions are critical for efficient mitochondrial metabolism, they are not accompanied by any net consumption of the nucleotide. On the contrary, NAD(+)-dependent signaling processes lead to its degradation. Three distinct families of enzymes consume NAD(+) as substrate: poly(ADP-ribose) polymerases, ADP-ribosyl cyclases (CD38 and CD157), and sirtuins (SIRT1-7). Because all of the above enzymes generate nicotinamide as a byproduct, mammalian cells have evolved an NAD(+) salvage pathway capable of resynthesizing NAD(+) from nicotinamide. Overexpression of the rate-limiting enzyme in this pathway, nicotinamide phosphoribosyltransferase, increases total and mitochondrial NAD(+) levels in astrocytes. Moreover, targeting nicotinamide phosphoribosyltransferase to the mitochondria also enhances NAD(+) salvage pathway in astrocytes. Supplementation with the NAD(+) precursors nicotinamide mononucleotide and nicotinamide riboside also increases NAD(+) levels in astrocytes. Amyotrophic lateral sclerosis (ALS) is caused by the progressive degeneration of motor neurons in the spinal cord, brain stem, and motor cortex. Superoxide dismutase 1 (SOD1) mutations account for up to 20% of familial ALS and 1-2% of apparently sporadic ALS cases. Primary astrocytes isolated from mutant human superoxide dismutase 1-overexpressing mice as well as human post-mortem ALS spinal cord-derived astrocytes induce motor neuron death in co-culture. Increasing total and mitochondrial NAD(+) content in ALS astrocytes increases oxidative stress resistance and reverts their toxicity toward co-cultured motor neurons. Taken together, our results suggest that enhancing the NAD(+) salvage pathway in astrocytes could be a potential therapeutic target to prevent astrocyte-mediated motor neuron death in ALS. © 2016 by The American Society for Biochemistry and Molecular
Hydrogen/Chlorine exchange reactions of gaseous carbanions.

Science.gov (United States)

Chen, Hao; Cooks, R Graham; Meurer, Eduardo C; Eberlin, Marcos N

2005-12-01

Gas-phase reactions of three typical carbanions CH(2)NO(2)(-), CH(2)CN(-), and CH(2)S(O)CH(3)(-) with the chloromethanes CH(2)Cl(2), CHCl(3), and CCl(4), examined by tandem mass spectrometry, show a novel hydrogen/chlorine exchange reaction. For example, reaction between the nitromethyl anion CH(2)NO(2)(-) and carbon tetrachloride CCl(4) forms the ion CHClNO(2)(-). The suggested reaction mechanism involves nucleophilic attack by CH(2)NO(2)(-) at the chlorine of CCl(4) followed by proton transfer within the resulting complex [CH(2)ClNO(2) + CCl(3)(-)] to form CHClNO(2)(-) and CHCl(3). Two other carbanions CH(2)CN(-) and CH(2)S(O)CH(3)(-) also undergo the novel hydrogen/chlorine exchange reactions with CCl(4) but to a much smaller extent, their higher nucleophilicities favoring competitive nucleophilic attack reactions. Proton abstraction is the exclusive pathway in the reactions of these carbanions with CHCl(3). While CH(2)CN(-) and CH(2)S(O)CH(3)(-) promote mainly proton abstraction and nucleophilic displacement in reactions with CH(2)Cl(2), CH(2)NO(2)(-) does not react.
Structural parameter identifiability analysis for dynamic reaction networks

DEFF Research Database (Denmark)

Davidescu, Florin Paul; Jørgensen, Sten Bay

2008-01-01

method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...... where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models....... The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...
Effect of trace elements on the interface reactions between two lead-free solders and copper or nickel substrates

Directory of Open Access Journals (Sweden)

Soares D.

2007-01-01

Full Text Available Traditional Sn-Pb solder alloys are being replaced, because of environmental and health concerns about lead toxicity. Among some alternative alloy systems, the Sn-Zn and Sn-Cu base alloy systems have been studied and reveal promising properties. The reliability of a solder joint is affected by the solder/substrate interaction and the nature of the layers formed at the interface. The solder/substrate reactions, for Sn-Zn and Sn-Cu base solder alloys, were evaluated in what concerns the morphology and chemical composition of the interface layers. The effect of the addition of P, at low levels, on the chemical composition of the layers present at the interface was studied. The phases formed at the interface between the Cu or Ni substrate and a molten lead-free solder at 250ºC, were studied for different stage times and alloy compositions. The melting temperatures, of the studied alloys, were determined by Differential Scanning Calorimetry (DSC. Identification of equilibrium phases formed at the interface layer, and the evaluation of their chemical composition were performed by Scanning Electron Microscopy (SEM/EDS. Different interface characteristics were obtained, namely for the alloys containing Zn. The obtained IML layer thickness was compared, for both types of alloy systems.
A board game to assist pharmacy students in learning metabolic pathways.

Science.gov (United States)

Rose, Tyler M

2011-11-10

To develop and evaluate a board game designed to increase students' enjoyment of learning metabolic pathways; their familiarity with pathway reactions, intermediates, and regulation; and, their understanding of how pathways relate to one another and to selected biological conditions. The board game, entitled Race to Glucose, was created as a team activity for first-year pharmacy students in the biochemistry curriculum. A majority of respondents agreed that the game was helpful for learning regulation, intermediates, and interpathway relationships but not for learning reactions, formation of energetic molecules, or relationships, to biological conditions. There was a significant increase in students' scores on game-related examination questions (68.8% pretest vs. 81.3% posttest), but the improvement was no greater than that for examination questions not related to the game (12.5% vs. 10.9%). First-year pharmacy students considered Race to Glucose to be an enjoyable and helpful tool for learning intermediates, regulation, and interpathway relationships.

Environmental pathways of radioactivity to man

International Nuclear Information System (INIS)

Johns, T.F.

1979-12-01

The report reviews and discusses the environmental pathways by which radioactive materials can lead to the irradiation of man, in a way that should be understood by non-specialists who have neither the time nor the knowledge to study all of the relevant literature on this subject. The role of these environmental pathways in the general structure of radiological protection is considered, and the various mechanisms which lead to the dispersion or re-concentration of radioactive materials are discussed at some length. Particular groups of radionuclides from the nuclear power industry are considered in some detail. Similarly the question of the corresponding pathways from naturally-occurring radioactive materials is covered. The doses to animals and plants resulting from the nuclear industry are examined, and it is concluded that there is no reason to expect that these doses will lead to significant harm. Finally a summary is presented, and it is noted that it has been possible to obtain a very extensive knowledge of the behaviour of radionuclides in the environment only because of the extreme sensitivity of the techniques available for their detection, identification and assay. As a result a fund of knowledge has been built up about the behaviour of radioactive materials in the environment which is far more extensive than our knowledge of the behaviour of many highly toxic chemicals which are also discharged into the environment. (UK)
The Azomethine Ylide Route to Amine C–H Functionalization: Redox-Versions of Classic Reactions and a Pathway to New Transformations

Science.gov (United States)

2016-01-01

Conspectus Redox-neutral methods for the functionalization of amine α-C–H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine α-C–H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine α-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet–Spengler, and Kabachnik–Fields reactions, Friedel–Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables α-C–H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic
The azomethine ylide route to amine C-H functionalization: redox-versions of classic reactions and a pathway to new transformations.

Science.gov (United States)

Seidel, Daniel

2015-02-17

Conspectus Redox-neutral methods for the functionalization of amine α-C-H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine α-C-H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine α-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet-Spengler, and Kabachnik-Fields reactions, Friedel-Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables α-C-H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic processes, have been
Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology (edited by Gerhard Michal)

Science.gov (United States)

Voige, Reviewed By William H.

2000-02-01

feature to the hyperlinks in an electronic document.) The book's index is comprehensive and useful. Entries for "phenylketonuria" and "sickle cell anemia", for example, lead to commendably concise summaries of these hereditary diseases (and the relevant metabolic pathway, in the former case). Looking up a specific molecule, however, is less helpful. The listing for fumarate hydratase, a citric acid cycle enzyme, directs the reader to the chapter on special bacterial metabolism but not to the section on the citric acid cycle itself. Literature references are included at the end of each section and are mainly from the 1990s, but they could be more useful. A long section on heme proteins, for example, concludes with eight citations, but their titles are not included, so it is impossible to determine what topic each one addresses. This book will be most useful to those with a good understanding of the fundamentals of biochemistry. Some of the information it presents could easily confuse less experienced readers. For example, it classifies selenocysteine as a standard amino acid in a figure but not in the accompanying text. In the diagram of anaerobic glycolysis, a double-headed arrow for the hexokinase reaction reinforces the frustratingly common student misperception that the phosphoryl group of glucose-6-phosphate can be used to phosphorylate ADP. Biochemical Pathways compiles a large amount of information in a single source. Its good index and clear, concise text and diagrams should make it a reliable way of gaining insight into many biochemical topics. With a price similar to that of most textbooks, it merits a place in the libraries of individuals and academic departments that teach biochemistry.
The Role of Psychological Stress Reactions in the Longitudinal Relation Between Workplace Bullying and Turnover

DEFF Research Database (Denmark)

Nabe-Nielsen, Kirsten; Grynderup, Matias Brødsgaard; Conway, Paul Maurice

2017-01-01

OBJECTIVES: To investigate the association between workplace bullying and change of job/unemployment, and to investigate whether psychological stress reactions constitute a potential pathway linking workplace bullying and change of job/unemployment. METHODS: We used questionnaire data on workplace...... bullying and psychological stress reactions and register data on change of job/unemployment. We applied a multiple pathway approach to estimate the proportion of the association between workplace bullying and subsequent change of job/unemployment that was potentially mediated by psychological stress...... reactions. RESULTS: Workplace bullying was associated with risk of change of job (odds ratio [OR] = 1.35; 95% confidence interval [CI]: 1.06-1.72; 24% potentially mediated by psychological stress reactions) and unemployment (OR = 4.90; 95% CI: 3.18-7.55; 19% potentially mediated by psychological stress...
Two-component multistep direct reactions: A microscopic approach

International Nuclear Information System (INIS)

Koning, A.J.; Chadwick, M.B.

1998-03-01

The authors present two principal advances in multistep direct theory: (1) A two-component formulation of multistep direct reactions, where neutron and proton excitations are explicitly accounted for in the evolution of the reaction, for all orders of scattering. While this may at first seem to be a formidable task, especially for multistep processes where the many possible reaction pathways becomes large in a two-component formalism, the authors show that this is not so -- a rather simple generalization of the FKK convolution expression 1 automatically generates these pathways. Such considerations are particularly relevant when simultaneously analyzing both neutron and proton emission spectra, which is always important since these processes represent competing decay channels. (2) A new, and fully microscopic, method for calculating MSD cross sections which does not make use of particle-hole state densities but instead directly calculates cross sections for all possible particle-hole excitations (again including an exact book-keeping of the neutron/proton type of the particle and hole at all stages of the reaction) determined from a simple non-interacting shell model. This is in contrast to all previous numerical approaches which sample only a small number of such states to estimate the DWBA strength, and utilize simple analytical formulae for the partial state density, based on the equidistant spacing model. The new approach has been applied, along with theories for multistep compound, compound, and collective reactions, to analyze experimental emission spectra for a range of targets and energies. The authors show that the theory correctly accounts for double-differential nucleon spectra
Aspartate aminotransferase: the kinetic barriers facing the covalent intermediates on the reaction pathway

International Nuclear Information System (INIS)

Kirsch, J.F.; Julin, D.A.; McLeish, M.; Wiesinger, H.

1986-01-01

The intermediates, aldimine (A), quinonoid (Q) and ketimine (K), along the transaminase reaction coordinate were probed by isotope transfer and solvent exchange kinetics. Less than 0.003% of 3 H is transferred from C/sub α/[ 3 H]-aspartate to pyridoxamine phosphate in the cytoplasmic aspartate aminotransferase (cAATase) reaction implying either that Q does not exist as a kinetically competent intermediate or that there is a rapid exchange of isotope with solvent. The ratio of the rate constants for C/sub α/ hydrogen exchange vs keto acid product formation (k/sub exge//k/sub prod/) are 2.5 and 0.5 for the reactions of cAATase with C/sub α/ [ 2 H]-aspartate and mitochondrial (m) AATase with C/sub α/[ 2 H]-glutamate respectively. The latter reaction was also probed from the α-keto-glutarate side with carbonyl 0-18 enriched keto acid. This experiment gave k/sub exge//k/sub prod/ = 1.0 for oxygen-18 exchange in α-ketoglutarate versus amino acid formation. The two exchange experiments with mAATase are interpreted in terms of a model in which the rate constant for diffusion of water from the active site is comparable with those for product forming steps
Secondary lead production

Energy Technology Data Exchange (ETDEWEB)

Hollis, R.G.

1990-10-16

This invention is concerned with the efficient recovery of soft lead from the paste component of used automobile lead-acid storage batteries. According to the invention, a scrap which contains lead oxide, lead sulfate, and antimony in an oxidized state is processed in the following steps to recover lead. A refractory lined reaction vessel is continuously charged with the scrap, along with a reductant effective for reducing lead oxide. The charged material is melted and agitated by means of a submerged lance at 900-1150{degree}C whereby some of the lead oxide of the scrap is reduced to form molten lead. A slag layer is then formed above the molten lead, and an amount of lead oxide is maintained in the slag layer. The molten lead, now containing under 0.5 wt % of antimony, is removed, and the antimony oxide in the scrap is concentrated as oxide in the slag layer. Preferred embodiments of the invention result in the production, in a single step, of a soft lead substantially free of antimony. The slag may be subsequently treated to reduce the antimony oxide and produce a valuable antimony-lead product. Further advantages of the process are that a wet battery paste may be used as the feed without prior drying, and the process can be conducted at a temperature 100-150{degree}C lower than in previously known methods. In addition, a smaller reactor can be employed which reduces both capital cost and fuel costs. The process of the invention is illustrated by descriptions of pilot plant tests. 1 fig.
Defining the Brittle Failure Envelopes of Individual Reaction Zones Observed in CO2-Exposed Wellbore Cement.

Science.gov (United States)

Hangx, Suzanne J T; van der Linden, Arjan; Marcelis, Fons; Liteanu, Emilia

2016-01-19

To predict the behavior of the cement sheath after CO2 injection and the potential for leakage pathways, it is key to understand how the mechanical properties of the cement evolves with CO2 exposure time. We performed scratch-hardness tests on hardened samples of class G cement before and after CO2 exposure. The cement was exposed to CO2-rich fluid for one to six months at 65 °C and 8 MPa Ptotal. Detailed SEM-EDX analyses showed reaction zones similar to those previously reported in the literature: (1) an outer-reacted, porous silica-rich zone; (2) a dense, carbonated zone; and (3) a more porous, Ca-depleted inner zone. The quantitative mechanical data (brittle compressive strength and friction coefficient) obtained for each of the zones suggest that the heterogeneity of reacted cement leads to a wide range of brittle strength values in any of the reaction zones, with only a rough dependence on exposure time. However, the data can be used to guide numerical modeling efforts needed to assess the impact of reaction-induced mechanical failure of wellbore cement by coupling sensitivity analysis and mechanical predictions.
Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

Science.gov (United States)

Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

2014-10-14

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a
Chlorination of tramadol: Reaction kinetics, mechanism and genotoxicity evaluation.

Science.gov (United States)

Cheng, Hanyang; Song, Dean; Chang, Yangyang; Liu, Huijuan; Qu, Jiuhui

2015-12-01

Tramadol (TRA) is one of the most detected analgesics in environmental matrices, and it is of high significance to study the reactivity of TRA during chlorination considering its potential toxicity to the environment. The chlorine/TRA reaction is first order with respect to the TRA concentration, and a combination of first-order and second-order with respect to chlorine concentration. The pH dependence of the observed rate constants (kobs) showed that the TRA oxidation reactivity increased with increasing pH. kobs can be quantitatively described by considering all active species including Cl2, Cl2O and HOCl, and the individual rate constants of HOCl/TRA(0), HOCl/TRAH(+), Cl2/TRA and Cl2O/TRA reactions were calculated to be (2.61±0.29)×10(3)M(-1)s(-1), 14.73±4.17M(-1)s(-1), (3.93±0.34)×10(5)M(-1)s(-1) and (5.66±1.83)×10(6)M(-1)s(-1), respectively. Eleven degradation products were detected with UPLC-Q-TOF-MS, and the corresponding structures of eight products found under various pH conditions were proposed. The amine group was proposed to be the initial attack site under alkaline pH conditions, where reaction of the deprotonated amine group with HOCl is favorable. Under acidic and neutral pH conditions, however, two possible reaction pathways were proposed. One is an electrophilic substitution on the aromatic ring, and another is an electrophilic substitution on the nitrogen, leading to an N-chlorinated intermediate, which can be further oxidized. Finally, the SOS/umu test showed that the genotoxicity of TRA chlorination products increased with increasing dosage of chlorine, which was mostly attributed to the formation of some chlorine substitution products. Copyright © 2015 Elsevier Ltd. All rights reserved.
The reaction of fluorine atoms with methanol: yield of CH3O/CH2OH and rate constant of the reactions CH3O + CH3O and CH3O + HO2.

Science.gov (United States)

Assaf, Emmanuel; Schoemaecker, Coralie; Vereecken, Luc; Fittschen, Christa

2018-04-25

Xenondifluoride, XeF2, has been photolysed in the presence of methanol, CH3OH. Two reaction pathways are possible: F + CH3OH → CH2OH + HF and F + CH3OH → CH3O + HF. Both products, CH2OH and CH3O, will be converted to HO2 in the presence of O2. The rate constants for the reaction of both radicals with O2 differ by more than 3 orders of magnitude, which allows an unequivocal distinction between the two reactions when measuring HO2 concentrations in the presence of different O2 concentrations. The following yields have then been determined from time-resolved HO2 profiles: φCH2OH = (0.497 ± 0.013) and φCH3O = (0.503 ± 0.013). Experiments under low O2 concentrations lead to reaction mixtures containing nearly equal amounts of HO2 (converted from the first reaction) and CH3O (from the second reaction). The subsequent HO2 decays are very sensitive to the rate constants of the reaction between these two radicals and the following rate constants have been obtained: k(CH3O + CH3O) = (7.0 ± 1.4) × 10-11 cm3 s-1 and k(CH3O + HO2) = (1.1 ± 0.2) × 10-10 cm3 s-1. The latter reaction has also been theoretically investigated on the CCSD(T)//M06-2X/aug-cc-pVTZ level of theory and CH3OH + O2 have been identified as the main products. Using μVTST, a virtually pressure independent rate constant of k(CH3O + HO2) = 4.7 × 10-11 cm3 s-1 has been obtained, in good agreement with the experiment.
A controlled vocabulary for pathway entities and events.

Science.gov (United States)

Jupe, Steve; Jassal, Bijay; Williams, Mark; Wu, Guanming

2014-01-01

Entities involved in pathways and the events they participate in require descriptive and unambiguous names that are often not available in the literature or elsewhere. Reactome is a manually curated open-source resource of human pathways. It is accessible via a website, available as downloads in standard reusable formats and via Representational State Transfer (REST)-ful and Simple Object Access Protocol (SOAP) application programming interfaces (APIs). We have devised a controlled vocabulary (CV) that creates concise, unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve. The CV could be reapplied in any situation where names are used for pathway entities and events. Adoption of this CV would significantly improve naming consistency and readability, with consequent benefits for searching and data mining within and between databases. Database URL: http://www.reactome.org. © The Author(s) 2014. Published by Oxford University Press.
A Unique (3+2) Annulation Reaction between Meldrum's Acid and Nitrones: Mechanistic Insight by ESI-IMS-MS and DFT Studies.

Science.gov (United States)

Lespes, Nicolas; Pair, Etienne; Maganga, Clisy; Bretier, Marie; Tognetti, Vincent; Joubert, Laurent; Levacher, Vincent; Hubert-Roux, Marie; Afonso, Carlos; Loutelier-Bourhis, Corinne; Brière, Jean-François

2018-03-15

The fragile intermediates of the domino process leading to an isoxazolidin-5-one, triggered by unique reactivity between Meldrum's acid and an N-benzyl nitrone in the presence of a Brønsted base, were determined thanks to the softness and accuracy of electrospray ionization mass spectrometry coupled to ion mobility spectrometry (ESI-IMS-MS). The combined DFT study shed light on the overall organocatalytic sequence that starts with a stepwise (3+2) annulation reaction that is followed by a decarboxylative protonation sequence encompassing a stereoselective pathway issue. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
ON THE RELATIVE ABUNDANCE OF LiH AND LiH+ MOLECULES IN THE EARLY UNIVERSE: NEW RESULTS FROM QUANTUM REACTIONS

International Nuclear Information System (INIS)

Bovino, Stefano; Tacconi, Mario; Gianturco, Franco A.; Galli, Daniele; Palla, Francesco

2011-01-01

The relative efficiencies of the chemical pathways that can lead to the destruction of LiH and LiH + molecules, conjectured to be present in the primordial gas and to control molecular cooling processes in the gravitational collapse of the post-recombination era, are revisited by using accurate quantum calculations for the several reactions involved. The new rates are employed to survey the behavior of the relative abundance of these molecules at redshifts of interest for early universe conditions. We find significant differences with respect to previous calculations, the present ones yielding LiH abundances higher than LiH + at all redshifts.
Reaction of winter oilseed rape varieties to elevated concentrations of lead

Directory of Open Access Journals (Sweden)

Oreščanin Bojana

2012-01-01

Full Text Available Remediation methods allow the removal of metals from contaminated soil, and phytoremediation a technology for cleaning contaminated soil and waste material by plants, is becoming increasingly used. Brassica napus L., as one of the main oilcrops and high-biomass producing species, is becoming more and more interesting for the use in phytoextraction as it is proved to be tolerant to higher concentrations of heavy metals. The aim of this study was to examine the specific responses of three commercial winter rapeseed varieties, Banaćanka, Slavica and Kata, to the increased concentrations of lead in vitro. Significant reduction in root length of plants treated with lead was observed only in the variety Slavica, indicating susceptibility of this variety to the increased concentrations of this heavy metal. As in variety Kata a significant reduction in the length of the above-ground part due to the treatment with lead was detected, it could be concluded that the variety Banaćanka is the most tolerant to the applied concentrations of lead since there were no significant changes in the growth and biomass accumulation in all treatments except one, and could be recommended for further use in phytoremediation studies. [Projekat Ministarstva nauke Republike Srbije, br. TR31025 i br. III43007
The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion: The Pathway for Oxygen.

Science.gov (United States)

Bassingthwaighte, James B; Raymond, Gary M; Dash, Ranjan K; Beard, Daniel A; Nolan, Margaret

2016-01-01

The 'Pathway for Oxygen' is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system's basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: (1) a 'one-alveolus lung' with airway resistance, lung volume compliance, (2) bidirectional transport of solute gasses like O2 and CO2, (3) gas exchange between alveolar air and lung capillary blood, (4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and (5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there.
Directing Reaction Pathways through Controlled Reactant Binding at Pd-TiO2 Interfaces.

Science.gov (United States)

Zhang, Jing; Wang, Bingwen; Nikolla, Eranda; Medlin, J Will

2017-06-01

Recent efforts to design selective catalysts for multi-step reactions, such as hydrodeoxygenation (HDO), have emphasized the preparation of active sites at the interface between two materials having different properties. However, achieving precise control over interfacial properties, and thus reaction selectivity, has remained a challenge. Here, we encapsulated Pd nanoparticles (NPs) with TiO 2 films of regulated porosity to gain a new level of control over catalyst performance, resulting in essentially 100 % HDO selectivity for two biomass-derived alcohols. This catalyst also showed exceptional reaction specificity in HDO of furfural and m-cresol. In addition to improving HDO activity by maximizing the interfacial contact between the metal and metal oxide sites, encapsulation by the nanoporous oxide film provided a significant selectivity boost by restricting the accessible conformations of aromatics on the surface. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Teaching Biochemical Pathways Using Concept Maps

Directory of Open Access Journals (Sweden)

Simon Brown

2013-08-01

Full Text Available The interesting paper by Dinarvand and Vaisi-Raygan (1 makes valuable points about a particularly challenging aspect of biochemistry learning and teaching. Their work prompts me to ask two questions and make a comment. First, what do the authors mean by a concept map (CM? A pathway map could be considered a CM, but a CM could cover modes of regulation and kinetics in relation to particular reactions or pathways and there are many other possibilities. Irrespective of this, a CM can get extremely complex if more than a few concepts are involved (2, as can be seen in examples given by Novak (3. This is the fundamental problem of teaching and learning biochemistry (4, which combines the network of pathways, compartmentation, macromol¬ecular structure, regulation, kinetics and some fairly sophisticated chemical concepts.Second, how did the students go about preparing CMs? My experience is that students prefer to use a computer for most tasks, but standard CM software (5 may not be suitable. For example, they often struggle unnec¬essarily to use software to prepare a graphical summary of the structural features of a protein, its precursors and the gene encoding it. This distracts them from the material. My suggestions that pencil and paper might be sufficient are usually met with amazement. Third, as Dinarvand and Vaisi-Raygan (1 make clear, a coherent summary of the metabolism considered in a course in metabolic biochemistry is crucial if students are to appreciate the pathways and their interconn-ection and regulation. For many years I have used an approach in which students collaborate in tutorials to achieve this. The sessions are usually initiated by me drawing the plasma membrane and the mitochondrial membranes on a large board and inviting the students to fill in the blanks (I provide large sheets of paper so that students can make copies. With coaxing, someone volunteers and I explain that the volunteer is not alone because everyone is
Guanine nucleotide exchange factor αPIX leads to activation of the Rac 1 GTPase/glycogen phosphorylase pathway in interleukin (IL)-2-stimulated T cells

DEFF Research Database (Denmark)

Llavero, Francisco; Urzelai, Bakarne; Osinalde, Nerea

2015-01-01

Recently, we have reported that the active form of Rac 1 GTPase binds to the glycogen phosphorylase muscle isoform (PYGM) and modulates its enzymatic activity leading to T cell proliferation. In the lymphoid system, Rac 1 and in general other small GTPases of the Rho family participate...... in the signaling cascades that are activated after engagement of the T cell antigen receptor. However, little is known about the IL-2-dependent Rac 1 activator molecules. For the first time, a signaling pathway leading to the activation of Rac 1/PYGM in response to IL-2-stimulated T cell proliferation is described....... More specifically, αPIX, a known guanine nucleotide exchange factor for the small GTPases of the Rho family, preferentially Rac 1, mediates PYGM activation in Kit 225 T cells stimulated with IL-2. Using directed mutagenesis, phosphorylation of αPIX Rho-GEF serines 225 and 488 is required for activation...

Photochemical Reactions of Particulate Organic Matter: Deciphering the Role of Direct and Indirect Processes

Science.gov (United States)

Carrasquillo, A. J.; Gelfond, C. E.; Kocar, B. D.

2016-12-01

Photochemical reactions of natural organic matter (NOM) represent potentially important pathways for biologically recalcitrant material to be chemically altered in aquatic systems. Irradiation can alter the physical state of organic matter by facilitating the cycling between the particulate (POM) and dissolved (DOM) pools, however, a molecular level understanding of this chemically dynamic system is currently lacking. Photochemical reactions of a target molecule proceed by the direct absorption of a photon, or through reaction with a second photolytically generated species (i.e. the hydroxyl radical, singlet oxygen, excited triplet state NOM, hydrogen peroxide, etc.). Here, we isolate the major direct and indirect photochemical reactions of a lignocellulose-rich POM material (Phragmites australis) to determine their relative importance in changing the the chemical structure of the parent POM, and in the production of DOM. We measured POM molecular structure using a combination of NMR and FTIR for bulk analyses and scanning transmission x-ray microscopy (STXM) for spatially resolved chemistry, while the chemical composition of photo-produced DOM was measured using ultra-high resolution mass spectrometry. Results are discussed in the context of the differences in chemical composition of both NOM pools resulting from the isolated photochemical pathways. All treatments result in an increase in DOM with reaction time, indicating that the larger POM matrix is likely fragmenting into smaller more soluble species. Spectroscopic measurements, on the other hand, point to functionalization reactions which increase the abundance of alcohol, acid, and carbonyl moieties in both carbon pools. This unique dataset provides new insight into how photochemical reactions alter the chemical composition of NOM while highlighting the relative importance of indirect pathways.
Probabilistic Modeling of Childhood Multimedia Lead Exposures: Examining the Soil Ingestion Pathway

Science.gov (United States)

BACKGROUND: Drinking water and other sources for lead are the subject of public health concerns around the Flint, Michigan, drinking water and East Chicago, Indiana, lead in soil crises. In 2015, the U.S. Environmental Protection Agency (EPA)’s National Drinking Water Advis...
Evaporation residue cross sections and average neutron multiplicities in the /sup 64/Ni+/sup 92/Zr and /sup 12/C+/sup 144/Sm reactions leading to /sup 156/Er

Energy Technology Data Exchange (ETDEWEB)

Janssens, R.V.F.; Holzmann, R.; Henning, W.; Khoo, T.L.; Lesko, K.T.; Stephans, G.S.F.; Radford, D.C.; Van den Berg, A.M.; Kuehn, W.; Ronningen, R.M.

1986-11-27

Evaporation residue cross sections and neutron multiplicity distributions have been measured for the /sup 12/C+/sup 144/Sm and /sup 64/Ni+/sup 92/Zr reactions leading to the same compound nucleous /sup 156/Er. Statistical model calculations can account for the data in the /sup 12/C-induced reaction. In contrast, the inhibition of neutron emission with respect to statistical model predictions seen in /sup 64/Ni+/sup 92/Zr cannot be explained even with the inclusion of the broad angular momentum distributions required to describe the fusion cross section data.
Charting an Alternate Pathway to Reaction Orders and Rate Laws in Introductory Chemistry Courses

Science.gov (United States)

Rushton, Gregory T.; Criswell, Brett A.; McAllister, Nicole D.; Polizzi, Samuel J.; Moore, Lamesha A.; Pierre, Michelle S.

2014-01-01

Reaction kinetics is an axiomatic topic in chemistry that is often addressed as early as the high school course and serves as the foundation for more sophisticated conversations in college-level organic, physical, and biological chemistry courses. Despite the fundamental nature of reaction kinetics, students can struggle with transforming their…
Effects of urban air pollution on the inflammatory reaction: involvement of the chemokine pathways; Impact de la pollution atmospherique urbaine sur la reponse inflammatoire: implication des chimiokines

Energy Technology Data Exchange (ETDEWEB)

Fahy, O.

2000-12-01

Urban air pollution is both gaseous and particulate, and diesel exhausts are now the main source of particles. Diesel particles consist of a carbon core with multiple adsorbed organic compounds, among witch poly-aromatic hydrocarbons. These diesel particles and associated poly-aromatic hydrocarbons are likely to play a role in the recent increase in allergic diseases. In this study, we evaluated the effects of diesel organic extracts on the initiation and the orientation of the allergen-dependent inflammatory reaction by analyzing the dis-regulation of a family of mediators involved in cellular recruitment: the chemokines. We demonstrated that mononuclear cells and alveolar macrophages from normal subjects displayed a dis-regulation in pro-inflammatory chemokine expression and production (IL-8, MCP-1, RANTES) when exposed to diesel organic extracts. In addition we observed a synergy between the effects of diesel and allergen when cells from allergic patients were exposed to both simultaneously, leading to a strong over-production of chemokines, and to the increased capacity of recruiting effector cells such as neutrophils and eosinophils. The MAP kinase pathways seemed largely involved in the transduction of diesel and allergen stimulus, since a specific inhibition almost abolished the dis-regulation of chemokine production. Diesel and allergen also appeared to favour the establishment of a type 2 immune response (pro-allergenic), by preferentially recruiting Th2 lymphocytes via the dis-regulation of chemokine expression (MDC and IP-10). Finally, the humanized SCID mouse model grafted with autologous human skin allowed the in vivo evaluation of a local over-production of chemokine, by analyzing the cellular recruitment in the skin after intra-dermal injection of recombinant chemokines. This model appears useful for the study of the mechanisms of cellular recruitment by chemokines and the potential therapeutic approaches. In conclusion, our study underlines the
Regio- and stereoselective carbometallation reactions of N-alkynylamides and sulfonamides

Directory of Open Access Journals (Sweden)

Yury Minko

2013-03-01

Full Text Available The carbocupration reactions of heterosubstituted alkynes allow the regio- and stereoselective formation of vinyl organometallic species. N-Alkynylamides (ynamides are particularly useful substrates for the highly regioselective carbocupration reaction, as they lead to the stereodefined formation of vinylcopper species geminated to the amide moiety. The latter species are involved in numerous synthetically useful transformations leading to valuable building blocks in organic synthesis. Here we describe in full the results of our studies related to the carbometallation reactions of N-alkynylamides.
Synthesis and reactions of deuterated 2-(alkylimino)-3-nitrosooxazolidines, 3-alkly-1-(2-hydroxyethyl)-1-nitrosoureas, and related compounds as possible intermediates in the aqueous decomposition of 3-alkyl-1-(2-chloroethyl)-1-nitrosoureas

International Nuclear Information System (INIS)

Lown, J.W.; Chauhan, S.M.S.

1981-01-01

Decomposition of 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea-α-d 2 (CCNU-α-d 2 ) (7) in pH 7.2 phosphate buffer or of CINO-α-d 2 (9) or CHNU-α-d 2 (8) with the addition of chloride ion gives rise to the same spectrum of products, including deuterium-free acetaldehyde (29), a mixture of the two deuterio-2-chloroethanols, 2-hydroxy-2,2-dideuterioethyl cyclohexyl carbamates, and vinyl chloride containing one deuterium (i.e., opposite the results obtained in the corresponding reaction of BCNU-α-d 4 ). The products were identified and the number and position of the deuterium labels determined by GC/MS. The results are interpreted in terms of two decomposition pathways for CCNU. The first decomposition pathway operating for CCNU is via an intermediate-2-chloroethanediazohydroxide or the equivalent 2-chloroethyl cation in agreement with the results of other workers. The second pathway may involve reversible conversion of CCNU-α-d 2 (7) to CINO-α-d 2 (9) and then ring opening of the latter to CHNU-α-d 2 (8). Independent decomposition of 8 provides evidence for its conversion to a 1.1-dideuterio-2-hydroxyethanediazohydroxide (41) leading to the isolated carbamates 36 and 44. The intermediacy of species 41 may account for the formation of 2-hydroxyethylated nucleosides observed when (2-chloroethyl)nitrosoureas react with DNA. An alternative ring-opening reaction of 9 leads to a 2-hydroxydiazoethyl cyclohexylcarbamate species (37), elimination of which and attack by halide ion may account for the vinyl halide species formed. Further evidence in support of these competing pathways employing additional specifically deuterated intermediates is described and discussed
Lead (Pb) isotopic fingerprinting and its applications in lead pollution studies in China: a review.

Science.gov (United States)

Cheng, Hefa; Hu, Yuanan

2010-05-01

As the most widely scattered toxic metal in the world, the sources of lead (Pb) observed in contamination investigation are often difficult to identify. This review presents an overview of the principles, analysis, and applications of Pb isotopic fingerprinting in tracing the origins and transport pathways of Pb in the environment. It also summarizes the history and current status of lead pollution in China, and illustrates the power of Pb isotopic fingerprinting with examples of its recent applications in investigating the effectiveness of leaded gasoline phase-out on atmospheric lead pollution, and the sources of Pb found in various environmental media (plants, sediments, and aquatic organisms) in China. The limitations of Pb isotopic fingerprinting technique are discussed and a perspective on its development is also presented. Further methodological developments and more widespread instrument availability are expected to make isotopic fingerprinting one of the key tools in lead pollution investigation. Copyright 2009 Elsevier Ltd. All rights reserved.
Rapid sonochemical preparation of shape-selective lead iodide

International Nuclear Information System (INIS)

Huang, Baojun; He, Qin; Fa, Wenjun; Li, Pinjiang; Zhang, Yange; Zheng, Zhi

2012-01-01

Graphical abstract: SEM morphologies of various PbI2 products obtained with the iodine concentration of 6.7 g/L and irradiation time of 1 minute at the reaction temperatures of 35 °C (a), 25 °C (b), and 15 °C (c). Highlights: ► PbI 2 with various morphologies were rapidly formed at room temperature. ► We could well control the morphologies of PbI 2 by changing reaction conditions. ► The PbI 2 films could better resist rolling in a liquid media. -- Abstract: Lead iodide (PbI 2 ) films/crystals with various nano/micro morphologies (e.g., Nanoflake, block and microrod) were rapidly synthesized by taking advantage of a simple sonochemical method. The PbI 2 crystals with uniform nanoflake structures could be fabricated directly on lead foils with the irradiation time as short as 36 s via interfacial reaction between lead foils and elemental iodine in ethanol at ambient temperature. It was found experimentally that the morphologies of the resulting thin films/crystals could be well controlled by the adjustment of several parameters including irradiation time, reaction solvents, iodine concentration, ultrasonic power, and reaction temperature. Most importantly, the resultant PbI 2 films are stable enough to resist rolling under the drastic ultrasound irradiation in a liquid media. This method is believed to be the fastest way for in situ fabrication of morphology-controlled semiconductor films on various metal substrates for subsequent applications related to the other metal iodide or metal sulfide semiconductor films.
Human plasmacytoid dentritic cells elicit a Type I Interferon response by sensing DNA via the cGAS-STING signaling pathway.

Science.gov (United States)

Bode, Christian; Fox, Mario; Tewary, Poonam; Steinhagen, Almut; Ellerkmann, Richard K; Klinman, Dennis; Baumgarten, Georg; Hornung, Veit; Steinhagen, Folkert

2016-07-01

Plasmacytoid dendritic cells (pDCs) are a major source of type I interferon (IFN) and are important for host defense by sensing microbial DNA via TLR9. pDCs also play a critical role in the pathogenesis of IFN-driven autoimmune diseases. Yet, this autoimmune reaction is caused by the recognition of self-DNA and has been linked to TLR9-independent pathways. Increasing evidence suggests that the cytosolic DNA receptor cyclic GMP-AMP (cGAMP) synthase (cGAS) is a critical component in the detection of pathogens and contributes to autoimmune diseases. It has been shown that binding of DNA to cGAS results in the synthesis of cGAMP and the subsequent activation of the stimulator of interferon genes (STING) adaptor to induce IFNs. Our results show that the cGAS-STING pathway is expressed and activated in human pDCs by cytosolic DNA leading to a robust type I IFN response. Direct activation of STING by cyclic dinucleotides including cGAMP also activated pDCs and knockdown of STING abolished this IFN response. These results suggest that pDCs sense cytosolic DNA and cyclic dinucleotides via the cGAS-STING pathway and that targeting this pathway could be of therapeutic interest. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Fe(II)/Fe(III)-Catalyzed Intramolecular Didehydro-Diels-Alder Reaction of Styrene-ynes.

Science.gov (United States)

Mun, Hyeon Jin; Seong, Eun Young; Ahn, Kwang-Hyun; Kang, Eun Joo

2018-02-02

The intramolecular didehydro-Diels-Alder reaction of styrene-ynes was catalyzed by Fe(II) and Fe(III) to produce various naphthalene derivatives under microwave heating conditions. Mechanistic calculations found that the Fe(II) catalyst activates the styrenyl diene in an inverse-electron-demand Diels-Alder reaction, and the consecutive dehydrogenation reaction can be promoted by either Fe(II)-catalyzed direct dehydrogenation or an Fe(III)-catalyzed rearomatization/dehydrogenation pathway.
Pathways to Sexual Risk Taking among Female Adolescent Detainees

Science.gov (United States)

Lopez, Vera; Kopak, Albert; Robillard, Alyssa; Gillmore, Mary Rogers; Holliday, Rhonda C.; Braithwaite, Ronald L.

2011-01-01

Sexual risk taking among female delinquents represents a significant public health problem. Research is needed to understand the pathways leading to sexual risk taking among this population. This study sought to address this issue by identifying and testing two pathways from child maltreatment to non-condom use among 329 White and 484 African…
The Atmospheric Oxidation of Volatile Organic Compounds Through Hydrogen Shift Reactions

DEFF Research Database (Denmark)

Knap, Hasse Christian

a radical is denoted as a H-shift reaction. Quantum chemical calculations were carried out to investigate the potential energy surface of the H-shift reactions and the subsequent decomposition pathways. The transition state theory including the Eckart quantum tunneling correction have been used to calculate...... the reaction rate constants of the H-shift reactions. The autoxidation of volatile organic compounds is an important oxidation mechanism that produces secondary organic aerosols (SOA) and recycles hydroxyl (OH) radicals. The autoxidation cycle produces a second generation peroxy radical (OOQOOH) through...... a series of H-shift reactions and O2 attachments. I have investigated the H-shift reactions in two OOQOOH radicals (hydroperoxy peroxy radicals and hydroperoxy acyl peroxy radicals). The H-shift reaction rate constants have been compared with the bimolecular reaction rate constants of the peroxy radicals...
Machine learning methods for metabolic pathway prediction

Directory of Open Access Journals (Sweden)

Karp Peter D

2010-01-01

Full Text Available Abstract Background A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism. Results To quantitatively validate methods for pathway prediction, we developed a large "gold standard" dataset of 5,610 pathway instances known to be present or absent in curated metabolic pathway databases for six organisms. We defined a collection of 123 pathway features, whose information content we evaluated with respect to the gold standard. Feature data were used as input to an extensive collection of machine learning (ML methods, including naïve Bayes, decision trees, and logistic regression, together with feature selection and ensemble methods. We compared the ML methods to the previous PathoLogic algorithm for pathway prediction using the gold standard dataset. We found that ML-based prediction methods can match the performance of the PathoLogic algorithm. PathoLogic achieved an accuracy of 91% and an F-measure of 0.786. The ML-based prediction methods achieved accuracy as high as 91.2% and F-measure as high as 0.787. The ML-based methods output a probability for each predicted pathway, whereas PathoLogic does not, which provides more information to the user and facilitates filtering of predicted pathways. Conclusions ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability. More advanced prediction methods and/or more sophisticated input features may improve the performance of ML methods. However, pathway prediction performance appears to be limited largely by the ability to correctly match enzymes to the reactions they catalyze based on genome annotations.
Machine learning methods for metabolic pathway prediction

Science.gov (United States)

2010-01-01

Background A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism. Results To quantitatively validate methods for pathway prediction, we developed a large "gold standard" dataset of 5,610 pathway instances known to be present or absent in curated metabolic pathway databases for six organisms. We defined a collection of 123 pathway features, whose information content we evaluated with respect to the gold standard. Feature data were used as input to an extensive collection of machine learning (ML) methods, including naïve Bayes, decision trees, and logistic regression, together with feature selection and ensemble methods. We compared the ML methods to the previous PathoLogic algorithm for pathway prediction using the gold standard dataset. We found that ML-based prediction methods can match the performance of the PathoLogic algorithm. PathoLogic achieved an accuracy of 91% and an F-measure of 0.786. The ML-based prediction methods achieved accuracy as high as 91.2% and F-measure as high as 0.787. The ML-based methods output a probability for each predicted pathway, whereas PathoLogic does not, which provides more information to the user and facilitates filtering of predicted pathways. Conclusions ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability. More advanced prediction methods and/or more sophisticated input features may improve the performance of ML methods. However, pathway prediction performance appears to be limited largely by the ability to correctly match enzymes to the reactions they catalyze based on genome annotations. PMID:20064214
Lead remediation and changes in human lead exposure: some physiological and biokinetic dimensions.

Science.gov (United States)

Mushak, Paul

2003-02-15

This paper presents a qualitative and quantitative analysis of the various aspects of lead remediation effectiveness with particular reference to human health risk assessment. One of the key elements of lead remediation efforts at such sites as those under the Superfund program deals with populations at elevated exposure and toxicity risk in the proximity of, or at, the site of remediation, especially remediation workers, workers at other tasks on sites that were remediated down to some action level of lead concentration in soils, and groups at risk in nearby communities. A second element has to do with how one measures or models lead exposure changes with special reference to baseline and post-remediation conditions. Various biomarkers of lead exposure can be employed, but their use requires detailed knowledge of what results using each means. The most commonly used approach is measurement of blood lead (Pb-B). Recognized limitations in the use of Pb-B has led to the use of predictive Pb exposure models, which are less vulnerable to the many behavioral, physiological, and environmental parameters that can distort isolated or 'single shot' Pb-B testings. A third aspect covered in this paper presents various physiological factors that affect the methods by which one evaluates Pb remediation effectiveness. Finally, this article offers an integrated look at how lead remediation actions directed at one lead source or pathway affect the total lead exposure picture for human populations at elevated lead exposure and toxicity risk.
Chemical Reactions of Molecules Promoted and Simultaneously Imaged by the Electron Beam in Transmission Electron Microscopy.

Science.gov (United States)

Skowron, Stephen T; Chamberlain, Thomas W; Biskupek, Johannes; Kaiser, Ute; Besley, Elena; Khlobystov, Andrei N

2017-08-15

The main objective of this Account is to assess the challenges of transmission electron microscopy (TEM) of molecules, based on over 15 years of our work in this field, and to outline the opportunities in studying chemical reactions under the electron beam (e-beam). During TEM imaging of an individual molecule adsorbed on an atomically thin substrate, such as graphene or a carbon nanotube, the e-beam transfers kinetic energy to atoms of the molecule, displacing them from equilibrium positions. Impact of the e-beam triggers bond dissociation and various chemical reactions which can be imaged concurrently with their activation by the e-beam and can be presented as stop-frame movies. This experimental approach, which we term ChemTEM, harnesses energy transferred from the e-beam to the molecule via direct interactions with the atomic nuclei, enabling accurate predictions of bond dissociation events and control of the type and rate of chemical reactions. Elemental composition and structure of the reactant molecules as well as the operating conditions of TEM (particularly the energy of the e-beam) determine the product formed in ChemTEM processes, while the e-beam dose rate controls the reaction rate. Because the e-beam of TEM acts simultaneously as a source of energy for the reaction and as an imaging tool monitoring the same reaction, ChemTEM reveals atomic-level chemical information, such as pathways of reactions imaged for individual molecules, step-by-step and in real time; structures of illusive reaction intermediates; and direct comparison of catalytic activity of different transition metals filmed with atomic resolution. Chemical transformations in ChemTEM often lead to previously unforeseen products, demonstrating the potential of this method to become not only an analytical tool for studying reactions, but also a powerful instrument for discovery of materials that can be synthesized on preparative scale.
Modeling position-specific isotope fractionation of organic micropollutants degradation via different reaction pathways

DEFF Research Database (Denmark)

Jin, Biao; Rolle, Massimo

: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model successfully reproduces the multi-element isotope data, and precisely captures the dual element isotope trends, characterizing the different degradation pathways. Besides illustrating the model capability of mechanistic evaluation...
Lead (Pb) isotopic fingerprinting and its applications in lead pollution studies in China: A review

International Nuclear Information System (INIS)

Cheng Hefa; Hu Yuanan

2010-01-01

As the most widely scattered toxic metal in the world, the sources of lead (Pb) observed in contamination investigation are often difficult to identify. This review presents an overview of the principles, analysis, and applications of Pb isotopic fingerprinting in tracing the origins and transport pathways of Pb in the environment. It also summarizes the history and current status of lead pollution in China, and illustrates the power of Pb isotopic fingerprinting with examples of its recent applications in investigating the effectiveness of leaded gasoline phase-out on atmospheric lead pollution, and the sources of Pb found in various environmental media (plants, sediments, and aquatic organisms) in China. The limitations of Pb isotopic fingerprinting technique are discussed and a perspective on its development is also presented. Further methodological developments and more widespread instrument availability are expected to make isotopic fingerprinting one of the key tools in lead pollution investigation. - This review presents an overview of the principles, applications, and limitations of Pb isotopic fingerprinting in lead pollution investigation, and provides a perspective on its future development.
Errors in Postural Preparation Lead to Increased Choice Reaction Times for Step Initiation in Older Adults

Science.gov (United States)

Nutt, John G.; Horak, Fay B.

2011-01-01

Background. This study asked whether older adults were more likely than younger adults to err in the initial direction of their anticipatory postural adjustment (APA) prior to a step (indicating a motor program error), whether initial motor program errors accounted for reaction time differences for step initiation, and whether initial motor program errors were linked to inhibitory failure. Methods. In a stepping task with choice reaction time and simple reaction time conditions, we measured forces under the feet to quantify APA onset and step latency and we used body kinematics to quantify forward movement of center of mass and length of first step. Results. Trials with APA errors were almost three times as common for older adults as for younger adults, and they were nine times more likely in choice reaction time trials than in simple reaction time trials. In trials with APA errors, step latency was delayed, correlation between APA onset and step latency was diminished, and forward motion of the center of mass prior to the step was increased. Participants with more APA errors tended to have worse Stroop interference scores, regardless of age. Conclusions. The results support the hypothesis that findings of slow choice reaction time step initiation in older adults are attributable to inclusion of trials with incorrect initial motor preparation and that these errors are caused by deficits in response inhibition. By extension, the results also suggest that mixing of trials with correct and incorrect initial motor preparation might explain apparent choice reaction time slowing with age in upper limb tasks. PMID:21498431

Copper-Catalyzed Oxidative Reaction of β-Keto Sulfones with Alcohols via C-S Bond Cleavage: Reaction Development and Mechanism Study.

Science.gov (United States)

Du, Bingnan; Wang, Wenmin; Wang, Yang; Qi, Zhenghang; Tian, Jiaqi; Zhou, Jie; Wang, Xiaochen; Han, Jianlin; Ma, Jing; Pan, Yi

2018-02-16

A Cu-catalyzed cascade oxidative radical process of β-keto sulfones with alcohols has been achieved by using oxygen as an oxidant. In this reaction, β-keto sulfones were converted into sulfinate esters under the oxidative conditions via cleavage of C-S bond. Experimental and computational studies demonstrate that a new pathway is involved in this reaction, which proceeds through the formation of the key four-coordinated Cu II intermediate, O-O bond homolysis induced C-S bond cleavage and Cu-catalyzed esterification to form the final products. This reaction provides a new strategy to sulfonate esters and enriches the research content of C-S bond cleavage and transformations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Lead induced dyslipidemia: The comparative effects of ascorbate ...

African Journals Online (AJOL)

R.N. UGBAJA

2013-04-10

Apr 10, 2013 ... Key words: Ascorbate, chelating agents, dyslipidemia, lead exposure, plumbism. .... elements like iron, zinc, calcium and a host of other divalent elements in ..... cholesterol synthesis and transport pathways may be adversely ...
Quantum Chemical Investigation on Photochemical Reactions of Nonanoic Acids at Air-Water Interface.

Science.gov (United States)

Xiao, Pin; Wang, Qian; Fang, Wei-Hai; Cui, Ganglong

2017-06-08

Photoinduced chemical reactions of organic compounds at the marine boundary layer have recently attracted significant experimental attention because this kind of photoreactions has been proposed to have substantial impact on local new particle formation and their photoproducts could be a source of secondary organic aerosols. In this work, we have employed first-principles density functional theory method combined with cluster models to systematically explore photochemical reaction pathways of nonanoic acids (NAs) to form volatile saturated and unsaturated C 9 and C 8 aldehydes at air-water interfaces. On the basis of the results, we have found that the formation of C 9 aldehydes is not initiated by intermolecular Norrish type II reaction between two NAs but by intramolecular T 1 C-O bond fission of NA generating acyl and hydroxyl radicals. Subsequently, saturated C 9 aldehydes are formed through hydrogenation reaction of acyl radical by another intact NA. Following two dehydrogenation reactions, unsaturated C 9 aldehydes are generated. In parallel, the pathway to C 8 aldehydes is initiated by T 1 C-C bond fission of NA, which generates octyl and carboxyl radicals; then, an octanol is formed through recombination reaction of octyl with hydroxyl radical. In the following, two dehydrogenation reactions result into an enol intermediate from which saturated C 8 aldehydes are produced via NA-assisted intermolecular hydrogen transfer. Finally, two dehydrogenation reactions generate unsaturated C 8 aldehydes. In these reactions, water and NA molecules are found to play important roles. They significantly reduce relevant reaction barriers. Our work has also explored oxygenation reactions of NA with molecular oxygen and radical-radical dimerization reactions.
The Atmospherically Important Reaction of Hydroxyl Radicals with Methyl Nitrate: A Theoretical Study Involving the Calculation of Reaction Mechanisms, Enthalpies, Activation Energies, and Rate Coefficients.

Science.gov (United States)

Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

2017-09-07

A theoretical study, involving the calculation of reaction enthalpies, activation energies, mechanisms, and rate coefficients, was made of the reaction of hydroxyl radicals with methyl nitrate, an important process for methyl nitrate removal in the earth's atmosphere. Four reaction channels were considered: formation of H 2 O + CH 2 ONO 2 , CH 3 OOH + NO 2 , CH 3 OH + NO 3 , and CH 3 O + HNO 3 . For all channels, geometry optimization and frequency calculations were performed at the M06-2X/6-31+G** level, while relative energies were improved at the UCCSD(T*)-F12/CBS level. The major channel is found to be the H abstraction channel, to give the products H 2 O + CH 2 ONO 2 . The reaction enthalpy (ΔH 298 K RX ) of this channel is computed as -17.90 kcal mol -1 . Although the other reaction channels are also exothermic, their reaction barriers are high (>24 kcal mol -1 ), and therefore these reactions do not contribute to the overall rate coefficient in the temperature range considered (200-400 K). Pathways via three transition states were identified for the H abstraction channel. Rate coefficients were calculated for these pathways at various levels of variational transition state theory including tunneling. The results obtained are used to distinguish between two sets of experimental rate coefficients, measured in the temperature range of 200-400 K, one of which is approximately an order of magnitude greater than the other. This comparison, as well as the temperature dependence of the computed rate coefficients, shows that the lower experimental values are favored. The implications of the results to atmospheric chemistry are discussed.
The reaction of Lupinus angustifolius L. root meristematic cell nucleoli to lead.

Science.gov (United States)

Balcerzak, Lucja; Glińska, Sława; Godlewski, Mirosław

2011-04-01

The effect of 2-48 h treatment of Lupinus angustifolius L. roots with lead nitrate at the concentration of 10(-4) M on the nucleoli in meristematic cells was investigated. In the lead presence the number of ring-shaped as well as segregated nucleoli increased especially after 12-48 h of treatment, while spindle-shaped nucleoli appeared after 24 h and 48 h. Lead presence also increased the frequency of cells with silver-stained particles in the nucleus and the number of these particles especially from the 12th hour of treatment. It was accompanied by significant decline of nucleolar area. Analysis of these cells in transmission electron microscope confirmed the presence of ring-shaped and segregated nucleoli. Moreover, electron microscopy revealed compact structure nucleoli without granular component. Additionally, one to three oval-shaped fibrillar structures attached to nucleolus or lying free in the nucleoplasm were visible. The possible mechanism of lead toxicity to the nucleolus is briefly discussed.
On the mechanism of photocatalytic reactions with eosin Y

Directory of Open Access Journals (Sweden)

Michal Majek

2014-04-01

Full Text Available A combined spectroscopic, synthetic, and apparative study has allowed a more detailed mechanistic rationalization of several recently reported eosin Y-catalyzed aromatic substitutions at arenediazonium salts. The operation of rapid acid–base equilibria, direct photolysis pathways, and radical chain reactions has been discussed on the basis of pH, solvent polarity, lamp type, absorption properties, and quantum yields. Determination of the latter proved to be an especially valuable tool for the distinction between radical chain and photocatalytic reactions.
Dehydrogenation of aromatic molecules under a scanning tunneling microscope: pathways and inelastic spectroscopy simulations.

Science.gov (United States)

Lesnard, Hervé; Bocquet, Marie-Laure; Lorente, Nicolas

2007-04-11

We have performed a theoretical study on the dehydrogenation of benzene and pyridine molecules on Cu(100) induced by a scanning tunneling microscope (STM). Density functional theory calculations have been used to characterize benzene, pyridine, and different dehydrogenation products. The adiabatic pathways for single and double dehydrogenation have been evaluated with the nudge elastic band method. After identification of the transition states, the analysis of the electronic structure along the reaction pathway yields interesting information on the electronic process that leads to H-scission. The adiabatic barriers show that the formation of double dehydrogenated fragments is difficult and probably beyond reach under the actual experimental conditions. However, nonadiabatic processes cannot be ruled out. Hence, in order to identify the final dehydrogenation products, the inelastic spectra are simulated and compared with the experimental ones. We can then assign phenyl (C6H5) and alpha-pyridil (alpha-C5H4N) as the STM-induced dehydrogenation products of benzene and pyridine, respectively. Our simulations permit us to understand why phenyl, pyridine, and alpha-pyridil present tunneling-active C-H stretch modes in opposition to benzene.
High Chloride Doping Levels Stabilize the Perovskite Phase of Cesium Lead Iodide.

Science.gov (United States)

Dastidar, Subham; Egger, David A; Tan, Liang Z; Cromer, Samuel B; Dillon, Andrew D; Liu, Shi; Kronik, Leeor; Rappe, Andrew M; Fafarman, Aaron T

2016-06-08

Cesium lead iodide possesses an excellent combination of band gap and absorption coefficient for photovoltaic applications in its perovskite phase. However, this is not its equilibrium structure under ambient conditions. In air, at ambient temperature it rapidly transforms to a nonfunctional, so-called yellow phase. Here we show that chloride doping, particularly at levels near the solubility limit for chloride in a cesium lead iodide host, provides a new approach to stabilizing the functional perovskite phase. In order to achieve high doping levels, we first co-deposit colloidal nanocrystals of pure cesium lead chloride and cesium lead iodide, thereby ensuring nanometer-scale mixing even at compositions that potentially exceed the bulk miscibility of the two phases. The resulting nanocrystal solid is subsequently fused into a polycrystalline thin film by chemically induced, room-temperature sintering. Spectroscopy and X-ray diffraction indicate that the chloride is further dispersed during sintering and a polycrystalline mixed phase is formed. Using density functional theory (DFT) methods in conjunction with nudged elastic band techniques, low-energy pathways for interstitial chlorine diffusion into a majority-iodide lattice were identified, consistent with the facile diffusion and fast halide exchange reactions observed. By comparison to DFT-calculated values (with the PBE exchange-correlation functional), the relative change in band gap and the lattice contraction are shown to be consistent with a Cl/I ratio of a few percent in the mixed phase. At these incorporation levels, the half-life of the functional perovskite phase in a humid atmosphere increases by more than an order of magnitude.
Formal modeling of a system of chemical reactions under uncertainty.

Science.gov (United States)

Ghosh, Krishnendu; Schlipf, John

2014-10-01

We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.
Increased bone calcium dissociation in lead-exposed rats

Directory of Open Access Journals (Sweden)

Eko Suhartono

2012-12-01

Full Text Available Background Lead is still a major environmental and occupational health hazard, since it is extensively used in the production of paints, gasoline and cosmetics. This causes the metal to be ubiquitous in the environment, being found in the air, soil, and water, from which it can enter the human body by inhalation or ingestion. Absorbed lead is capable of altering the calcium levels in bone. The aim of this study was to demonstrate the effect of lead on bone calcium levels by measuring the reaction constant, Gibbs free energy, and enthalpy. Methods This study was of pure experimental design using 100 male albino rats (Rattus norvegicus. The experimental animals were assigned by simple randomization to two groups, one group receiving lead acetate orally at a dosage of 100 mg/kgBW, while the other group did not receive lead acetate. The intervention was given for 4 weeks and the rats were observed weekly for measurement of bone calcium levels by the permanganometric method. Results This study found that k1 (hydroxyapatite dissociation rate constant was 0.90 x 10-3 dt-1, and that k2 (hydroxyapatite association rate constant was 6.16 x 10-3 dt-1 for the control group, whereas for the intervention group k1 = 26.20 x 10-3 dt-1 and k2 = 16.75 x 10-3 dt-1. Thermodynamically, the overall reaction was endergonic and endothermic (DG > 0 and DH > 0. ConclusionS Lead exposure results in increased dissociation rate of bone in comparison with its association rate. Overall, the reaction was endergonic and endothermic (DG > 0 and DH > 0.
Increased bone calcium dissociation in lead-exposed rats

Directory of Open Access Journals (Sweden)

Eko Suhartono

2015-12-01

Full Text Available BACKGROUND Lead is still a major environmental and occupational health hazard, since it is extensively used in the production of paints, gasoline and cosmetics. This causes the metal to be ubiquitous in the environment, being found in the air, soil, and water, from which it can enter the human body by inhalation or ingestion. Absorbed lead is capable of altering the calcium levels in bone. The aim of this study was to demonstrate the effect of lead on bone calcium levels by measuring the reaction constant, Gibbs free energy, and enthalpy. METHODS This study was of pure experimental design using 100 male albino rats (Rattus norvegicus. The experimental animals were assigned by simple randomization to two groups, one group receiving lead acetate orally at a dosage of 100 mg/ kgBW, while the other group did not receive lead acetate. The intervention was given for 4 weeks and the rats were observed weekly for measurement of bone calcium levels by the permanganometric method. RESULTS This study found that k1 (hydroxyapatite dissociation rate constant was 0.90 x 10-3 dt-1, and that k2 (hydroxyapatite association rate constant was 6.16 x 10-3 dt-1 for the control group, whereas for the intervention group k1 = 26.20 x 10-3 dt-1 and k2 = 16.75 x 10-3 dt-1. Thermodynamically, the overall reaction was endergonic and endothermic (ΔG > 0 and ΔH > 0. CONCLUSIONS Lead exposure results in increased dissociation rate of bone in comparison with its association rate. Overall, the reaction was endergonic and endothermic (ΔG > 0 and ΔH > 0.
Neutron Production in Spallation Reactions of 0.9 and 1.5 GeV Protons on a Thick Lead Target. Comparison between Experimental Data and Monte-Carlo Simulations

CERN Document Server

Krasa, A; Bradnova, V; Caloun, P; Chultem, D; Henzl, V; Henzlová, D; Kalinnikov, V G; Krivopustov, M I; Krízek, F; Kugler, A; Majerle, M; Solnyshkin, A A; Stegailov, V I; Tsoupko-Sitnikov, V M; Tumendelger, T; Vasilev, S I; Wagner, V; Nuclear Physics Institute of Academy of Sciences of Czech Republic, Rez, Czech Republic

2005-01-01

This paper reports on two experiments performed at the Synchrophasotron/Nuclotron accelerator complex at JINR. Relativistic protons with energies 885 MeV and 1.5 GeV hit a massive cylindrical lead target. The spatial and energetic distributions of the neutron field produced by the spallation reactions were measured by the activation of Al, Au, Bi, Co, and Cu foils placed on the surface of the target and close to it. The yields of the radioactive nuclei produced by threshold reactions in these foils were determined by the analyses of their $\\gamma$ spectra. The comparison with Monte-Carlo based simulations was performed both with the LAHET+MCNP code and the MCNPX code.
Neutron production in spallation reactions of 0.9 and 1.5 GeV protons on a thick lead target. Comparison between experimental data and Monte-Carlo simulations

International Nuclear Information System (INIS)

Krasa, A.; Krizek, F.; Wagner, V.; Kugler, A.; Henzl, V.; Henzlova, D.; Majerle, M.; Adam, J.; Caloun, P.; Bradnova, V.; Chultem, D.; Kalinnikov, V.G.; Krivopustov, M.I.; Solnyshkin, A.A.; Stegajlov, V.I.; Tsupko-Sitnikov, V.M.; Tumehndehlgehr, Ts.; Vasil'ev, S.I.

2005-01-01

This paper reports on two experiments performed at the Synchrophasotron/Nuclotron accelerator complex at JINR. Relativistic protons with energies 885 MeV and 1.5 GeV hit a massive cylindrical lead target. The spatial and energetic distributions of the neutron field produced by the spallation reactions were measured by the activation of Al, Au, Bi, Co, and Cu foils placed on the surface of the target and close to it. The yields of the radioactive nuclei produced by threshold reactions in these foils were determined by the analyses of their γ spectra. The comparison with Monte-Carlo based simulations was performed both with the LAHET+MCNP code and the MCNPX code
Environmental pathways of radioactivity to man

International Nuclear Information System (INIS)

Johns, T.F.

1983-01-01

An attempt has been made to discuss environmental pathways and their significance in a way which will be understood by non-specialists. The role of these pathways in the general structure of radiological protection is explained and the more important pathways to man from releases into the air and the aquatic environment are discussed generally. The various mechanisms which lead to the dispersion or reconstruction of radioactive materials are discussed and their importance stressed. The more important pathways for particular groups of radionuclides from the nuclear power industry are dealt with in detail and information resulting from many theoretical and practical studies of the situations at particular locations summarized. There is detailed discussion about the doses to local population groups and about worldwide doses as a result of the release of certain long-lived radioactive species. The corresponding pathways and resulting doses from natural radiation are detailed to illustrate that the doses from the nuclear power industry are small in comparison, and brief consideration is given to animal and plant doses from the industry. (U.K.)
[Various pathways leading to the progression of chronic liver diseases].

Science.gov (United States)

Egresi, Anna; Lengyel, Gabriella; Somogyi, Anikó; Blázovics, Anna; Hagymási, Krisztina

2016-02-21

As the result of various effects (viruses, metabolic diseases, nutritional factors, toxic agents, autoimmune processes) abnormal liver function, liver steatosis and connective tissue remodeling may develop. Progression of this process is complex including various pathways and a number of factors. The authors summarize the factors involved in the progression of chronic liver disease. They describe the role of cells and the produced inflammatory mediators and cytokines, as well as the relationship between the disease and the intestinal flora. They emphasize the role of oxidative stress, mitochondrial dysfunction and cell death in disease progression. Insulin resistance and micro-elements (iron, copper) in relation to liver damage are also discussed, and genetic and epigenetic aspects underlying disease progression are summarized. Discovery of novel treatment options, assessment of the effectiveness of treatment, as well as the success and proper timing of liver transplantation may depend on a better understanding of the process of disease progression.
The TyrA family of aromatic-pathway dehydrogenases in phylogenetic context

Directory of Open Access Journals (Sweden)

Wolinsky Murray

2005-05-01

Full Text Available Abstract Background The TyrA protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to L-tyrosine and a third reaction that is not part of tyrosine biosynthesis. Family members share a catalytic core region of about 30 kDa, where inhibitors operate competitively by acting as substrate mimics. This protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size. Results Phylogenetic relationships of TyrA domains were evaluated in the context of combinatorial patterns of specificity for the two substrates, as well as the presence or absence of a variety of fusions. An interactive tool is provided for prediction of substrate specificity. Interactive alignments for a suite of catalytic-core TyrA domains of differing specificity are also provided to facilitate phylogenetic analysis. tyrA membership in apparent operons (or supraoperons was examined, and patterns of conserved synteny in relationship to organismal positions on the 16S rRNA tree were ascertained for members of the domain Bacteria. A number of aromatic-pathway genes (hisHb, aroF, aroQ have fused with tyrA, and it must be more than coincidental that the free-standing counterparts of all of the latter fused genes exhibit a distinct trace of syntenic association. Conclusion We propose that the ancestral TyrA dehydrogenase had broad specificity for both the cyclohexadienyl and pyridine nucleotide substrates. Indeed, TyrA proteins of this type persist today, but it is also common to find instances of narrowed substrate specificities, as well as of acquisition via gene fusion of additional catalytic domains or regulatory domains. In some clades a qualitative change associated with either narrowed substrate specificity or gene fusion has produced an evolutionary "jump" in the vertical genealogy of TyrA homologs. The evolutionary history of gene organizations that include
A barrier-free atomic radical-molecule reaction: N (2D) NO2 (2A1) mechanistic study

Science.gov (United States)

Zuo, Ming-Hui; Liu, Hui-Ling; Huang, Xu-Ri; Zhan, Jin-Hui; Sun, Chia-Chung

The reaction of N (2D) radical with NO2 molecule has been studied theoretically using density functional theory and ab initio quantum chemistry method. Singlet electronic state [N2O2] potential energy surfaces (PES) are calculated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311+G(d) + ZPE and G3B3 levels of theory. All the involved transition states for generation of (2NO) and (O2 + N2) lie much lower than the reactants. Thus, the novel reaction N + NO2 can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction.
Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.

Science.gov (United States)

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D

2008-11-25

o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered bi uni uni bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first half-reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the "F" form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered bi uni uni bi iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogues with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogues tested as none were active except 4-[2-(trifluoromethyl)phenyl]-4-oxobutyric acid which exhibited a 100-fold decrease in k(cat)/K(m). On the basis of an understanding of OSB-CoA synthetase's kinetic mechanism and substrate specificity, a reaction intermediate analogue of OSB-AMP, 5'-O-{N-[2-(trifluoromethyl)phenyl]-4-oxobutyl}adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase
Randomness in multi-step direct reactions

International Nuclear Information System (INIS)

Koning, A.J.; Akkermans, J.M.

1991-01-01

The authors propose a quantum-statistical framework that provides an integrated perspective on the differences and similarities between the many current models for multi-step direct reactions in the continuum. It is argued that to obtain a statistical theory two physically different approaches are conceivable to postulate randomness, respectively called leading-particle statistics and residual-system statistics. They present a new leading-particle statistics theory for multi-step direct reactions. It is shown that the model of Feshbach et al. can be derived as a simplification of this theory and thus can be founded solely upon leading-particle statistics. The models developed by Tamura et al. and Nishioka et al. are based upon residual-system statistics and hence fall into a physically different class of multi-step direct theories, although the resulting cross-section formulae for the important first step are shown to be the same. The widely used semi-classical models such as the generalized exciton model can be interpreted as further phenomenological simplification of the leading-particle statistics theory
Adverse reactions associated with acetylcysteine.

Science.gov (United States)

Sandilands, E A; Bateman, D N

2009-02-01

Paracetamol (acetaminophen) is one of the most common agents deliberately ingested in self-poisoning episodes and a leading cause of acute liver failure in the western world. Acetylcysteine is widely acknowledged as the antidote of choice for paracetamol poisoning, but its use is not without risk. Adverse reactions, often leading to treatment delay, are frequently associated with both intravenous and oral acetylcysteine and are a common source of concern among treating physicians. A systematic literature review investigating the incidence, clinical features, and mechanisms of adverse effects associated with acetylcysteine. A variety of adverse reactions to acetylcysteine have been described ranging from nausea to death, most of the latter due to incorrect dosing. The pattern of reactions differs with oral and intravenous dosing, but reported frequency is at least as high with oral as intravenous. The reactions to the intravenous preparation result in similar clinical features to true anaphylaxis, including rash, pruritus, angioedema, bronchospasm, and rarely hypotension, but are caused by nonimmunological mechanisms. The precise nature of this reaction remains unclear. Histamine now seems to be an important mediator of the response, and there is evidence of variability in patient susceptibility, with females, and those with a history of asthma or atopy are particularly susceptible. Quantity of paracetamol ingestion, measured through serum paracetamol concentration, is also important as higher paracetamol concentrations protect patients against anaphylactoid effects. Most anaphylactoid reactions occur at the start of acetylcysteine treatment when concentrations are highest. Acetylcysteine also affects clotting factor activity, and this affects the interpretation of minor disturbances in the International Normalized Ratio in the context of paracetamol overdose. This review discusses the incidence, clinical features, underlying pathophysiological mechanisms, and

Reaction pathway towards formation of cobalt single chain magnets and nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Balaji, G.; Desilva, Rohini M.; Palshin, V. [Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806 (United States); Desilva, N. [Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 (United States); Palmer, G. [Department of Biochemistry and Cell Biology, Rice University, MS 140, 6100 Main street, Houston, TX 77251 (United States); Kumar, Challa S.S.R., E-mail: ckumar1@lsu.ed [Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806 (United States)

2010-03-15

With the advent of molecular magnets the quest for suitable high density magnetic storage materials has fuelled further research in this area. Here in this report, we present a detailed mechanistic investigation of thermal decomposition of cyclopentadienyl cobalt [CoCp(CO){sub 2}] precursor where Cp is the cyclopentadienyl moiety. The reaction revealed the formation of cobalt nanoparticles (Co-NPs) through an isolable reaction intermediate characterized as a Single Chain Magnet (SCM), [Co(Cp){sub 2}]{sub 2}CoCl{sub 4} (1). The SQUID magnetic measurements showed the presence of very strong antiferromagnetic interactions between Co{sup 2+} ions. The zero-field cooled (ZFC) and field cooled (FC) magnetization curves branch out below 5 K and there is evidence for frequency dependent complex susceptibility along with a maximum observed around 2.5 K. The optical studies indicated that the Co{sup 2+} d-d transition is influenced by the polarity of the solvents. The cobalt nanoparticles (Co-NPs) were obtained, either directly from 1 or from its precursor. They are spherical in shape with a mean size 15 nm, have fcc crystal structure and were found to be ferromagnetic at room temperature.
Medium effects in direct reactions

International Nuclear Information System (INIS)

Karakoc, M; Bertulani, C

2013-01-01

We discuss medium corrections of the nucleon-nucleon (NN) cross sections and their influence on direct reactions at intermediate energies ≳50 MeV/nucleon. The results obtained with free NN cross sections are compared with those obtained with a geometrical treatment of Pauli-blocking and Dirac-Bruecker methods. We show that medium corrections may lead to sizable modifications for collisions at intermediate energies and that they are more pronounced in reactions involving weakly bound nuclei.
Transesterification of Jatropha curcas oil glycerides: Theoretical and experimental studies of biodiesel reaction

Energy Technology Data Exchange (ETDEWEB)

Neyda C. Om Tapanes; Donato A. Gomes Aranda; Jose W. de Mesquita Carneiro; Octavio A. Ceva Antunes [Universidade Federal do Rio de Janeiro, Rio de Janeiro (Brazil). Laboratorio GREENTEC

2008-08-15

Vegetal oil, also known as triglycerides, is a mixture of fatty acid triesters of glycerol. In the triglycerides alkyl chains of Jatropha curcas oil, predominate the palmitic, oleic and linoleic fatty acids. The process usually used to convert these triglycerides to biodiesel is called transesterification. The overall process is a sequence of three equivalent, consecutive and reversible reactions, in which di- and monoglycerides are formed as intermediates. Semi-empirical AM1 molecular orbital calculations were used to investigate the reaction pathways of base-catalyzed transesterification of glycerides of palmitic, oleic and linoleic acid. The most probable pathway and the rate determining-step of the reactions were estimated from the molecular orbital calculations. Our results suggest the formation of only one tetrahedral intermediate, which in a subsequent step rearranges to form the products. The rate determining-step is the break of this tetrahedral intermediate. 27 refs., 6 figs., 4 tabs.
Protein degradation pathways in Parkinson's disease: curse or blessing.

Science.gov (United States)

Ebrahimi-Fakhari, Darius; Wahlster, Lara; McLean, Pamela J

2012-08-01

Protein misfolding, aggregation and deposition are common disease mechanisms in many neurodegenerative diseases including Parkinson's disease (PD). Accumulation of damaged or abnormally modified proteins may lead to perturbed cellular function and eventually to cell death. Thus, neurons rely on elaborated pathways of protein quality control and removal to maintain intracellular protein homeostasis. Molecular chaperones, the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway (ALP) are critical pathways that mediate the refolding or removal of abnormal proteins. The successive failure of these protein degradation pathways, as a cause or consequence of early pathological alterations in vulnerable neurons at risk, may present a key step in the pathological cascade that leads to spreading neurodegeneration. A growing number of studies in disease models and patients have implicated dysfunction of the UPS and ALP in the pathogenesis of Parkinson's disease and related disorders. Deciphering the exact mechanism by which the different proteolytic systems contribute to the elimination of pathogenic proteins, like α-synuclein, is therefore of paramount importance. We herein review the role of protein degradation pathways in Parkinson's disease and elaborate on the different contributions of the UPS and the ALP to the clearance of altered proteins. We examine the interplay between different degradation pathways and provide a model for the role of the UPS and ALP in the evolution and progression of α-synuclein pathology. With regards to exciting recent studies we also discuss the putative potential of using protein degradation pathways as novel therapeutic targets in Parkinson's disease.
Phosphite radicals and their reactions. Examples of redox, substitution, and addition reactions

International Nuclear Information System (INIS)

Schaefer, K.; Asmus, K.D.

1980-01-01

Phosphite radicals HPO 3 - and PO 3 2 -, which exist in an acid-base equilibrium with pK = 5.75, are shown to take part in various types of reactions. In the absence of scavengers, they disappear mainly by second-order disproportionation and combination; a first-order contribution to the decay is also indicated. HPO 3 - and PO 3 2 - are good reductants toward electron acceptors such as tetranitromethane. In this reaction phosphate and C(NO 2 ) 3 - are formed. Phosphite radicals can, however, also act as good oxidants, e.g., toward thiols and thiolate ions. These reactions lead to the formation of RS. radicals which were identified either directly, as in the case of penicillamine, through the optical absorption of PenS. or more indirectly through equilibration of RS. with RS- to the optically absorbing RSSR-. disulfide radical anion. A homolytic substitution reaction (S/sub H/2) occurs in the reaction of the phosphite radicals with aliphatic disulfides, yielding RS. radicals and phosphate thioester RSPO 3 2 -. Lipoic acid, as an example of a cyclic disulfide, is reduced to the corresponding RSSR-. radical anion and also undergoes the S/sub H/2 reaction with about equal probability. An addition reaction is observed between phosphite radicals and molecular oxygen. The resulting peroxo phosphate radicals establish an acid-base equilibrium HPO 5 - . reversible PO 5 2- . + H+ with a pK = 3.4. Absolute rate constants were determined for all reactions discussed
Pathway analysis: State of the art

Directory of Open Access Journals (Sweden)

Miguel Angel eGarcía-Campos

2015-12-01

Full Text Available Pathway analysis is a set of widely used tools for research in life sciences intended to give meaning to high-throughput biological data. The methodology of these tools settles in the gathering and usage of knowledge that comprise biomolecular functioning, coupled with statistical testing and other algorithms. Despite their wide employment, pathway analysis foundations and overall background may not be fully understood, leading to misinterpretation of analysis results. This review attempts to comprise the fundamental knowledge to take into consideration when using pathway analysis as a hypothesis generation tool. We discuss the key elements that are part of these methodologies, their capabilities and current deficiencies. We also present an overview of current and all-time popular methods, highlighting different classes across them. In doing so, we show the exploding diversity of methods that pathway analysis encompasses, point out commonly overlooked caveats, and direct attention to a potential new class of methods that attempt to zoom the analysis scope to the sample scale.
Isotopic ratio based source apportionment of children's blood lead around coking plant area.

Science.gov (United States)

Cao, Suzhen; Duan, Xiaoli; Zhao, Xiuge; Wang, Beibei; Ma, Jin; Fan, Delong; Sun, Chengye; He, Bin; Wei, Fusheng; Jiang, Guibin

2014-12-01

Lead exposure in the environment is a major hazard affecting human health, particularly for children. The blood lead levels in the local children living around the largest coking area in China were measured, and the source of blood lead and the main pathways of lead exposure were investigated based on lead isotopic ratios ((207)Pb/(206)Pb and (208)Pb/(206)Pb) in blood and in a variety of media, including food, airborne particulate matter, soil, dust and drinking water. The children's blood lead level was 5.25 (1.59 to 34.36 as range) μg dL(-1), lower than the threshold in the current criteria of China defined by the US Centers for Disease Control (10 μg dL(-1)). The isotopic ratios in the blood were 2.111±0.018 for (208)Pb/(206)Pb and 0.864±0.005 for (207)Pb/(206)Pb, similar to those of vegetables, wheat, drinking water, airborne particulate matter, but different from those of vehicle emission and soil/dust, suggesting that the formers were the main pathway of lead exposure among the children. The exposure pathway analysis based on the isotopic ratios and the human health risk assessment showed that dietary intake of food and drinking water contributed 93.67% of total exposed lead. The study further indicated that the coal used in the coking plant is the dominant pollution source of lead in children's blood. Copyright © 2014 Elsevier Ltd. All rights reserved.
Iodinated Contrast Media and the Alleged "Iodine Allergy": An Inexact Diagnosis Leading to Inferior Radiologic Management and Adverse Drug Reactions.

Science.gov (United States)

Böhm, Ingrid; Nairz, Knud; Morelli, John N; Keller, Patricia Silva Hasembank; Heverhagen, Johannes T

2017-04-01

Purpose To test the hypothesis that the incomplete diagnosis "iodine allergy" is a possibly dangerous concept for patients under routine radiologic conditions. Materials and Methods 300 patients with a history of an "iodine allergy" were retrospectively screened and compared with two age-, sex-, and procedure-matched groups of patients either diagnosed with a nonspecific "iodine contrast medium (ICM) allergy" or an allergy to a specific ICM agent. For all groups, the clinical symptoms of the most recent past adverse drug reaction (ADR), prophylactic actions taken for subsequent imaging, and ultimate outcome were recorded and analyzed. Results The diagnosis "iodine allergy" was not otherwise specified in 84.3 % patients. For this group, in most cases, the symptoms of the previous ADRs were not documented. In contrast, the type of ADR was undocumented in only a minority of patients in the comparison groups. In the group of patients with an "iodine allergy" the percentage of unenhanced CT scans was greater than within the other two groups (36.7 % vs. 28.7 %/18.6 %). ADRs following prophylactic measures were only observed in the "iodine allergy" group (OR of 9.24 95 % CI 1.16 - 73.45; p contrast media containing covalently bound iodine.. · There is a clear correlation between the exactness of the diagnosis - from the alleged "iodine allergy" to "contrast media allergy" to naming the exact culprit CM - and the quality of documentation of the symptoms.. · Management of patients diagnosed with "iodine allergy" was associated with uncertainty leading to unenhanced scans and sometimes unnecessary prophylactic actions.. · The term "iodine allergy" should be omitted, because it is potentially dangerous and can decrease the quality of radiology exams.. Citation Format · Böhm Ingrid, Nairz Knud, Morelli John N et al. Iodinated Contrast Media and the Alleged "Iodine Allergy": An Inexact Diagnosis Leading to Inferior Radiologic Management and
Activation barriers for series of exothermic homologous reactions. VI. Reactions of lanthanide and transition metal atoms.

Science.gov (United States)

Blue, Alan S.; Fontijn, Arthur

2001-09-01

Semiempirical configuration interaction (SECI) theory to predict activation barriers, E, as given by k(T)=ATn exp(-E(RT), has been applied to homologous series of lanthanide (LN) and transition metal (TM) atom oxidation reactions. This was achieved by considering as homologous series reactions of elements differing only by the number of electrons in one subshell. Comparison between SECI and experimental results leads to an average deviation for the LN+N2O reactions of 0.66 kJ mol-1, and up to 5.5 kJ mol-1 for other series. Thirty-one activation barriers are reported.
Insights into the Diels-Alder Reaction between 3-Vinylindoles and Methyleneindolinone without and with the Assistance of Hydrogen-Bonding Catalyst Bisthiourea: Mechanism, Origin of Stereoselectivity, and Role of Catalyst.

Science.gov (United States)

Yan, Chao-Xian; Yang, Fan; Yang, Xing; Zhou, Da-Gang; Zhou, Pan-Pan

2017-03-17

The Diels-Alder reaction between 3-vinylindoles and methyleneindolinone can proceed both under catalyst-free conditions and with bisthiourea as the catalyst. The reaction with bisthiourea is much faster and results in higher stereoselectivity of the product. The reaction mechanism, origin of stereoselectivity, and role of the catalyst were elaborated based on quantum mechanical calculations and theoretical methods of reactivity indices, NCI, QTAIM, and distortion/interaction models. In the uncatalyzed reaction, the two C-C bonds that are formed undergo conversion from noncovalent to covalent bonding via a concerted asynchronous mechanism. The weak intermolecular interactions formed in the transition state play important roles. The difference between the interaction and distortion energies is responsible for the stereoselectivity. In the catalyzed reaction, bisthiourea induces both the diene and dienophile to approach it via weak intermolecular interactions, which greatly lowers the energy barrier of the reaction and leads to the product with excellent stereoselectivity. The possible pathways of this reaction were explored, which suggested that the formation of the two C-C bonds goes through either a stepwise or concerted asynchronous mechanism. These results detail the reaction mechanism and shed light on both the significant role of the bisthiourea catalyst and the origin of stereoselectivity for this type of Diels-Alder reaction and related ones.
Allergic reactions in anaesthesia

DEFF Research Database (Denmark)

Krøigaard, M; Garvey, L H; Menné, T

2005-01-01

a significant number of patients at unnecessary risk. Some patients may be labelled with a wrong allergy, leading to unnecessary warnings against harmless substances, and some patients may be put at risk of subsequent re-exposure to the real allergen. Patients with suspected allergic reactions during...
Cross sections of (p, xn) reactions in the isotopes of lead and bismuth

Energy Technology Data Exchange (ETDEWEB)

Bell, R E [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada); Skarsgard, H M [Atomic Energy Research Establishment, Reactor Research Div., Harwell (United Kingdom)

1956-07-01

Measurements have been made by the activation method of cross sections of (p, xn) reactions in Bi{sup 209}, Pb{sup 206}, Pb{sup 207}, and Pb{sup 208}. The present results cover x = 3 to 7 in Bi{sup 209}, 2 to 6 in Pb{sup 206}, 2 to 4 in Pb{sup 207}, and 3 and 4 in Pb{sup 208}, over a total proton energy range from 12 to 85 Mev. The absolute accuracy is about 15%. Each cross section plotted as a function of proton energy rises above its threshold to a peak whose height is of the order of one barn, and then falls again to a low and fairly constant value. The results from x = 3 to 7 are consistent with a compound nucleus plus prompt nucleon-nucleon cascade model using reasonable nuclear parameters, but the experimental (p, 2n) cross section appears to be almost double the value so predicted. Since (p, xn) reactions are dominant in the energy range 10 to 40 Mev., their sum approximates the total reaction cross section; the experimental sum fluctuates around the smooth curve computed for the compound nucleus model with r{sub 0} = 1.3 X 10{sup -13} cm. The fluctuations are similar to, but more marked than, those in the total neutron cross section of heavy elements in the same energy range. A more detailed theoretical discussion of these results is given by Jackson in the paper immediately following. (author)
Reaction of tellurium with Zircaloy-4

International Nuclear Information System (INIS)

Boer, R. de; Cordfunke, E.H.P.

1994-09-01

Interaction of tellurium vapour with Zircaloy during the initial stage of an accident will lead to retention of tellurium in the core. For reliable estimation of the release behaviour of tellurium, it is necessary to know which zirconium tellurides are formed during this interaction. In this work the reaction of tellurium with Zircaloy-4 has been studied, using various reaction temperatures and tellurium vapour pressures. The compound ZrTe 2-x is formed on the surface of the Zircaloy in a broad range of reaction temperatures and vapour pressures. It is found that the formation of the more zirconium-rich compound Zr 5 Te 4 is favoured at high reaction temperatures is combination with low tellurium vapour pressures. (orig.)
Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

Science.gov (United States)

Asgharzadeh, Somaie; Vahedpour, Morteza

2018-06-01

Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.
Reaction of phosphorus ylides with carbonyl compounds in supercritical carbon dioxide

International Nuclear Information System (INIS)

Jeong, Kyung Il; Kim, Hak Do; Shim, Jae Jin; Ra, Choon Sup

2004-01-01

The condensation reaction of (benzylene)triphenylphosphoranes with carbonyl compounds in supercritical carbon dioxide was examined. Reactions of (benzylene)phosphoranes (ca. 1 mmol) with several benzaldehydes in a supercritical carbon dioxide (80 .deg. C, 2,000 psi) containing THF entrainer (5%) in a 24 mL reactor proceed smoothly to yield olefination products in fairly good to excellent yields but slower, compared to reactions in a conventional THF solvent. Generally, phosphoranes that are not substituted with a nitro group show more (Z)-selective reactions with aromatic aldehydes under scCO 2 condition than in THF. The reaction of (benzylene)triphenylphosphosphoranes with 4-t-butylcyclohexanone gave the corresponding olefin compounds with a low conversion under both the supercritical carbon dioxide and the organic THF solvent. Our preliminary study showed the Wittig reaction carries out smoothly in supercritical carbon dioxide medium and also a possible tunability of this reaction pathway by adding a entrainer. The results would be useful for devising a novel process for the environmentally friendly Wittig reaction
Eryptosis in lead-exposed workers.

Science.gov (United States)

Aguilar-Dorado, Itzel-Citlalli; Hernández, Gerardo; Quintanar-Escorza, Martha-Angelica; Maldonado-Vega, María; Rosas-Flores, Margarita; Calderón-Salinas, José-Víctor

2014-12-01

Eryptosis is a physiological phenomenon in which old and damaged erythrocytes are removed from circulation. Erythrocytes incubated with lead have exhibited major eryptosis. In the present work we found evidence of high levels of eryptosis in lead exposed workers possibly via oxidation. Blood samples were taken from 40 male workers exposed to lead (mean blood lead concentration 64.8μg/dl) and non-exposed workers (4.2μg/dl). The exposure to lead produced an intoxication characterized by 88.3% less δ-aminolevulinic acid dehydratase (δALAD) activity in lead exposed workers with respect to non-lead exposed workers. An increment of oxidation in lead exposed workers was characterized by 2.4 times higher thiobarbituric acid-reactive substance (TBARS) concentration and 32.8% lower reduced/oxidized glutathione (GSH/GSSG) ratio. Oxidative stress in erythrocytes of lead exposed workers is expressed in 192% higher free calcium concentration [Ca(2+)]i and 1.6 times higher μ-calpain activity with respect to non-lead exposed workers. The adenosine triphosphate (ATP) concentration was not significantly different between the two worker groups. No externalization of phosphatidylserine (PS) was found in non-lead exposed workers (lead exposed workers showed 2.82% externalization. Lead intoxication induces eryptosis possibly through a molecular pathway that includes oxidation, depletion of reduced glutathione (GSH), increment of [Ca(2+)], μ-calpain activation and externalization of PS in erythrocytes. Identifying molecular signals that induce eryptosis in lead intoxication is necessary to understand its physiopathology and chronic complications. Copyright © 2014 Elsevier Inc. All rights reserved.
ASSET RECOVERY OF HAZARDOUS MATERIALS BENEFICIAL REUSE OF RADIOLOGICALLY ENCUMBERED LEAD STOCKS

International Nuclear Information System (INIS)

Lloyd, E.R.; Meehan, R.W.

2003-01-01

Underutilized and surplus lead stocks and leaded components are a common legacy environmental problem across much of the Department of Energy (DOE) Complex. While seeking to dispose of these items through its Environmental Management Program, DOE operational programs continue to pursue contemporary mission requirements such as managing and/or storing radioactive isotopes that require lead materials for shielding. This paradox was identified in late 1999 when DOE's policies for managing scrap metal were assessed. In January 2000, the Secretary of Energy directed the National Center of Excellence for Materials Recycle (NMR) to develop and implement a comprehensive lead reuse program for all of DOE. Fluor Hanford, contractor for DOE Richland Operations, subsequently contacted NMR to pilot lead reclamation and reuse at the Hanford Site. This relationship resulted in the development of a beneficial reuse pathway for lead reclaimed from spent fuel transport railcars being stored at Hanford. The 1.3 million pounds of lead in the railcars is considered radiologically encumbered due to its prior use. Further, the material was considered a mixed Resource Conservation and Recovery Act (RCRA) low-level radioactive waste that would require expensive storage or macro encapsulation to meet land disposal restrictions prior to burial. Working closely with Flour Hanford and the Office of Air, Water, and Radiation (EH-412), NMR developed a directed reuse pathway for this and other radiologically encumbered lead. When derived supplemental release limits were used, the lead recovered from these railcars became eligible for reuse in shielding products to support DOE and commercial nuclear industry operations. Using this disposition pathway has saved Hanford one third of the cost of disposing of the lead and the cost of acquiring additional lead for nuclear shielding applications. Furthermore, the environmental costs associated with mining and producing new lead for shielding products a
A thermodynamic solution model for calcium carbonate: Towards an understanding of multi-equilibria precipitation pathways

OpenAIRE

Donnet, Marcel; Bowen, Paul; Lemaître, Jacques

2009-01-01

Thermodynamic solubility calculations are normally only related to thermodynamic equilibria in solution. In this paper, we extend the use of such solubility calculations to help elucidate possible precipitation reaction pathways during the entire reaction. We also estimate the interfacial energy of particles using only solubility data by a modification of Mersmann’s approach. We have carried this out by considering precipitation reactions as a succession of small quasi-equilibrium states. Thu...
Measuring protection of aromatic wine thiols from oxidation by competitive reactions vs wine preservatives with ortho-quinones.

Science.gov (United States)

Nikolantonaki, Maria; Magiatis, Prokopios; Waterhouse, Andrew L

2014-11-15

Quinones are central intermediates in wine oxidation that can degrade the quality of wine by reactions with varietal thiols, such as 3-sulfanylhexanol, decreasing desirable aroma. Protection by wine preservatives (sulphur dioxide, glutathione, ascorbic acid and model tannin, phloroglucinol) was assessed by competitive sacrificial reactions with 4-methyl-1,2-benzoquinone, quantifying products and ratios by HPLC-UV-MS. Regioselectivity was assessed by product isolation and identification by NMR spectroscopy. Nucleophilic addition reactions compete with two electron reduction of quinones by sulphur dioxide or ascorbic acid, and both routes serve as effective quenching pathways, but minor secondary products from coupled redox reactions between the products and reactants are also observed. The wine preservatives were all highly reactive and thus all very protective against 3-sulfanylhexanol loss to the quinone, but showed only additive antioxidant effects. Confirmation of these reaction rates and pathways in wine is needed to assess the actual protective action of each tested preservative. Copyright © 2014 Elsevier Ltd. All rights reserved.
Three Rate-Constant Kinetic Model for Permanganate Reactions Autocatalyzed by Colloidal Manganese Dioxide: The Oxidation of L-Phenylalanine.

Science.gov (United States)

Perez-Benito, Joaquin F; Ferrando, Jordi

2014-12-26

The reduction of permanganate ion to MnO(2)-Mn(2)O(3) soluble colloidal mixed oxide by l-phenylalanine in aqueous phosphate-buffered neutral solutions has been followed by a spectrophotometric method, monitoring the decay of permanganate ion at 525 nm and the formation of the colloidal oxide at 420 nm. The reaction is autocatalyzed by the manganese product, and three rate constants have been required to fit the experimental absorbance-time kinetic data. The reaction shows base catalysis, and the values of the activation parameters at different pHs have been determined. A mechanism including both the nonautocatalytic and the autocatalytic reaction pathways, and in agreement with the available experimental data, has been proposed. Some key features of this mechanism are the following: (i) of the two predominant forms of the amino acid, the anionic form exhibits a stronger reducing power than the zwitterionic form; (ii) the nonautocatalytic reaction pathway starts with the transfer of the hydrogen atom in the α position of the amino acid to permanganate ion; and (iii) the autocatalytic reaction pathway involves the reduction of Mn(IV) to Mn(II) by the amino acid and the posterior reoxidation of Mn(II) to Mn(IV) by permanganate ion.

Formation of phosphonates and pyrophosphates in the reactions of ...

Indian Academy of Sciences (India)

Bu-4-Me-C6H2O)2P(O)]2O (8) could be isolated, although the reaction mixture showed several other compounds in the phosphorus NMR. A possible pathway for the formation of phosphonate salts is proposed. The X-ray crystal structures of 4, ...
Partial equilibrium in induced redox reactions of plutonium

Energy Technology Data Exchange (ETDEWEB)

Nikol' skii, B P; Posvol' skii, M V; Krylov, L I; Morozova, Z P

1975-01-01

A study was made of oxidation-reduction reactions of Pu in buffer solutions containing bichromate and a reducing agent which reacted with hexavalent chromium at pH=3.5. In most cases sodium nitrite was used. A rather slow reduction of Pu (6) with NaNO/sub 2/ in the course of which tetravalent plutonium was formed via disproportionation reaction of plutonium (5), became very rapid upon the addition of bichromate to the solution. The yield of tetravalent plutonium increased with an increase in the concentration of NaNO/sub 2/ and the bichromate but never reached 100%. This was due to a simultaneous occurrenc of the induced oxidation reaction of Pu(4), leading to a partial equilibrium between the valence forms of plutonium in the nitrite-bichromate system which on the whole was in a nonequilibrium state. It was shown that in the series of reactions leading to the reduction of plutonium the presence of bivalent chromium was a necessary link.
Vibrio Phage KVP40 Encodes a Functional NAD+ Salvage Pathway.

Science.gov (United States)

Lee, Jae Yun; Li, Zhiqun; Miller, Eric S

2017-05-01

The genome of T4-type Vibrio bacteriophage KVP40 has five genes predicted to encode proteins of pyridine nucleotide metabolism, of which two, nadV and natV , would suffice for an NAD + salvage pathway. NadV is an apparent nicotinamide phosphoribosyltransferase (NAmPRTase), and NatV is an apparent bifunctional nicotinamide mononucleotide adenylyltransferase (NMNATase) and nicotinamide-adenine dinucleotide pyrophosphatase (Nudix hydrolase). Genes encoding the predicted salvage pathway were cloned and expressed in Escherichia coli , the proteins were purified, and their enzymatic properties were examined. KVP40 NadV NAmPRTase is active in vitro , and a clone complements a Salmonella mutant defective in both the bacterial de novo and salvage pathways. Similar to other NAmPRTases, the KVP40 enzyme displayed ATPase activity indicative of energy coupling in the reaction mechanism. The NatV NMNATase activity was measured in a coupled reaction system demonstrating NAD + biosynthesis from nicotinamide, phosphoribosyl pyrophosphate, and ATP. The NatV Nudix hydrolase domain was also shown to be active, with preferred substrates of ADP-ribose, NAD + , and NADH. Expression analysis using reverse transcription-quantitative PCR (qRT-PCR) and enzyme assays of infected Vibrio parahaemolyticus cells demonstrated nadV and natV transcription during the early and delayed-early periods of infection when other KVP40 genes of nucleotide precursor metabolism are expressed. The distribution and phylogeny of NadV and NatV proteins among several large double-stranded DNA (dsDNA) myophages, and also those from some very large siphophages, suggest broad relevance of pyridine nucleotide scavenging in virus-infected cells. NAD + biosynthesis presents another important metabolic resource control point by large, rapidly replicating dsDNA bacteriophages. IMPORTANCE T4-type bacteriophages enhance DNA precursor synthesis through reductive reactions that use NADH/NADPH as the electron donor and NAD
Mass spectrometric study of thermodynamic properties of gaseous lead tellurates. Estimation of formation enthalpies of gaseous lead polonates

Energy Technology Data Exchange (ETDEWEB)

Shugurov, S.M., E-mail: s.shugurov@spbu.ru; Panin, A.I.; Lopatin, S.I.; Emelyanova, K.A.

2016-10-15

Gaseous reactions involving lead oxides, tellurium oxide and lead tellurates were studied by the Knudsen effusion mass spectrometry. Equilibrium constants and reaction enthalpies were evaluated. Structures, molecular parameters and thermodynamic functions of gaseous PbTeO{sub 3} and Pb{sub 2}TeO{sub 4} were calculated by quantum chemistry methods. The formation enthalpies Δ{sub f}H{sup 0} (298.15) = −294 ± 13 for gaseous PbTeO{sub 3} and Δ{sub f}H{sup 0} (298.15) = −499 ± 12 for gaseous Pb{sub 2}TeO{sub 4} were obtained. On the base of these results the formation enthalpies of gaseous PbPoO{sub 3} and Pb{sub 2}PoO{sub 4} were estimated as −249 ± 34 and −478 ± 38, respectively. - Highlights: • Gaseous lead tellurates PbTeO{sub 3}, Pb{sub 2}TeO{sub 4} were discovered. • Their thermodynamic properties were studied using both high temperature mass spectrometry and quantum chemistry computations. • The obtained data allows to predict the formation enthalpies of gaseous lead polonates PbPoO{sub 3}, Pb{sub 2}PoO{sub 4}.
The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism.

Science.gov (United States)

Igamberdiev, Abir U; Kleczkowski, Leszek A

2018-01-01

Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.
Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate †

Science.gov (United States)

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D.

2009-01-01

O-succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered Bi Uni Uni Bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct-binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first-half reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the ‘F’ form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered Bi Uni Uni Bi Iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogs with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogs tested as none were active except 4-(2-trifluoromethylphenyl)-4-oxobutyric acid which exhibited a 100-fold decrease in kcat/Km. Based on an understanding of OSB-CoA synthetase’s kinetic mechanism and substrate specificity, a reaction intermediate analog of OSB-AMP, 5’-O-(N-(2-trifluoromethylphenyl)-4-oxobutyl) adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of
Photogeochemical reactions of manganese under anoxic conditions

Science.gov (United States)

Liu, W.; Yee, N.; Piotrowiak, P.; Falkowski, P. G.

2017-12-01

Photogeochemistry describes reactions involving light and naturally occurring chemical species. These reactions often involve a photo-induced electron transfer that does not occur in the absence of light. Although photogeochemical reactions have been known for decades, they are often ignored in geochemical models. In particular, reactions caused by UV radiation during an ozone free early Earth could have influenced the available oxidation states of manganese. Manganese is one of the most abundant transition metals in the crust and is important in both biology and geology. For example, the presence of manganese (VI) oxides in the geologic record has been used as a proxy for oxygenic photosynthesis; however, we suggest that the high oxidation state of Mn can be produced abiotically by photochemical reactions. Aqueous solutions of manganese (II) as well as suspensions of rhodochrosite (MnCO3) were irradiated under anoxic condition using a 450 W mercury lamp and custom built quartz reaction vessels. The photoreaction of the homogeneous solution of Mn(II) produced H2 gas and akhtenskite (ɛ-MnO2) as the solid product . This product is different than the previously identified birnessite. The irradiation of rhodochrosite suspensions also produced H2 gas and resulted in both a spectral shift as well as morphology changes of the mineral particles in the SEM images. These reactions offer alternative, abiotic pathways for the formation of manganese oxides.
Prenatal inhibition of the kynurenine pathway leads to structural changes in the hippocampus of adult rat offspring

OpenAIRE

Khalil, Omari S; Pisar, Mazura; Forrest, Caroline M; Vincenten, Maria C J; Darlington, L Gail; Stone, Trevor W

2014-01-01

Glutamate receptors for N-methyl-d-aspartate (NMDA) are involved in early brain development. The kynurenine pathway of tryptophan metabolism includes the NMDA receptor agonist quinolinic acid and the antagonist kynurenic acid. We now report that prenatal inhibition of the pathway in rats with 3,4-dimethoxy-N-[4-(3-nitrophenyl)thiazol-2-yl]benzenesulphonamide (Ro61-8048) produces marked changes in hippocampal neuron morphology, spine density and the immunocytochemical localisation of developme...
Deoxygenation of Palmitic and Lauric Acids over Pt/ZIF-67 Membrane/Zeolite 5A Bead Catalysts.

Science.gov (United States)

Yang, Liqiu; Carreon, Moises A

2017-09-20

The deoxygenation of palmitic and lauric acids over 0.5 wt % Pt/ZIF-67 membrane/zeolite 5A bead catalysts is demonstrated. Almost complete conversion (% deoxygenation of ≥95%) of these two fatty acids was observed over both fresh and recycled catalyst after a 2 h reaction time. The catalysts displayed high selectivity to pentadecane and undecane via decarboxylation reaction pathway even at low 0.5 wt % Pt loading. Selectivity to pentadecane and undecane as high as ∼92% and ∼94% was observed under CO 2 atmosphere when palmitic and lauric acids were used respectively as reactants. Depending on the reaction gas atmosphere, two distinctive reaction pathways were observed: decarboxylation and hydrodeoxygenation. Specifically, it was found that decarboxylation reaction pathway was more favorable in the presence of helium and CO 2 , while hydrodeoxygenation pathway strongly competed against the decarboxylation pathway when hydrogen was employed during the deoxygenation reactions. Esters were identified as the key reaction intermediates leading to decarboxylation and hydrodeoxygenation pathways.
Pathway Distiller - multisource biological pathway consolidation.

Science.gov (United States)

Doderer, Mark S; Anguiano, Zachry; Suresh, Uthra; Dashnamoorthy, Ravi; Bishop, Alexander J R; Chen, Yidong

2012-01-01

One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow
Multinucleation during C. trachomatis infections is caused by the contribution of two effector pathways.

Directory of Open Access Journals (Sweden)

Heather M Brown

Full Text Available Chlamydia trachomatis is an obligate intracellular bacterial pathogen and the second leading cause of sexually transmitted infections in the US. Infections cause significant morbidity and can lead to serious reproductive sequelae, including an epidemiological link to increased rates of reproductive cancers. One of the overt changes that infected cells exhibit is the development of genomic instability leading to multinucleation. Here we demonstrate that the induction of multinucleation is not conserved equally across chlamydial species; C. trachomatis L2 caused high levels of multinucleation, C. muridarum intermediate levels, and C. caviae had very modest effects on multinucleation. Our data show that at least two effector pathways together cause genomic instability during infection leading to multinucleation. We find that the highly conserved chlamydial protease CPAF is a key effector for one of these pathways. CPAF secretion is required for the loss of centrosome duplication regulation as well as inducing early mitotic exit. The second effector pathway involves the induction of centrosome position errors. This function is not conserved in three chlamydial species tested. Together these two pathways contribute to the induction of high levels of genomic instability and multinucleation seen in C. trachomatis infections.
Using Physical Organic Chemistry To Shape the Course of Electrochemical Reactions.

Science.gov (United States)

Moeller, Kevin D

2018-05-09

While organic electrochemistry can look quite different to a chemist not familiar with the technique, the reactions are at their core organic reactions. As such, they are developed and optimized using the same physical organic chemistry principles employed during the development of any other organic reaction. Certainly, the electron transfer that triggers the reactions can require a consideration of new "wrinkles" to those principles, but those considerations are typically minimal relative to the more traditional approaches needed to manipulate the pathways available to the reactive intermediates formed downstream of that electron transfer. In this review, three very different synthetic challenges-the generation and trapping of radical cations, the development of site-selective reactions on microelectrode arrays, and the optimization of current in a paired electrolysis-are used to illustrate this point.
Reaction mechanism for the free-edge oxidation of soot by O 2

KAUST Repository

Raj, Abhijeet

2012-11-01

The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.
Reaction mechanism for the free-edge oxidation of soot by O 2

KAUST Repository

Raj, Abhijeet; da Silva, Gabriel; Chung, Suk-Ho

2012-01-01

The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.
Theoretical characterizations of novel C2H5O+ reactions

Science.gov (United States)

Hudson, Charles E.; McAdoo, David J.

2004-03-01

Assorted reactions of C2H5O+ isomers are characterized by theory, including tracing their courses by means of intrinsic reaction coordinate computations. We establish that CH3CH=OH+ eliminates methane by transferring H from oxygen to a methyl hydrogen and then to the CC bond to produce CHO++CH4. This adds to the limited knowledge of the involvement of hypervalent structures in the reactions of cations in the gas phase. Second, we characterized the course of CH3CH=OH+-->H3O++HC[triple bond; length as m-dash]CH. In this dissociation, H first migrates from the methyl to the oxygen to give O-protonated vinyl alcohol, a stable intermediate. Then the H2O swings outward to over the middle of the CC bond while one of the two hydrogens on the non-O-bearing carbon revolves to between the oxygen and the two carbons, leading to formation of a [H3O+ HC[triple bond; length as m-dash]CH] complex. This complex contains sufficient energy to dissociate its partners because a high barrier is crossed in its formation. Third, we found that methane elimination from CH3O+=CH2 involves stretching of the CH3---O bond and then rotation of the methyl so that a methyl hydrogen is pointed directly toward the oxygen. This reaction is completed by further rotation of the methyl to abstract a methylene hydrogen to the opposite side of the methyl from that initially bonded to oxygen. This clearly establishes that this dissociation takes place through an ion-neutral complex. Each of the reaction coordinates for the three preceding reactions traverses a novel bonding stage involving H, evidence that such are not unusual in gas phase ion chemistry. Finally, we showed that in the rearrangement CH3O+=CH2-->CH2=O+CH3, before Ht is transferred CH2 rotates around the C=C bond from being in the skeletal plane to being perpendicular to it, and Ht remains in the skeletal plane throughout its transfer. This pathway appears to balance avoiding an orbital symmetry-forbidden suprafacial transition state with
Transfer and breakup reactions at intermediate energies

International Nuclear Information System (INIS)

Stokstad, R.G.

1986-04-01

The origin of the quasi-elastic peak in peripheral heavy-ion reactions is discussed in terms of inelastic scattering and transfer reactions to unbound states of the primary projectile-like fragment. The situation is analogous to the use of reverse kinematics in fusion reactions, a technique in which the object of study is moving with nearly the beam velocity. It appears that several important features of the quasi-elastic peak may be explained by this approach. Projectile-breakup reactions have attractive features for the study of nuclear structure. They may also be used to determine the partition of excitation energy in peripheral reactions. At intermediate energies, neutron-pickup reactions leading to four-body final states become important. Examples of experiments are presented that illustrate these points. 15 refs., 14 figs
Front propagation in Rayleigh-Taylor systems with reaction

International Nuclear Information System (INIS)

Scagliarini, A; Biferale, L; Sbragaglia, M; Mantovani, F; Pivanti, M; Schifano, S F; Tripiccione, R; Pozzati, F; Toschi, F

2011-01-01

A special feature of Rayleigh-Taylor systems with chemical reactions is the competition between turbulent mixing and the 'burning processes', which leads to a highly non-trivial dynamics. We studied the problem performing high resolution numerical simulations of a 2d system, using a thermal lattice Boltzmann (LB) model. We spanned the various regimes emerging at changing the relative chemical/turbulent time scales, from slow to fast reaction; in the former case we found numerical evidence of an enhancement of the front propagation speed (with respect to the laminar case), providing a phenomenological argument to explain the observed behaviour. When the reaction is very fast, instead, the formation of sharp fronts separating patches of pure phases, leads to an increase of intermittency in the small scale statistics of the temperature field.
CO2 as an Oxidant for High Temperature Reactions

Directory of Open Access Journals (Sweden)

Sibudjing eKawi

2015-03-01

Full Text Available This paper presents a review on the developments in catalyst technology for the reactions utilizing CO2 for high temperature applications. These include dehydrogenation of alkanes to olefins, the dehydrogenation of ethylbenzene to styrene and finally CO2 reforming of hydrocarbon feedstock (i.e. methane and alcohols. Aspects on the various reaction pathways are also highlighted. The literature on the role of promoters and catalyst development is critically evaluated. Most of the reactions discussed in this review are exploited in industries and related to on-going processes, thus providing extensive data from literature. However some reactions, such as CO2 reforming of ethanol and glycerol which have not reached industrial scale are also reviewed owing to their great potential in terms of sustainability which are essential as energy for the future. This review further illustrates the building-up of knowledge which shows the role of support and catalysts for each reaction and the underlying linkage between certain catalysts which can be adapted for the multiple CO2-related reactions.
Quantum mechanical/molecular mechanical calculated reactivity networks reveal how cytochrome P450cam and Its T252A mutant select their oxidation pathways.

Science.gov (United States)

Wang, Binju; Li, Chunsen; Dubey, Kshatresh Dutta; Shaik, Sason

2015-06-17

Quantum mechanical/molecular mechanical calculations address the longstanding-question of a "second oxidant" in P450 enzymes wherein the proton-shuttle, which leads to formation of the "primary-oxidant" Compound I (Cpd I), was severed by mutating the crucial residue (in P450cam: Threonine-252-to-Alanine, hence T252A). Investigating the oxidant candidates Cpd I, ferric hydroperoxide, and ferric hydrogen peroxide (Fe(III)(O2H2)), and their reactions, generates reactivity networks which enable us to rule out a "second oxidant" and at the same time identify an additional coupling pathway that is responsible for the epoxidation of 5-methylenylcamphor by the T252A mutant. In this "second-coupling pathway", the reaction starts with the Fe(III)(O2H2) intermediate, which transforms to Cpd I via a O-O homolysis/H-abstraction mechanism. The persistence of Fe(III)(O2H2) and its oxidative reactivity are shown to be determined by interplay of substrate and protein. The substrate 5-methylenylcamphor prevents H2O2 release, while the protein controls the Fe(III)(O2H2) conversion to Cpd I by nailing-through hydrogen-bonding interactions-the conformation of the HO(•) radical produced during O-O homolysis. This conformation prevents HO(•) attack on the porphyrin's meso position, as in heme oxygenase, and prefers H-abstraction from Fe(IV)OH thereby generating H2O + Cpd I. Cpd I then performs substrate oxidations. Camphor cannot prevent H2O2 release and hence the T252A mutant does not oxidize camphor. This "second pathway" transpires also during H2O2 shunting of the cycle of wild-type P450cam, where the additional hydrogen-bonding with Thr252 prevents H2O2 release, and contributes to a successful Cpd I formation. The present results lead to a revised catalytic cycle of Cytochrome P450cam.
Lead in school children from Morelos, Mexico: levels, sources and feasible interventions.

Science.gov (United States)

Farías, Paulina; Álamo-Hernández, Urinda; Mancilla-Sánchez, Leonardo; Texcalac-Sangrador, José Luis; Carrizales-Yáñez, Leticia; Riojas-Rodríguez, Horacio

2014-12-01

Lead is a pervasive pollutant, associated at low levels to many adverse health effects. To investigate lead levels, exposure pathways and intervention possibilities in school children from Alpuyeca, in Morelos, Mexico. Blood lead concentrations (BPb) were measured in 226 children in 2011. Exposure pathways were assessed through a questionnaire, lead measurements in different environmental matrices and spatial aggregation analysis of lead concentrations. BPb ranged from 1.5 to 36.5 ìg/dL, with a mean (SD) of 7.23 (4.9) ìg/dL. Sixty-four and 18% of the children had BPb > 5 ìg/dL and > 10 ìg/dL, respectively. The use of lead glazed ceramics was reported in almost half of the households; it was the main BPb determinant and it was associated with an increased risk of having BPb > 5 g/dL by 2.7 times (p = 0.001). Environmental samples were within US EPA’s lead recommended limits, and blood lead levels were randomly distributed in the community. Lead remains a public health problem in Alpuyeca, Mexico. Unlike other local pollutant lead exposure prevention can be achieved inexpensively and in a short term. Interventions should make mothers aware of lead's health effects and empower them to safeguard their children's health by avoiding the culturally ingrained use of lead glazed pottery.

Some links on this page may take you to non-federal websites. Their policies may differ from this site.