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.

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...

Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

International Nuclear Information System (INIS)

Kurosaki, Yuzuru; Ho, Tak-San; Rabitz, Herschel

2014-01-01

We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O 2 + O asymptote on the ground-state 1 A ′ potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excited electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization

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

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.

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.

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

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.

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.

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 ...

Electron transfer reactions induced by the triplet state of thiacarbocyanine dimers

International Nuclear Information System (INIS)

Chibisov, Alexander K.; Slavnova, Tatyana D.; Goerner, Helmut

2004-01-01

The photoinduced electron transfer between either cationic 5,5 ' -dichloro-3,3 ' ,9-triethylthiacarbocyanine (1) or a structurally similar anionic dye (2) and appropriate donors, e.g. ascorbic acid, and acceptors, e.g. methyl viologen, was studied by ns-laser photolysis. In aqueous solution the dyes in the ground state are present as an equilibrated mixture of dimers and monomers, whereas the triplet state is mainly populated from dimers. The triplet states of both dimers and monomers are quenched by electron donors or acceptors and the rate constant for quenching is generally 2-4 times higher for dimers than for monomers. The kinetics of triplet decay and radical formation and decay as a result of primary and secondary electron transfer were analyzed. While the one-electron reduced dimer decays due to back reactions, the one-electron oxidized dimer rapidly dissociates into the monomer and the monomeric dye radical. For the dimeric dye/donor/acceptor systems the primary photoinduced electron transfer occurs either from the donor or to the acceptor yielding the dimeric dye radicals. The one-electron reduced dimer can be efficiently oxidized by acceptors, e.g. the rate constant for reaction of the dimeric dye radical of 1 with methyl viologen (photoreductive pathway of sensitization) is 1.6x10 9 M -1 s -1 . The photooxidative pathway of sensitization is more complicated; after dissociation of the dimeric dye radical, the monomeric dye radical is reduced in a secondary electron transfer from ascorbic acid, e.g. with a rate constant of 1x10 9 M -1 s -1 for 2, yielding the monomer. On increasing the donor concentration the photooxidative pathway of sensitization is switched to a photoreductive one

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.

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.

Steady-state isotopic transient kinetic analysis investigation of CO-O2 and CO-NO reactions over a commercial automotive catalyst

International Nuclear Information System (INIS)

Oukaci, R.; Blackmond, D.G.; Goodwin, J.G. Jr.; Gallaher, G.R.

1992-01-01

In this paper, steady-state isotopic transient kinetic analysis (SSITKA) is used to study two model reactions, CO oxidation and CO-NO reactions, on a typical formulation of a three-way auto-catalyst. Under steady-state conditions, abrupt switches in the isotopic composition of CO ( 12 C 16 O/ 13 C 18 O) were carried out to produce isotopic transients in both labeled reactants and products. Along with the determination of the average surface lifetimes and concentrations of reaction intermediates, an analysis of the transient responses along the carbon reaction pathway indicated that the distribution of active sites for the formation of CO 2 was bimodal for both reactions. Furthermore, relatively few surface sites contributed to the overall reaction rate

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...

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.

Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway.

Science.gov (United States)

Viswanathan, Vasanthi S; Ryan, Matthew J; Dhruv, Harshil D; Gill, Shubhroz; Eichhoff, Ossia M; Seashore-Ludlow, Brinton; Kaffenberger, Samuel D; Eaton, John K; Shimada, Kenichi; Aguirre, Andrew J; Viswanathan, Srinivas R; Chattopadhyay, Shrikanta; Tamayo, Pablo; Yang, Wan Seok; Rees, Matthew G; Chen, Sixun; Boskovic, Zarko V; Javaid, Sarah; Huang, Cherrie; Wu, Xiaoyun; Tseng, Yuen-Yi; Roider, Elisabeth M; Gao, Dong; Cleary, James M; Wolpin, Brian M; Mesirov, Jill P; Haber, Daniel A; Engelman, Jeffrey A; Boehm, Jesse S; Kotz, Joanne D; Hon, Cindy S; Chen, Yu; Hahn, William C; Levesque, Mitchell P; Doench, John G; Berens, Michael E; Shamji, Alykhan F; Clemons, Paul A; Stockwell, Brent R; Schreiber, Stuart L

2017-07-27

Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with resistance to multiple treatment modalities across diverse cancer lineages, but the mechanistic underpinning for this state has remained incompletely understood. Here we molecularly characterize this therapy-resistant high-mesenchymal cell state in human cancer cell lines and organoids and show that it depends on a druggable lipid-peroxidase pathway that protects against ferroptosis, a non-apoptotic form of cell death induced by the build-up of toxic lipid peroxides. We show that this cell state is characterized by activity of enzymes that promote the synthesis of polyunsaturated lipids. These lipids are the substrates for lipid peroxidation by lipoxygenase enzymes. This lipid metabolism creates a dependency on pathways converging on the phospholipid glutathione peroxidase (GPX4), a selenocysteine-containing enzyme that dissipates lipid peroxides and thereby prevents the iron-mediated reactions of peroxides that induce ferroptotic cell death. Dependency on GPX4 was found to exist across diverse therapy-resistant states characterized by high expression of ZEB1, including epithelial-mesenchymal transition in epithelial-derived carcinomas, TGFβ-mediated therapy-resistance in melanoma, treatment-induced neuroendocrine transdifferentiation in prostate cancer, and sarcomas, which are fixed in a mesenchymal state owing to their cells of origin. We identify vulnerability to ferroptic cell death induced by inhibition of a lipid peroxidase pathway as a feature of therapy-resistant cancer cells across diverse mesenchymal cell-state contexts.

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.

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.

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 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.

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.

Prioritizing Acquisition Pathways in the State Level Concept

Energy Technology Data Exchange (ETDEWEB)

Murphy, Chantell L. [Los Alamos National Laboratory; Budlong-Sylvester, Kory [Los Alamos National Laboratory; Pilat, Joseph F. [Los Alamos National Laboratory

2012-06-27

The International Atomic Energy Agency's (IAEA) Department of Safeguards has launched a project to further develop the State-level concept for the planning, implementation, and evaluation of safeguards activities. In order to further evolve the safeguards system an emphasis is placed on integrating inspection-related activities and the State evaluation process to draw safeguards conclusions in the most efficient way. The credible implementation of acquisition pathway analysis is central to the success of the IAEA's State-level concept. NNSA's Office of Nuclear Safeguards and Security (NA-241) The Next Generation Safeguards Initiative (NGSI) is sponsoring Los Alamos National Laboratory (LANL) to produce a study that will examine the use of acquisition pathway analysis in: (1) Developing a State-specific, State-level approach (SLA) and Annual Implementation Plan (AIP); (2) Maximizing the utility of the physical model; and (3) Supporting resource allocation decisions through a pathway prioritization. To deal with the challenge of developing an effective and efficient SLA, this study looks at: (1) Prioritizing proliferation pathways based on an assessment of a State's capabilities and assumed proliferation strategies; and (2) Relevant State behavior (e.g., transparency, cooperation, etc.) while avoiding subjective judgments about States themselves. The study makes use of case studies and concrete examples in order to illustrate how new concepts and approaches will be implemented, and how they may differ from more traditional safeguards approaches.

Effect of excited states on thermonuclear reaction rates

International Nuclear Information System (INIS)

Sargood, D.G.

1983-01-01

Values of the ratio of the thermonuclear reaction rate of a reaction, with target nuclei in a thermal distribution of energy states, to the reaction rate with all target nuclei in their ground states are tabulated for neutron, proton and α-particle induced reactions on the naturally occurring nuclei from 20 Ne to 70 Zn, at temperatures of 1, 2, 3.5 and 5x10 9 K. The ratios are determined from reaction rates based on statistical model cross sections

Communication: State-to-state dynamics of the Cl + H2O → HCl + OH reaction: Energy flow into reaction coordinate and transition-state control of product energy disposal.

Science.gov (United States)

Zhao, Bin; Sun, Zhigang; Guo, Hua

2015-06-28

Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H2O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H2O → H2 + OH reaction. The strong enhancement of reactivity by the H2O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal.

Communication: State-to-state dynamics of the Cl + H2O → HCl + OH reaction: Energy flow into reaction coordinate and transition-state control of product energy disposal

International Nuclear Information System (INIS)

Zhao, Bin; Guo, Hua; Sun, Zhigang

2015-01-01

Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H 2 O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H 2 O → H 2 + OH reaction. The strong enhancement of reactivity by the H 2 O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal

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.

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

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.

Reactions of Ground State Nitrogen Atoms N(4S) with Astrochemically-Relevant Molecules on Interstellar Dusts

Science.gov (United States)

Krim, Lahouari; Nourry, Sendres

2015-06-01

In the last few years, ambitious programs were launched to probe the interstellar medium always more accurately. One of the major challenges of these missions remains the detection of prebiotic compounds and the understanding of reaction pathways leading to their formation. These complex heterogeneous reactions mainly occur on icy dust grains, and their studies require the coupling of laboratory experiments mimicking the extreme conditions of extreme cold and dilute media. For that purpose, we have developed an original experimental approach that combine the study of heterogeneous reactions (by exposing neutral molecules adsorbed on ice to non-energetic radicals H, OH, N...) and a neon matrix isolation study at very low temperatures, which is of paramount importance to isolate and characterize highly reactive reaction intermediates. Such experimental approach has already provided answers to many questions raised about some astrochemically-relevant reactions occurring in the ground state on the surface of dust grain ices in dense molecular clouds. The aim of this new present work is to show the implication of ground state atomic nitrogen on hydrogen atom abstraction reactions from some astrochemically-relevant species, at very low temperatures (3K-20K), without providing any external energy. Under cryogenic temperatures and with high barrier heights, such reactions involving N(4S) nitrogen atoms should not occur spontaneously and require an initiating energy. However, the detection of some radicals species as byproducts, in our solid samples left in the dark for hours at 10K, proves that hydrogen abstraction reactions involving ground state N(4S) nitrogen atoms may occur in solid phase at cryogenic temperatures. Our results show the efficiency of radical species formation stemming from non-energetic N-atoms and astrochemically-relevant molecules. We will then discuss how such reactions, involving nitrogen atoms in their ground states, might be the first key step

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.

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/.

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

Activation energies as the validity criterion of a model for complex reactions that can be in oscillatory states

Directory of Open Access Journals (Sweden)

Anić S.

2007-01-01

Full Text Available Modeling of any complex reaction system is a difficult task. If the system under examination can be in various oscillatory dynamic states, the apparent activation energies corresponding to different pathways may be of crucial importance for this purpose. In that case the activation energies can be determined by means of the main characteristics of an oscillatory process such as pre-oscillatory period, duration of the oscillatory period, the period from the beginning of the process to the end of the last oscillation, number of oscillations and others. All is illustrated on the Bray-Liebhafsky oscillatory reaction.

Nanocrystalline spinel ferrites by solid state reaction route

Indian Academy of Sciences (India)

Wintec

Nanocrystalline spinel ferrites by solid state reaction route. T K KUNDU* and S MISHRA. Department of Physics, Visva-Bharati, Santiniketan 731 235, India. Abstract. Nanostructured NiFe2O4, MnFe2O4 and (NiZn)Fe2O4 were synthesized by aliovalent ion doping using conventional solid-state reaction route. With the ...

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.

Single-particle and collective states in transfer reactions

International Nuclear Information System (INIS)

Lhenry, I.; Suomijaervi, T.; Giai, N. van

1993-01-01

The possibility to excite collective states in transfer reactions induced by heavy ions is studied. Collective states are described within the Random Phase Approximation (RPA) and the collectivity is defined according to the number of configurations contributing to a given state. The particle transfer is described within the Distorted Wave Born Approximation (DWBA). Calculations are performed for two different stripping reactions: 207 Pb( 20 Ne, 19 Ne) 208 Pb and 59 Co( 20 Ne, 19 F) 60 Ni at 48 MeV/nucleon for which experimental data are available. The calculation shows that a sizeable fraction of collective strength can be excited in these reactions. The comparison with experiment shows that this parameter-free calculation qualitatively explains the data. (author) 19 refs.; 10 figs

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

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.

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.

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

Iron based superconductors and related compounds synthesized by solid state metathesis and high temperature reactions

International Nuclear Information System (INIS)

Frankovsky, Rainer

2013-01-01

The results of this thesis can be divided into three major topics, which can also be seen as different approaches of solid state chemistry to reveal interesting features of known and unknown compounds and to develop alternative synthesis routes. Firstly, known compounds with related structural motifs to the superconducting iron-arsenides were investigated regarding their structural and physical properties. In case of La 3 Pd 4 Ge 4 the influence of Fe doping on the properties was studied, whereas in the series ZrMAs (M=Ti,V) the physical properties have not yet been reported at all and were investigated for the first time. Secondly, an alternative synthesis route has been developed for the synthesis of superconducting LaFeAsO 1-x F x . This solid state metathesis reaction distinctly increased the quality of the samples compared to conventionally prepared products. Furthermore, the reaction pathway was investigated and clarified, which helps to understand the processes during high temperature solid state metathesis reactions in general. Thirdly, this alternative synthesis route was expanded to other systems and new compounds like co-substituted LaFe 1-x Mn x AsO 1-y F y were prepared and thoroughly investigated. This led to a complex study of the interplay of magnetism, electronic and structural conditions and the occurrence of superconducting properties. The investigation and understanding of such complex coherences will probably be decisive for the further understanding of the superconducting mechanism in iron based superconductors.

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.

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

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

Solid-state reaction mechanism and microwave dielectric properties of CaTiO3–LaAlO3 ceramics

International Nuclear Information System (INIS)

Jiang, Juan; Fang, Danhua; Lu, Chao; Dou, Zhanming; Wang, Gan; Zhang, Fan; Zhang, Tianjin

2015-01-01

Highlights: • CaTiO 3 –LaAlO 3 perovskite ceramics were prepared by four sintering reaction routes. • The solid-state reaction mechanism was investigated by XRD and TG/DSC techniques. • Sintering routes had more influence on the parameters of Q × f and τ f than on ε r . - Abstract: 0.675CaTiO 3 –0.325LaAlO 3 perovskite ceramics were prepared by a conventional sintering process through four reaction routes. The solid-state reaction mechanisms were investigated by X-ray diffraction and thermogravimetric/differential scanning calorimetric analysis techniques. The results show that interactions occurred between mixtures of CaCO 3 and TiO 2 as well as La 2 O 3 and Al 2 O 3 , and they can influence the sintering behavior of the mixtures. Prior to the formation of solid solutions, the perovskite phases CaTiO 3 and LaAlO 3 were formed regardless of the combination of oxide powders used as reagents. From the powder mixtures which were calcined at 1200 °C, a Ca-rich Ca 9 Al 6 O 18 phase was present at 1400 °C if free La 2 O 3 and Al 2 O 3 used in the reaction mixtures. Ca-rich phases were also formed at higher temperature (1450 °C) if LaAlO 3 was present. The densities of the ceramics obtained by the four routes were different at specific sintering temperatures, and the highest density was obtained for the reaction route two. Results indicated that the preparation pathways had more influence on Q × f and temperature coefficient of the resonant frequency (τ f ) than on the dielectric constants (ε r ), and Q × f decreased and τ f increased rapidly when the secondary phase presented. Route four is considered as an optimal pathway for the preparation of 0.675CaTiO 3 –0.325LaAlO 3 ceramics.

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

The factor that determines photo-induced crystalline-state reaction

International Nuclear Information System (INIS)

Takenaka, Y.

1995-01-01

The photo-induced crystalline-state reaction of cobaloxime complexes were investigated by X-ray diffraction method. The reactivity or the reaction rate is dependent only on the volume of the reaction cavity. The hydrogen bond formation of the reactive group and the difference of the base ligand have no effect. (author)

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.

Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

International Nuclear Information System (INIS)

Kustova, Elena V.; Kremer, Gilberto M.

2014-01-01

Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N 2 flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure

Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

Energy Technology Data Exchange (ETDEWEB)

Kustova, Elena V., E-mail: e.kustova@spbu.ru [Department of Mathematics and Mechanics, Saint Petersburg State University, 198504 Universitetskiy pr. 28, Saint Petersburg (Russian Federation); Kremer, Gilberto M., E-mail: kremer@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba (Brazil)

2014-12-05

Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N{sub 2} flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure.

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.

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

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.

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.

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.

The effect of interfaces on solid-state reactions between oxides

International Nuclear Information System (INIS)

Johnson, M.T.; Carter, C.B.

1998-01-01

A thin-film geometry has been used to study fundamental solid-state reaction processes occurring at interfaces in two spinel-forming oxide systems. In the first system, NiO/Al 2 O 3 , epitactic NiO films were deposited on various orientations of single-crystal α-Al 2 O 3 . In this case, the reaction kinetics were studied and correlated with the interfacial structure (or substrate orientation). In the second, In 2 O 3 /MgO, solid-state reactions were studied under the influence of an electric field. The electric field provides a driving force for mass transport that affects both the reaction process and the morphological stability of an interface

Selective population of high-j states via heavy-ion-induced transfer reactions

International Nuclear Information System (INIS)

Bond, P.D.

1982-01-01

One of the early hopes of heavy-ion-induced transfer reactions was to populate states not seen easily or at all by other means. To date, however, I believe it is fair to say that spectroscopic studies of previously unknown states have had, at best, limited success. Despite the early demonstration of selectivity with cluster transfer to high-lying states in light nuclei, the study of heavy-ion-induced transfer reactions has emphasized the reaction mechanism. The value of using two of these reactions for spectroscopy of high spin states is demonstrated: 143 Nd( 16 O, 15 O) 144 Nd and 170 Er( 16 O, 15 Oγ) 171 Er

A critical assessment of theoretical methods for finding reaction pathways and transition states of surface processes

International Nuclear Information System (INIS)

Klimes, JirI; Michaelides, Angelos; Bowler, David R

2010-01-01

The performance of a variety of techniques for locating transition states on potential energy surfaces is evaluated within the density functional theory framework. Diffusion of a water molecule across NaCl(001) and HCl bond breaking on the same surface are treated as general test cases; the former is an example of a low barrier diffusion process and the latter an example of a relatively high barrier covalent bond rupture event. The methods considered include the nudged elastic band (NEB), Dewar, Healy and Stewart (DHS), dimer, constrained optimization (CO), activation-relaxation technique (ART) and one-side growing string (OGS) as well as novel combinations of the DHS with growing string (DHS + GS) and DHS plus climbing image (CI-DHS). A key conclusion to come from this study is that the NEB method is relatively fast, especially when just a single (climbing) image is used. Indeed, using more images represents an unnecessary computational burden for our set of processes. The dimer method exhibits variable performance; being poor for the water diffusion processes, which have small activation energies, but much more efficient for the HCl bond breaking process which has a higher barrier. When only a poor initial guess of the transition state geometry is available, the CI-DHS scheme is one of the most efficient techniques considered. And as a means to quickly establish an approximate minimum energy pathway the DHS + GS scheme offers some potential.

Study of highly excited high spin states via the (HI, α) reaction

International Nuclear Information System (INIS)

Kubono, S.

1982-01-01

Three subjects are discussed in this paper. 1) The mechanism of (HI, α) reactions is briefly studied. 2) Possible excitation of molecular resonance states of 12 C- 12 C in 24 Mg through the 12 C( 16 O, α) 24 Mg reaction were investigated. A precise measurement of the level widths in 24 Mg did not support the previous report that the molecular states seen in 12 C + 12 C scattering had been excited in the transfer reaction 12 C( 16 O, α) 24 Mg. 3) Highly excited states in 28 Si, which have a large parentage of 12 C- 16 O, were also studied via the 12 C( 20 Ne, α) 28 Si reaction. An angular correlation measurement revealed the lowest 8 + and 10 + states at 14.00 and 15.97 MeV, respectively, which were selectively excited in the 12 C( 20 Ne, α) reaction. These results suggest a possible new band in 28 Si. (author)

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.

Atom-radical reaction dynamics of O(3P)+C3H5→C3H4+OH: Nascent rovibrational state distributions of product OH

Science.gov (United States)

Park, Jong-Ho; Lee, Hohjai; Kwon, Han-Cheol; Kim, Hee-Kyung; Choi, Young-Sang; Choi, Jong-Ho

2002-08-01

The reaction dynamics of ground-state atomic oxygen [O(3P)] with allyl radicals (C3H5) has been investigated by applying a combination of crossed beams and laser induced fluorescence techniques. The reactants O(3P) and C3H5 were produced by the photodissociation of NO2 and the supersonic flash pyrolysis of precursor allyl iodide, respectively. A new exothermic channel of O(3P)+C3H5→C3H4+OH was observed and the nascent internal state distributions of the product OH (X 2Π:υ″=0,1) showed substantial bimodal internal excitations of the low- and high-N″ components without Λ-doublet and spin-orbit propensities in the ground and first excited vibrational states. With the aid of the CBS-QB3 level of ab initio theory and Rice-Ramsperger-Kassel-Marcus calculations, it is predicted that on the lowest doublet potential energy surface the major reaction channel of O(3P) with C3H5 is the formation of acrolein (CH2CHCHO)+H, which is consistent with the previous bulk kinetic experiments performed by Gutman et al. [J. Phys. Chem. 94, 3652 (1990)]. The counterpart C3H4 of the probed OH product in the title reaction is calculated to be allene after taking into account the factors of reaction enthalpy, barrier height and the number of intermediates involved along the reaction pathway. On the basis of population analyses and comparison with prior calculations, the statistical picture is not suitable to describe the reactive atom-radical scattering processes, and the dynamics of the title reaction is believed to proceed through two competing dynamical pathways. The major low N″-components with significant vibrational excitation may be described by the direct abstraction process, while the minor but extraordinarily hot rotational distribution of high N″-components implies that some fraction of reactants is sampled to proceed through the indirect short-lived addition-complex forming process.

Surface-Activated Coupling Reactions Confined on a Surface.

Science.gov (United States)

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

2015-10-20

Chemical reactions may take place in a pure phase of gas or liquid or at the interface of two phases (gas-solid or liquid-solid). Recently, the emerging field of "surface-confined coupling reactions" has attracted intensive attention. In this process, reactants, intermediates, and products of a coupling reaction are adsorbed on a solid-vacuum or a solid-liquid interface. The solid surface restricts all reaction steps on the interface, in other words, the reaction takes place within a lower-dimensional, for example, two-dimensional, space. Surface atoms that are fixed in the surface and adatoms that move on the surface often activate the surface-confined coupling reactions. The synergy of surface morphology and activity allow some reactions that are inefficient or prohibited in the gas or liquid phase to proceed efficiently when the reactions are confined on a surface. Over the past decade, dozens of well-known "textbook" coupling reactions have been shown to proceed as surface-confined coupling reactions. In most cases, the surface-confined coupling reactions were discovered by trial and error, and the reaction pathways are largely unknown. It is thus highly desirable to unravel the mechanisms, mechanisms of surface activation in particular, of the surface-confined coupling reactions. Because the reactions take place on surfaces, advanced surface science techniques can be applied to study the surface-confined coupling reactions. Among them, scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) are the two most extensively used experimental tools. The former resolves submolecular structures of individual reactants, intermediates, and products in real space, while the latter monitors the chemical states during the reactions in real time. Combination of the two methods provides unprecedented spatial and temporal information on the reaction pathways. The experimental findings are complemented by theoretical modeling. In particular, density

Bridge mediated two-electron transfer reactions: Analysis of stepwise and concerted pathways

International Nuclear Information System (INIS)

Petrov, E.G.; May, V.

2004-01-01

A theory of nonadiabatic donor (D)-acceptor (A) two-electron transfer (TET) mediated by a single regular bridge (B) is developed. The presence of different intermediate two-electron states connecting the reactant state D -- BA with the product state DBA -- results in complex multiexponential kinetics. The conditions are discussed at which a reduction to two-exponential as well as single-exponential kinetics becomes possible. For the latter case the rate K TET is calculated, which describes the bridge-mediated reaction as an effective two-electron D-A transfer. In the limit of small populations of the intermediate TET states D - B - A, DB -- A, D - BA - , and DB - A - , K TET is obtained as a sum of the rates K TET (step) and K TET (sup) . The first rate describes stepwise TET originated by transitions of a single electron. It starts at D -- BA and reaches DBA -- via the intermediate state D - BA - . These transitions cover contributions from sequential as well as superexchange reactions all including reduced bridge states. In contrast, a specific two-electron superexchange mechanism from D -- BA to DBA -- defines K TET (sup) . An analytic dependence of K TET (step) and K TET (sup) on the number of bridging units is presented and different regimes of D-A TET are studied

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.

Characterization of excited-state reactions with instant spectra of fluorescence kinetics

International Nuclear Information System (INIS)

Tomin, Vladimir I.; Ushakou, Dzmitryi V.

2015-01-01

Comprehensible knowledge of the excited-state proton transfer processes in organic compounds is overwhelmingly important not only for physics, but also chemistry and Life Sciences, since they play a key role in main processes of photosynthesis and functioning of biological organisms. Moreover compounds with Excited-State Intramolecular Proton Transfer (ESIPT) are in the focus of the interest of scientists throughout the world, because dual fluorescence spectra of such objects corresponding to two forms of molecular structure (normal and photoproduct) are very sensitive to characteristics of molecular microenvironment. This property allows to use such substances as fluorescent probes for diverse applications in chemistry and Life Sciences. But at the same time studying of proton transfer processes is not simple, because this process is characterized by extremely fast times (on picoseconds time scale and less order) and very often contribution of reverse reactions is essentially complicates an interpretation of observed properties of dual fluorescence. Hence, understanding of a role of reversible reactions is crucial for a comprehensive description of all processes accompanying excited state reactions. We discuss new approach for treatment ESIPT reaction on the basis of experimentally measured instant spectra of dual fluorescence and temporal behavior of ratiometric signal of normal to tautomer form intensities. Simple analytical expressions show in transparent way how to distinguish a degree of reverse reaction contribution to ratiometric signal. A validation of the approach under consideration is fulfilled with two different flavonols – 3-hydroxyflavone and 4′-(Dimethylamino)-3-hydroxyflavone – representing two extreme cases in affecting reversible reaction on dual emission. A comparing of new approach and traditional method when we analyze kinetics of separate the N* and T* fluorescence bands decays, has been carried out. - Highlights: • The excited-state

Characterization of excited-state reactions with instant spectra of fluorescence kinetics

Energy Technology Data Exchange (ETDEWEB)

Tomin, Vladimir I., E-mail: tomin@apsl.edu.pl; Ushakou, Dzmitryi V.

2015-10-15

Comprehensible knowledge of the excited-state proton transfer processes in organic compounds is overwhelmingly important not only for physics, but also chemistry and Life Sciences, since they play a key role in main processes of photosynthesis and functioning of biological organisms. Moreover compounds with Excited-State Intramolecular Proton Transfer (ESIPT) are in the focus of the interest of scientists throughout the world, because dual fluorescence spectra of such objects corresponding to two forms of molecular structure (normal and photoproduct) are very sensitive to characteristics of molecular microenvironment. This property allows to use such substances as fluorescent probes for diverse applications in chemistry and Life Sciences. But at the same time studying of proton transfer processes is not simple, because this process is characterized by extremely fast times (on picoseconds time scale and less order) and very often contribution of reverse reactions is essentially complicates an interpretation of observed properties of dual fluorescence. Hence, understanding of a role of reversible reactions is crucial for a comprehensive description of all processes accompanying excited state reactions. We discuss new approach for treatment ESIPT reaction on the basis of experimentally measured instant spectra of dual fluorescence and temporal behavior of ratiometric signal of normal to tautomer form intensities. Simple analytical expressions show in transparent way how to distinguish a degree of reverse reaction contribution to ratiometric signal. A validation of the approach under consideration is fulfilled with two different flavonols – 3-hydroxyflavone and 4′-(Dimethylamino)-3-hydroxyflavone – representing two extreme cases in affecting reversible reaction on dual emission. A comparing of new approach and traditional method when we analyze kinetics of separate the N* and T* fluorescence bands decays, has been carried out. - Highlights: • The excited-state

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

Features of Speech Reactions to Mental State Concepts

Directory of Open Access Journals (Sweden)

Ekaterina M. Alekseeva

2017-11-01

Full Text Available The article is devoted to the problem of mental state associative speech representation. The study involved 31 Russian-speaking subjects (27 females and 4 males at the age of 18 - 22 years old. The experimental procedure using DMDX program allowed to measure the time of speech response to stimuli - the concepts of 25 mental states. The average reaction time to the concepts of mental states, shown on the computer monitor, made 2114.68 milliseconds. The most rapid associative speech response was the response to the following stimuli: "ecstasy" (1452.54 msec, "meditation" (1569.26 msec, "tranquility" (1685.21 msec, the slowest response is the response to "interest" (2517.5 msec and "indecision" (2454.63 msec. In total, 448 associations were given to the concepts of 25 mental states by tested subjects - speech reactions, i.e. 17.9 associations per mental state on the average. The greatest number of speech associations (24 was given to the concept of love. The smallest number was given to the concept of ecstasy (11 associations. Associative fields of mental states (meditation, ecstasy, melancholy, tiredness, loneliness have the most pronounced core. The prospects of the study consist in the performance of a similar associative experiment among the representatives of another culture, as well as in the studying of an estimated and situational associative representation of mental states.

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

Singlet versus Triplet Excited State Mediated Photoinduced Dehalogenation Reactions of Itraconazole in Acetonitrile and Aqueous Solutions.

Science.gov (United States)

Zhu, Ruixue; Li, Ming-de; Du, Lili; Phillips, David Lee

2017-04-06

Photoinduced dehalogenation of the antifungal drug itraconazole (ITR) in acetonitrile (ACN) and ACN/water mixed solutions was investigated using femtosecond and nanosecond time-resolved transient absorption (fs-TA and ns-TA, respectively) and nanosecond time-resolved resonance Raman spectroscopy (ns-TR 3 ) experiments. An excited resonance energy transfer is found to take place from the 4-phenyl-4,5-dihydro-3H-1,2,4-triazol-3-one part of the molecule to the 1,3-dichlorobenzene part of the molecule when ITR is excited by ultraviolet light. This photoexcitation is followed by a fast carbon-halogen bond cleavage that leads to the generation of radical intermediates via either triplet and/or singlet excited states. It is found that the singlet excited state-mediated carbon-halogen cleavage is the predominant dehalogenation process in ACN solvent, whereas a triplet state-mediated carbon-halogen cleavage prefers to occur in the ACN/water mixed solutions. The singlet-to-triplet energy gap is decreased in the ACN/water mixed solvents and this helps facilitate an intersystem crossing process, and thus, the carbon-halogen bond cleavage happens mostly through an excited triplet state in the aqueous solutions examined. The ns-TA and ns-TR 3 results also provide some evidence that radical intermediates are generated through a homolytic carbon-halogen bond cleavage via predominantly the singlet excited state pathway in ACN but via mainly the triplet state pathway in the aqueous solutions. In strong acidic solutions, protonation at the oxygen and/or nitrogen atoms of the 1,2,4-triazole-3-one group appears to hinder the dehalogenation reactions. This may offer the possibility that the phototoxicity of ITR due to the generation of aryl or halogen radicals can be reduced by protonation of certain moieties in suitably designed ITR halogen-containing derivatives.

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

α-particle D-state effects in (d,α) reactions

International Nuclear Information System (INIS)

Santos, F.D.; Tonsfelt, S.A.; Clegg, T.B.; Ludwig, E.J.; Tagishi, Y.; Wilkerson, J.F.

1982-01-01

It is shown that the tensor analyzing powers for (d,α) reactions are sensitive to the D-state component in the α-particle wave function. The D to S-state asymptotic ratio extracted from T 20 and T 22 data in J = L +- 1 transitions is discussed using an α-particle D state generated with the Jackson and Riska model

Periodic-orbit formula for quantum reactions through transition states

NARCIS (Netherlands)

Schubert, Roman; Waalkens, Holger; Goussev, Arseni; Wiggins, Stephen

2010-01-01

Transition state theory forms the basis of computing reaction rates in chemical and other systems. Recently, it has been shown how transition state theory can rigorously be realized in phase space by using an explicit algorithm. The quantization has been demonstrated to lead to an efficient

Solid-state reaction mechanism and microwave dielectric properties of CaTiO{sub 3}–LaAlO{sub 3} ceramics

Energy Technology Data Exchange (ETDEWEB)

Jiang, Juan [Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Science & Engineering, Hubei University, Wuhan 430062 (China); Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Hubei University, Wuhan 430062 (China); Fang, Danhua; Lu, Chao; Dou, Zhanming; Wang, Gan; Zhang, Fan [Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Science & Engineering, Hubei University, Wuhan 430062 (China); Zhang, Tianjin, E-mail: zhangtj@hubu.edu.cn [Ministry of Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Science & Engineering, Hubei University, Wuhan 430062 (China); Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Hubei University, Wuhan 430062 (China)

2015-07-25

Highlights: • CaTiO{sub 3}–LaAlO{sub 3} perovskite ceramics were prepared by four sintering reaction routes. • The solid-state reaction mechanism was investigated by XRD and TG/DSC techniques. • Sintering routes had more influence on the parameters of Q × f and τ{sub f} than on ε{sub r}. - Abstract: 0.675CaTiO{sub 3}–0.325LaAlO{sub 3} perovskite ceramics were prepared by a conventional sintering process through four reaction routes. The solid-state reaction mechanisms were investigated by X-ray diffraction and thermogravimetric/differential scanning calorimetric analysis techniques. The results show that interactions occurred between mixtures of CaCO{sub 3} and TiO{sub 2} as well as La{sub 2}O{sub 3} and Al{sub 2}O{sub 3}, and they can influence the sintering behavior of the mixtures. Prior to the formation of solid solutions, the perovskite phases CaTiO{sub 3} and LaAlO{sub 3} were formed regardless of the combination of oxide powders used as reagents. From the powder mixtures which were calcined at 1200 °C, a Ca-rich Ca{sub 9}Al{sub 6}O{sub 18} phase was present at 1400 °C if free La{sub 2}O{sub 3} and Al{sub 2}O{sub 3} used in the reaction mixtures. Ca-rich phases were also formed at higher temperature (1450 °C) if LaAlO{sub 3} was present. The densities of the ceramics obtained by the four routes were different at specific sintering temperatures, and the highest density was obtained for the reaction route two. Results indicated that the preparation pathways had more influence on Q × f and temperature coefficient of the resonant frequency (τ{sub f}) than on the dielectric constants (ε{sub r}), and Q × f decreased and τ{sub f} increased rapidly when the secondary phase presented. Route four is considered as an optimal pathway for the preparation of 0.675CaTiO{sub 3}–0.325LaAlO{sub 3} ceramics.

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.

Dynamical structure analysis of crystalline-state reaction and elucidation of chemical reactivity in crystalline environment

International Nuclear Information System (INIS)

Ohashi, Yuji

2010-01-01

It was found that a chiral alkyl group bonded to the cobalt atom in a cobalt complex crystal was racemized with retention of the single crystal form on exposure to visible light. Such reactions, which are called crystalline-state reactions, have been found in a variety of cobalt complex crystals. The concept of reaction cavity was introduced to explain the reaction rate quantitatively and the chirality of the photo-product. The new diffractometers and detectors were made for rapid data collection. The reaction mechanism was also elucidated using neutron diffraction analysis. The unstable reaction intermediates were analyzed using cryo-trapping method. The excited-state structures were obtained at the equilibrium state between ground and excited states. (author)

Quantum mechanical calculations of state-to-state cross sections and rate constants for the F + DCl → Cl + DF reaction.

Science.gov (United States)

Bulut, Niyazi; Kłos, Jacek; Roncero, Octavio

2015-06-07

We present accurate state-to-state quantum wave packet calculations of integral cross sections and rate constants for the title reaction. Calculations are carried out on the best available ground 1(2)A' global adiabatic potential energy surface of Deskevich et al. [J. Chem. Phys. 124, 224303 (2006)]. Converged state-to-state reaction cross sections have been calculated for collision energies up to 0.5 eV and different initial rotational and vibrational excitations, DCl(v = 0, j = 0 - 1; v = 1, j = 0). Also, initial-state resolved rate constants of the title reaction have been calculated in a temperature range of 100-400 K. It is found that the initial rotational excitation of the DCl molecule does not enhance reactivity, in contract to the reaction with the isotopologue HCl in which initial rotational excitation produces an important enhancement. These differences between the isotopologue reactions are analyzed in detail and attributed to the presence of resonances for HCl(v = 0, j), absent in the case of DCl(v = 0, j). For vibrational excited DCl(v = 1, j), however, the reaction cross section increases noticeably, what is also explained by another resonance.

Vibrational-state-selected ion--molecule reaction cross sections at thermal energies

NARCIS (Netherlands)

Pijkeren, D. van; Boltjes, E.; Eck, J. van; Niehaus, A.

1984-01-01

A method designed to measure relative ion—molecule reaction rates at thermal collision energies for selected reactant ion vibrational states is described. Relative reaction rates are determined for the three endothermic reactions: H2+ (υ)(He,H)HeH+, H2+ (υ)(Ne,H)NeH+, D2+(υ)(Ne, D)NeD+, and for the

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.

Oxygen entry through multiple pathways in T-state human hemoglobin.

Science.gov (United States)

Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

2013-05-23

The heme oxygen (O2) binding site of human hemoglobin (HbA) is buried in the interior of the protein, and there is a debate over the O2 entry pathways from solvent to the binding site. As a first step to understand HbA O2 binding process at the atomic level, we detected all significant multiple O2 entry pathways from solvent to the binding site in the α and β subunits of the T-state tetramer HbA by utilizing ensemble molecular dynamics (MD) simulation. By executing 128 independent 8 ns MD trajectories in O2-rich aqueous solvent, we simulated the O2 entry processes and obtained 141 and 425 O2 entry events in the α and β subunits of HbA, respectively. We developed the intrinsic pathway identification by clustering method to achieve a persuasive visualization of the multiple entry pathways including both the shapes and relative importance of each pathway. The rate constants of O2 entry estimated from the MD simulations correspond to the experimentally observed values, suggesting that O2 ligands enter the binding site through multiple pathways. The obtained multiple pathway map can be utilized for future detailed analysis of HbA O2 binding process.

State Strategies for Sustaining and Scaling Grades 9-14 Career Pathways: Toward a Policy Set for Pathways to Prosperity

Science.gov (United States)

Cahill, Charlotte; Hoffman, Nancy; Loyd, Amy; Vargas, Joel

2014-01-01

This brief begins with a discussion of the composition of state leadership teams and organizing structures for supporting a Pathways to Prosperity Network initiative, and then describes effective strategies currently at play in the network states for jumpstarting work in the regions. It goes on to review state policies that support 9-14…

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.

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

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.

Crystalline state photoreactions direct observation of reaction processes and metastable intermediates

CERN Document Server

Ohashi, Yuji

2014-01-01

Offering some 300 references, this book focuses on chemical reactions in the crystalline state. The reactions span many fields in inorganic and organic chemistry, making this a useful resource for inorganic, organic and physical chemists and graduate students.

Exchange reaction between hydrogen and deuterium. I. Importance of surface reactions in the steady-state mechanism

Energy Technology Data Exchange (ETDEWEB)

Marteau, C; Gaillard-Cusin, F; James, H [Centre National de la Recherche Scientifique, 45 - Orleans-la-Source (France). Centre de Recherches sur la Chimie de Combustion et des Hautes Temperatures

1978-05-01

Investigation of heterogeneous initiation process of gas phase linear chain reactions is carried out through the study of H/sub 2/-D/sub 2/ exchange reaction. Experimental data under study concern mainly the stationary rate of HD formation and the prestationary proceeding. Steady-state method accounts for the first one of these data; it allows to clearly compare the wall process part to the part played by the homogeneous chain reaction towards HD formation. Activation energy of exchange elementary step between chemisorbed hydrogen (on silica) and gaseous deuterium has been evaluated: Esub(e1)=52+-1 Kcal/mole.

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.

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

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...

Action-reaction based parameters identification and states estimation of flexible systems

OpenAIRE

Khalil, Islam; Kunt, Emrah Deniz; Şabanoviç, Asif; Sabanovic, Asif

2012-01-01

This work attempts to identify and estimate flexible system's parameters and states by a simple utilization of the Action-Reaction law of dynamical systems. Attached actuator to a dynamical system or environmental interaction imposes an action that is instantaneously followed by a dynamical system reaction. The dynamical system's reaction carries full information about the dynamical system including system parameters, dynamics and externally applied forces that arise due to system interaction...

The Photoconversion of Phytochrome Includes an Unproductive Shunt Reaction Pathway.

Science.gov (United States)

Buhrke, David; Kuhlmann, Uwe; Michael, Norbert; Hildebrandt, Peter

2018-03-05

Phytochromes are modular bimodal photoswitches that control gene expression for morphogenetic processes in plants. These functions are triggered by photoinduced conversions between the inactive and active states of the photosensory module, denoted as Pr and Pfr, respectively. In the present time-resolved resonance Raman spectroscopic study of bacterial representatives of this photoreceptor family, we demonstrate that these phototransformations do not represent linear processes but include a branching reaction back to the initial state, prior to (de)activation of the output module. Thus, only a fraction of the photoreceptors undergoing the phototransformations can initiate the downstream signaling process, consistent with phytochrome's function as a sensor for more durable changes of light conditions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Search for low spin superdeformed states by transfer reactions

Energy Technology Data Exchange (ETDEWEB)

Blons, J; Goutte, D; Lepretre, A; Lucas, R; Meot, V; Paya, D; Phan, X H [DAPNIA SPhN CE Saclay 91191 Gif sur Yvette (France); Barreau, G; Doan, T P; Pedemay, G [CENBG, 33175 Gradignan (France); Becker, J A; Stoyer, M A [LLNL, Livermore, CA (United States)

1992-08-01

We present a specific experimental technique aiming to observe superdeformed isomeric states. Preliminary results on two proton transfer reaction on platinum targets leading to {sup 194}Hg are shown. (author). 6 refs., 5 figs.

Excited State Spectra and Dynamics of Phenyl-Substituted Butadienes

DEFF Research Database (Denmark)

Wallace-Williams, Stacie E.; Schwartz, Benjamin J.; Møller, Søren

1994-01-01

indicate that phenyl torsional motion is not important to the excited-state dynamics and reveal alternative excited-state reaction pathways. The results demonstrate how molecular systems that are structually similar can exhibit different electronic properties and excited-state dynamics....

Studies of combustion reactions at the state-resolved differential cross section level

Energy Technology Data Exchange (ETDEWEB)

Houston, P.L.; Suits, A.G.; Bontuyan, L.S.; Whitaker, B.J. [Cornell Univ., Ithaca, NY (United States)

1993-12-01

State-resolved differential reaction cross sections provide perhaps the most detailed information about the mechanism of a chemical reaction, but heretofore they have been extremely difficult to measure. This program explores a new technique for obtaining differential cross sections with product state resolution. The three-dimensional velocity distribution of state-selected reaction products is determined by ionizing the appropriate product, waiting for a delay while it recoils along the trajectory imparted by the reaction, and finally projecting the spatial distribution of ions onto a two dimensional screen using a pulsed electric field. Knowledge of the arrival time allows the ion position to be converted to a velocity, and the density of velocity projections can be inverted mathematically to provide the three-dimensional velocity distribution for the selected product. The main apparatus has been constructed and tested using photodissociations. The authors report here the first test results using crossed beams to investigate collisions between Ar and NO. Future research will both develop further the new technique and employ it to investigate methyl radical, formyl radical, and hydrogen atom reactions which are important in combustion processes. The authors intend specifically to characterize the reactions of CH{sub 3} with H{sub 2} and H{sub 2}CO; of HCO with O{sub 2}; and of H with CH{sub 4}, CO{sub 2}, and O{sub 2}.

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.

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.

Coupled-reaction-channel analysis of the (d,6Li) reaction on 24Mg and 26Mg to low-lying states

International Nuclear Information System (INIS)

Oelert, W.

1986-01-01

Experimental spectroscopic factors of the alpha-transfer reaction on nuclei of the sd-shell show rather strong inconsistencies and scatter much more strongly than explainable by the quoted errors. The poorer the quality of agreement between experimental and theoretical angular distribution shapes, the more inconsistent the comparison of spectroscopic factors either between different experiments or between theory and experiment. In view of the strong deformation of nuclei in the lower part of the sd-shell, higher-order reaction mechanisms are expected. A coupled-reaction-channel analysis for the transitions to the 0 + , 2 + , and 4 + states of the ground-state bands in 20 Ne and 22 Ne excited via the (d, 6 Li) reaction yields good agreement between experimental and theoretical angular distribution shapes as well as spectroscopic information. (orig.)

Action-reaction based parameters identification and states estimation of flexible systems

OpenAIRE

Khalil, Islam Shoukry Mohammed; Şabanoviç, Asif; Sabanovic, Asif

2010-01-01

This work attempts to identify and estimate flexible system’s parameters and states by a simple utilization of the Action-Reaction law of dynamical systems. Attached actuator to a dynamical system or environmental interaction imposes an action that is instantaneously followed by a dynamical system reaction. The dynamical system’s reaction carries full information about the dynamical system including system parameters, dynamics and externally applied forces that arise due to system interaction...

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).

Ambient Mechanochemical Solid-State Reactions of Carbon Nanotubes and Their Reactions via Covalent Coordinate Bond in Solution

Science.gov (United States)

Kabbani, Mohamad A.

In its first part, this thesis deals with ambient mechanochemical solid-state reactions of differently functionalized multiple walled carbon nanotubes (MWCNTs) while in its second part it investigates the cross-linking reactions of CNTs in solution via covalent coordinate bonds with transitions metals and carboxylate groups decorating their surfaces. In the first part a series of mechanochemical reactions involving different reactive functionalities on the CNTs such as COOH/OH, COOH/NH2 and COCl/OH were performed. The solid-state unzipping of CNTs leading to graphene formation was confirmed using spectroscopic, thermal and electron microscopy techniques. The non-grapheme products were established using in-situ quadruple mass spectroscopy. The experimental results were confirmed by theoretical simulation calculations using the 'hot spots' protocol. The kinetics of the reaction between MWCNT-COOH and MWCNT-OH was monitored using variable temperature Raman spectroscopy. The low activation energy was discussed in terms of hydrogen bond mediated proton transfer mechanism. The second part involves the reaction of MWCNTII COOH with Zn (II) and Cu (II) to form CNT metal-organic frame (MOFs) products that were tested for their effective use as counter-electrodes in dyes sensitized solar cells (DSSC). The thesis concludes by the study of the room temperature reaction between the functionalized graphenes, GOH and G'-COOH followed by the application of compressive loads. The 3D solid graphene pellet product ( 0.6gm/cc) is conductive and reflective with a 35MPa ultimate strength as compared to 10MPa strength of graphite electrode ( 2.2gm/cc).

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.

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

Graph-representation of oxidative folding pathways

Directory of Open Access Journals (Sweden)

Kaján László

2005-01-01

Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.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...

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.

Radioactive nuclide production and isomeric state branching ratios in P + W reactions to 200 mev

International Nuclear Information System (INIS)

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

1995-01-01

Calculations of nuclide yields from spallation reactions usually assume that the products are formed in their ground states. We are performing calculations of product yields from proton reactions on tungsten isotopes that explicitly account for formation of the residual nuclei in excited states. The Hauser-Feshbach statistical/preequilibrium code GNASH, with full accounting for angular momentum conservation and electromagnetic transitions, is utilized in the calculations. We present preliminary results for isomer branching ratios for proton reactions to 200 MeV for several products including the 31-y, 16+ state in l78 Hf and the 25-d, 25/2- state in 179 Hf. Knowledge of such branching ratios, might be important for concepts such as accelerator production of tritium that utilize intermediate-energy proton reactions on tungsten

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.

Chemical equilibrium and reaction modeling of arsenic and selenium in soils

Science.gov (United States)

The chemical processes and soil factors that affect the concentrations of As and Se in soil solution were discussed. Both elements occur in two redox states differing in toxicity and reactivity. Methylation and volatilization reactions occur in soils and can act as detoxification pathways. Precip...

State-to-state quantum dynamics of the F + HCl (vi = 0, ji = 0) → HF(vf, jf) + Cl reaction on the ground state potential energy surface.

Science.gov (United States)

Li, Anyang; Guo, Hua; Sun, Zhigang; Kłos, Jacek; Alexander, Millard H

2013-10-07

The state-to-state reaction dynamics of the title reaction is investigated on the ground electronic state potential energy surface using two quantum dynamical methods. The results obtained using the Chebyshev real wave packet method are in excellent agreement with those obtained using the time-independent method, except at low translational energies. It is shown that this exothermic hydrogen abstraction reaction is direct, resulting in a strong back-scattered bias in the product angular distribution. The HF product is highly excited internally. Agreement with available experimental data is only qualitative. We discuss several possible causes of disagreement with experiment.

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.

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.

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

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.

Structure of states in 12Be via the 11Be( d,p) reaction

Science.gov (United States)

Kanungo, R.; Gallant, A. T.; Uchida, M.; Andreoiu, C.; Austin, R. A. E.; Bandyopadhyay, D.; Ball, G. C.; Becker, J. A.; Boston, A. J.; Boston, H. C.; Brown, B. A.; Buchmann, L.; Colosimo, S. J.; Clark, R. M.; Cline, D.; Cross, D. S.; Dare, H.; Davids, B.; Drake, T. E.; Djongolov, M.; Finlay, P.; Galinski, N.; Garrett, P. E.; Garnsworthy, A. B.; Green, K. L.; Grist, S.; Hackman, G.; Harkness, L. J.; Hayes, A. B.; Howell, D.; Hurst, A. M.; Jeppesen, H. B.; Leach, K. G.; Macchiavelli, A. O.; Oxley, D.; Pearson, C. J.; Pietras, B.; Phillips, A. A.; Rigby, S. V.; Ruiz, C.; Ruprecht, G.; Sarazin, F.; Schumaker, M. A.; Shotter, A. C.; Sumitharachchi, C. S.; Svensson, C. E.; Tanihata, I.; Triambak, S.; Unsworth, C.; Williams, S. J.; Walden, P.; Wong, J.; Wu, C. Y.

2010-01-01

The s-wave neutron fraction of the 0 levels in 12Be has been investigated for the first time through the 11Be(d,p) transfer reaction using a 5 A MeV11Be beam at TRIUMF, Canada. The reaction populated all the known bound states of 12Be. The ground state s-wave spectroscopic factor was determined to be 0.28-0.07+0.03 while that for the long-lived 02+ excited state was 0.73-0.40+0.27. This observation, together with the smaller effective separation energy indicates enhanced probability for an extended density tail beyond the 10Be core for the 02+ excited state compared to the ground state.

A Glimpse into a State Technical College System's POS Pathways

Science.gov (United States)

Frazier, Stephanie D.; Swygert, N. Maria

2012-01-01

The South Carolina Technical College System (SCTCS) has embraced POS, providing students across the state with pathways into careers ranging from nuclear systems technology to health care to industrial technology. The SCTCS has strived, over the last 50 years, to foster a bridge between business and education. The colleges coordinate and…

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

An alternative preparation method for ion exchanged catalysts: Solid state redox reaction

DEFF Research Database (Denmark)

Schneider, E.; Hagen, A.; Grunwaldt, J.-D.

2004-01-01

A new method for modifying zeolites with zinc is proposed. The solid state redox reaction between metallic zinc and ZSM-5 zeolites with different Si/Al ratios was investigated by temperature programmed hydrogen evolution (TPHE), X-ray absorption near edge structure (XANES) and diffuse reflectance...... infrared Fourier transform spectroscopy (DRIFTS). The evolution of hydrogen was detected at temperatures above 620 K. The source of hydrogen was the solid state redox reaction of the metal with protons of the support. The samples exhibit catalytic activity in ethane aromatization indicating that zinc...... should be located at the same sites as in catalysts prepared by conventional methods. Combination of XANES and catalytic activity point to zinc being mainly present in tetrahedral geometry under reaction conditions....

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.

Direct single-molecule dynamic detection of chemical reactions.

Science.gov (United States)

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

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

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.

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.

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...

Concluding remarks of international symposium on highly excited states in nuclear reactions

Energy Technology Data Exchange (ETDEWEB)

Bernstein, A. M.; Ikegami, H.; Muraoka, M. [eds.

1980-01-01

This is the concluding remarks in the international symposium on highly excited states in nuclear reactions. The remarks concentrate on the giant quadrupole states. In the framework of the distorted wave Born approximation (DWB), the differential cross section can be deduced. The relevant transition matrix elements are defined, and the quantities which are measured in inelastic hadron (h, h') reactions are shown. These are used to obtain both neutron and proton transition multipole matrix elements. This is equivalent to make the isospin decomposition of the electromagnetic transition matrix elements. The ratios of the transition matrix elements of neutrons and protons of the lowest 2/sup +/ states in even-even single closed shell nuclei are evaluated and compared with experimental results. For each nucleus, the consistency between various measurements is generally good. The effect of the virtual excitation of giant 2/sup +/ states into the ground and first excited states of even-even nuclei is discussed. The accuracy of (h, h') results can be tested.

Particle-hole state densities for statistical multi-step compound reactions

International Nuclear Information System (INIS)

Oblozinsky, P.

1986-01-01

An analytical relation is derived for the density of particle-hole bound states applying the equidistant-spacing approximation and the Darwin-Fowler statistical method. The Pauli exclusion principle as well as the finite depth of the potential well are taken into account. The set of densities needed for calculations of multi-step compound reactions is completed by deriving the densities of accessible final states for escape and damping. (orig.)

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].

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.

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.

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.

Pre-steady-state kinetic analysis of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis reveals partially rate-limiting product release by parallel pathways.

Science.gov (United States)

Liu, Juan; Murkin, Andrew S

2012-07-03

As part of the non-mevalonate pathway for the biosynthesis of the isoprenoid precursor isopentenyl pyrophosphate, 1-deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR) catalyzes the conversion of DXP into 2-C-methyl-D-erythritol 4-phosphate (MEP) by consecutive isomerization and NADPH-dependent reduction reactions. Because this pathway is essential to many infectious organisms but is absent in humans, DXR is a target for drug discovery. In an attempt to characterize its kinetic mechanism and identify rate-limiting steps, we present the first complete transient kinetic investigation of DXR. Stopped-flow fluorescence measurements with Mycobacterium tuberculosis DXR (MtDXR) revealed that NADPH and MEP bind to the free enzyme and that the two bind together to generate a nonproductive ternary complex. Unlike the Escherichia coli orthologue, MtDXR exhibited a burst in the oxidation of NADPH during pre-steady-state reactions, indicating a partially rate-limiting step follows chemistry. By monitoring NADPH fluorescence during these experiments, the transient generation of MtDXR·NADPH·MEP was observed. Global kinetic analysis supports a model involving random substrate binding and ordered release of NADP(+) followed by MEP. The partially rate-limiting release of MEP occurs via two pathways--directly from the binary complex and indirectly via the MtDXR·NADPH·MEP complex--the partitioning being dependent on NADPH concentration. Previous mechanistic studies, including kinetic isotope effects and product inhibition, are discussed in light of this kinetic mechanism.

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

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution.

Science.gov (United States)

Ou, Yang; Shi, Wenjing; Smith, Steven J; Ledna, Catherine M; West, J Jason; Nolte, Christopher G; Loughlin, Daniel H

2018-04-15

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the energy system to compare environmental impacts of alternative low-carbon pathways for the United States. One set of pathways emphasizes nuclear energy and carbon capture and storage, while another set emphasizes renewable energy, including wind, solar, geothermal power, and bioenergy. These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter smaller than 2.5 μm in diameter, and energy-related water demands are evaluated for 50% and 80% carbon dioxide reduction targets in 2050. The renewable low-carbon pathways require less water withdrawal and consumption than the nuclear and carbon capture pathways. However, the renewable low-carbon pathways modeled in this study produce higher particulate matter-related mortality costs due to greater use of biomass in residential heating. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies.

Geometric phase and quantum interference in photosynthetic reaction center: Regulation of electron transfer

Energy Technology Data Exchange (ETDEWEB)

Sun, Yuming, E-mail: ymsun@ytu.edu.cn; Su, Yuehua; Dai, Zhenhong; Wang, WeiTian

2016-10-20

Photosynthesis is driven by electron transfer in reaction centers in which the functional unit is composed of several simple molecules C{sub 2}-symmetrically arranged into two branches. In view of quantum mechanism, both branches are possible pathways traversed by the transferred electron. Due to different evolution of spin state along two pathways in transmembrane electric potential (TEP), quantum state of the transferred electron at the bridged site acquires a geometric phase difference dependent on TEP, the most efficient electron transport takes place in a specific range of TEP beyond which electron transfer is dramatically suppressed. What’s more, reaction center acts like elaborately designed quantum device preparing polarized spin dependent on TEP for the transferred electron to regulate the reduction potential at bridged site. In brief, electron transfer generates the TEP, reversely, TEP modulates the efficiency of electron transfer. This may be an important approach to maintaining an appreciable pH environment in photosynthesis.

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.

Nucleon transfer reactions to rotational states induced by 206,208PB projectiles

International Nuclear Information System (INIS)

Wollersheim, H.J.; DeBoer, F.W.N.; Emling, H.; Grein, H.; Grosse, E.; Spreng, W.; Eckert, G.; Elze, Th.W.; Stelzer, K.; Lauterbach, Ch.

1986-01-01

In a systematic study of nucleon transfer reactions accompanied by Coulomb excitation the authors bombarded 152 Sm, 160 Gd and 232 Th with 206, 208 Pb beams at incident energies close to the Coulomb barrier. Particle-gamma coincidence techniques were used to identify excited states of reaction products populated through inelastic scattering and in nucleon transfer reactions. Large cross sections were observed for one- and two-neutron pick-up from 232 Th at an incident energy of 6.4 MeV/μ. The results are analyzed in the framework of semiclassical models

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

Investigation of the O+allyl addition/elimination reaction pathways from the OCH2CHCH2 radical intermediate

International Nuclear Information System (INIS)

FitzPatrick, Benjamin L.; Lau, K.-C.; Butler, Laurie J.; Lee, S.-H.; Lin, Jim Jr-Min

2008-01-01

These experiments study the preparation of and product channels resulting from OCH 2 CHCH 2 , a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH 2 CHCH 2 radicals; these undergo a facile ring opening to the OCH 2 CHCH 2 radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH 2 CHCH 2 radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C 3 H 4 O (acrolein)+H, C 2 H 4 +HCO (formyl radical), and H 2 CO (formaldehyde)+C 2 H 3 . A small signal from C 2 H 2 O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C 2 H 5 +CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to

Investigation of the O+allyl addition/elimination reaction pathways from the OCH2CHCH2 radical intermediate

Science.gov (United States)

Fitzpatrick, Benjamin L.; Lau, Kai-Chung; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim-Min, Jr.

2008-08-01

These experiments study the preparation of and product channels resulting from OCH2CHCH2, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH2CHCH2 radicals; these undergo a facile ring opening to the OCH2CHCH2 radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH2CHCH2 radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C3H4O (acrolein)+H, C2H4+HCO (formyl radical), and H2CO (formaldehyde)+C2H3. A small signal from C2H2O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C2H5+CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to each of these product channels

Reactions of carbon atoms in pulsed molecular beams

Energy Technology Data Exchange (ETDEWEB)

Reisler, H. [Univ. of Southern California, Los Angeles (United States)

1993-12-01

This research program consists of a broad scope of experiments designed to unravel the chemistry of atomic carbon in its two spin states, P and D, by using well-controlled initial conditions and state-resolved detection of products. Prerequisite to the proposed studies (and the reason why so little is known about carbon atom reactions), is the development of clean sources of carbon atoms. Therefore, in parallel with the studies of its chemistry and reaction dynamics, the authors continuously explore new, state-specific and efficient ways of producing atomic carbon. In the current program, C({sup 3}P) is produced via laser ablation of graphite, and three areas of study are being pursued: (i) exothermic reactions with small inorganic molecules (e.g., O{sub 2}, N{sub 2}O, NO{sub 2}) that can proceed via multiple pathways; (ii) the influence of vibrational and translational energy on endothermic reactions involving H-containing reactants that yield CH products (e.g., H{sub 2}O H{sub 2}CO); (iii) reactions of C({sup 3}P) with free radicals (e.g., HCO, CH{sub 3}O). In addition, the authors plan to develop a source of C({sup 1}D) atoms by exploiting the pyrolysis of diazotetrazole and its salts in the ablation source. Another important goal involves collaboration with theoreticians in order to obtain relevant potential energy surfaces, rationalize the experimental results and predict the roles of translational and vibrational energies.

Densities of accessible final states for multi-step compound reactions

International Nuclear Information System (INIS)

Maoming De; Guo Hua

1993-01-01

The densities of accessible final states for calculations of multi-step compound reactions are derived. The Pauli exclusion principle is taken into account in the calculations. The results are compared with a previous author's results and the effect of the Pauli exclusion principle is investigated. (Author)

Reactions to Graphic Health Warnings in the United States

Science.gov (United States)

Nonnemaker, James M.; Choiniere, Conrad J.; Farrelly, Matthew C.; Kamyab, Kian; Davis, Kevin C.

2015-01-01

This study reports consumer reactions to the graphic health warnings selected by the Food and Drug Administration to be placed on cigarette packs in the United States. We recruited three sets of respondents for an experimental study from a national opt-in e-mail list sample: (i) current smokers aged 25 or older, (ii) young adult smokers aged 18-24…

[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

Single particle transfer reactions: what can they tell us about vibrational states

International Nuclear Information System (INIS)

Hering, W.R.

1975-01-01

The topic discussed concerns single particle transfer reactions (SPTR) which are, in general, used to study SP states. However, good SP states are rare objects in nature and people who try to look for them have often to settle with something less than ideal. Indeed the picture of a pure SP state is physically not even reasonable. It means that a nucleon is moving around a core nucleus which stays in its ground state: a process which one could call equivalent to elastic scattering of a nucleon which is not free but rather in a bound state. However it is shown that inelastic scattering is a very strong competitor to elastic scattering if the nucleus possesses states of high collectivity. Thus one would expect inelastic scattering to happen also while the nucleon is bound. This is a very intuitive picture of what is called the fragmentation of SP states. A final state psi sub(B) is populated by the transfer reaction A + a → B + b where psi sub(B) = α 1 phi 1 phi sub(A)(0) + α 2 phi 2 phi sub(A)(lambda). Hence the population of psi sub(B) automatically involves the collective state phi sub(A)(lambda). A discussion of how one can get information about phi sub(A)(lambda) out of the experimental data is given. (Auth.)

Effects of Methylphenidate on Resting-State Functional Connectivity of the Mesocorticolimbic Dopamine Pathways in Cocaine Addiction

Energy Technology Data Exchange (ETDEWEB)

Konova, Anna B.; Moeller, Scott J.; Tomasi, Dardo; Volkow, Nora D.; Goldstein, Rita Z.

2013-08-01

Cocaine addiction is associated with altered resting-state functional connectivity among regions of the mesocorticolimbic dopamine pathways. Methylphenidate hydrochloride, an indirect dopamine agonist, normalizes task-related regional brain activity and associated behavior in cocaine users; however, the neural systems–level effects of methylphenidate in this population have not yet been described. To use resting-state functional magnetic resonance imaging to examine changes in mesocorticolimbic connectivity with methylphenidate and how connectivity of affected pathways relates to severity of cocaine addiction.

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.

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

International Nuclear Information System (INIS)

Wang Zhan-Feng; Liu Yu-Ru; Wang Peng-Ye; Xie Ping

2017-01-01

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson–Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA–RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP. (paper)

Synthesisofc-lifepo4 composite by solid state reaction method

Science.gov (United States)

Rahayu, I.; Hidayat, S.; Noviyanti, A. R.; Rakhmawaty, D.; Ernawati, E.

2017-02-01

In this research, the enhancement of LiFePO4 conductivity was conducted by doping method with carbon materials. Carbon-based materials were obtained from the mixture of sucrose, and the precursor of LiH2PO4 and α-Fe2O3 was synthesized by solid state reaction. Sintering temperature was varied at 700°C, 800°C, 900°C and 1,000°C. The result showed that C-LiFePO4 could be synthesized by using solid state reaction method. Based on the XRD and FTIR spectrums, C-LiFePO4 can be identified as the type of crystal, characterized by the appearance of sharp signal on (011), (211) and typical peak of LiFePO4 materials. The result of conductivity measurement from C-LiFePO4 at sintering temperature of 900°C and 1,000°C was 2×10-4 S/cm and 4×10-4S/cm, respectively. The conductivity value at sintering temperature of 700°C and 800°C was very small (<10-6 S/cm), which cannot be measured by the existing equipment.

On the nature of organic and inorganic centers that bifurcate electrons, coupling exergonic and endergonic oxidation-reduction reactions.

Science.gov (United States)

Peters, John W; Beratan, David N; Schut, Gerrit J; Adams, Michael W W

2018-04-19

Bifurcating electrons to couple endergonic and exergonic electron-transfer reactions has been shown to have a key role in energy conserving redox enzymes. Bifurcating enzymes require a redox center that is capable of directing electron transport along two spatially separate pathways. Research into the nature of electron bifurcating sites indicates that one of the keys is the formation of a low potential oxidation state to satisfy the energetics required of the endergonic half reaction, indicating that any redox center (organic or inorganic) that can exist in multiple oxidation states with sufficiently separated redox potentials should be capable of electron bifurcation. In this Feature Article, we explore a paradigm for bifurcating electrons down independent high and low potential pathways, and describe redox cofactors that have been demonstrated or implicated in driving this unique biochemistry.

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.

Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

Science.gov (United States)

Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

2016-02-11

The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br.

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.

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...

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.

Excited-State N2 Dissociation Pathway on Fe-Functionalized Au.

Science.gov (United States)

Martirez, John Mark P; Carter, Emily A

2017-03-29

Localized surface plasmon resonances (LSPRs) offer the possibility of light-activated chemical catalysis on surfaces of strongly plasmonic metal nanoparticles. This technology relies on lower-barrier bond formation and/or dissociation routes made available through energy transfer following the eventual decay of LSPRs. The coupling between these decay processes and a chemical trajectory (nuclear motion, charge-transfer, intersystem crossing, etc.) dictates the availability of these alternative (possibly lower barrier) excited-state channels. The Haber-Bosch method of NH 3 synthesis from N 2 and H 2 is notoriously energy intensive. This is due to the difficulty of N 2 dissociation despite the overall reaction being thermodynamically favorable at ambient temperatures and pressures. LSPRs may provide means to improve the kinetics of N 2 dissociation via induced resonance electronic excitation. In this work, we calculate, via embedded n-electron valence second-order perturbation theory within the density functional embedding theory, the excited-state potential energy surfaces for dissociation of N 2 on an Fe-doped Au(111) surface. This metal alloy may take advantage simultaneously of the strong LSPR of Au and the catalytic activity of Fe toward N 2 dissociation. We find the ground-state dissociation activation energy to be 4.74 eV/N 2 , with Fe as the active site on the surface. Consecutive resonance energy transfers (RETs) may be accessed due to the availability of many electronically excited states with intermediate energies arising from the metal surface that may couple to states induced by the Fe-dopant and the adsorbate molecule, and crossing between excited states may effectively lower the dissociation barrier to 1.33 eV. Our work illustrates that large energetic barriers, prohibitive toward chemical reaction, may be overcome through multiple RETs facilitating an otherwise difficult chemical process.

Search for antiproton-nucleus states with (anti p,p) reactions

International Nuclear Information System (INIS)

Garreta, D.; Birien, P.; Bruge, G.; Chaumeaux, A.; Drake, D.M.; Janouin, S.; Legrand, D.; Lemaire, M.C.; Mayer, B.; Pain, J.; Peng, J.C.; Berrada, M.; Bocquet, J.P.; Monnand, E.; Mougey, J.; Perrin, P.

1985-01-01

We have studied (anti p,p) reactions on 12 C, 63 Cu, and 209 Bi to search for possible nuclear states formed by antiprotons and nuclei. The experiments used the 180 MeV antiproton beam from LEAR, and the high-resolution magnetic spectrometer, SPES II, to detect the outgoing protons. No evidence of antiproton-nucleus states was found. The gross features of the proton spectra are reasonably well described by intranuclear cascade model calculations, which consider proton emission following antiproton annihilations in the target nucleus. (orig.)

The Reaction Mechanism of Claisen Rearrangement Obtained by Transition State Spectroscopy and Single Direct-Dynamics Trajectory

Directory of Open Access Journals (Sweden)

Takayoshi Kobayashi

2013-02-01

Full Text Available Chemical bond breaking and formation during chemical reactions can be observed using “transition state spectroscopy”. Comparing the measurement result of the transition state spectroscopy with the simulation result of single direct-dynamics trajectory, we have elucidated the reaction dynamics of Claisen rearrangement of allyl vinyl ether. Observed the reaction of the neat sample liquid, we have estimated the time constants of transformation from straight-chain structure to aromatic-like six-membered ring structure forming the C1-C6 bond. The result clarifies that the reaction proceeds via three steps taking longer time than expected from the gas phase calculation. This finding provides new hypothesis and discussions, helping the development of the field of reaction mechanism analysis.

Relative state, social comparison reactions, and the behavioral constellation of deprivation.

Science.gov (United States)

Novakowski, Dallas; Mishra, Sandeep

2017-01-01

Pepper & Nettle compellingly synthesize evidence indicating that temporal discounting is a functional, adaptive response to deprivation. In this commentary, we underscore the importance of the psychology of relative state, which is an index of relative competitive (dis)advantage. We then highlight two proximate emotional social comparison reactions linked with relative state - personal relative deprivation and envy - that may play an important role in the deprivation-discounting link.

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.

Impact of organic-mineral matter interactions on thermal reaction pathways for coal model compounds

Energy Technology Data Exchange (ETDEWEB)

Buchanan, A.C. III; Britt, P.F.; Struss, J.A. [Oak Ridge National Lab., TN (United States). Chemical and Analytical Sciences Div.

1995-07-01

Coal is a complex, heterogeneous solid that includes interdispersed mineral matter. However, knowledge of organic-mineral matter interactions is embryonic, and the impact of these interactions on coal pyrolysis and liquefaction is incomplete. Clay minerals, for example, are known to be effective catalysts for organic reactions. Furthermore, clays such as montmorillonite have been proposed to be key catalysts in the thermal alteration of lignin into vitrinite during the coalification process. Recent studies by Hatcher and coworkers on the evolution of coalified woods using microscopy and NMR have led them to propose selective, acid-catalyzed, solid state reaction chemistry to account for retained structural integrity in the wood. However, the chemical feasibility of such reactions in relevant solids is difficult to demonstrate. The authors have begun a model compound study to gain a better molecular level understanding of the effects in the solid state of organic-mineral matter interactions relevant to both coal formation and processing. To satisfy the need for model compounds that remain nonvolatile solids at temperatures ranging to 450 C, model compounds are employed that are chemically bound to the surface of a fumed silica (Si-O-C{sub aryl}linkage). The organic structures currently under investigation are phenethyl phenyl ether (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}OC{sub 6}H{sub 5}) derivatives, which serve as models for {beta}-alkyl aryl ether units that are present in lignin and lignitic coals. The solid-state chemistry of these materials at 200--450 C in the presence of interdispersed acid catalysts such as small particle size silica-aluminas and montmorillonite clay will be reported. Initial focus will be on defining the potential impact of these interactions on coal pyrolysis and liquefaction.

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

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.

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).

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

Complete active space second order perturbation theory (CASPT2) study of N({sup 2}D) + H{sub 2}O reaction paths on D{sub 1} and D{sub 0} potential energy surfaces: Direct and roaming pathways

Energy Technology Data Exchange (ETDEWEB)

Isegawa, Miho; Liu, Fengyi [Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Kyoto 606-8103 (Japan); Maeda, Satoshi [Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan); Morokuma, Keiji, E-mail: morokuma@fukui.kyoto-u.ac.jp [Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Kyoto 606-8103 (Japan); Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States)

2014-10-21

We report reaction paths starting from N({sup 2}D) + H{sub 2}O for doublet spin states, D{sub 0} and D{sub 1}. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H{sub 2}ON → H–O(H)N → H–HON → NO({sup 2}Π) + H{sub 2}, (2) cis-HNOH → HNO–H → H–HNO → NO + H{sub 2}, (3) H{sub 2}NO → H–HNO → HNO–H → trans-HNOH, are confirmed on the D{sub 0} surface.

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.

Reaction pathways of photoexcited retinal in proteorhodopsin studied by pump-dump-probe spectroscopy.

Science.gov (United States)

Rupenyan, Alisa; van Stokkum, Ivo H M; Arents, Jos C; van Grondelle, Rienk; Hellingwerf, Klaas J; Groot, Marie Louise

2009-12-17

Proteorhodopsin (pR) is a membrane-embedded proton pump from the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization on the femtosecond to picosecond time scales. Here, we report a study on the photoisomerization dynamics of the retinal chromophore of pR, using dispersed ultrafast pump-dump-probe spectroscopy. The application of a pump pulse initiates the photocycle, and with an appropriately tuned dump pulse applied at a time delay after the dump, the molecules in the initial stages of the photochemical process can be de-excited and driven back to the ground state. In this way, we were able to resolve an intermediate on the electronic ground state that represents chromophores that are unsuccessful in isomerization. In particular, the fractions of molecules that undergo slow isomerization (20 ps) have a high probability to enter this state rather than the isomerized K-state. On the ground state reaction surface, return to the stable ground state conformation via a structural or vibrational relaxation occurs in 2-3 ps. Inclusion of this intermediate in the kinetic scheme led to more consistent spectra of the retinal-excited state, and to a more accurate estimation of the quantum yield of isomerization (Phi = 0.4 at pH 6).

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.

Re-examining the 26Mg(α ,α')26Mg reaction: Probing astrophysically important states in 26Mg

Science.gov (United States)

Adsley, P.; Brümmer, J. W.; Li, K. C. W.; Marín-Lámbarri, D. J.; Kheswa, N. Y.; Donaldson, L. M.; Neveling, R.; Papka, P.; Pellegri, L.; Pesudo, V.; Pool, L. C.; Smit, F. D.; van Zyl, J. J.

2017-11-01

Background: The 22Ne(α ,n )25Mg reaction is one of the neutron sources for the s process in massive stars. The properties of levels in 26Mg above the α -particle threshold control the strengths of the 22Ne(α ,n )25Mg and 22Ne(α ,γ )26Mg reactions. The strengths of these reactions as functions of temperature are one of the major uncertainties in the s process. Purpose: Information on the existence, spin, and parity of levels in 26Mg can assist in constraining the strengths of the 22Ne(α ,γ )26Mg and 22Ne(α ,n )25Mg reactions, and therefore in constraining s -process abundances. Methods: Inelastically scattered α particles from a 26Mg target were momentum-analyzed in the K600 magnetic spectrometer at iThemba LABS, South Africa. The differential cross sections of states were deduced from the focal-plane trajectory of the scattered α particles. Based on the differential cross sections, spin and parity assignments to states are made. Results: A newly assigned 0+ state was observed in addition to a number of other states, some of which can be associated with states observed in other experiments. Some of the deduced Jπ values of the states observed in the present study show discrepancies with those assigned in a similar experiment performed at RCNP Osaka. The reassignments and additions of the various states can strongly affect the reaction rate at low temperatures. Conclusion: The number, location, and assignment of levels in 26Mg that may contribute to the 22Ne+α reactions are not clear. Future experimental investigations of 26Mg must have an extremely good energy resolution to separate the contributions from different levels. Coincidence experiments of 26Mg provide a possible route for future investigations.

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

Pathways of fish invasions in the Mid-Atlantic region of the United States

Science.gov (United States)

Lapointe, Nicolas W. R.; Fuller, Pam; Neilson, Matthew; Murphy, Brian R.; Angermeier, Paul

2016-01-01

Non-native fish introductions are a major threat to biodiversity and fisheries, and occur through numerous pathways that vary regionally in importance. A key strategy for managing invasions is to focus prevention efforts on pathways posing the greatest risk of future introductions. We identified high-risk pathways for fish establishment in the Mid-Atlantic region of the United States based on estimates of probability of establishment and records of previous introductions, which were considered in the context of emerging socioeconomic trends. We used estimates of propagule pressure, species’ environmental tolerance, and size of species pool to assess the risk of establishment by pathway. Pathways varied considerably in historic importance and species composition, with the majority of species introduced intentionally via stocking (primarily for sport, forage, or biocontrol) or bait release. Bait release, private stocking, illegal introductions intended to establish reproducing populations (e.g., of sport fish), aquaculture, and the sale of live organisms all create risks for future invasions in the Mid-Atlantic region. Of these pathways, bait release probably poses the greatest risk of introductions for the Mid-Atlantic region because propagule pressure is moderate, most released species are tolerant of local environmental conditions, and the pool of species available for transplantation is large. Our findings differ considerably from studies in other regions (e.g., bait release is a dominant pathway in the Mid-Atlantic region, whereas illegal introduction of sport fish is dominant in the western US and aquarium releases are dominant in Florida), demonstrating the need for regional-scale assessments of, and management strategies for, introduction pathways.

Low-lying states and structure of the exotic 8He via direct reactions on the proton

International Nuclear Information System (INIS)

Skaza, F.; Lapoux, V.; Keeley, N.; Alamanos, N.; Auger, F.; Beaumel, D.; Becheva, E.; Blumenfeld, Y.; Delaunay, F.; Drouart, A.; Gillibert, A.; Giot, L.; Khan, E.; Nalpas, L.; Pakou, A.; Pollacco, E.; Raabe, R.; Roussel-Chomaz, P.; Rusek, K.; Scarpaci, J.-A.; Sida, J.-L.; Stepantsov, S.; Wolski, R.

2007-01-01

The structure of the light exotic nucleus 8 He was investigated using direct reactions of the 8 He SPIRAL beam on a proton-rich target. The (p,p') scattering to the 2 1 + state, the (p,d) 7 He and (p,t) 6 He transfer reactions, were measured at the energy E lab =15.7 A.MeV. The light charged particles (p,d,t) were detected in the MUST Si-strip telescope array. The excitation spectrum of 8 He was extracted from the (p,p') reaction. Above the known 2 1 + excited state at 3.6 MeV, a second resonance was found around 5.4 MeV. The cross sections were analyzed within the coupled-reaction channels framework, using microscopic potentials. It is inferred that the 8 He ground state has a more complex neutron-skin structure than suggested by previous α+4n models assuming a pure (1p 3/2 ) 4 configuration

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

Hydronium-Ion-Catalyzed Elimination Pathways of Substituted Cyclohexanols in Zeolite H-ZSM5

Energy Technology Data Exchange (ETDEWEB)

Hintermeier, Peter H. [Department; Eckstein, Sebastian [Department; Mei, Donghai [Institute; Olarte, Mariefel V. [Institute; Camaioni, Donald M. [Institute; Baráth, Eszter [Department; Lercher, Johannes A. [Department; Institute

2017-10-02

Hydronium ions in the pores of zeolite H-ZSM5 show high catalytic activity in the elimination of water from cyclohexanol in aqueous phase. Substitution induces subtle changes in rates and reaction pathways, which are concluded to be related to steric effects. Exploring the reaction pathways of 2-, 3-, and 4-methylcyclohexanol (2-McyOH, 3-McyOH, and 4-McyOH), 2- and 4-ethylcyclohexanol (2-EcyOH and 4-EcyOH), 2-n-propylcyclohexanol (2-PcyOH), and cyclohexanol (CyOH) it is shown that the E2 character increases with closer positioning of the alkyl and hydroxyl groups. Thus, 4-McyOH dehydration proceeds via an E1-type elimination, while cis-2-McyOH preferentially reacts via an E2 pathway. The entropy of activation decreased with increasing alkyl chain length (ca. 20 J mol^-1 K^-1 per CH₂ unit) for 2-substituted alcohols, which is concluded to result from constraints influencing the configurational entropy of the transition states.

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.

Microstructure and growth kinetics of nickel silicide ultra-thin films synthesized by solid-state reactions

Science.gov (United States)

Coia, Cedrik

The objective of the thesis is to develop a detailed fundamental understanding of the thermally induced solid-state reactions that lead to the formation of the NiSi. We use in situ synchrotron x-ray diffraction as well as wafer curvature measurements to monitor reactions as they occur during the annealing treatment. These analyses are complemented by ex situ transmission electron microscopy, Rutherford backscattering spectroscopy, and secondary ions mass spectroscopy. The solid-state reactions between 4 to 500 nm-thick Ni films and Si (001) are considerably more complex than previously believed. In addition to the commonly observed phases listed above, we observe the formation of three additional compounds---θ-Ni2Si, Ni31Si12 and Ni3Si2---before the complete transformation of the reacted film into NiSi. These compounds are found to co-exist laterally (within the same layer) with delta-Ni2Si and/or NiSi. The metastable compound θ-Ni2Si, which formation results from texture inheritance and rapid growth through vacancy diffusion, is present in all samples and forms at the same temperature (300+/-10°C) regardless of the initial Ni thickness. Indeed, this compound forms rapidly during ramps anneals, apparently consuming all the delta-Ni2Si for initial Ni films thickness of up to 10 nm. Its disappearance is also rapid and is correlated to both the growth of NiSi and to a surprising return of the orthorhombic delta-Ni 2Si. The formation sequence is therefore not monotonic in composition in contrast to what is usually expected in solid-state reactions. An investigation of the effect of alloying elements (Pt and Co) and impurities (B, P, As, F, N) on the Ni-Si reactions enables us to determine that nucleation plays a limiting role in the growth of metastable θ-Ni2Si and that the template provided by delta-Ni2Si is crucial in promoting this nucleation. Furthermore, reactions with amorphized and amorphous substrates indicate that the possibility of epitaxy with the Si

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)

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.

Synthesis of LaO1-xFxFeAs (x=0-0.15) via solid state metathesis reaction

Science.gov (United States)

Frankovsky, Rainer; Marchuk, Alexey; Pobel, Roman; Johrendt, Dirk

2012-04-01

LaOFeAs and superconducting LaO1-xFxFeAs have been synthesized via salt metathesis reactions and characterized by X-ray powder diffraction and magnetic susceptibility measurements. The process uses LaOCl and NaFeAs as precursors and yielded very pure samples. Superconductivity was confirmed in samples with x=0.05, 0.10 and 0.15 at critical temperatures of 11 K, 26 K and 9 K, respectively. According to temperature-dependent X-ray diffraction data, the reaction pathway is not topotactic in contrast to earlier suggestions.

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.

The role of the excited electronic states in the C++H2O reaction

International Nuclear Information System (INIS)

Flores, Jesus R.; Gonzalez, Adan B.

2008-01-01

The electronic excited states of the [COH 2 ] + system have been studied in order to establish their role in the dynamics of the C + +H 2 O→[COH] + +H reaction, which is a prototypical ion-molecule reaction. The most relevant minima and saddle points of the lowest excited state have been determined and energy profiles for the lowest excited doublet and quartet electronic states have been computed along the fragmentation and isomerization coordinates. Also, nonadiabatic coupling strengths between the ground and the first excited state have been computed where they can be large. Our analysis suggests that the first excited state could play an important role in the generation of the formyl isomer, which has been detected in crossed beam experiments [D. M. Sonnenfroh et al., J. Chem. Phys. 83, 3985 (1985)], but could not be explained in quasiclassical trajectory computations [Y. Ishikawa et al., Chem. Phys. Lett. 370, 490 (2003); J. R. Flores, J. Chem. Phys. 125, 164309 (2006)

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

Spectroscopy and reactions of vibrationally excited transient molecules

Energy Technology Data Exchange (ETDEWEB)

Dai, H.L. [Univ. of Pennsylvania, Philadelphia (United States)

1993-12-01

Spectroscopy, energy transfer and reactions of vibrationally excited transient molecules are studied through a combination of laser-based excitation techniques and efficient detection of emission from the energized molecules with frequency and time resolution. Specifically, a Time-resolved Fourier Transform Emission Spectroscopy technique has been developed for detecting dispersed laser-induced fluorescence in the IR, visible and UV regions. The structure and spectroscopy of the excited vibrational levels in the electronic ground state, as well as energy relaxation and reactions induced by specific vibronic excitations of a transient molecule can be characterized from time-resolved dispersed fluorescence in the visible and UV region. IR emissions from highly vibrational excited levels, on the other hand, reveal the pathways and rates of collision induced vibrational energy transfer.

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.

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.

Unveiling the excited state energy transfer pathways in peridinin-chlorophyll a-protein by ultrafast multi-pulse transient absorption spectroscopy.

Science.gov (United States)

Redeckas, Kipras; Voiciuk, Vladislava; Zigmantas, Donatas; Hiller, Roger G; Vengris, Mikas

2017-04-01

Time-resolved multi-pulse methods were applied to investigate the excited state dynamics, the interstate couplings, and the excited state energy transfer pathways between the light-harvesting pigments in peridinin-chlorophyll a-protein (PCP). The utilized pump-dump-probe techniques are based on perturbation of the regular PCP energy transfer pathway. The PCP complexes were initially excited with an ultrashort pulse, resonant to the S 0 →S 2 transition of the carotenoid peridinin. A portion of the peridinin-based emissive intramolecular charge transfer (ICT) state was then depopulated by applying an ultrashort NIR pulse that perturbed the interaction between S 1 and ICT states and the energy flow from the carotenoids to the chlorophylls. The presented data indicate that the peridinin S 1 and ICT states are spectrally distinct and coexist in an excited state equilibrium in the PCP complex. Moreover, numeric analysis of the experimental data asserts ICT→Chl-a as the main energy transfer pathway in the photoexcited PCP systems. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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

Transmission Coefficients for Chemical Reactions with Multiple States: Role of Quantum Decoherence

Czech Academy of Sciences Publication Activity Database

de la Lande, A.; Řezáč, Jan; Lévy, B.; Sanders, B. C.; Salahub, D. R.

2011-01-01

Roč. 133, č. 11 (2011), s. 3883-3894 ISSN 0002-7863 Institutional research plan: CEZ:AV0Z40550506 Keywords : decoherence * transition state theory * nonadiabatic reactions Subject RIV: CC - Organic Chemistry Impact factor: 9.907, year: 2011

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

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.

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

Low-temperature synthesis of actinide tetraborides by solid-state metathesis reactions

Science.gov (United States)

Lupinetti, Anthony J [Los Alamos, NM; Garcia, Eduardo [Los Alamos, NM; Abney, Kent D [Los Alamos, NM

2004-12-14

The synthesis of actinide tetraborides including uranium tetraboride (UB.sub.4), plutonium tetraboride (PuB.sub.4) and thorium tetraboride (ThB.sub.4) by a solid-state metathesis reaction are demonstrated. The present method significantly lowers the temperature required to .ltoreq.850.degree. C. As an example, when UCl.sub.4 is reacted with an excess of MgB.sub.2, at 850.degree. C., crystalline UB.sub.4 is formed. Powder X-ray diffraction and ICP-AES data support the reduction of UCl.sub.3 as the initial step in the reaction. The UB.sub.4 product is purified by washing water and drying.

Growth behavior of LiMn2O4 particles formed by solid-state reactions in air and water vapor

International Nuclear Information System (INIS)

Kozawa, Takahiro; Yanagisawa, Kazumichi; Murakami, Takeshi; Naito, Makio

2016-01-01

Morphology control of particles formed during conventional solid-state reactions without any additives is a challenging task. Here, we propose a new strategy to control the morphology of LiMn 2 O 4 particles based on water vapor-induced growth of particles during solid-state reactions. We have investigated the synthesis and microstructural evolution of LiMn 2 O 4 particles in air and water vapor atmospheres as model reactions; LiMn 2 O 4 is used as a low-cost cathode material for lithium-ion batteries. By using spherical MnCO 3 precursor impregnated with LiOH, LiMn 2 O 4 spheres with a hollow structure were obtained in air, while angulated particles with micrometer sizes were formed in water vapor. The pore structure of the particles synthesized in water vapor was found to be affected at temperatures below 700 °C. We also show that the solid-state reaction in water vapor is a simple and valuable method for the large-scale production of particles, where the shape, size, and microstructure can be controlled. - Graphical abstract: This study has demonstrated a new strategy towards achieving morphology control without the use of additives during conventional solid-state reactions by exploiting water vapor-induced particle growth. - Highlights: • A new strategy to control the morphology of LiMn 2 O 4 particles is proposed. • Water vapor-induced particle growth is exploited in solid-state reactions. • The microstructural evolution of LiMn 2 O 4 particles is investigated. • The shape, size and microstructure can be controlled by solid-state reactions.

Final-state interactions and relativistic effects in the quasielastic (e,e') reaction

International Nuclear Information System (INIS)

Chinn, C.R.; Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545); Picklesimer, A.; Van Orden, J.W.

1989-01-01

The longitudinal and transverse response functions for the inclusive quasielastic (e,e') reaction are analyzed in detail. A microscopic theoretical framework for the many-body reaction provides a clear conceptual (nonrelativistic) basis for treating final-state interactions and goes far beyond simple plane-wave or Hermitean potential models. The many-body physics of inelastic final-state channels as described by optical and multiple scattering theories is properly included by incorporating a full complex optical potential. Explicit nonrelativistic and relativistic momentum-space calculations quantitatively demonstrate the importance of such a treatment of final-state interactions for both the transverse and longitudinal response. Nonrelativistic calculations are performed using final-state interactions based on phenomenology, local density models, and microscopic multiple scattering theory. Relativistic calculations span a similar range of models and employ Dirac bound-state wave functions. The theoretical extension to relativistic dynamics is of course not clear, but is done in obvious parallel to elastic proton scattering. Extensive calculations are performed for 40 Ca at momentum transfers of 410, 550, and 700 MeV/c. A number of interesting physical effects are observed, including significant relativistic suppressions (especially for R L ), large off-shell and virtual pair effects, enhancement of the tails of the response by the final-state interactions, and large qualitative and even shape distinctions between the predictions of the various models of the final-state interactions. None of the models is found to be able to simultaneously predict the data for both response functions. This strongly suggests that additional physical mechanisms are of qualitative importance in inclusive quasielastic electron scattering

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.

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.

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.

Communication: Photodissociation of CH3CHO at 308 nm: Observation of H-roaming, CH3-roaming, and transition state pathways together along the ground state surface

Science.gov (United States)

Li, Hou-Kuan; Tsai, Po-Yu; Hung, Kai-Chan; Kasai, Toshio; Lin, King-Chuen

2015-01-01

Following photodissociation of acetaldehyde (CH3CHO) at 308 nm, the CO(v = 1-4) fragment is acquired using time-resolved Fourier-transform infrared emission spectroscopy. The CO(v = 1) rotational distribution shows a bimodal feature; the low- and high-J components result from H-roaming around CH3CO core and CH3-roaming around CHO radical, respectively, in consistency with a recent assignment by Kable and co-workers (Lee et al., Chem. Sci. 5, 4633 (2014)). The H-roaming pathway disappears at the CO(v ≥ 2) states, because of insufficient available energy following bond-breaking of H + CH3CO. By analyzing the CH4 emission spectrum, we obtained a bimodal vibrational distribution; the low-energy component is ascribed to the transition state (TS) pathway, consistent with prediction by quasiclassical trajectory calculations, while the high-energy component results from H- and CH3-roamings. A branching fraction of H-roaming/CH3-roaming/TS contribution is evaluated to be (8% ± 3%)/(68% ± 10%)/(25% ± 5%), in which the TS pathway was observed for the first time. The three pathways proceed concomitantly along the electronic ground state surface.

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.

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.

Investigation of α-cluster states in 13C via the (6Li,d) reaction

CERN Document Server

Rodrigues, M R D; Horodynski-Matsushigue, L B; Cunsolo, A; Cappuzzello, F; Duarte, J L M; Rodrigues, C L; Ukita, G M; Souza, M A; Miyake, H

2010-01-01

The 9Be(6Li,d)13C reaction was used to investigate possible α-cluster states in 13C. The reaction was measured at 25.5 MeV incident energy, employing the São Paulo Pelletron-Enge-Spectrograph facility and the nuclear emulsion detection technique. Ten out of sixteen known levels of 13C, up to 11 MeV of excitation, were observed and, due to the much improved energy resolution of 50 keV, at least three doublets could be resolved. This work presents a preliminary analysis of five of the most intensely populated states, also in comparison with the results of former transfer studies.

Kinetics of ion/molecule reactions in Xe++acteone system

International Nuclear Information System (INIS)

Vinogradov, P.S.; Misharin, A.S.

2002-01-01

A reaction of Xe+ ion with acetone and subsequent transformations of the product ions at a buffer gas pressure (He) of 1.1 Torr were studied by the flow reactor technique mass spectrometry. A kinetic scheme describing the evolution of the ionic composition has been determined. The rate constants of the key reactions involved in the scheme have been evaluated. A channel of the production of acetone cation in A state in a charge transfer reaction was observed. A production of slowly reacting isomer of the acetone cation in secondary reactions was detected. Its product in the reaction with acetone is the 'nonprotonated dimer'. The kinetics of the production of ternary ions - ( CH 3 CO + CH 3 COCH 3 )(m/e=101), CH 3 COCH 3 H + (m/e=59) as well as the production of ions of the fourth generation ( CH 3 CO + (CH 3 COCH 3 ) 2 ) (m/e=159) and (CH 3 COCH 3 ) 2 H + was observed. CH 3 CO + ion (m/e=43) was found as the main reaction product. The main pathways scheme of ionic transformations is shown. (nevyjel)

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.

Doorway states in nuclear reactions as a manifestation of the 'super-radiant' mechanism

International Nuclear Information System (INIS)

Auerbach, N.; Zelevinsky, V.

2007-01-01

A mechanism is considered for generating doorway states and intermediate structure in low-energy nuclear reactions as a result of collectivization of widths of unstable intrinsic states coupled to common decay channels. At the limit of strong continuum coupling, the segregation of broad ('super-radiating') and narrow ('trapped') states occurs revealing the separation of direct and compound processes. We discuss the conditions for the appearance of intermediate structure in this process and doorways related to certain decay channels

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

Reaction diffusion and solid state chemical kinetics handbook

CERN Document Server

Dybkov, V I

2010-01-01

This monograph deals with a physico-chemical approach to the problem of the solid-state growth of chemical compound layers and reaction-diffusion in binary heterogeneous systems formed by two solids; as well as a solid with a liquid or a gas. It is explained why the number of compound layers growing at the interface between the original phases is usually much lower than the number of chemical compounds in the phase diagram of a given binary system. For example, of the eight intermetallic compounds which exist in the aluminium-zirconium binary system, only ZrAl3 was found to grow as a separate

Ion-beam mixing and solid-state reaction in Zr-Fe multilayers

International Nuclear Information System (INIS)

Paesano, A. Jr.; Motta, A.T.; Birtcher, R.C.; Ryan, E.A.; Teixeira, S.R.; Bruckmann, M.E.; Amaral, L.

1997-01-01

Vapor-deposited Zr-Fe multilayered thin films with various wavelengths and of overall composition either 50% Fe or Fe-rich up to 57% Fe were either irradiated with 300 keV Kr ions at temperatures from 25 K to 623 K to fluences up to 2 x 10 16 cm -2 , or simply annealed at 773 K in-situ in the Intermediate Voltage Electron microscope At Argonne National Laboratory. Under irradiation, the final reaction product is the amorphous phase in all cases studied, but the dose to amorphization depends on the temperature and on the wavelength. In the purely thermal case (annealing at 773 K), the 50-50 composition produces the amorphous phase but for the Fe-rich multilayers the reaction products depend on the multilayer wavelength. For small wavelength, the amorphous phase is still formed, but at large wavelength the Zr-Fe crystalline intermetallic compounds appear. These results are discussed in terms of existing models of irradiation kinetics and phase selection during solid state reaction

First-principles calculated decomposition pathways for LiBH4 nanoclusters

Science.gov (United States)

Huang, Zhi-Quan; Chen, Wei-Chih; Chuang, Feng-Chuan; Majzoub, Eric H.; Ozoliņš, Vidvuds

2016-05-01

We analyze thermodynamic stability and decomposition pathways of LiBH4 nanoclusters using grand-canonical free-energy minimization based on total energies and vibrational frequencies obtained from density-functional theory (DFT) calculations. We consider (LiBH4)n nanoclusters with n = 2 to 12 as reactants, while the possible products include (Li)n, (B)n, (LiB)n, (LiH)n, and Li2BnHn; off-stoichiometric LinBnHm (m ≤ 4n) clusters were considered for n = 2, 3, and 6. Cluster ground-state configurations have been predicted using prototype electrostatic ground-state (PEGS) and genetic algorithm (GA) based structural optimizations. Free-energy calculations show hydrogen release pathways markedly differ from those in bulk LiBH4. While experiments have found that the bulk material decomposes into LiH and B, with Li2B12H12 as a kinetically inhibited intermediate phase, (LiBH4)n nanoclusters with n ≤ 12 are predicted to decompose into mixed LinBn clusters via a series of intermediate clusters of LinBnHm (m ≤ 4n). The calculated pressure-composition isotherms and temperature-pressure isobars exhibit sloping plateaus due to finite size effects on reaction thermodynamics. Generally, decomposition temperatures of free-standing clusters are found to increase with decreasing cluster size due to thermodynamic destabilization of reaction products.

Quasi-steady-state voltammetry of rapid electron transfer reactions at the macroscopic substrate of the scanning electrochemical microscope.

Science.gov (United States)

Nioradze, Nikoloz; Kim, Jiyeon; Amemiya, Shigeru

2011-02-01

We report on a novel theory and experiment for scanning electrochemical microscopy (SECM) to enable quasi-steady-state voltammetry of rapid electron transfer (ET) reactions at macroscopic substrates. With this powerful approach, the substrate potential is cycled widely across the formal potential of a redox couple while the reactant or product of a substrate reaction is amperometrically detected at the tip in the feedback or substrate generation/tip collection mode, respectively. The plot of tip current versus substrate potential features the retraceable sigmoidal shape of a quasi-steady-state voltammogram although a transient voltammogram is obtained at the macroscopic substrate. Finite element simulations reveal that a short tip-substrate distance and a reversible substrate reaction (except under the tip) are required for quasi-steady-state voltammetry. Advantageously, a pair of quasi-steady-state voltammograms is obtained by employing both operation modes to reliably determine all transport, thermodynamic, and kinetic parameters as confirmed experimentally for rapid ET reactions of ferrocenemethanol and 7,7,8,8-tetracyanoquinodimethane at a Pt substrate with ∼0.5 μm-radius Pt tips positioned at 90 nm-1 μm distances. Standard ET rate constants of ∼7 cm/s were obtained for the latter mediator as the largest determined for a substrate reaction by SECM. Various potential applications of quasi-steady-state voltammetry are also proposed.

Quantum measurement corrections to CIDNP in photosynthetic reaction centers

International Nuclear Information System (INIS)

Kominis, Iannis K

2013-01-01

Chemically induced dynamic nuclear polarization is a signature of spin order appearing in many photosynthetic reaction centers. Such polarization, significantly enhanced above thermal equilibrium, is known to result from the nuclear spin sorting inherent in the radical pair mechanism underlying long-lived charge-separated states in photosynthetic reaction centers. We will show here that the recently understood fundamental quantum dynamics of radical-ion-pair reactions open up a new and completely unexpected pathway toward obtaining chemically induced dynamic nuclear polarization signals. The fundamental decoherence mechanism inherent in the recombination process of radical pairs is shown to produce nuclear spin polarizations of the order of 10 4 times (or more) higher than the thermal equilibrium value at the Earth's magnetic field relevant to natural photosynthesis. This opens up the possibility of a fundamentally new exploration of the biological significance of high nuclear polarizations in photosynthesis. (paper)

Nuclear reactions

International Nuclear Information System (INIS)

Lane, A.M.

1980-01-01

In reviewing work at Harwell over the past 25 years on nuclear reactions it is stated that a balance has to be struck in both experiment and theory between work on cross-sections of direct practical relevance to reactors and on those relevant to an overall understanding of reaction processes. The compound nucleus and direct process reactions are described. Having listed the contributions from AERE, Harwell to developments in nuclear reaction research in the period, work on the optical model, neutron capture theory, reactions at doorway states with fine structure, and sum-rules for spectroscopic factors are considered in more detail. (UK)

Nonequilibrium photochemical reactions induced by lasers. Technical progress report

International Nuclear Information System (INIS)

Steinfeld, J.I.

1978-04-01

Research has progressed in six principal subject areas of interest to DOE advanced (laser) isotope separation efforts. These are (1) Infrared double resonance spectroscopy of molecules excited by multiple infrared photon absorption, particularly SF 6 and vinyl chloride. (2) Infrared multiphoton excitation of metastable triplet-state molecules, e.g., biacetyl. (3) An Information Theory analysis of multiphoton excitation and collisional deactivation has been carried out. (4) The mechanism of infrared energy deposition and multiphoton-induced reactions in chlorinated ethylene derivatives; and RRKM (statistical) model accounts for all observed behavior of the system, and a deuterium-specific reaction pathway has been identified. (5) Diffusion-enhanced laser isotope separation in N 16 O/N 18 O. (6) A technical evaluation of laser-induced chemistry and isotope separation

States With Medically Needy Pathways: Differences in Long-Term and Temporary Medicaid Entry for Low-Income Medicare Beneficiaries.

Science.gov (United States)

Keohane, Laura M; Trivedi, Amal; Mor, Vincent

2017-10-01

Medically needy pathways may provide temporary catastrophic coverage for low-income Medicare beneficiaries who do not otherwise qualify for full Medicaid benefits. Between January 2009 and June 2010, states with medically needy pathways had a higher percentage of low-income beneficiaries join Medicaid than states without such programs (7.5% vs. 4.1%, p < .01). However, among new full Medicaid participants, living in a state with a medically needy pathway was associated with a 3.8 percentage point (adjusted 95% confidence interval [1.8, 5.8]) increase in the probability of switching to partial Medicaid and a 4.5 percentage point (adjusted 95% confidence interval [2.9, 6.2]) increase in the probability of exiting Medicaid within 12 months. The predicted risk of leaving Medicaid was greatest when new Medicaid participants used only hospital services, rather than nursing home services, in their first month of Medicaid benefits. Alternative strategies for protecting low-income Medicare beneficiaries' access to care could provide more stable coverage.

Probing the 8He ground state via the 8He(p,t)6He reaction

International Nuclear Information System (INIS)

Keeley, N.; Skaza, F.; Lapoux, V.; Alamanos, N.; Auger, F.; Beaumel, D.; Becheva, E.; Blumenfeld, Y.; Delaunay, F.; Drouart, A.; Gillibert, A.; Giot, L.; Kemper, K.W.; Nalpas, L.; Pakou, A.; Pollacco, E.C.; Raabe, R.; Roussel-Chomaz, P.; Rusek, K.; Scarpaci, J.-A.; Sida, J.-L.; Stepantsov, S.; Wolski, R.

2007-01-01

The weakly-bound 8 He nucleus exhibits a neutron halo or thick neutron skin and is generally considered to have an α+4n structure in its ground state, with the four valence neutrons each occupying 1p 3/2 states outside the α core. The 8 He(p,t) 6 He reaction is a sensitive probe of the ground state structure of 8 He, and we present a consistent analysis of new and existing data for this reaction at incident energies of 15.7 and 61.3A MeV, respectively. Our results are incompatible with the usual assumption of a pure (1p 3/2 ) 4 structure and suggest that other configurations such as (1p 3/2 ) 2 (1p 1/2 ) 2 may be present with significant probability in the ground state wave function of 8 He

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

High spin states excited by the (p, t) reaction on lead isotopes

Energy Technology Data Exchange (ETDEWEB)

Kumabe, I.; Hyakutake, M. [Kyushu Univ., Fukuoka (Japan). Faculty of Engineering; Yuasa, K.; Yamagata, T.; Kishimoto, S.; Ikegami, H.; Muraoka, M [eds.

1980-01-01

In order to find high spin states the sup(204, 206, 208)Pb (p, t) reactions have been investigated with RCNP isochronous cyclotron and a high resolution magnetic spectrograph ''RAIDEN''. The experimental angular distributions were analyzed by DWBA calculations, and the lowest 10/sup +/, 12/sup +/ (i sub(13/2))/sup 2/ and 11/sup -/ (i sub(13/2), h sub(9/2)) states in /sup 202/Pb, /sup 204/Pb and /sup 206/Pb were established.

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

Science.gov (United States)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

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.

A Chemical Activation Study of the Unimolecular Reactions of CD3CD2CHCl2 and CHCl2CHCl2 with Analysis of the 1,1-HCl Elimination Pathway.

Science.gov (United States)

Larkin, Allie C; Nestler, Matthew J; Smith, Caleb A; Heard, George L; Setser, Donald W; Holmes, Bert E

2016-10-03

Chemically activated C2D5CHCl2 molecules were generated with 88 kcal mol-1 of vibrational energy by the recombination of C2D5 and CHCl2 radicals in a room temperature bath gas. The competing 2,1-DCl and 1,1-HCl unimolecular reactions were identified by the observation of the CD3CD=CHCl and CD3CD=CDCl products. The initial CD3CD2C-Cl carbene product from 1,1-HCl elimination rearranges to CD3CD=CDCl under the conditions of the experiments. The experimental rate constants were 2.7 x107 and 0.47 x107 s-1 for 2,1-DCl and 1,1-HCl elimination reactions, respectively, which corresponds to branching fractions of 0.84 and 0.16. The experimental rate constants were compared to calculated statistical rate constants to assign threshold energies of 54 and ≈ 66 kcal mol-1 for the 1,2-DCl and 1,1-HCl reactions, respectively. The statistical rate constants were obtained from models developed from electronic-structure calculations for the molecule and its transition states. The rate constant (5.3 x 107 s-1) for the unimolecular decomposition of CHCl2CHCl2 molecules formed with 82 kcal mol-1 of vibrational energy by the recombination of CHCl2 radicals also is reported. Based upon the magnitude of the calculated rate constant, 1,1-HCl elimination must contribute less than 15% to the reaction; 1,2-HCl elimination is the major reaction and the threshold energy is 59 kcal mol-1. Calculations also were done to analyze previously published rate constants for chemically activated CD2Cl-CHCl2 molecules with 86 kcal mol-1 of energy in order to obtain a better overall description of the nature of the 1,1-HCl pathway for 1,1-dichloroalkanes. The interplay of the threshold energies for the 2,1-HCl and 1,1-HCl reactions and the available energy determines the product branching fractions for individual molecules. The unusual nature of the transition state for 1,1-HCl elimination is discussed.

Chemical degradation of proteins in the solid state with a focus on photochemical reactions.

Science.gov (United States)

Mozziconacci, Olivier; Schöneich, Christian

2015-10-01

Protein pharmaceuticals comprise an increasing fraction of marketed products but the limited solution stability of proteins requires considerable research effort to prepare stable formulations. An alternative is solid formulation, as proteins in the solid state are thermodynamically less susceptible to degradation. Nevertheless, within the time of storage a large panel of kinetically controlled degradation reactions can occur such as, e.g., hydrolysis reactions, the formation of diketopiperazine, condensation and aggregation reactions. These mechanisms of degradation in protein solids are relatively well covered by the literature. Considerably less is known about oxidative and photochemical reactions of solid proteins. This review will provide an overview over photolytic and non-photolytic degradation reactions, and specially emphasize mechanistic details on how solid structure may affect the interaction of protein solids with light. Copyright © 2014 Elsevier B.V. All rights reserved.

On the theory of direct reactions with many particle final states

International Nuclear Information System (INIS)

Trautmann, D.; Baur, G.

1977-01-01

We study the theory of direct reactions with many particle final states. First, we concentrate on the DWBA formulation of the break-up of deuterons on heavy nuclei below the Coulomb barrier. Because there are no free parameters, this permits a clean test of the theory by comparing it to the experimental data. The agreement is very good. The theory is applied to the break-up of antideuteronic atoms. Then the effect of virtual deuteron break-up on Rutherford scattering is studied. It is small, but it seems to be measurable. Also the deuteron break-up above the Coulomb barrier can be well explained theoretically. In this context, small effects are studied briefly. A semiclassical theory of the break-up process is given, which results in an intuitive picture and a fast computational method. Our theory lends itself in a natural way to the study of stripping reactions to unbound states. The relation of stripping into the continuum to elastic scattering of the transferred particle on the same target nucleus is explained. Then the connection of stripping to bound and unbound states is established. Finally various examples of stripping of uncharged and charged particles into the continuum are given to illustrate the theory. Resonance wave functions describing the transferred particle are discussed. In a conclusion an outlook for possible future developments of experiment and theory is given. (author)

Realisation and crossed molecular beams study of H2/O chemical reactions at several excited states

International Nuclear Information System (INIS)

Marx, Jacqueline

1986-01-01

This work is devoted to the study of the reactive collision O + H 2 OH + H in a crossed beam experiment. This process including several channels taken a part in the chemistry of the upper atmosphere as well as in the combustion of hydrogen. According to the electronic or vibrational state of the reactants, the OH radical is produced in its ground electronic state OH (X 2 π) or in its first excited state OH (A 2 Σ + ). When the reactants are in their ground state, the reaction is endothermic in the conditions of the experiment (center of mass kinetic energy ≅ 0.12 eV). The following reactions have been obtained: O( 1 D) +H 2 (v=O) → OH (X 2 π) +H( 2 S) and O( 1 D) +H 2 (v≥5) → OH (A 2 Σ + ) +H( 2 S). The atomic oxygen is produced in its excited state O( 1 D) in a radio-frequency discharge which dissociates the molecular oxygen seeded in a carrier gas (He or Ar) and the hydrogen molecules are excited vibrationally by electron bombardment. The first reaction is studied by time-of-flight measurements. In this way, it has been possible to observe the different vibrational levels on which the OH radical is produced. The analysis of this vibrational distribution shows the competition between the abstraction and insertion-dissociation mechanisms. In the second reaction, the analysis of the spontaneous fluorescence of OH (A 2 Σ + ) reveals a very hot and non-Boltzmann rotational excitation. (author) [fr

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.

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.

A green synthesis of a layered titanate, potassium lithium titanate; lower temperature solid-state reaction and improved materials performance

International Nuclear Information System (INIS)

Ogawa, Makoto; Morita, Masashi; Igarashi, Shota; Sato, Soh

2013-01-01

A layered titanate, potassium lithium titanate, with the size range from 0.1 to 30 µm was prepared to show the effects of the particle size on the materials performance. The potassium lithium titanate was prepared by solid-state reaction as reported previously, where the reaction temperature was varied. The reported temperature for the titanate preparation was higher than 800 °C, though 600 °C is good enough to obtain single-phase potassium lithium titanate. The lower temperature synthesis is cost effective and the product exhibit better performance as photocatalysts due to surface reactivity. - Graphical abstract: Finite particle of a layered titanate, potassium lithium titanate, was prepared by solid-state reaction at lower temperature to show modified materials performance. Display Omitted - Highlights: • Potassium lithium titanate was prepared by solid-state reaction. • Lower temperature reaction resulted in smaller sized particles of titanate. • 600 °C was good enough to obtain single phased potassium lithium titanate. • The product exhibited better performance as photocatalyst

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.

A potential role of substrate as a base for deprotonation pathway in Rh-catalysed C-H amination of heteroArenes: DFT insights

KAUST Repository

Ajitha, Manjaly John

2016-03-29

The possibility of direct introduction of a new functionality through C–H bond activation is an attractive strategy in covalent synthesis. Here, we investigated the mechanism of Rh-catalysed C-H amination of the hetero-aryl substrate (2-phenylpyridine) using phenyl azide as nitrogen source by density functional theory (DFT). For the deprotocyclometallation and protodecyclometallation processes of the title reaction, we propose a stepwise base-assisted mechanism (pathway I) instead of previously reported concerted mechanism (pathway II). In the new mechanism proposed here, 2-phenylpyridine acts as a base in the initial deprotonation step (C-H bond cleavage) and transports the proton towards the final protonation step. In fact, the N-H bond of the strong conjugate acid (formed during initial C-H bond cleavage) considered in pathway I (via TS4) is more acidic than the C-H bond of the neutral substrate considered in pathway II (via TS5). The higher activation barrier of TS5 mainly originates from the ring strain of the four membered cyclic transition state. The vital role of base, as disclosed here, can potentially have broader mechanistic implications for the development of reaction conditions of transition metal catalysed reactions.

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.

Deciphering Selectivity in Organic Reactions: A Multifaceted Problem.

Science.gov (United States)

Balcells, David; Clot, Eric; Eisenstein, Odile; Nova, Ainara; Perrin, Lionel

2016-05-17

Computational chemistry has made a sustained contribution to the understanding of chemical reactions. In earlier times, half a century ago, the goal was to distinguish allowed from forbidden reactions (e.g., Woodward-Hoffmann rules), that is, reactions with low or high to very high activation barriers. A great achievement of computational chemistry was also to contribute to the determination of structures with the bonus of proposing a rationalization (e.g., anomeric effect, isolobal analogy, Gillespie valence shell pair electron repulsion rules and counter examples, Wade-Mingos rules for molecular clusters). With the development of new methods and the constant increase in computing power, computational chemists move to more challenging problems, close to the daily concerns of the experimental chemists, in determining the factors that make a reaction both efficient and selective: a key issue in organic synthesis. For this purpose, experimental chemists use advanced synthetic and analytical techniques to which computational chemists added other ways of determining reaction pathways. The transition states and intermediates contributing to the transformation of reactants into the desired and undesired products can now be determined, including their geometries, energies, charges, spin densities, spectroscopy properties, etc. Such studies remain challenging due to the large number of chemical species commonly present in the reactive media whose role may have to be determined. Calculating chemical systems as they are in the experiment is not always possible, bringing its own share of complexity through the large number of atoms and the associated large number of conformers to consider. Modeling the chemical species with smaller systems is an alternative that historically led to artifacts. Another important topic is the choice of the computational method. While DFT is widely used, the vast diversity of functionals available is both an opportunity and a challenge. Though

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution

Energy Technology Data Exchange (ETDEWEB)

Ou, Yang; Shi, Wenjing; Smith, Steven J.; Ledna, Catherine M.; West, J. Jason; Nolte, Christopher G.; Loughlin, Daniel H.

2018-04-01

There are many technological pathways that can lead to reduced carbon dioxide (CO₂) emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the U.S. energy system to compare environmental impacts of alternative low-carbon pathways. One set of pathways emphasizes nuclear energy and carbon capture and storage (NUC/CCS), while another set emphasizes renewable energy (RE). These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter less than 2.5 microns in diameter (PM2.5), and energy-related water demands are evaluated for 50% and 80% CO₂ reduction targets in the U.S. in 2050. The RE low-carbon pathways require less water withdrawal and consumption than the NUC/CCS pathways because of the large cooling demands of nuclear power and CCS. However, the NUC/CCS low-carbon pathways produce greater health benefits, mainly because the NUC/CCS assumptions result in less primary PM2.5 emissions from residential wood combustion. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies. An important finding is that biomass in the building sector can offset some of the health co-benefits of the low-carbon pathways even though it plays only a minor role in reducing CO₂ emissions.

Quantum Chemical Investigation of the Transition States and Intermediates for the Reaction of the Nitrosonium Ion with the Pentaammineazidocobalt(III) Ion.

Science.gov (United States)

Rotzinger, François P

2016-12-19

The water exchange reaction on Co(NH 3 ) 5 OH 2 3+ was investigated with various density functionals and basis sets. A Gibbs activation energy (ΔG ⧧ ) agreeing with experiment was obtained with the long-range-corrected functionals ωB97X-D3 and LC-BOP-LRD, SMD hydration, and modified Karlsruhe def2-TZVP basis sets. This computational technique was then applied to the reaction of NO + with Co(NH 3 ) 5 N 3 2+ . All of the possible pathways were investigated, NO + attack at the terminal N of Co(NH 3 ) 5 N 3 2+ via the E and the Z isomers of the transition states, and NO + attack at the bound N of azide, also via both isomers. The most favorable pathway proceeds via the attack at the bound N via the Z isomer. This leads to the intermediate with an oxatetrazole ligand bound to Co(III) at the N in the 3-position, Co(NH 3 ) 5 (cycl-N 4 O) 3+ , which undergoes N 2 elimination to yield the Co(NH 3 ) 5 N 2 O 3+ intermediate. The subsequent substitution of N 2 O by water follows the I d mechanism with retention of the configuration. No evidence for the existence of the square-pyramidal pentacoordinated intermediate Co(NH 3 ) 5 3+ was found. All of the investigated intermediates, Co(NH 3 ) 5 N 2 3+ , Co(NH 3 ) 5 [E-N(N 2 )(NO)] 3+ , Co(NH 3 ) 5 (E-ON 4 ) 3+ , Co(NH 3 ) 5 ON 2 3+ , Co(NH 3 ) 5 (cycl-N 4 O) 3+ , and Co(NH 3 ) 5 N 2 O 3+ , exhibit short lifetimes of less than ∼60 μs and react via the I d mechanism.

Solid state reaction in alumina nanoparticles/LZSA glass-ceramic composites

International Nuclear Information System (INIS)

Montedo, O.K.; Oliveira, A.N. de; Raupp-Pereira, F.

2016-01-01

Full text: The aim of this work is to present results related to solid state reactions on LZSA glass-ceramic composites containing alumina reinforcement nano-particles. A LZSA (Li2O-ZrO2-SiO2-Al2O3) glass-ceramic has been prepared by sintering of powders and characterized. Composites containing 0 to 77 vol.% of alumina nanoparticles (27-43 nm APS, 35 m2.g-1 SSA) and a 16.9Li2O•5.0ZrO2•65.1SiO2•8.6Al2O3 glass-ceramic matrix have been prepared. X-ray diffractometry studies have been performed in order of investigating the solid state reactions occurring in LZSA-based composites. Results of the XRD patterns have been related to the coefficient of thermal expansion (CTE), Young modulus, and dielectric constant, showing that, in comparison with the glass-ceramic composition, the composites showed a decrease of CTE with the alumina concentration increasing, due to the increasing of beta-spodumeness formation (solid solution of beta-spodumene, Li2O.Al2O3.4-10SiO2). The performance of the glass-ceramic was improved with the alumina nano-particles addition, showing potential of using in the preparation of Low Thermal Co-fired Ceramics (LTCC). (author)

A computational approach to extinction events in chemical reaction networks with discrete state spaces.

Science.gov (United States)

Johnston, Matthew D

2017-12-01

Recent work of Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist of a series of systems of equalities and inequalities on the edges of a modified reaction network called a domination-expanded reaction network. In this paper, we present a computational implementation of these conditions written in Python and apply the program on examples drawn from the biochemical literature. We also run the program on 458 models from the European Bioinformatics Institute's BioModels Database and report our results. Copyright © 2017 Elsevier Inc. All rights reserved.

Photoinduced dynamics of a cyanine dye: parallel pathways of non-radiative deactivation involving multiple excited-state twisted transients.

Science.gov (United States)

Upadhyayula, Srigokul; Nuñez, Vicente; Espinoza, Eli M; Larsen, Jillian M; Bao, Duoduo; Shi, Dewen; Mac, Jenny T; Anvari, Bahman; Vullev, Valentine I

2015-04-01

Cyanine dyes are broadly used for fluorescence imaging and other photonic applications. 3,3'-Diethylthiacyanine (THIA) is a cyanine dye composed of two identical aromatic heterocyclic moieties linked with a single methine, -CH 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 . The torsional degrees of freedom around the methine bonds provide routes for non-radiative decay, responsible for the inherently low fluorescence quantum yields. Using transient absorption spectroscopy, we determined that upon photoexcitation, the excited state relaxes along two parallel pathways producing three excited-state transients that undergo internal conversion to the ground state. The media viscosity impedes the molecular modes of ring rotation and preferentially affects one of the pathways of non-radiative decay, exerting a dominant effect on the emission

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.

Greigite: a true intermediate on the polysulfide pathway to pyrite

Directory of Open Access Journals (Sweden)

Benning Liane G

2007-03-01

Full Text Available Abstract The formation of pyrite (FeS2 from iron monosulfide precursors in anoxic sediments has been suggested to proceed via mackinawite (FeS and greigite (Fe3S4. Despite decades of research, the mechanisms of pyrite formation are not sufficiently understood because solid and dissolved intermediates are oxygen-sensitive and poorly crystalline and therefore notoriously difficult to characterize and quantify. In this study, hydrothermal synchrotron-based energy dispersive X-ray diffraction (ED-XRD methods were used to investigate in situ and in real-time the transformation of mackinawite to greigite and pyrite via the polysulfide pathway. The rate of formation and disappearance of specific Bragg peaks during the reaction and the changes in morphology of the solid phases as observed with high resolution microscopy were used to derive kinetic parameters and to determine the mechanisms of the reaction from mackinawite to greigite and pyrite. The results clearly show that greigite is formed as an intermediate on the pathway from mackinawite to pyrite. The kinetics of the transformation of mackinawite to greigite and pyrite follow a zero-order rate law indicating a solid-state mechanism. The morphology of greigite and pyrite crystals formed under hydrothermal conditions supports this conclusion and furthermore implies growth of greigite and pyrite by oriented aggregation of nanoparticulate mackinawite and greigite, respectively. The activation enthalpies and entropies of the transformation of mackinawite to greigite, and of greigite to pyrite were determined from the temperature dependence of the rate constants according to the Eyring equation. Although the activation enthalpies are uncharacteristic of a solid-state mechanism, the activation entropies indicate a large increase of order in the transition state, commensurate with a solid-state mechanism.

Looking for chemical reaction networks exhibiting a drift along a manifold of marginally stable states.

Science.gov (United States)

Brogioli, Doriano

2013-02-07

I recently reported some examples of mass-action equations that have a continuous manifold of marginally stable stationary states [Brogioli, D., 2010. Marginally stable chemical systems as precursors of life. Phys. Rev. Lett. 105, 058102; Brogioli, D., 2011. Marginal stability in chemical systems and its relevance in the origin of life. Phys. Rev. E 84, 031931]. The corresponding chemical reaction networks show nonclassical effects, i.e. a violation of the mass-action equations, under the effect of the concentration fluctuations: the chemical system drifts along the marginally stable states. I proposed that this effect is potentially involved in abiogenesis. In the present paper, I analyze the mathematical properties of mass-action equations of marginally stable chemical reaction networks. The marginal stability implies that the mass-action equations obey some conservation law; I show that the mathematical properties of the conserved quantity characterize the motion along the marginally stable stationary state manifold, i.e. they allow to predict if the fluctuations give rise to a random walk or a drift under the effect of concentration fluctuations. Moreover, I show that the presence of the drift along the manifold of marginally stable stationary-states is a critical property, i.e. at least one of the reaction constants must be fine tuned in order to obtain the drift. Copyright © 2012 Elsevier Ltd. All rights reserved.

Lifetime and g-factor measurements of excited states using Coulomb excitation and alpha transfer reactions

Energy Technology Data Exchange (ETDEWEB)

Guevara, Z. E., E-mail: zjguevaram@unal.edu.co; Torres, D. A., E-mail: datorresg@unal.edu.co [Physics Department, Universidad Nacional de Colombia, Bogotá D.C. (Colombia)

2016-07-07

In this contribution the challenges in the use of a setup to simultaneously measure lifetimes and g-factor values will be presented. The simultaneous use of the transient field technique and the Doppler Shift Attenuation Method, to measure magnetic moments and lifetimes respectively, allows to obtain a complete characterization of the currents of nucleons and the deformation in excited states close to the ground state. The technique is at the moment limited to Coulomb excitation and alpha-transfer reactions, what opens an interesting perspective to consider this type of experiments with radioactive beams. The use of deep-inelastic and fusion-evaporation reactions will be discussed. An example of a setup that makes use of a beam of {sup 106}Cd to study excited states of {sup 110}Sn and the beam nuclei itself will be presented.

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.

Facile and efficient room temperature solid state reaction enabled synthesis of antimony nanoparticles embedded within reduced graphene oxide for enhanced sodium-ion storage

Science.gov (United States)

Zhang, Xiukui; Wu, Ping; Jiang, Li; Zhang, Xiaofang; Shi, Hongxia; Zhu, Xiaoshu; Wei, Shaohua; Zhou, Yiming

2018-06-01

Herein, a very simple and cost-effective solid state reaction method is employed to obtain, for the first time, the antimony nanoparticles embedded within reduced graphene oxide matrices (designated as Sb/rGO). By directly grinding antimony chloride and sodium hydroxide together at room temperature in the presence of graphene oxide (GO), Sb4O5Cl2 precursor was quickly obtained, which is evenly incorporated in the graphene oxide matrices. After subsequent chemical reduction by NaBH4, the Sb/rGO composite was successfully synthesized. The as-prepared Sb/rGO composite consists of uniform Sb nanoparticles of sub-20 nm, all of which have been wrapped in and protected by the rGO matrices. The Sb nanoparticles serve as a sufficient sodium ion reservoir while the rGO matrices provide highly efficient pathways for transport of sodium ions and electrons. Moreover, the volume expansion of Sb during sodiation can be buffered in the rGO matrices. As a result, the Sb/rGO composite exhibits excellent electrochemical performance in sodium-ion batteries (SIBs), including an enhanced cycling stability with a highly reversible charge capacity of 455 mA h g-1 after 45 cycles at 100 mA g-1, and a coulombic efficiency exceeding 98% during cycling. The findings in the present work pave the way to not only synthesize the designated promising electrode materials for high performance SIBs, but also thoroughly understand the solid-state reaction.

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.

Ground-state and isomeric-state cross sections for the {sup 138}Ce(n,2n){sup 137}Ce reaction from its threshold to 20 MeV

Energy Technology Data Exchange (ETDEWEB)

Luo, Junhua [Hexi Univ., Zhangye (China). Inst. of Theoretical Physics; Hexi Univ., Zhangye (China). School of Physics and Electromechanical Engineering; An, Li; Jiang, Li [Chinese Academy of Engineering Physics, Mianyang (China). Inst. of Nuclear Physics and Chemistry

2015-07-01

The cross sections of the {sup 138}Ce(n,2n){sup 137}Ce reactions and their isomeric cross section ratios σ{sub m}/σ{sub g} were measured at three neutron energies between 13.5 and 14.8 MeV using the activation technique. CeO{sub 2} samples and Nb monitor foils were activated together to determine the reaction cross section and the incident neutron flux. The monoenergetic neutron beams were formed via the {sup 3}H(d,n){sup 4}He reaction. The activities induced in the reaction products were measured using high-resolution γ-ray spectroscopy. The pure cross section of the ground-state was derived from the absolute cross section of the metastable state and the residual nuclear decay analysis. The cross sections were also estimated using the nuclear model code, TALYS-1.6 with different level density options at neutron energies varying from the reaction threshold to 20 MeV. Results are discussed and compared with the corresponding literature data.

Rotational and neutron-hole states in 43S via the neutron knockout and fragmentation reactions

International Nuclear Information System (INIS)

Riley, L. A.; Hosier, K. E.; Adrich, P.; Baugher, T. R.; Bazin, D.; Diget, C. A.; Weisshaar, D.; Brown, B. A.; Cook, J. M.; Gade, A.; Garland, D. A.; Glasmacher, T.; Ratkiewicz, A.; Siwek, K. P.; Cottle, P. D.; Kemper, K. W.; Tostevin, J. A.

2009-01-01

The recent assertion that shape coexistence occurs in the neutron-rich isotope 43 S implies that a state observed at 940 keV in a previous study is a rotational excitation of the deformed ground state. Here we use results from two intermediate-energy reactions to demonstrate that this state--assigned an energy of 971 keV in the present work--is indeed a rotational state. This result strengthens the case for shape coexistence in 43 S.

In-beam study of the rotational states in actinides after alpha-induced nuclear reactions

International Nuclear Information System (INIS)

Hardt, K.

1983-01-01

In the experiments described in this thesis the ground state rotational bands of a whole series of actinide isotopes has been studied by means of α-induced nuclear reactions. The rotational bands studied in the even isotopes could be identified up to a spin of about 16 (h/2π). With this data it was now possible to establish a broad systematic of the rotational energies up to relatively high angular momenta. Also in the odd isotopes 233 U and 239 Pu it was possible to follow the ground state rotational bands up to higher spins and to compare them with predictions of the rotational model. By means of the (α,α'2n) reaction the nuclei 230 Th and especially 228 Th could by populated. (orig./HSI) [de

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.

Reactions of Ferrous Coproheme Decarboxylase (HemQ) with O2 and H2O2 Yield Ferric Heme b.

Science.gov (United States)

Streit, Bennett R; Celis, Arianna I; Shisler, Krista; Rodgers, Kenton R; Lukat-Rodgers, Gudrun S; DuBois, Jennifer L

2017-01-10

A recently discovered pathway for the biosynthesis of heme b ends in an unusual reaction catalyzed by coproheme decarboxylase (HemQ), where the Fe(II)-containing coproheme acts as both substrate and cofactor. Because both O 2 and H 2 O 2 are available as cellular oxidants, pathways for the reaction involving either can be proposed. Analysis of reaction kinetics and products showed that, under aerobic conditions, the ferrous coproheme-decarboxylase complex is rapidly and selectively oxidized by O 2 to the ferric state. The subsequent second-order reaction between the ferric complex and H 2 O 2 is slow, pH-dependent, and further decelerated by D 2 O 2 (average kinetic isotope effect of 2.2). The observation of rapid reactivity with peracetic acid suggested the possible involvement of Compound I (ferryl porphyrin cation radical), consistent with coproheme and harderoheme reduction potentials in the range of heme proteins that heterolytically cleave H 2 O 2 . Resonance Raman spectroscopy nonetheless indicated a remarkably weak Fe-His interaction; how the active site structure may support heterolytic H 2 O 2 cleavage is therefore unclear. From a cellular perspective, the use of H 2 O 2 as an oxidant in a catalase-positive organism is intriguing, as is the unusual generation of heme b in the Fe(III) rather than Fe(II) state as the end product of heme synthesis.

Accurate Quantum Wave Packet Study of the Deep Well D+ + HD Reaction: Product Ro-vibrational State-Resolved Integral and Differential Cross Sections.

Science.gov (United States)

He, Haixiang; Zhu, Weimin; Su, Wenli; Dong, Lihui; Li, Bin

2018-03-08

The H + + H 2 reaction and its isotopic variants as the simplest triatomic ion-molecule reactive system have been attracting much interests, however there are few studies on the titled reaction at state-to-state level until recent years. In this work, accurate state-to-state quantum dynamics studies of the titled reaction have been carried out by a reactant Jacobi coordinate-based time-dependent wave packet approach on diabatic potential energy surfaces constructed by Kamisaka et al. Product ro-vibrational state-resolved information has been calculated for collision energies up to 0.2 eV with maximal total angular momentum J = 40. The necessity of including all K-component for accounting the Coriolis coupling for the reaction has been illuminated. Competitions between the two product channels, (D + + HD' → D' + + HD and D + + HD' → H + + DD') were investigated. Total integral cross sections suggest that resonances enhance the reactivity of channel D + + HD'→ H + + DD', however, resonances depress the reactivity of the another channel D + + HD' → D' + + HD. The structures of the differential cross sections are complicated and depend strongly on collision energies of the two channels and also on the product rotational states. All of the product ro-vibrational state-resolved differential cross sections for this reaction do not exhibit rigorous backward-forward symmetry which may indicate that the lifetimes of the intermediate resonance complexes should not be that long. The dynamical observables of this deuterated isotopic reaction are quite different from the reaction of H + + H 2 → H 2 + H + reported previously.

Kynurenine Pathway Metabolites in Humans: Disease and Healthy States

Directory of Open Access Journals (Sweden)

Yiquan Chen

2009-01-01

Full Text Available Tryptophan is an essential amino acid that can be metabolised through different pathways, a major route being the kynurenine pathway. The first enzyme of the pathway, indoleamine-2,3-dioxygenase, is strongly stimulated by inflammatory molecules, particularly interferon gamma. Thus, the kynurenine pathway is often systematically up-regulated when the immune response is activated. The biological significance is that 1 the depletion of tryptophan and generation of kynurenines play a key modulatory role in the immune response; and 2 some of the kynurenines, such as quinolinic acid, 3-hydroxykynurenine and kynurenic acid, are neuroactive. The kynurenine pathway has been demonstrated to be involved in many diseases and disorders, including Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease, AIDS dementia complex, malaria, cancer, depression and schizophrenia, where imbalances in tryptophan and kynurenines have been found. This review compiles most of these studies and provides an overview of how the kynurenine pathway might be contributing to disease development, and the concentrations of tryptophan and kynurenines in the serum, cerebrospinal fluid and brain tissues in control and patient subjects.

Moving Towards a State of the Art Charge-Exchange Reaction Code

Science.gov (United States)

Poxon-Pearson, Terri; Nunes, Filomena; Potel, Gregory

2017-09-01

Charge-exchange reactions have a wide range of applications, including late stellar evolution, constraining the matrix elements for neutrinoless double β-decay, and exploring symmetry energy and other aspects of exotic nuclear matter. Still, much of the reaction theory needed to describe these transitions is underdeveloped and relies on assumptions and simplifications that are often extended outside of their region of validity. In this work, we have begun to move towards a state of the art charge-exchange reaction code. As a first step, we focus on Fermi transitions using a Lane potential in a few body, Distorted Wave Born Approximation (DWBA) framework. We have focused on maintaining a modular structure for the code so we can later incorporate complications such as nonlocality, breakup, and microscopic inputs. Results using this new charge-exchange code will be shown compared to the analysis in for the case of 48Ca(p,n)48Sc. This work was supported in part by the National Nuclear Security Administration under the Stewardship Science Academic Alliances program through the U.S. DOE Cooperative Agreement No. DE- FG52-08NA2855.

Growth behavior of LiMn{sub 2}O{sub 4} particles formed by solid-state reactions in air and water vapor

Energy Technology Data Exchange (ETDEWEB)

Kozawa, Takahiro, E-mail: t-kozawa@jwri.osaka-u.ac.jp [Joining and Welding Research Institute, Osaka University, 11–1 Mihogaoka, Ibaraki, Osaka 567-0047 (Japan); Yanagisawa, Kazumichi [Research Laboratory of Hydrothermal Chemistry, Faculty of Science, Kochi University, 2–5-1 Akebono-cho, Kochi 780-8520 (Japan); Murakami, Takeshi; Naito, Makio [Joining and Welding Research Institute, Osaka University, 11–1 Mihogaoka, Ibaraki, Osaka 567-0047 (Japan)

2016-11-15

Morphology control of particles formed during conventional solid-state reactions without any additives is a challenging task. Here, we propose a new strategy to control the morphology of LiMn{sub 2}O{sub 4} particles based on water vapor-induced growth of particles during solid-state reactions. We have investigated the synthesis and microstructural evolution of LiMn{sub 2}O{sub 4} particles in air and water vapor atmospheres as model reactions; LiMn{sub 2}O{sub 4} is used as a low-cost cathode material for lithium-ion batteries. By using spherical MnCO{sub 3} precursor impregnated with LiOH, LiMn{sub 2}O{sub 4} spheres with a hollow structure were obtained in air, while angulated particles with micrometer sizes were formed in water vapor. The pore structure of the particles synthesized in water vapor was found to be affected at temperatures below 700 °C. We also show that the solid-state reaction in water vapor is a simple and valuable method for the large-scale production of particles, where the shape, size, and microstructure can be controlled. - Graphical abstract: This study has demonstrated a new strategy towards achieving morphology control without the use of additives during conventional solid-state reactions by exploiting water vapor-induced particle growth. - Highlights: • A new strategy to control the morphology of LiMn{sub 2}O{sub 4} particles is proposed. • Water vapor-induced particle growth is exploited in solid-state reactions. • The microstructural evolution of LiMn{sub 2}O{sub 4} particles is investigated. • The shape, size and microstructure can be controlled by solid-state reactions.

Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis.

Science.gov (United States)

Hattersley, J G; Pérez-Velázquez, J; Chappell, M J; Bearup, D; Roper, D; Dowson, C; Bugg, T; Evans, N D

2011-11-01

An important question in Systems Biology is the design of experiments that enable discrimination between two (or more) competing chemical pathway models or biological mechanisms. In this paper analysis is performed between two different models describing the kinetic mechanism of a three-substrate three-product reaction, namely the MurC reaction in the cytoplasmic phase of peptidoglycan biosynthesis. One model involves ordered substrate binding and ordered release of the three products; the competing model also assumes ordered substrate binding, but with fast release of the three products. The two versions are shown to be distinguishable; however, if standard quasi-steady-state assumptions are made distinguishability cannot be determined. Once model structure uniqueness is ensured the experimenter must determine if it is possible to successfully recover rate constant values given the experiment observations, a process known as structural identifiability. Structural identifiability analysis is carried out for both models to determine which of the unknown reaction parameters can be determined uniquely, or otherwise, from the ideal system outputs. This structural analysis forms an integrated step towards the modelling of the full pathway of the cytoplasmic phase of peptidoglycan biosynthesis. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

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

Solid-state polymerisation via [2+2] cycloaddition reaction involving coordination polymers.

Science.gov (United States)

Medishetty, Raghavender; Park, In-Hyeok; Lee, Shim Sung; Vittal, Jagadese J

2016-03-14

Highly crystalline metal ions containing organic polymers are potentially useful to manipulate the magnetic and optical properties to make advanced multifunctional materials. However, it is challenging to synthesise monocrystalline metal complexes of organic polymers and single-phase hybrid materials made up of both coordination and organic polymers by traditional solution crystallisation. This requires an entirely different approach in the solid-state by thermal or photo polymerisation of the ligands. Among the photochemical methods available, [2+2] cycloaddition reaction has been recently employed to generate cyclobutane based coordination polymers from the metal complexes. Cyclobutane polymers have also been integrated into coordination polymers in this way. Recent advancements in the construction of polymeric chains of cyclobutane rings through photo-dimerisation reaction in the monocrystalline solids containing metal complexes, coordination polymers and metal-organic framework structures are discussed here.

Electron transfer reactions

CERN Document Server

Cannon, R D

2013-01-01

Electron Transfer Reactions deals with the mechanisms of electron transfer reactions between metal ions in solution, as well as the electron exchange between atoms or molecules in either the gaseous or solid state. The book is divided into three parts. Part 1 covers the electron transfer between atoms and molecules in the gas state. Part 2 tackles the reaction paths of oxidation states and binuclear intermediates, as well as the mechanisms of electron transfer. Part 3 discusses the theories and models of the electron transfer process; theories and experiments involving bridged electron transfe

Pathways of hepatic glycogen formation in humans following ingestion of a glucose load in the fed state

International Nuclear Information System (INIS)

Magnusson, I.; Chandramouli, V.; Schumann, W.C.; Kumaran, K.; Wahren, J.; Landau, B.R.

1989-01-01

The relative contributions of the direct and the indirect pathways to hepatic glycogen formation following a glucose load given to humans four hours after a substantial breakfast have been examined. Glucose loads labeled with [6-( 14 )C]glucose were given to six healthy volunteers along with diflunisal (1 g) or acetaminophen (1.5 g), drugs excreted in urine as glucuronides. Distribution of 14 C in the glucose unit of the glucuronide was taken as a measure of the extent to which glucose was deposited directly in liver glycogen (ie, glucose----glucose-6-phosphate----glycogen) rather than indirectly (ie, glucose----C3-compound----glucose-6-phosphate----glycogen). The maximum contribution to glycogen formation by the direct pathway was estimated to be 77% +/- 4%, which is somewhat higher than previous estimates in humans fasted overnight (65% +/- 1%, P less than 0.05). Thus, the indirect pathway of liver glycogen formation following a glucose load is operative in both the overnight fasted and the fed state, although its contribution may be somewhat less in the fed state

The formation of urea in space. I. Ion-molecule, neutral-neutral, and radical gas-phase reactions

Science.gov (United States)

Brigiano, Flavio Siro; Jeanvoine, Yannick; Largo, Antonio; Spezia, Riccardo

2018-02-01

Context. Many organic molecules have been observed in the interstellar medium thanks to advances in radioastronomy, and very recently the presence of urea was also suggested. While those molecules were observed, it is not clear what the mechanisms responsible to their formation are. In fact, if gas-phase reactions are responsible, they should occur through barrierless mechanisms (or with very low barriers). In the past, mechanisms for the formation of different organic molecules were studied, providing only in a few cases energetic conditions favorable to a synthesis at very low temperature. A particularly intriguing class of such molecules are those containing one N-C-O peptide bond, which could be a building block for the formation of biological molecules. Urea is a particular case because two nitrogen atoms are linked to the C-O moiety. Thus, motivated also by the recent tentative observation of urea, we have considered the synthetic pathways responsible to its formation. Aims: We have studied the possibility of forming urea in the gas phase via different kinds of bi-molecular reactions: ion-molecule, neutral, and radical. In particular we have focused on the activation energy of these reactions in order to find possible reactants that could be responsible for to barrierless (or very low energy) pathways. Methods: We have used very accurate, highly correlated quantum chemistry calculations to locate and characterize the reaction pathways in terms of minima and transition states connecting reactants to products. Results: Most of the reactions considered have an activation energy that is too high; but the ion-molecule reaction between NH2OHNH2OH2+ and formamide is not too high. These reactants could be responsible not only for the formation of urea but also of isocyanic acid, which is an organic molecule also observed in the interstellar medium.

Nonmonotonic Temperature Dependence of the Pressure-Dependent Reaction Rate Constant and Kinetic Isotope Effect of Hydrogen Radical Reaction with Benzene Calculated by Variational Transition-State Theory.

Science.gov (United States)

Zhang, Hui; Zhang, Xin; Truhlar, Donald G; Xu, Xuefei

2017-11-30

The reaction between H and benzene is a prototype for reactions of radicals with aromatic hydrocarbons. Here we report calculations of the reaction rate constants and the branching ratios of the two channels of the reaction (H addition and H abstraction) over a wide temperature and pressure range. Our calculations, obtained with an accurate potential energy surface, are based on variational transition-state theory for the high-pressure limit of the addition reaction and for the abstraction reaction and on system-specific quantum Rice-Ramsperger-Kassel theory calibrated by variational transition-state theory for pressure effects on the addition reaction. The latter is a very convenient way to include variational effects, corner-cutting tunneling, and anharmonicity in falloff calculations. Our results are in very good agreement with the limited experimental data and show the importance of including pressure effects in the temperature interval where the mechanism changes from addition to abstraction. We found a negative temperature effect of the total reaction rate constants at 1 atm pressure in the temperature region where experimental data are missing and accurate theoretical data were previously missing as well. We also calculated the H + C 6 H 6 /C 6 D 6 and D + C 6 H 6 /C 6 D 6 kinetic isotope effects, and we compared our H + C 6 H 6 results to previous theoretical data for H + toluene. We report a very novel nonmonotonic dependence of the kinetic isotope effect on temperature. A particularly striking effect is the prediction of a negative temperature dependence of the total rate constant over 300-500 K wide temperature ranges, depending on the pressure but generally in the range from 600 to 1700 K, which includes the temperature range of ignition in gasoline engines, which is important because aromatics are important components of common fuels.

Synthesising and comparing electrical properties of NTC thermistors prepared from nano powder and solid state reaction

International Nuclear Information System (INIS)

Azad, N.; Ghanbari Shohany, B.; Hosseini, S. M.; Kompany, A.

2011-01-01

In this research, NTC thermistors with composition of NiMn 2-x Co x O 4 (x = 0.4, 0.8, 1.2, 1.6) prepared by two methods: solid state reaction and sol-gel (gel-combustion). The average particle size was monitored and structure of the calcinated powders have been investigated using x-ray diffraction and tunneling electron microscopy techniques. The average particle size was estimated to be about 65 nm with the cubic and cubic + tetragonal phases for low and high cobalt concentrations, respectively. The grain size of samples verifies with scanning electron microscopy images. Upon increasing the cobalt fraction, the grain size of samples increases from about 2μm to a few μm in size. The electrical properties of these thermistors depend on the grain size. The grain size of samples made from sol-gel is smaller than from solid state reaction under the same condition. For longer sintering time of the samples prepared by gel-combustion method, the grain size was increased then the electrical parameters of nano powder improved and we obtain better results than the samples prepared from solid state 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.

Stability and isomerization reactions of phenyl cation C{sub 6}H{sub 5}{sup +} isomers

Energy Technology Data Exchange (ETDEWEB)

Shi, Dandan [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Yang, Xue [College of Science, Jilin Institute of Chemical Technology, Jilin 132022 (China); Zhang, Xiaomei; Shan, Shimin [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Xu, Haifeng, E-mail: xuhf@jlu.edu.cn [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Yan, Bing, E-mail: yanbing@jlu.edu.cn [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China)

2016-03-01

Highlights: • A total of 60 isomers of C{sub 6}H{sub 5}{sup +} cations were obtained at density functional theory. • The stability and isomerization reactions of C{sub 6}H{sub 5}{sup +} isomers were performed. • The structures, frequencies, thermodynamic properties of isomers were summarized. • Ring to ring or chain isomerization pathways were investigated using IRC method. • Result shows reactions contain hydrogen transfer, bond broken and reconstruction. - Abstract: As a key polyatomic molecular cation that plays a pivotal role in growth of the polycyclic aromatic hydrocarbons, phenyl cation C{sub 6}H{sub 5}{sup +} exhibits various isomers and isomerization reactions. Investigation on the structure and stability of the isomers as well as the isomerization is important for better understanding the chemical reactions involving C{sub 6}H{sub 5}{sup +} cations. In this work, we have performed a theoretical study on the stability and isomerization reactions of C{sub 6}H{sub 5}{sup +} isomers at density functional theory B3LYP/6-311G (d, p) level. We have obtained a total of 60 isomers of C{sub 6}H{sub 5}{sup +} cations, most of which are reported for the first time. The geometries, vibrational frequencies, thermodynamic properties and stability of 28 out of 60 isomers have been summarized in detail. Different ring-to-ring and ring-to-chain isomerization pathways, which are connected via 28 transition states, have been investigated using the intrinsic reaction coordinate method. The results show that the isomerization reactions occur via hydrogen migration followed by bond-breaking and reconstruction.

Reactive ground-state pathways are not ubiquitous in red/green cyanobacteriochromes.

Science.gov (United States)

Chang, Che-Wei; Gottlieb, Sean M; Kim, Peter W; Rockwell, Nathan C; Lagarias, J Clark; Larsen, Delmar S

2013-09-26

Recent characterization of the red/green cyanobacteriochrome (CBCR) NpR6012g4 revealed a high quantum yield for its forward photoreaction [J. Am. Chem. Soc. 2012, 134, 130-133] that was ascribed to the activity of hidden, productive ground-state intermediates. The dynamics of the pathways involving these ground-state intermediates was resolved with femtosecond dispersed pump-dump-probe spectroscopy, the first such study reported for any CBCR. To address the ubiquity of such second-chance initiation dynamics (SCID) in CBCRs, we examined the closely related red/green CBCR NpF2164g6 from Nostoc punctiforme. Both NpF2164g6 and NpR6012g4 use phycocyanobilin as the chromophore precursor and exhibit similar excited-state dynamics. However, NpF2164g6 exhibits a lower quantum yield of 32% for the generation of the isomerized Lumi-R primary photoproduct, compared to 40% for NpR6012g4. This difference arises from significantly different ground-state dynamics between the two proteins, with the SCID mechanism deactivated in NpF2164g6. We present an integrated inhomogeneous target model that self-consistently fits the pump-probe and pump-dump-probe signals for both forward and reverse photoreactions in both proteins. This work demonstrates that reactive ground-state intermediates are not ubiquitous phenomena in CBCRs.

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 ...

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

Possible reaction pathways of the lincomycin molecule according to the DFT calculation method

Directory of Open Access Journals (Sweden)

Eren Bahar

2017-01-01

Full Text Available Human-used antibiotics are eliminated from the body with little or no transformation at all. Traces of eliminated antibiotics enter the receiving environment directly since they cannot be treated in prevalent wastewater treatment facilities. Thus, wastewaters containing traces of antibiotics have to be treated accordingly. Lincomycin is subsequently isolated from Streptomyces lincolnensis. Lincomycin and its derivatives are antibiotics exhibiting biological activity against Gram-positive bacteria, and are natural antibiotics in the environment as pollutants. This study aims to predict the degradation mechanism of lincomycin molecule in the gaseous phase and aqueous media. Probable reaction path of lincomycin molecule with OH radicals was analyzed. Optimized geometry was calculated via Gauss View 5. Subsequently, the lowest energy status was determined through geometric optimization via Gaussian 09 program. Aiming to determine the intermediates in photocatalytic degradation mechanism of lincomycin, geometric optimization of the molecule was realized through DFT method. Activation energy for the probable reaction path was calculated, and their most stable state from the thermodynamic perspective determined for the gaseous phase and aqueous media. Impact of water solvent was investigated using the conductor-like screening solvation model (COSMO. The predicted mechanism was confirmed by comparison with experimental results on simple structures reported in literature.

The TDF System for Thermonuclear Plasma Reaction Rates, Mean Energies and Two-Body Final State Particle Spectra

International Nuclear Information System (INIS)

Warshaw, S I

2001-01-01

The rate of thermonuclear reactions in hot plasmas as a function of local plasma temperature determines the way in which thermonuclear ignition and burning proceeds in the plasma. The conventional model approach to calculating these rates is to assume that the reacting nuclei in the plasma are in Maxwellian equilibrium at some well-defined plasma temperature, over which the statistical average of the reaction rate quantity σv is calculated, where σ is the cross-section for the reaction to proceed at the relative velocity v between the reacting particles. This approach is well-understood and is the basis for much nuclear fusion and astrophysical nuclear reaction rate data. The Thermonuclear Data File (TDF) system developed at the Lawrence Livermore National Laboratory (Warshaw 1991), which is the topic of this report, contains data on the Maxwellian-averaged thermonuclear reaction rates for various light nuclear reactions and the correspondingly Maxwellian-averaged energy spectra of the particles in the final state of those reactions as well. This spectral information closely models the output particle and energy distributions in a burning plasma, and therefore leads to more accurate computational treatments of thermonuclear burn, output particle energy deposition and diagnostics, in various contexts. In this report we review and derive the theoretical basis for calculating Maxwellian-averaged thermonuclear reaction rates, mean particle energies, and output particle spectral energy distributions for these reactions in the TDF system. The treatment of the kinematics is non-relativistic. The current version of the TDF system provides exit particle energy spectrum distributions for two-body final state reactions only. In a future report we will discuss and describe how output particle energy spectra for three- and four-body final states can be developed for the TDF system. We also include in this report a description of the algorithmic implementation of the TDF

Dynamics of anion-molecule reactions at low energy

International Nuclear Information System (INIS)

Mikosch, J.

2007-11-01

Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S N 2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S N 2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S N 2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S N 2 mechanism involving CH 3 -rotation. (orig.)

Dynamics of anion-molecule reactions at low energy

Energy Technology Data Exchange (ETDEWEB)

Mikosch, J.

2007-11-15

Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S{sub N}2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S{sub N}2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S{sub N}2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S{sub N}2 mechanism involving CH{sub 3}-rotation. (orig.)

Efficient Computation of Transition State Resonances and Reaction Rates from a Quantum Normal Form

NARCIS (Netherlands)

Schubert, Roman; Waalkens, Holger; Wiggins, Stephen

2006-01-01

A quantum version of a recent formulation of transition state theory in phase space is presented. The theory developed provides an algorithm to compute quantum reaction rates and the associated Gamov-Siegert resonances with very high accuracy. The algorithm is especially efficient for

Formation of amorphous Ti-50at.%Pt by solid state reactions during mechanical alloying

CSIR Research Space (South Africa)

Mahlatji, ML

2013-10-01

Full Text Available Mechanical alloying of an equiatomic mixture of crystalline elemental powders of Ti and Pt in a high-energy ball mill results in formation of an amorphous alloy by solid-state reactions. Mechanical alloying was carried out in an argon atmosphere...

Generalized transition state theory. Quantum effects for collinear reactions of hydrogen molecules and isotopically substituted hydrogen molecules

International Nuclear Information System (INIS)

Garrett, B.C.; Truhlar, D.G.

1979-01-01

Canonical variational transition state theory, microcanonical variational transition state theory, and Miller's unified statistical theory were used in an attempt to correct two major deficiencies of the conventional transition state theory. These are: (1) the necessity of extra assumptions to include quantum mechanical tunneling effects and (2) the fundamental assumption that trajectories crossing a dividing surface in phase space proceed directly to products. The accuracy of these approximate methods were tested by performing calculations for several collinear reactions of hydrogen, deuterium, chlorine, or iodine, with five isotopes of hydrogen molecules and comparison of these results with those from accurate quantitative calculations of the reaction probabilities as functions of energy and of the thermal rate constants as functions of temperature. 49 references, 28 figures, 17 tables

Photo- and radiation chemical studies of intermediates involved in excited-state electron-transfer reactions

International Nuclear Information System (INIS)

Hoffman, M.Z.

1985-01-01

Excited-state inter- and intramolecular electron-transfer reactions lie at the heart of the most photochemical solar energy conversion schemes. The authors research, which has utilized the techniques of continuous and pulsed photolysis and radiolysis, has focused on three general aspects of these reactions involving transition metal coordination complexes and electron donor-acceptor complexes: i) the effect of solution medium on the properties and quenching of the excited states; ii) the control of the quantum yields of formation of redox products; iii) the mechanism by which reduced species interact with water to yield H 2 homogeneously and heterogeneously. EDTA is among the most popular sacrificial electron donors used in model systems. Its role is to scavenge the oxidized form of the photosensitizer in order to prevent its rapid reaction with the reduced form of the electron relay species that results from the electron-transfer quenching of the excited photosensitizer. In systems involving MV 2+ , the radicals resulting from the oxidation of EDTA can eventually lead to the generation of a second equivalent of MV + ; the reducing agent is believed to be a radical localized on the carbon atom alpha to the carboxylate group. The reaction of radiolytically-generated OH/H with EDTA produces this radical directly via H-abstraction or indirectly via deprotonation of the carbon atom adjacent to the nitrogen radical site in the oxidized amine moiety; it reduces MV 2+ with rate constants of 2.8 x 10 9 , 7.6 x 10 9 , and 8.5 x 10 6 M -1 s -1 at pH 12.5, 8.3, and 4.7, respectively. Degradative decarboxylation of EDTA-radicals and their back electron-transfer reactions are enhanced in acidic solution causing the yield of MV + to be severely diminished

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.

Rotational state dependence of ion-polar molecule reactions at very low temperature

International Nuclear Information System (INIS)

Dubernet, M.L.; McCarroll, R.

1989-01-01

The adiabatic rotational state method is used to investigate the rotational state dependence of the rate coefficients for ion-polar molecule reactions in the very low temperature regime characteristic of interstellar molecular clouds. Results obtained for the systems H 3 + +HCl and H 3 + +HCN indicate that all the methods based on the adiabatic separation of the rotational and radial motion of the collision complex - adiabatic capture centrifugal sudden approximation (ACCSA), statistical adiabatic channel model, classical adiabatic invariance method - agree very satisfactorily in the low temperature limit. Discrepancies observed between some of the published data would appear to arise from numerical inaccuracies rather than from any defect of the theory. (orig.)

Theoretical study of the oxidation mechanisms of naphthalene initiated by hydroxyl radicals: the O2 addition reaction pathways.

Science.gov (United States)

Shiroudi, A; Deleuze, M S; Canneaux, S

2015-05-28

Atmospheric oxidation of the naphthalene-OH adduct [C10H8OH]˙ (R1) by molecular oxygen in its triplet electronic ground state has been studied using density functional theory along with the B3LYP, ωB97XD, UM05-2x and UM06-2x exchange-correlation functionals. From a thermodynamic viewpoint, the most favourable process is O2 addition at the C2 position in syn mode, followed by O2 addition at the C2 position in anti mode, O2 addition at the C4 position in syn mode, and O2 addition at the C4 position in anti mode, as the second, third and fourth most favourable processes. The syn modes of addition at these positions are thermodynamically favoured over the anti ones by the formation of an intramolecular hydrogen bond between the hydroxyl and peroxy substituents. Analysis of the computed structures, bond orders and free energy profiles demonstrate that the reaction steps involved in the oxidation of the naphthalene-OH adduct by O2 satisfy Hammond's principle. Kinetic rate constants and branching ratios under atmospheric pressure and in the fall-off regime have been supplied, using transition state and RRKM theories. By comparison with experiment, these data confirm the relevance of a two-step reaction mechanism. Whatever the addition mode, O2 addition in C4 position is kinetically favoured over O2 addition in C2 position, in contrast with the expectations drawn from thermodynamics and reaction energies. Under a kinetic control of the reaction, and in line with the computed reaction energy barriers, the most efficient process is O2 addition at the C4 position in syn mode, followed by O2 addition at the C2 position in syn mode, O2 addition at the C4 position in anti mode, and O2 addition at the C2 position in anti mode as the second, third and fourth most rapid processes. The computed branching ratios also indicate that the regioselectivity of the reaction decreases with increasing temperatures and decreasing pressures.

0+ analogue state in 118Sb from 117Sn(p,nγ) reaction

International Nuclear Information System (INIS)

Pal, J.; Dey, C.C.; Bose, S.; Sinha, B.K.; Chatterjee, M.B.; Mahapatra, D.P.

1996-01-01

The analogue of the 0 + ground state in 118 Sn has been observed in the compound nucleus 118 Sb through 117 Sn(p,nγ) 117 Sb reaction. The neutron decays of this analogue resonance have been studied from the deexciting γ-rays of the residual nucleus 117 Sb. From off resonance excitation functions, spin assignments have been made to states in 117 Sb, on the basis of Hauser-Feshbach formalism. The resonance parameters of the isobaric analogue resonance have been determined, including the total, proton and neutron decay widths. (orig.)

Studies in the reaction dynamics of beam-gas chemiluminescent reactions

International Nuclear Information System (INIS)

Prisant, M.G.

1984-01-01

This thesis develops techniques for the analysis and interpretation of data obtained from beam-gas chemiluminescence experiments. These techniques are applied to experimental studies of atom transfer reactions of the type A + BC → AB + C. A procedure is developed for determining the product rotational alignment in the center-of-mass frame from polarization measurements of chemiluminescent atom-diatom exchange reactions under beam-gas conditions. Knowledge of a vector property of a reaction, such as product alignment, provides information on the disposition of angular momentum by a chemical reaction. Fluorescence polarization and hence product alignment are measured for two prototype reactions. The reaction of metastable calcium atoms with hydrogen-chloride gas yields highly aligned calcium-chloride product which exhibits little variation of alignment with vibrational state. The reaction of ground-state calcium with fluorine gas yields moderately aligned product which shows strong variation of alignment with vibration. A multi-surface direct-interaction model is developed to interpret product alignment and population data. The predictions of this model for the reaction of calcium with fluorine show reasonable agreement with experiment

Comparison of 3D Classical Trajectory and Transition-State Theory Reaction Cross Sections

Science.gov (United States)

Koeppl, G. W.; Karplus, Martin

1970-10-01

Although there is excellent agreement for a system such as H+H{sub 2} --> H{sub 2}+H, in which both the potential and the particle masses are symmetric, significant deviations occur for more asymmetric reactions. A detailed analysis show that the calculated differences are from the violation of two assumptions of transition-state theory.

An ab initio potential energy surface for the reaction N+ + H2→ NH+ + H

International Nuclear Information System (INIS)

Gittins, M.A.; Hirst, D.M.

1975-01-01

Preliminary results of ab initio unrestricted Hartree-Fock calculations for the potential energy surface for the reaction N + + H 2 →NH + + H are reported. For the collinear approach of N + to H 2 , the 3 Σ - surface has no activation barrier and has a shallow well (ca.1eV). For perpendicular approach (Csub(2V)symmetry) the 3 B 2 states is of high energy, the 3 A 2 state has a shallow well but as the bond angle increases the 3 B 1 states decreases in energy to become the state of lowest energy. Neither the collinear nor the perpendicular approaches give adiabatic pathways to the deep potential well of 3 B 1 (HNH) + . (auth.)

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).

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 ...

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.

Coating of graphite flakes with MgO/carbon nanocomposite via gas state reaction

International Nuclear Information System (INIS)

Sharif, M.; Faghihi-Sani, M.A.; Golestani-Fard, F.; Saberi, A.; Soltani, Ali Khalife

2010-01-01

Coating of graphite flakes with MgO/carbon nanocomposite was carried out via gaseous state reaction between mixture of Mg metal, CO gas and graphite flakes at 1000 o C. XRD and FE-SEM analysis of coating showed that the coating was comprised of MgO nano particles and amorphous carbon distributed smoothly and covered the graphite surface evenly. Thermodynamic calculations were employed to predict the reaction sequences as well as phase stability. The effect of coating on water wettability and oxidation resistance of graphite was studied using contact angle measurement and TG analysis, respectively. It was demonstrated that the reaction between Mg and CO could result in MgO/C nanocomposite deposition. The coating improved water wettability of graphite and also enhanced the oxidation resistance of graphite flakes significantly. Also the graphite coating showed significant phenolic resin-wettabilty owing to high surface area of such hydrophilic nano composite coating. The importance of graphite coating is explained with emphasis on its potential application in graphite containing refractories.

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...

Quantitative Assays for RAS Pathway Proteins and Phosphorylation States

Science.gov (United States)

The NCI CPTAC program is applying its expertise in quantitative proteomics to develop assays for RAS pathway proteins. Targets include key phosphopeptides that should increase our understanding of how the RAS pathway is regulated.

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.

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles.

Science.gov (United States)

Kitayama, Tomoya; Kinoshita, Ayako; Sugimoto, Masahiro; Nakayama, Yoichi; Tomita, Masaru

2006-07-17

In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles.

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles

Directory of Open Access Journals (Sweden)

Sugimoto Masahiro

2006-07-01

Full Text Available Abstract Background In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. Results The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. Conclusion The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles.

Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation.

Directory of Open Access Journals (Sweden)

Andrea Ciliberto

2007-03-01

Full Text Available In metabolic networks, metabolites are usually present in great excess over the enzymes that catalyze their interconversion, and describing the rates of these reactions by using the Michaelis-Menten rate law is perfectly valid. This rate law assumes that the concentration of enzyme-substrate complex (C is much less than the free substrate concentration (S0. However, in protein interaction networks, the enzymes and substrates are all proteins in comparable concentrations, and neglecting C with respect to S0 is not valid. Borghans, DeBoer, and Segel developed an alternative description of enzyme kinetics that is valid when C is comparable to S0. We extend this description, which Borghans et al. call the total quasi-steady state approximation, to networks of coupled enzymatic reactions. First, we analyze an isolated Goldbeter-Koshland switch when enzymes and substrates are present in comparable concentrations. Then, on the basis of a real example of the molecular network governing cell cycle progression, we couple two and three Goldbeter-Koshland switches together to study the effects of feedback in networks of protein kinases and phosphatases. Our analysis shows that the total quasi-steady state approximation provides an excellent kinetic formalism for protein interaction networks, because (1 it unveils the modular structure of the enzymatic reactions, (2 it suggests a simple algorithm to formulate correct kinetic equations, and (3 contrary to classical Michaelis-Menten kinetics, it succeeds in faithfully reproducing the dynamics of the network both qualitatively and quantitatively.

Vibronic coupling in ionized organic molecules. Structural distortions and chemical reactions

International Nuclear Information System (INIS)

Williams, F.

2002-01-01

Complete text of publication follows. Ionized organic molecules (radical cations, RC) are prone to undergo vibronic coupling whenever there is a relatively small energy gap ( 2v point group of the neutral parent molecule by twisting at the olefinic π bond to the lower C 2 symmetry in the RC (Chem. Eur. J. 2002, 8, 1074). These experiments clearly revealed a double minimum in the potential energy surface along the a 2 torsional mode. This is in accord with the coupling of the 2 B 1 and 2 B 2 Born-Oppenheimer states in C 2v symmetry, this mixing of the 2 B 1 π-ionized ground state and the 2 B 2 δ-ionized excited state being facilitated by the low (∼ 1.0 eV) gap between these states, as estimated from photoelectron spectroscopy. Turning to the second class of RC where unimolecular rearrangement reactions are promoted by vibronic interaction, several cases have emerged where the rearrangement would not be expected if it were based only on the ground-state properties of the RC. It was found (Chem. Phy. Lett. 1988, 143, 521) that the ethylene oxide RC undergoes C-C ring opening to the oxallyl species despite the fact that the ground state corresponds to ionization from the nonbonding oxygen π lone-pair orbital. The reaction develops excited-state character as a result of the vibronic mixing so that the activation barrier to ring opening is lowered. We will discuss the unusual rearrangements of the bicyclo[1.1.1.]pentane and [1.1.1]propellane RC from a similar perspective, emphasis being placed on the decisive role of symmetry in predicting the course of these rearrangements. We illustrate how this approach can reconcile conflicting considerations on some of the 'unexpected' reaction pathways followed by highly strained organic RC

Computer simulation of the steam--graphite reaction under isothermal and steady-state conditions

International Nuclear Information System (INIS)

Joy, D.S.; Stem, S.C.

1975-05-01

A mathematical model was formulated to describe the isothermal, steady-state diffusion and reaction of steam in a graphite matrix. A generalized Langmuir-Hinshelwood equation is used to represent the steam-graphite reaction rate. The model also includes diffusion in the gas phase adjacent to the graphite matrix. A computer program, written to numerically integrate the resulting differential equations, is described. The coupled nonlinear differential equations in the graphite phase are solved using the IBM Continuous System Modeling Program. Classical finite difference techniques are used for the gas-phase calculations. An iterative procedure is required to couple the two sets of calculations. Several sample problems are presented to demonstrate the utility of the model. (U.S.)

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.

Carbonyl-Olefin Exchange Reaction: Present State and Outlook

Science.gov (United States)

Kalinova, Radostina; Jossifov, Christo

The carbonyl-olefin exchange reaction (COER) is a new reaction between carbonyl group and olefin double bond, which has a formal similarity with the olefin metathesis (OM) - one carbon atom in the latter is replaced with an oxygen atom. Till now the new reaction is performed successfully only when the two functional groups (carbonyl group and olefin double bond) are in one molecule and are conjugated. The α, β-unsaturated carbonyl compounds (substituted propenones) are the compounds with such a structure. They polymerize giving substituted polyacetylenes. The chain propagation step of this polymerization is in fact the COER. The question arises: is it possible the COER to take place when the two functional groups are not in one molecule and are not conjugated, and could this reaction became an alternative of the existing carbonyl olefination reactions?

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.

Nucleophilic radioiodination of 6-bromocholesterol via non-isotopic exchange reaction in molten state

International Nuclear Information System (INIS)

El-Shaboury, G.; Farah, K.; El-Tawoosy, M.

2001-01-01

A synthetic method for preparing radioiodinated 6-[ 125 I]iodocholesterol [CL-6- 125 I] for adrenal evaluation is described. The radioiodine atom was incorporated onto the cholesterol molecule via non-isotopic exchange between 6-bromocholesterol [CL-6-Br] and radioiodine as iodide ion [ 125 I - ] in a molten state. The different parameters affecting the yield of exchange were investigated using 125 I (T 1/2 ≅ 60 d) to centralize the different physical and chemical reaction conditions and purification of the final product as pure as 6-[ 125 I]iodocholesterol. The method was suitable to either 131 I (T 1/2 ≅ 8 d) nucleophilic radioiodination which facilitates the scanning of the adrenal for a few days after administration or the use of 124 I (T 1/2 ≅ 4.16 d) nucleophilic radioiodination for PET evaluation of the adrenal. TLC as well as HPLC chromatographic analysis is used to determine the efficiency of the exchange reactions under different chemical reaction conditions and to monitor the stability of the final product as pure as CL-6- 125 I with radiochemical purity of ≅99%. This no-carrier-added method improved the speed of the reaction and affords high radiochemical yield of 90% and suitable specific activity due to the use of CL-6-Br rather than CL-6-I as substrate. Kinetic studies revealed second order iodine-bromine exchange reaction. The activation energy for the exchange reaction in ammonium acetate (m.p. 114 deg C) was calculated to be 4.576 kcal/mole. (author)

Characteristic 7- and 5- states observed in the (p,t) reactions on even-even rare earth nuclei

International Nuclear Information System (INIS)

Ishizaki, Y.; Kubono, S.; Iwasaki, Y.

1984-01-01

The (p,t) reactions have been studied for the even-even rare earth nuclei with 40 MeV proton beam from the INS SF cyclotron. A pair of 7 - and 5 - states was observed with large cross sections in each of the nuclei with the neutron number (N) ranging from 86 to 100. For sup(140,142)Nd of N = 80 and 82 the data were obtained at KVI in Groningen, and the data for 152 Sm of N = 90 at MSU. Q value systematics of (p,t) reactions to these states seem to suggest that these are excited by the two neutron pick-up from the neutron core of N = 82. The (p,t) cross sections leading to these states of N from 82 to 96 are nearly constant. (author)

Thermal rate coefficients in collinear versus bent transition state reactions: the N+N{sub 2} case study

Energy Technology Data Exchange (ETDEWEB)

Lagana, Antonio; Faginas Lago, Noelia; Rampino, Sergio [Dipartimento di Chimica, Universita di Perugia, 06123 Perugia (Italy); Huarte-Larranaga, FermIn [Computer Simulation and Modeling Lab (CoSMoLab), Parc CientIfic de Barcelona, 08028 Barcelona (Spain); GarcIa, Ernesto [Departamento de Quimica Fisica, Universidad del PaIs Vasco, 01006 Vitoria (Spain)], E-mail: lagana05@gmail.com, E-mail: fhuarte@pcb.ub.es, E-mail: e.garcia@ehu.es

2008-10-15

Zero total angular momentum exact quantum calculations of the probabilities of the N+N{sub 2} reaction have been performed on the L3 potential energy surface having a bent transition state. This has allowed us to work out J-shifting estimates of the thermal rate coefficient based on the calculation of either detailed (state-to-state) or cumulative (multiconfiguration) probabilities. The results obtained are used to compare the numerical outcomes and the concurrent computational machineries of both quantum and semiclassical approaches as well as to exploit the potentialities of the J-shifting model. The implications of moving the barrier to reaction from the previously proposed collinear geometry of the LEPS to the bent one of L3 are also investigated by comparing the related detailed reactive probabilities.

The effect of B_2O_3 flux on growth NLBCO superconductor by solid state reaction and wet-mixing methods

International Nuclear Information System (INIS)

Suharta, W. G.; Wendri, N.; Ratini, N.; Suarbawa, K. N.

2016-01-01

The synthesis of B_2O_3 flux substituted NLBCO superconductor NdBa_1_._7_5La_0_._2_5Cu_3O_7_-_∂ has been done using solid state reaction and wet-mixing methods in order to obtain homogeneous crystals and single phase. From DTA/TGA characteritations showed the synthesis process by wet-mixing requires a lower temperature than the solid state reaction in growing the superconductor NdBa_1_._7_5La_0_._2_5Cu_3O_7_-_∂. Therefore, in this research NdBa_1_._7_5La_0_._2_5Cu_3O_7_-_∂ sample calcinated at 650°C for wet-mixing method and 820°C for solid state reaction methods. The all samples was sintered at 950°C for ten hours. Crystallinity of the sample was confirmed using X-ray techniques and generally obtained sharp peaks that indicates the sample already well crystallized. Search match analyses for diffraction data gave weight fractions of impurity phase of the solid state reaction method higher than wet-mixing method. In this research showed decreasing the price of the lattice parameter about 1% with the addition of B_2O_3 flux for the both synthesis process and 2% of wet mixing process for all samples. Characterization using scanning electron microscopy (SEM) showed the distribution of crystal zise for wet-mixing method more homogeneous than solid state reaction method, with he grain size of samples is around 150–250 nm. The results of vibrating sample magnetometer (VSM) showed the paramagnetic properties for all samples.

CuInSe2 nano-crystallite reaction kinetics using solid state reaction from Cu2Se and In2Se3 powders

International Nuclear Information System (INIS)

Hsiang, Hsing-I; Lu, Li-Hsin; Chang, Yu-Lun; Ray, Dahtong; Yen, Fu-Su

2011-01-01

Highlights: → CuInSe 2 phase increased gradually accompanied with a decrease in γ-In 2 Se 3 and no intermediate phase during calcination. → CuInSe 2 formation from Cu 2 Se and In 2 Se 3 powders follows a one-dimensional diffusion-controlled reaction with apparent activation energy of about 122.5 kJ/mol. → The solid reaction kinetics may be dominated by the diffusion of In 3+ ions. - Abstract: The reaction mechanism and CuInSe 2 formation kinetics using a solid state reaction from Cu 2 Se and In 2 Se 3 powders synthesized using a heating up process were investigated using X-ray diffractomy (XRD) and transmission electron microscopy (TEM). It was observed that the CuInSe 2 phase increased gradually, accompanied with a decrease in γ-In 2 Se 3 with no intermediate phase as the calcination temperature and soaking time were increased. The reaction kinetics was analyzed using the Avrami and polynomial kinetic model, suggesting that CuInSe 2 formation from Cu 2 Se and In 2 Se 3 powders follows a diffusion-controlled reaction with an apparent activation energy of about 122.5-182.3 kJ/mol. Cu 2 Se and In 2 Se 3 phases react and directly transform into CIS without the occurrence of any intermediate phase and the size of the newly formed CuInSe 2 crystallites was close to that of the Cu 2 Se reactant particle based on the TEM results, which indicated that the solid reaction kinetics may be dominated by the diffusion of In 3+ ions.

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.

Methylation reactions, the redox balance and atherothrombosis: the search for a link with hydrogen sulfide.

Science.gov (United States)

Lupoli, Roberta; Di Minno, Alessandro; Spadarella, Gaia; Franchini, Massimo; Sorrentino, Raffaella; Cirino, Giuseppe; Di Minno, Giovanni

2015-06-01

It is now clear that homocysteine (Hcy) is irreversibly degraded to hydrogen sulfide (H(2)S), an endogenous gasotransmitter that causes in vivo platelet activation via upregulation of phospholipase A2 and downstream boost of the arachidonate cascade. This mechanism involves a transsulfuration pathway. Based on these new data, clinical and experimental models on the relationships between Hcy and folate pathways in vascular disease and information on the Hcy controversy have been reanalyzed in the present review. Most interventional trials focused on Hcy lowering by folate administration did not exclude patients routinely taking the arachidonate inhibitor aspirin. This may have influenced the results of some of these trials. It is also clear that nutritional intake of folate affects several enzymatic reactions of the methionine-Hcy cycle and associated one-carbon metabolism and, thereby, both methylation reactions and redox balance. Hence, it is conceivable that the abnormally high Hcy levels seen in pathologic states reflect a poorly elucidated perturbation of such reactions and of such balance. While it is unknown whether there is an interplay between H2S, methylation reactions, and redox balance, measuring the sole reduction of blood Hcy that follows folate administration may well be an oversimplified approach to a complex biologic perturbation. The need to investigate this complex framework is thoroughly discussed in this article. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

On experimental determination of characteristics of nuclear fusion reactions from mu-molecular resonance states

International Nuclear Information System (INIS)

Bystritskij, V.M.; Pen'kov, F.M.

1997-01-01

Charge-nonsymmetrical deuterium-helium muon complexes (dμHe) are studied. A method is proposed for experimentally determining the rates of nuclear fusion reactions in dμHe molecules in the J=1 and J=0 states (J is the orbital moment of the system) and the partial rates for radiative decay of these complexes in these states. Experiments are supposed to be carried out at meson factories with gaseous and cryogenic targets filled with a mixture of deuterium and helium

Theoretical investigation of the oxidation pathways of the Cl-initiated reaction of 2-methyl-3-buten-2-ol

Science.gov (United States)

Zhang, Weichao; Zhang, Dongju

2012-12-01

The mechanism and products of the reaction of 2-methyl-3-buten-2-ol (MBO232) with Cl atoms in the presence of O2 have been elucidated by performing high-level quantum chemistry calculations. The geometries of the reactants, intermediates, transition states, and products are optimized at the MP2(full)/6-311G(d, p) level, and their single-point energies are refined at the CCSD(T)/6-311 + G(d, p) level. The potential energy surface profiles have been constructed at the CCSD(T)/6-311 + G(d, p)//MP2(full)/6-311G(d, p) + 0.95 × ZPE level of theory, and the possible channels involved in the reaction are also discussed. The calculations indicate that the reaction predominantly proceeds via the addition of Cl atoms to the double bond rather than the direct abstraction of the H atoms in MBO232. The nascent adducts (CH3)2C(OH)CHCH2Cl (IM1) and (CH3)2C(OH)CHClCH2 (IM2) do not undergo subsequent isomerization and dissociation reactions, but rather react with O2. The theoretical results show that the major products are CH2ClCHO and CH3C(O)CH3 for the reaction of MBO232 + Cl in the presence of O2, which is in good agreement with the experimental finding.

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

Quenching reactions of electronically excited atoms

International Nuclear Information System (INIS)

Setser, D.W.

2001-01-01

The two-body, thermal quenching reactions of electronically excited atoms are reviewed using excited states of Ar, Kr, and Xe atoms as examples. State-specific interstate relaxation and excitation-transfer reactions with atomic colliders are discussed first. These results then are used to discuss quenching reactions of excited-state atoms with diatomic and polyatomic molecules, the latter have large cross sections, and the reactions can proceed by excitation transfer and by reactive quenching. Excited states of molecules are not considered; however, a table of quenching rate constants is given for six excited-state molecules in an appendix

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.

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

A procurement-based pathway for promoting public health: innovative purchasing approaches for state and local government agencies.

Science.gov (United States)

Noonan, Kathleen; Miller, Dorothy; Sell, Katherine; Rubin, David

2013-11-01

Through their purchasing powers, government agencies can play a critical role in leveraging markets to create healthier foods. In the United States, state and local governments are implementing creative approaches to procuring healthier foods, moving beyond the traditional regulatory relationship between government and vendors. They are forging new partnerships between government, non-profits, and researchers to increase healthier purchasing. On the basis of case examples, this article proposes a pathway in which state and local government agencies can use the procurement cycle to improve healthy eating.

Quadrupole-octupole coupled states in 112Cd populated in the 111Cd(d ⃗,p ) reaction

Science.gov (United States)

Jamieson, D. S.; Garrett, P. E.; Bildstein, V.; Demand, G. A.; Finlay, P.; Green, K. L.; Leach, K. G.; Phillips, A. A.; Sumithrarachchi, C. S.; Svensson, C. E.; Triambak, S.; Ball, G. C.; Faestermann, T.; Hertenberger, R.; Wirth, H.-F.

2014-11-01

States in 112Cd have been studied with the 111Cd(d ⃗,p ) 12Cd reaction using 22 MeV polarized deuterons. The protons from the reaction were momentum analyzed with a Q3D magnetic spectrograph, and spectra have been recorded with a position-sensitive detector located on the focal plane. Angular distributions of cross sections and analyzing powers have been constructed for the low-lying negative-parity states observed, including the 3-,4-, and 5- members of the previously assigned quadrupole-octupole quintuplet. The 5- member at 2373-keV possess the second largest spectroscopic strength observed, and is reassigned as having the s1/2⊗h11/2 two-quasineutron configuration as the dominate component of its wave function.

Populations of excited states and reaction mechanisms in the emission of complex fragments

International Nuclear Information System (INIS)

Gomez del Campo, J.

1990-01-01

Cross sections for emission of complex fragments (Z>2) in their ground and excited states are presented for several heavy-ion reactions at bombarding energies above 10 MeV/nucleon. Data presented are mostly on the cross sections extracted by γ-ray techniques. It is shown that a simple statistical approach to associate the ratio, of cross sections for excited states and ground states, to the temperature of the emitter fails to give the expected temperatures. However, it is shown that this is mostly due to the fact that the fragments that γ decay are secondary fragments, produced by the particle decay of the primary emitted complex fragments. A Hauser-Feshbach analysis accounts well for the cross sections and extracted temperatures. 22 refs., 6 figs

How Glassy States Affect Brown Carbon Production?

Science.gov (United States)

Liu, P.; Li, Y.; Wang, Y.; Bateman, A. P.; Zhang, Y.; Gong, Z.; Gilles, M. K.; Martin, S. T.

2015-12-01

Secondary organic material (SOM) can become light-absorbing (i.e. brown carbon) via multiphase reactions with nitrogen-containing species such as ammonia and amines. The physical states of SOM, however, potentially slow the diffusion of reactant molecules in organic matrix under conditions that semisolids or solids prevail, thus inhibiting the browning reaction pathways. In this study, the physical states and the in-particle diffusivity were investigated by measuring the evaporation kinetics of both water and organics from aromatic-derived SOMs using a quartz-crystal-microbalance (QCM). The results indicate that the SOMs derived from aromatic precursors toluene and m-xylene became solid (glassy) and the in particle diffusion was significantly impeded for sufficiently low relative humidity ( toluene-derived SOM after ammonia exposure at varied RHs. The results suggest that the production of light-absorbing nitrogen-containing compounds from multiphase reactions with ammonia was kinetically limited in the glassy organic matrix, which otherwise produce brown carbon. The results of this study have significant implications for production and optical properties of brown carbon in urban atmospheres that ultimately influence the climate and tropospheric photochemistry.

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

Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states.

Directory of Open Access Journals (Sweden)

Andrea De Martino

Full Text Available Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at stationarity the system minimizes a global function of the reaction fluxes with the form of a Hopfield Hamiltonian with hebbian couplings, that is explicitly seen to correspond to the rate of decay of entropy production over time. Guided by this analogy, we show that reaction networks can be formally re-cast as systems of interacting reactions that optimize the use of the available compounds by competing for substrates, akin to agents competing for a limited resource in an optimal allocation problem. As an illustration, we analyze the scenario that emerges in two simple cases: that of toy (random reaction networks and that of a metabolic network model of the human red blood cell.

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.

Kinetics of Hydrogen Abstraction and Addition Reactions of 3-Hexene by ȮH Radicals.

Science.gov (United States)

Yang, Feiyu; Deng, Fuquan; Pan, Youshun; Zhang, Yingjia; Tang, Chenglong; Huang, Zuohua

2017-03-09

Rate coefficients of H atom abstraction and H atom addition reactions of 3-hexene by the hydroxyl radicals were determined using both conventional transition-state theory and canonical variational transition-state theory, with the potential energy surface (PES) evaluated at the CCSD(T)/CBS//BHandHLYP/6-311G(d,p) level and quantum mechanical effect corrected by the compounded methods including one-dimensional Wigner method, multidimensional zero-curvature tunneling method, and small-curvature tunneling method. Results reveal that accounting for approximate 70% of the overall H atom abstractions occur in the allylic site via both direct and indirect channels. The indirect channel containing two van der Waals prereactive complexes exhibits two times larger rate coefficient relative to the direct one. The OH addition reaction also contains two van der Waals complexes, and its submerged barrier results in a negative temperature coefficient behavior at low temperatures. In contrast, The OH addition pathway dominates only at temperatures below 450 K whereas the H atom abstraction reactions dominate overwhelmingly at temperature over 1000 K. All of the rate coefficients calculated with an uncertainty of a factor of 5 were fitted in a quasi-Arrhenius formula. Analyses on the PES, minimum reaction path and activation free Gibbs energy were also performed in this study.

Studies of Silyl-Transfer Photochemical Reactions of N-[(Trimethylsilyl)alkyl]saccharins

Energy Technology Data Exchange (ETDEWEB)

Cho, Dae Won; Oh, Sun Wha; Park, Hea Jung; Yoon, Ung Chan [Pusan National University, Busan (Korea, Republic of); Kim, Dong Uk [Daegu National University of Education, Daegu (Korea, Republic of); Xue, Jin Ying [Harbin Normal University, Harbin (China); Mariano, Patrick S. [University of New Mexico, Albuquerque (United States)

2010-09-15

Photochemical studies of N-[(trimethylsilyl)alkyl]saccharins were carried out to investigate their photochemical behavior. Depending on the nature of the substrate and the solvent system employed, reactions of these substances can take place by either SET-promoted silyl migration from carbon to either the amide carbonyl or sulfonyl oxygen or by a N-S homolysis route. The results of the current studies show that an azomethine ylide, arising from a SET-promoted silyl migration pathway, is generated in photoreactions of N-[(trimethylsilyl)methyl]saccharin and this intermediate reacts to give various photoproducts depending on the conditions employed. In addition, irradiation of N-[(trimethylsily)ethyl]saccharin produces an excited state that reacts through two pathways, the relative importance is governed by solvent polarity and protic nature. Finally, photoirradiation of N-[(trimethylsilyl)propyl]saccharin in a highly polar solvent system comprised of 35% aqueous MeOH gives rise to formation of a tricyclic pyrrolizidine and saccharin that generated via competitive SET-promoted silyl transfer and γ-hydrogen abstraction pathways.

Studies of Silyl-Transfer Photochemical Reactions of N-[(Trimethylsilyl)alkyl]saccharins

International Nuclear Information System (INIS)

Cho, Dae Won; Oh, Sun Wha; Park, Hea Jung; Yoon, Ung Chan; Kim, Dong Uk; Xue, Jin Ying; Mariano, Patrick S.

2010-01-01

Photochemical studies of N-[(trimethylsilyl)alkyl]saccharins were carried out to investigate their photochemical behavior. Depending on the nature of the substrate and the solvent system employed, reactions of these substances can take place by either SET-promoted silyl migration from carbon to either the amide carbonyl or sulfonyl oxygen or by a N-S homolysis route. The results of the current studies show that an azomethine ylide, arising from a SET-promoted silyl migration pathway, is generated in photoreactions of N-[(trimethylsilyl)methyl]saccharin and this intermediate reacts to give various photoproducts depending on the conditions employed. In addition, irradiation of N-[(trimethylsily)ethyl]saccharin produces an excited state that reacts through two pathways, the relative importance is governed by solvent polarity and protic nature. Finally, photoirradiation of N-[(trimethylsilyl)propyl]saccharin in a highly polar solvent system comprised of 35% aqueous MeOH gives rise to formation of a tricyclic pyrrolizidine and saccharin that generated via competitive SET-promoted silyl transfer and γ-hydrogen abstraction pathways

Single-particle states in ^112Cd probed with the ^111Cd(d,p) reaction

Science.gov (United States)

Garrett, P. E.; Jamieson, D.; Demand, G. A.; Finlay, P.; Green, K. L.; Leach, K. G.; Phillips, A. A.; Sumithrarachchi, C. S.; Svensson, C. E.; Triambak, S.; Wong, J.; Ball, G. C.; Hertenberger, R.; Wirth, H.-F.; Kr"Ucken, R.; Faestermann, T.

2009-10-01

As part of a program of detailed spectroscopy of the Cd isotopes, the single-particle neutron states in ^112Cd have been probed with the ^111Cd(d,p) reaction. Beams of polarized 22 MeV deuterons, obtained from the LMU/TUM Tandem Accelerator, bombarded a target of ^111Cd. The protons from the reaction, corresponding to excitation energies up to 3 MeV in ^112Cd, were momentum analyzed with the Q3D spectrograph. Cross sections and analyzing powers were fit to results of DWBA calculations, and spectroscopic factors were determined. The results from the experiment, and implications for the structure of ^112Cd, will be presented.

Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 1, Catalyzed reactions with wood models and wood polymers

Science.gov (United States)

Daniel J. Yelle; John Ralph; Charles R. Frihart

2011-01-01

To better understand adhesive interactions with wood, reactions between model compounds of wood and a model compound of polymeric methylene diphenyl diisocyanate (pMDI) were characterized by solution-state NMR spectroscopy. For comparison, finely ground loblolly pine sapwood, milled-wood lignin and holocellulose from the same wood were isolated and derivatized with...

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.

Quantum control of quasi-collision states: A protocol for hybrid fusion

Science.gov (United States)

Vilela Mendes, R.

2018-04-01

When confined to small regions quantum systems exhibit electronic and structural properties different from their free space behavior. These properties are of interest, for example, for molecular insertion, hydrogen storage and the exploration of new pathways for chemical and nuclear reactions. Here, a confined three-body problem is studied, with emphasis on the study of the “quantum scars” associated to dynamical collisions. For the particular case of nuclear reactions, it is proposed that a molecular cage might simply be used as a confining device with the collision states accessed by quantum control techniques.

Coating of graphite flakes with MgO/carbon nanocomposite via gas state reaction

Energy Technology Data Exchange (ETDEWEB)

Sharif, M., E-mail: Sharif_m@metaleng.iust.ac.i [Iran University of Science and Technology, Tehran (Iran, Islamic Republic of); Faghihi-Sani, M.A. [Sharif University of Technology, Tehran (Iran, Islamic Republic of); Golestani-Fard, F. [Iran University of Science and Technology, Tehran (Iran, Islamic Republic of); Saberi, A. [Tabriz University (Iran, Islamic Republic of); Soltani, Ali Khalife [Iran University of Science and Technology, Tehran (Iran, Islamic Republic of)

2010-06-18

Coating of graphite flakes with MgO/carbon nanocomposite was carried out via gaseous state reaction between mixture of Mg metal, CO gas and graphite flakes at 1000 {sup o}C. XRD and FE-SEM analysis of coating showed that the coating was comprised of MgO nano particles and amorphous carbon distributed smoothly and covered the graphite surface evenly. Thermodynamic calculations were employed to predict the reaction sequences as well as phase stability. The effect of coating on water wettability and oxidation resistance of graphite was studied using contact angle measurement and TG analysis, respectively. It was demonstrated that the reaction between Mg and CO could result in MgO/C nanocomposite deposition. The coating improved water wettability of graphite and also enhanced the oxidation resistance of graphite flakes significantly. Also the graphite coating showed significant phenolic resin-wettabilty owing to high surface area of such hydrophilic nano composite coating. The importance of graphite coating is explained with emphasis on its potential application in graphite containing refractories.

Structures and reaction pathways of the molybdenum centres of sulfite-oxidizing enzymes by pulsed EPR spectroscopy.

Science.gov (United States)

Enemark, John H; Astashkin, Andrei V; Raitsimring, Arnold M

2008-12-01

SOEs (sulfite-oxidizing enzymes) are physiologically vital and occur in all forms of life. During the catalytic cycle, the five-co-ordinate square pyramidal oxo-molybdenum active site passes through the Mo(V) state, and intimate details of the structure can be obtained from variable frequency pulsed EPR spectroscopy through the hyperfine and nuclear quadrupole interactions of nearby magnetic nuclei. By employing variable spectrometer operational frequencies, it is possible to optimize the measurement conditions for difficult quadrupolar nuclei of interest (e.g. (17)O, (33)S, (35)Cl and (37)Cl) and to simplify the interpretation of the spectra. Isotopically labelled model Mo(V) compounds provide further insight into the electronic and geometric structures and chemical reactions of the enzymes. Recently, blocked forms of SOEs having co-ordinated sulfate, the reaction product, were detected using (33)S (I=3/2) labelling. This blocking of product release is a possible contributor to fatal human sulfite oxidase deficiency in young children.

Antecedents of and Reactions to Emotions in the United States and Japan

OpenAIRE

Matsumoto, David; Kudoh, Tsutomu; Scherer, Klaus R.; Wallbott, Harald

1988-01-01

In this study, we examined the degree of cultural similarity and specificity in emotional experience by asking subjects in the United States and Japan to report their experiences and reactions concerning seven different emotions. The data used for this study were part of a larger cross-cultural study of emotion antecedents and reaxtions involving more than 2 000 subjects in 27 countries (Wallbott & Scherer, 1986). The American-Japanese comparison is a particularly interesting onem given t...

CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

Science.gov (United States)

Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

2013-07-01

Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

Chemical kinetics and reaction mechanism

International Nuclear Information System (INIS)

Jung, Ou Sik; Park, Youn Yeol

1996-12-01

This book is about chemical kinetics and reaction mechanism. It consists of eleven chapters, which deal with reaction and reaction speed on reaction mechanism, simple reaction by rate expression, reversible reaction and simultaneous reaction, successive reaction, complicated reaction mechanism, assumption for reaction mechanism, transition state theory, successive reaction and oscillating reaction, reaction by solution, research method high except kinetics on reaction mechanism, high reaction of kinetics like pulsed radiolysis.

High-Resolution State-Selected Ion-Molecule Reaction Studies Using Pulsed Field Ionization Photoelectron-Secondary Ion Coincidence Method

National Research Council Canada - National Science Library

Qian, X

2003-01-01

We have developed an octopole-quadrupole photoionization apparatus at the Advanced Light Source for absolute integral cross-section measurements of rovibrational-state-selected ion-molecule reactions...

Photodissociation of ultracold diatomic strontium molecules with quantum state control.

Science.gov (United States)

McDonald, M; McGuyer, B H; Apfelbeck, F; Lee, C-H; Majewska, I; Moszynski, R; Zelevinsky, T

2016-07-07

Chemical reactions at ultracold temperatures are expected to be dominated by quantum mechanical effects. Although progress towards ultracold chemistry has been made through atomic photoassociation, Feshbach resonances and bimolecular collisions, these approaches have been limited by imperfect quantum state selectivity. In particular, attaining complete control of the ground or excited continuum quantum states has remained a challenge. Here we achieve this control using photodissociation, an approach that encodes a wealth of information in the angular distribution of outgoing fragments. By photodissociating ultracold (88)Sr2 molecules with full control of the low-energy continuum, we access the quantum regime of ultracold chemistry, observing resonant and nonresonant barrier tunnelling, matter-wave interference of reaction products and forbidden reaction pathways. Our results illustrate the failure of the traditional quasiclassical model of photodissociation and instead are accurately described by a quantum mechanical model. The experimental ability to produce well-defined quantum continuum states at low energies will enable high-precision studies of long-range molecular potentials for which accurate quantum chemistry models are unavailable, and may serve as a source of entangled states and coherent matter waves for a wide range of experiments in quantum optics.

Two-Electron Transfer Pathways.

Science.gov (United States)

Lin, Jiaxing; Balamurugan, D; Zhang, Peng; Skourtis, Spiros S; Beratan, David N

2015-06-18

The frontiers of electron-transfer chemistry demand that we develop theoretical frameworks to describe the delivery of multiple electrons, atoms, and ions in molecular systems. When electrons move over long distances through high barriers, where the probability for thermal population of oxidized or reduced bridge-localized states is very small, the electrons will tunnel from the donor (D) to acceptor (A), facilitated by bridge-mediated superexchange interactions. If the stable donor and acceptor redox states on D and A differ by two electrons, it is possible that the electrons will propagate coherently from D to A. While structure-function relations for single-electron superexchange in molecules are well established, strategies to manipulate the coherent flow of multiple electrons are largely unknown. In contrast to one-electron superexchange, two-electron superexchange involves both one- and two-electron virtual intermediate states, the number of virtual intermediates increases very rapidly with system size, and multiple classes of pathways interfere with one another. In the study described here, we developed simple superexchange models for two-electron transfer. We explored how the bridge structure and energetics influence multielectron superexchange, and we compared two-electron superexchange interactions to single-electron superexchange. Multielectron superexchange introduces interference between singly and doubly oxidized (or reduced) bridge virtual states, so that even simple linear donor-bridge-acceptor systems have pathway topologies that resemble those seen for one-electron superexchange through bridges with multiple parallel pathways. The simple model systems studied here exhibit a richness that is amenable to experimental exploration by manipulating the multiple pathways, pathway crosstalk, and changes in the number of donor and acceptor species. The features that emerge from these studies may assist in developing new strategies to deliver multiple

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

Alpha cluster states in light nuclei populated through the (6Li,d) reaction

Energy Technology Data Exchange (ETDEWEB)

Borello-Lewin, Thereza; Rodrigues, M.R.D.; Horodynski-Matsushigue, L.B.; Duarte, J.L.M.; Rodrigues, C.L.; Souza, M.A. [Universidade de Sao Paulo (IF/USP), SP (Brazil). Inst. de Fisica; Cunsolo, A.; Cappuzzello, F. [Universita di Catania (Italy). Istituto Nazionale di Fisica Nucleare. Lab. Nazionali del Sud; Ukita, Gilberto Mitsuo [Universidade de Santo Amaro (UNISA), Sao Paulo, SP (Brazil). Fac. de Psicologia

2011-07-01

Full text: The alpha cluster correlation is an important concept in the nuclear physics of light nuclei. The main purpose of the research program in progress is the investigation of the alpha clustering phenomenon in (x{alpha}) and(x{alpha}+{nu}) nuclei through the ({sup 6}Li,d) alpha transfer reaction. In fact, there is scarce experimental information on the subject, in particular associated with resonant states predicted near (x{alpha}) and (x{alpha}+{nu}) thresholds. Measurements of the {sup 12},{sup 13}C({sup 6}Li,d) {sup 16},{sup 17}O reactions, at an incident energy of 25.5 MeV, have been performed employing the Sao Paulo Pelletron-Enge Split-Pole facility and the nuclear emulsion detection technique. The work is under way and an experimental energy resolution of 30 keV was obtained. Near the (4{alpha}) breakup threshold in {sup 16}O, three narrow alpha resonances, not previously measured, were detected, revealing important {alpha} + {sup 12}C(G.S.) components. One of these resonances corresponds to the known 0{sup +} state at 15.1 MeV[5] of excitation that has probably, according to Funaki et al., the gas like configuration of the 4{alpha} condensate state, with a very dilute density and a large component of {alpha} + {sup 12}C(Hoyle) configuration. As was already mentioned, our experimental information points to the necessity of including the {alpha} + {sup 12}C(G.S.) component in the wave function. (author)

Alpha cluster states in light nuclei populated through the (6Li,d) reaction

International Nuclear Information System (INIS)

Borello-Lewin, Thereza; Rodrigues, M.R.D.; Horodynski-Matsushigue, L.B.; Duarte, J.L.M.; Rodrigues, C.L.; Souza, M.A.; Cunsolo, A.; Cappuzzello, F.; Ukita, Gilberto Mitsuo

2011-01-01

Full text: The alpha cluster correlation is an important concept in the nuclear physics of light nuclei. The main purpose of the research program in progress is the investigation of the alpha clustering phenomenon in (xα) and(xα+ν) nuclei through the ( 6 Li,d) alpha transfer reaction. In fact, there is scarce experimental information on the subject, in particular associated with resonant states predicted near (xα) and (xα+ν) thresholds. Measurements of the 12 , 13 C( 6 Li,d) 16 , 17 O reactions, at an incident energy of 25.5 MeV, have been performed employing the Sao Paulo Pelletron-Enge Split-Pole facility and the nuclear emulsion detection technique. The work is under way and an experimental energy resolution of 30 keV was obtained. Near the (4α) breakup threshold in 16 O, three narrow alpha resonances, not previously measured, were detected, revealing important α + 12 C(G.S.) components. One of these resonances corresponds to the known 0 + state at 15.1 MeV[5] of excitation that has probably, according to Funaki et al., the gas like configuration of the 4α condensate state, with a very dilute density and a large component of α + 12 C(Hoyle) configuration. As was already mentioned, our experimental information points to the necessity of including the α + 12 C(G.S.) component in the wave function. (author)

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.

A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

Science.gov (United States)

Han, Junwei; Li, Chunquan; Yang, Haixiu; Xu, Yanjun; Zhang, Chunlong; Ma, Jiquan; Shi, Xinrui; Liu, Wei; Shang, Desi; Yao, Qianlan; Zhang, Yunpeng; Su, Fei; Feng, Li; Li, Xia

2015-01-01

Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools (http://bioinfo.hrbmu.edu.cn/PAGI). PMID:25551156

Excited states in 22Mg via the 12C(12C,2n)22Mg reaction

International Nuclear Information System (INIS)

Jewett, Cybele; Baktash, Cyrus; Bardayan, Daniel W.; Blackmon, Jeff C.; Chipps, K.; Galindo-Uribarri, Alfredo; Greife, U.; Gross, Carl J.; Jones, K. L.; Liang, Junjien; Livesay, Jake; Kozub, R. L.; Nesaraja, Caroline D; Radford, David C.; Sarazin, F.; Smith, Michael Scott; Thomas, J. S.; Yu, Chang-Hong

2007-01-01

The 12C(12C, 2n)22Mg reaction was measured with the CLARION array and the RMS separator at the Holifield Facility of Oak Ridge National Laboratory. This experiment was performed to gather more information on the excited states in 22Mg, which might be of relevance to recent radioactive ion beam measurements of the astrophysically important 21Na(p,γ)22Mg reaction. The results are compared to direct measurements, transfer experiments and a competing experiment performed with Gammasphere

F/Cl + C2H2 reactions: Are the addition and hydrogen abstraction direct processes?

International Nuclear Information System (INIS)

Li Jilai; Geng Caiyun; Huang Xuri; Zhan Jinhui; Sun Chiachung

2006-01-01

The reactions of atomic radical F and Cl with acetylene have been studied theoretically using ab initio quantum chemistry methods and transition state theory. The doublet potential energy surfaces were calculated at the CCSD(T)/aug-cc-pVDZ//CCSD/6-31G(d,p), CCSD(T)/aug-cc-pVDZ//UMP2/6-311++G(d,p) and compound method Gaussian-3 levels. Two reaction mechanisms including the addition-elimination and the hydrogen abstraction reaction mechanisms are considered. In the addition-elimination reactions, the halogen atoms approach C 2 H 2 , perpendicular to the C≡C triple bond, forming the pre-reactive complex C1 at the reaction entrance. C1 transforms to intermediate isomer I1 via transition state TSC1/1 with a negative/small barrier for C 2 H 2 F/C 2 H 2 Cl system, which can proceed by further eliminating H atom endothermally. While the hydrogen abstraction reactions also involve C1 for the fluorine atom abstraction of hydrogen, yet the hydrogen abstraction by chlorine atom first forms a collinear hydrogen-bonded complex C2. The other reaction pathways on the doublet PES are less competitive due to thermodynamical or kinetic factors. According to our results, the presence of pre-reactive complexes indicates that the simple hydrogen abstraction and addition in the halogen atoms reaction with unsaturated hydrocarbon should be more complex. Furthermore, based on the analysis of the kinetics of all channels through which the addition and abstraction reactions proceed, we expect that the actual feasibility of the reaction channels may depend on the reaction conditions in the experiment. The present study may be helpful for probing the mechanisms of the title reactions and understanding the halogen chemistry

Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks

OpenAIRE

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido

2011-01-01

Stochastic effects from correlated noise non-trivially modulate the kinetics of non-linear chemical reaction networks. This is especially important in systems where reactions are confined to small volumes and reactants are delivered in bursts. We characterise how the two noise sources confinement and burst modulate the relaxation kinetics of a non-linear reaction network around a non-equilibrium steady state. We find that the lifetimes of species change with burst input and confinement. Confi...

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 ...

Solid-state reaction in Ti/Ni multilayered films studied by using magneto-optical spectroscopy

CERN Document Server

Lee, Y P; Kim, K W; Kim, C G; Kudryavtsev, Y V; Nemoshkalenko, V V; Szymanski, B

2000-01-01

A comparative study of the solid-state reaction (SSR) in a series of Ti/Ni multilayered films (MLDs) with bilayer periods of 0.65-22.2 nm and a constant Ti to Ni sublayer thickness ratio was performed by using experimental and computer-simulated magneto-optical (MO) spectroscopy based on different models of MLFs, as well as x-ray diffraction (XRD). The spectral and sublayer thickness dependences of the MO properties of the Ti/Ni MLFs were explained on the basis of the electromagnetic theory. The existence of a threshold nominal Ni-sublayer thickness of about 3 nm for the as-deposited Ti/Ni MLF to observe of the equatorial Kerr effect was explained by a solid-state reaction which formed nonmagnetic alloyed regions between pure components during the MLF deposition. The SSR in the Ti/Ni MLFs, which was caused by the low temperature annealing, led to the formation of an amorphous Ti-Ni alloy and took place mainly in the Ti/Ni MLFs with ''thick'' sublayers. For the caes of Ti/Ni MLFs, the MO approach turned out to...

A treatment of the final-state interaction for photonuclear reactions

International Nuclear Information System (INIS)

Eden, J.A.; Thompson, M.N.

1991-01-01

The final state interaction is considered for the Gottfried factorized cross section. Numerical examples are presented for the 40 Ca(γ,pn) and 40 Ca(γ,n) reactions. The surface refraction process, allowing photonucleons to refract as they emerge from the nuclear potential well, cannot change the magnitude of the total cross section, but may redistribute the strength in the angular dependence of the differential cross section. The absorption process accounts for the loss of photonucleons as a result of inelastic collisions while escaping the nucleus. The surface refraction correction is calculated in a plane-wave Born approximation and the absorption correction is presented as a simple development of earlier phenomenological treatments. 12 refs., 7 figs

Isobaric analogue states of 73Ge via 72Ge(3He,d)73As reaction

International Nuclear Information System (INIS)

Ramaswamy, C.R.; Puttaswamy, N.G.; Sarma, N.

1974-01-01

The 72 Ge( 3 He,d) 73 As reaction has been studied at 20 MeV incident 3 He energy using an MP tandem and a multigap spectrograph. The energy spectrum of deuterons in the region between 9 to 10.5 MeV excitation energy of 73 As shows analogue states corresponding to G.S., 570, 673, 805, 900, 1050, and 1350 KeV states of 73 Ge. Angular distributions for the analogue states and 1-values of the transferred protons are extracted. The results are compared with available data on the levels of 73 Ge. (author)

Experimental study of high spin states in low-medium mass nuclei by use of charge particle induced reactions

International Nuclear Information System (INIS)

Alenius, N.G.

1975-01-01

For the test of nuclear models the study of the properties of nuclear states of high angular momentum is especially important, because such states can often be given very simple theoretical descriptions. High spin states are easily populated by use of reactions initiated by alpha particles or heavy ions. In this thesis a number of low-medium mass nuclei have been studied, with emphasis on high spin states. (Auth.)

[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.

The hydrogen atom-deuterium molecule reaction: Experimental determination of product quantum state distributions

International Nuclear Information System (INIS)

Rinnen, K.

1989-01-01

The H + H 2 atom exchange reaction (and its isotopic analogs) is the simplest neutral bimolecular chemical reaction because of the small number of electrons in the system and the lightness of the nuclei. The H 3 potential energy surface (PES) is the most accurately known reactive surface (LSTH surface); there have been both quasiclassical trajectory (QCT) and quantal calculations performed on it. This is one of the few systems for which theory is ahead of experiment, and many theoretical predictions await experimental comparison. The H + D 2 → HD + D reaction is studied using thermal D 2 (∼298 K) and translationally hot hydrogen atoms. Photolysis of HI at 266 nm generates H atoms with center-of-mass collision energies of 1.3 and 0.55 eV, both of which are above the classical reaction barrier of 0.42 eV. The rovibrational population distribution of the molecular product is measured by (2+1) resonance-enhanced multiphoton ionization (REMPI). A major effort has been directed toward calibrating the (2+1) REMPI detection procedure, to determine quantitatively the relationship between ion signals and relative quantum state populations for HD. An effusive, high-temperature nozzle has been constructed to populate thermally the high rovibrational levels observed in the reaction. The results are compared to theoretical calculations of the E,F 1 Σ g + - X 1 Σ g + two-photon transition moments. For the H + D 2 reaction, the populations of all energetically accessible HD product levels are measured. Specifically, the following levels are observed: HD(v = 0, J = 0-15), HD(v = 1, J = 0-12), and HD(v = 2, J = 0-8). Of the available energy, 73% is partitioned into product translation, 18% into HD rotation, and 9% into HD vibration

Vibronic coupling in ionized organic molecules: structural distortions and chemical reactions

International Nuclear Information System (INIS)

Williams, Ffrancon

2003-01-01

Ionized organic molecules (radical cations) in radiation chemistry are liable to undergo vibronic coupling whenever there is a relatively small energy gap (∼0.5-1.5 eV) between their ground and excited states. As a result of this mixing, the force constant for the symmetry-allowed vibrational mode that couples these states is lowered in the ground state of the radical cation so that deformation can take place more easily along this specific mode. This pseudo-Jahn-Teller effect can then result in a permanent structural distortion of the radical cation relative to the symmetry of the parent neutral molecule. It can also bring about an energetically favored pathway for a facile chemical rearrangement along a reaction coordinate defined by the coupling mode. Examples taken from matrix-isolation studies are used to illustrate these dramatic consequences of vibronic coupling in radical cations. Thus, the bicyclo[2.2.2]oct-2-ene and tetramethylurea radical cations are found to have twisted structures departing from the C 2v symmetry of their parent molecules, while the oxirane and bicyclo[1.1.1]pentane radical cations undergo ring-opening rearrangements along reaction coordinates that correspond to the deformational modes predicted by the pseudo-Jahn-Teller effect

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

Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity

International Nuclear Information System (INIS)

Kuramitsu, Seiki; Hiromi, Keitaro; Hayashi, Hideyuki; Morino, Yoshimasa; Kagamiyama, Hiroyuki

1990-01-01

The four half-transamination reactions [the pyridoxal form of Escherichia coli aspartate aminotransferase (AspAT) with aspartate or glutamate and the pyridoxamine form of the enzyme with oxalacetate or 2-oxoglutarate] were followed in a stopped-flow spectrometer by monitoring the absorbance change at either 333 or 358 nm. The reaction progress curves in all cases gave fits to a monophasic exponential process. Kinetic analyses of these reactions showed that each half-reaction is composed of the following three processes: (1) the rapid binding of an amino acid substrate to the pyridoxal form of the enzyme; (2) the rapid binding of the corresponding keto acid to the pyridoxamine form of the enzyme; (3) the rate-determining interconversion between the two complexes. This mechanism was supported by the findings that the equilibrium constants for half- and overall-transamination reactions and the steady-state kinetic constants agreed well with the predicted values on the basis of the above mechanism using pre-steady-state kinetic parameters. The significant primary kinetic isotope effect observed in the reaction with deuterated amino acid suggests that the withdrawal of the α-proton of the substrates is rate determining. The pyridoxal form of E. coli AspAT reacted with a variety of amino acids as substrates. The substrate specificity of the E. coli enzyme was much broader than that of pig isoenzymes, reflecting some subtle but distinct difference in microenvironment accommodating the side chain of the substrate between e. coli and mammalian AspATs

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.

Coherence, energy and charge transfers in de-excitation pathways of electronic excited state of biomolecules in photosynthesis

DEFF Research Database (Denmark)

Bohr, Henrik; Malik, F. Bary

2013-01-01

The observed multiple de-excitation pathways of photo-absorbed electronic excited state in the peridinin–chlorophyll complex, involving both energy and charge transfers among its constituents, are analyzed using the bio-Auger (B-A) theory. It is also shown that the usually used F¨orster–Dexter...

Interference of the two spin components of the capture state in the (n, [gamma]) reaction

NARCIS (Netherlands)

Kamp, A.M.F. op den; Kopecky, J.; Stecher-Rasmussen, F.; Abrahams, K.; Endt, P.M.

1972-01-01

Measurements of the circularγ-ray polarization for primary transitions in the 39K(n, γ)40K and 57Fe(n, γ)58Fe reactions induced by thermal neutrons give strong evidence for the interference of components in the capture state with different J=values.

High resolution 148Nd(3He, ny) two proton stripping reaction and the structure of the O2+ state in 150Sm

International Nuclear Information System (INIS)

Sharpey-Schafer, J.F.; Dinoko, T.S.; Herbert, M.S.; Orce, J.N.; Papka, P.; Kheswa, B.V.; Ndayishimye, J.; Bvumbi, S.P.; Jones, P.M.; Bucher, T.D.; Lawrie, E.A.; Lawrie, J.J.; Negi, D.; Shirinda, O.; Wiedeking, M.; Vymers, P.; Easton, J.L.; Noncolela, S.P.; Sithole, P.; Khumalo, N.; Majola, S.N.T.; Stankiewicz, M.A.

2014-01-01

The challenge of achieving high resolution in binary reactions involving an outgoing high energy neutron is solved by detecting the γ-ray decay of populated excited states in an array of escape suppressed HPGe detectors in coincidence with fast neutrons detected in a wall of scintillator detectors 2 m down beam of the target. The selectivity of the arrangement is of the order of 1 in 1000. The time-of-flight difference is sufficient to separate fast neutrons from direct reactions from a large background of statistical neutrons from fusion-evaporation reactions. Our interest is in the wavefunction of the 0 2 + state at 740 keV in the N=88 nucleus 150 Sm which, with the 0 2 + state in 100 Ru, are the only two excited states observed in 2β2ν double β-decay. (authors)

Crossed-beam reaction of carbon atoms with hydrocarbon molecules. IV. Chemical dynamics of methylpropargyl radical formation, C4H5, from reaction of C(3Pj) with propylene, C3H6 (X1A)

International Nuclear Information System (INIS)

Kaiser, R.I.; Stranges, D.; Bevsek, H.M.; Lee, Y.T.; Suits, A.G.

1997-01-01

The reaction between ground state carbon atoms and propylene, C 3 H 6 , was studied at average collision energies of 23.3 and 45.0 kJmol -1 using the crossed molecular beam technique. Product angular distributions and time-of-flight spectra of C 4 H 5 at m/e=53 were recorded. Forward-convolution fitting of the data yields a maximum energy release as well as angular distributions consistent with the formation of methylpropargyl radicals. Reaction dynamics inferred from the experimental results suggest that the reaction proceeds on the lowest 3 A surface via an initial addition of the carbon atom to the π-orbital to form a triplet methylcyclopropylidene collision complex followed by ring opening to triplet 1,2-butadiene. Within 0.3 endash 0.6 ps, 1,2-butadiene decomposes through carbon endash hydrogen bond rupture to atomic hydrogen and methylpropargyl radicals. The explicit identification of C 4 H 5 under single collision conditions represents a further example of a carbon endash hydrogen exchange in reactions of ground state carbon with unsaturated hydrocarbons. This versatile machine represents an alternative pathway to build up unsaturated hydrocarbon chains in combustion processes, chemical vapor deposition, and in the interstellar medium. copyright 1997 American Institute of Physics

A new pathway for transmembrane electron transfer in photosynthetic reaction centers of Rhodobacter sphaeroides not involving the excited special pair.

NARCIS (Netherlands)

van Brederode, M.E.; Jones, M.R.; van Mourik, F.; van Stokkum, I.H.M.; van Grondelle, R.

1997-01-01

It is generally accepted that electron transfer in bacterial photosynthesis is driven by the first singlet excited state of a special pair of bacteriochlorophylls (P*). We have examined the first steps of electron transfer in a mutant of the Rhodobacter sphaeroides reaction center in which charge

A new pathway for transmembrane electron transfer in photosyntetic reaction centers of Rhodobacter sphaeroides not involving the excited special pair.

NARCIS (Netherlands)

van Brederode, M.E.; Jones, M.R.; van Mourik, F.; van Stokkum, I.H.M.; van Grondelle, R.

1997-01-01

It is generally accepted that electron transfer in bacterial photosynthesis is driven by the first singlet excited state of a special pair of bacteriochlorophylls (P*). We have examined the first steps of electron transfer in a mutant of the Rhodobacter sphaeroides reaction center in which charge

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.