Reaction Decoder Tool (RDT): extracting features from chemical reactions.

PubMed

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.

Experimental Demonstrations in Teaching Chemical Reactions.

ERIC Educational Resources Information Center

Hugerat, Muhamad; Basheer, Sobhi

2001-01-01

Presents demonstrations of chemical reactions by employing different features of various compounds that can be altered after a chemical change occurs. Experimental activities include para- and dia-magnetism in chemical reactions, aluminum reaction with base, reaction of acid with carbonates, use of electrochemical cells for demonstrating chemical…

Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs.

PubMed

Dodsworth, Jeremy A; McDonald, Austin I; Hedlund, Brian P

2012-08-01

To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Chemical reactions in low-g

NASA Technical Reports Server (NTRS)

Grodzka, P. G.; Facemire, B. R.

1978-01-01

The Apollo-Soyuz flight experiment, 'Chemical Foams' demonstrated that foams and air/liquid dispersions are much more stable in low-gravity than on the ground. It thus should be possible to conduct unique chemical reactions in space foams. The low-g results and subsequent ground work on the formaldehyde clock reaction indicate that the reaction is strongly influenced by (1) dissociated and undissociated solution species being adsorbed at solid/liquid and gas/liquid surfaces and (2) chemical reaction rates apparently being affected by long-range forces determined by the liquid mass and the extent and nature of all surface interfaces.

Fission Reaction Event Yield Algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hagmann, Christian; Verbeke, Jerome; Vogt, Ramona

FREYA (Fission Reaction Event Yield Algorithm) is a code that simulated the decay of a fissionable nucleus at specified excitation energy. In its present form, FREYA models spontaneous fission and neutron-induced fission up to 20 MeV. It includes the possibility of neutron emission from the nuclear prior to its fussion (nth chance fission).

Tunneling chemical reactions D+H{sub 2}{yields}DH+H and D+DH{yields}D{sub 2}+H in solid D{sub 2}-H{sub 2} and HD-H{sub 2} mixtures: An electron-spin-resonance study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumada, Takayuki

2006-03-07

Tunneling chemical reactions D+H{sub 2}{yields}DH+H and D+DH{yields}D{sub 2}+H in solid HD-H{sub 2} and D{sub 2}-H{sub 2} mixtures were studied in the temperature range between 4 and 8 K. These reactions were initiated by UV photolysis of DI molecules doped in these solids for 30 s and followed by measuring the time course of electron-spin-resonance (ESR) intensities of D and H atoms. ESR intensity of D atoms produced by the photolysis decreases but that of H atoms increases with time. Time course of the D and H intensities has the fast and slow processes. The fast process, which finishes within {approx}300more » s after the photolysis, is assigned to the reaction of D atom with one of its nearest-neighboring H{sub 2} molecules, D(H{sub 2}){sub n}(HD){sub 12-n}{yields}H(H{sub 2}){sub n-1}(HD){sub 13-n} or D(H{sub 2}){sub n}(D{sub 2}){sub 12-n}{yields}H(HD)(H{sub 2}){sub n-1}(D{sub 2}){sub 12-n} for 12{>=}n{>=}1. Rate constant for the D+H{sub 2} reaction between neighboring D atom-H{sub 2} molecule pair is determined to be (7.5{+-}0.7)x10{sup -3} s{sup -1} in solid HD-H{sub 2} and (1.3{+-}0.3)x10{sup -2} s{sup -1} in D{sub 2}-H{sub 2} at 4.1 K, which is very close to that calculated based on the theory of chemical reaction in gas phase by Hancock et al. [J. Chem. Phys. 91, 3492 (1989)] and Takayanagi and Sato [J. Chem. Phys. 92, 2862 (1990)]. This rate constant was found to be independent of temperature up to 7 K within experimental error of {+-}30%. The slow process is assigned to the reaction of D atom produced in a cage fully surrounded by HD or D{sub 2} molecules, D(HD){sub 12} or D(D{sub 2}){sub 12}. This D atom undergoes the D+DH reaction with one of its nearest-neighboring HD molecules in solid HD-H{sub 2} or diffuses to the neighbor of H{sub 2} molecules to allow the D+H{sub 2} reaction in solid HD-H{sub 2} and D{sub 2}-H{sub 2}. The former is the main channel in solid HD-H{sub 2} below 6 K where D atoms diffuse very slowly, whereas the latter dominates

Chemical potential and reaction electronic flux in symmetry controlled reactions.

PubMed

Vogt-Geisse, Stefan; Toro-Labbé, Alejandro

2016-07-15

In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Diabatic models with transferrable parameters for generalized chemical reactions

NASA Astrophysics Data System (ADS)

Reimers, Jeffrey R.; McKemmish, Laura K.; McKenzie, Ross H.; Hush, Noel S.

2017-05-01

Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical

Modeling chemical reactions for drug design.

PubMed

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.

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

PubMed

Fooshee, David; Andronico, Alessio; Baldi, Pierre

2013-11-25

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

Learning to Predict Chemical Reactions

PubMed Central

Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

2011-01-01

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

Learning to predict chemical reactions.

PubMed

Kayala, Matthew A; Azencott, Chloé-Agathe; Chen, Jonathan H; Baldi, Pierre

2011-09-26

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are not generalizable or scalable, and lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry data set consisting of 1630 full multistep reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top-ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of nonproductive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches.

PubMed

de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre

2012-09-24

This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.

Adenine specific DNA chemical sequencing reaction.

PubMed Central

Iverson, B L; Dervan, P B

1987-01-01

Reaction of DNA with K2PdCl4 at pH 2.0 followed by a piperidine workup produces specific cleavage at adenine (A) residues. Product analysis revealed the K2PdCl4 reaction involves selective depurination at adenine, affording an excision reaction analogous to the other chemical DNA sequencing reactions. Adenine residues methylated at the exocyclic amine (N6) react with lower efficiency than unmethylated adenine in an identical sequence. This simple protocol specific for A may be a useful addition to current chemical sequencing reactions. Images PMID:3671067

The reaction between CH 3O 2 and OH radicals: Product yields and atmospheric implications

DOE PAGES

Assaf, Emmanuel; Sheps, Leonid; Whalley, Lisa; ...

2017-01-25

The reaction between CH 3O 2 and OH radicals has been shown to be fast and to play an appreciable role for the removal of CH 3O 2 radials in remote environments such as the marine boundary layer. Two different experimental techniques have been used here to determine the products of this reaction. The HO 2 yield has been obtained from simultaneous time-resolved measurements of the absolute concentration of CH 3O 2, OH, and HO 2 radicals by cw-CRDS. The possible formation of a Criegee intermediate has been measured by broadband cavity enhanced UV absorption. A yield of Φ HO2more » = (0.8 ± 0.2) and an upper limit for Φ Criegee = 0.05 has been determined for this reaction, suggesting a minor yield of methanol or stabilized trioxide as a product. The impact of this reaction on the composition of the remote marine boundary layer has been determined by implementing these findings into a box model utilizing the Master Chemical Mechanism v3.2, and constraining the model for conditions found at the Cape Verde Atmospheric Observatory in the remote tropical Atlantic Ocean. Inclusion of the CH 3O 2+OH reaction into the model results in up to 30% decrease in the CH 3O 2 radical concentration while the HO 2 concentration increased by up to 20%. Finally, production and destruction of O 3 are also influenced by these changes, and the model indicates that taking into account the reaction between CH 3O 2 and OH leads to a 6% decrease of O 3.« less

The reaction between CH 3O 2 and OH radicals: Product yields and atmospheric implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Assaf, Emmanuel; Sheps, Leonid; Whalley, Lisa

The reaction between CH 3O 2 and OH radicals has been shown to be fast and to play an appreciable role for the removal of CH 3O 2 radials in remote environments such as the marine boundary layer. Two different experimental techniques have been used here to determine the products of this reaction. The HO 2 yield has been obtained from simultaneous time-resolved measurements of the absolute concentration of CH 3O 2, OH, and HO 2 radicals by cw-CRDS. The possible formation of a Criegee intermediate has been measured by broadband cavity enhanced UV absorption. A yield of Φ HO2more » = (0.8 ± 0.2) and an upper limit for Φ Criegee = 0.05 has been determined for this reaction, suggesting a minor yield of methanol or stabilized trioxide as a product. The impact of this reaction on the composition of the remote marine boundary layer has been determined by implementing these findings into a box model utilizing the Master Chemical Mechanism v3.2, and constraining the model for conditions found at the Cape Verde Atmospheric Observatory in the remote tropical Atlantic Ocean. Inclusion of the CH 3O 2+OH reaction into the model results in up to 30% decrease in the CH 3O 2 radical concentration while the HO 2 concentration increased by up to 20%. Finally, production and destruction of O 3 are also influenced by these changes, and the model indicates that taking into account the reaction between CH 3O 2 and OH leads to a 6% decrease of O 3.« less

Chemical reactions involved in the initiation of hot corrosion of IN-738

NASA Technical Reports Server (NTRS)

Fryburg, G. C.; Kohl, F. J.; Stearns, C. A.

1984-01-01

Sodium-sulfate-induced hot corrosion of preoxidized IN-738 was studied at 975 C with special emphasis placed on the processes occurring during the long induction period. Thermogravimetric tests were run for predetermined periods of time, and then one set of specimens was washed with water. Chemical analysis of the wash solutions yielded information about water soluble metal salts and residual sulfate. A second set of samples was cross sectioned dry and polished in a nonaqueous medium. Element distributions within the oxide scale were obtained from electron microprobe X-ray micrographs. Evolution of SO was monitored throughout the thermogravimetric tests. Kinetic rate studies were performed for several pertinent processes; appropriate rate constants were obtained from the following chemical reactions; Cr203 + 2 Na2S04(1) + 3/2 02 yields 2 Na2Cr04(1) + 2 S03(g)n TiO2 + Na2S04(1) yields Na20(T102)n + 503(g)n T102 + Na2Cro4(1) yields Na2(T102)n + Cr03(g).

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model.

PubMed

Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir

2018-04-10

We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

DOE PAGES

Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco; ...

2018-03-15

Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco

Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

Peptide Bond Synthesis by a Mechanism Involving an Enzymatic Reaction and a Subsequent Chemical Reaction*

PubMed Central

Abe, Tomoko; Hashimoto, Yoshiteru; Zhuang, Ye; Ge, Yin; Kumano, Takuto; Kobayashi, Michihiko

2016-01-01

We recently reported that an amide bond is unexpectedly formed by an acyl-CoA synthetase (which catalyzes the formation of a carbon-sulfur bond) when a suitable acid and l-cysteine are used as substrates. DltA, which is homologous to the adenylation domain of nonribosomal peptide synthetase, belongs to the same superfamily of adenylate-forming enzymes, which includes many kinds of enzymes, including the acyl-CoA synthetases. Here, we demonstrate that DltA synthesizes not only N-(d-alanyl)-l-cysteine (a dipeptide) but also various oligopeptides. We propose that this enzyme catalyzes peptide synthesis by the following unprecedented mechanism: (i) the formation of S-acyl-l-cysteine as an intermediate via its “enzymatic activity” and (ii) subsequent “chemical” S → N acyl transfer in the intermediate, resulting in peptide formation. Step ii is identical to the corresponding reaction in native chemical ligation, a method of chemical peptide synthesis, whereas step i is not. To the best of our knowledge, our discovery of this peptide synthesis mechanism involving an enzymatic reaction and a subsequent chemical reaction is the first such one to be reported. This new process yields peptides without the use of a thioesterified fragment, which is required in native chemical ligation. Together with these findings, the same mechanism-dependent formation of N-acyl compounds by other members of the above-mentioned superfamily demonstrated that all members most likely form peptide/amide compounds by using this novel mechanism. Each member enzyme acts on a specific substrate; thus, not only the corresponding peptides but also new types of amide compounds can be formed. PMID:26586916

Microfabricated sleeve devices for chemical reactions

DOEpatents

Northrup, M. Allen

2003-01-01

A silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and non-silicon based materials to provide the thermal properties desired. For example, the chamber may combine a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

Plasmon-driven sequential chemical reactions in an aqueous environment.

PubMed

Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

2014-06-24

Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H(+) in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight.

Plasmon-driven sequential chemical reactions in an aqueous environment

PubMed Central

Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

2014-01-01

Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H+ in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight. PMID:24958029

Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.

PubMed

Mallory, Emily K; Acharya, Ambika; Rensi, Stefano E; Turnbaugh, Peter J; Bright, Roselie A; Altman, Russ B

2018-01-01

Bacteria in the human gut have the ability to activate, inactivate, and reactivate drugs with both intended and unintended effects. For example, the drug digoxin is reduced to the inactive metabolite dihydrodigoxin by the gut Actinobacterium E. lenta, and patients colonized with high levels of drug metabolizing strains may have limited response to the drug. Understanding the complete space of drugs that are metabolized by the human gut microbiome is critical for predicting bacteria-drug relationships and their effects on individual patient response. Discovery and validation of drug metabolism via bacterial enzymes has yielded >50 drugs after nearly a century of experimental research. However, there are limited computational tools for screening drugs for potential metabolism by the gut microbiome. We developed a pipeline for comparing and characterizing chemical transformations using continuous vector representations of molecular structure learned using unsupervised representation learning. We applied this pipeline to chemical reaction data from MetaCyc to characterize the utility of vector representations for chemical reaction transformations. After clustering molecular and reaction vectors, we performed enrichment analyses and queries to characterize the space. We detected enriched enzyme names, Gene Ontology terms, and Enzyme Consortium (EC) classes within reaction clusters. In addition, we queried reactions against drug-metabolite transformations known to be metabolized by the human gut microbiome. The top results for these known drug transformations contained similar substructure modifications to the original drug pair. This work enables high throughput screening of drugs and their resulting metabolites against chemical reactions common to gut bacteria.

Study of Horseradish Peroxidase Fixed on Mesoporous Materials as a Chemical Reaction Catalyst

NASA Astrophysics Data System (ADS)

Gao, Mengdan; Dai, Rongji

2017-12-01

Nanostructured mesoporous materials is a new type of porous materials, which has been widely used. It has excellent capability in enzymes immobilization, but modification on the chemical bonds of the enzyme reduce the enzymatic activity and rarely used in chemical reactions. The horseradish peroxidase was immobilized on the mesoporous materials with appropriate aperture and its activity and stability was evaluated when catalyzing the nitration reaction of amines and oxidation reaction of thiourea. The optimum mesoporous material to fix the horseradish peroxidase can be obtained by mixing polyoxyethylene - polyoxypropylene-pol, yoxyethylene(P123), 1,3,5-trimethylbenzene(TMB), and tetramethoxysilane (TMOS) at a ratio of 10:1:1, whose surface area and pore volume and pore diameter calculated by BET and BJH model were 402.903m2/g, 1.084cm2/g, 1.084cm2/g respectively. The horseradish peroxidase, immobilized on the mesoporous materials, was applied for catalyzing the nitration reaction of anilines and oxidation reaction of thiourea, produced a high product yield and can be recycled. Thus, it is a strong candidate as a catalysts for oxidation reactions, to be produced at industral scale, due to its high efficiency and low cost.

Mixing and non-equilibrium chemical reaction in a compressible mixing layer. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Steinberger, Craig J.

1991-01-01

The effects of compressibility, chemical reaction exothermicity, and non-equilibrium chemical modeling in a reacting plane mixing layer were investigated by means of two dimensional direct numerical simulations. The chemical reaction was irreversible and second order of the type A + B yields Products + Heat. The general governing fluid equations of a compressible reacting flow field were solved by means of high order finite difference methods. Physical effects were then determined by examining the response of the mixing layer to variation of the relevant non-dimensionalized parameters. The simulations show that increased compressibility generally results in a suppressed mixing, and consequently a reduced chemical reaction conversion rate. Reaction heat release was found to enhance mixing at the initial stages of the layer growth, but had a stabilizing effect at later times. The increased stability manifested itself in the suppression or delay of the formation of large coherent structures within the flow. Calculations were performed for a constant rate chemical kinetics model and an Arrhenius type kinetic prototype. The choice of the model was shown to have an effect on the development of the flow. The Arrhenius model caused a greater temperature increase due to reaction than the constant kinetic model. This had the same effect as increasing the exothermicity of the reaction. Localized flame quenching was also observed when the Zeldovich number was relatively large.

Runaway chemical reaction exposes community to highly toxic chemicals.

PubMed

Kaszniak, Mark; Vorderbrueggen, John

2008-11-15

The U.S. Chemical Safety and Hazard Investigation Board (CSB) conducted a comprehensive investigation of a runaway chemical reaction at MFG Chemical (MFG) in Dalton, Georgia on April 12, 2004 that resulted in the uncontrolled release of a large quantity of highly toxic and flammable allyl alcohol and allyl chloride into the community. Five people were hospitalized and 154 people required decontamination and treatment for exposure to the chemicals. This included police officers attempting to evacuate the community and ambulance personnel who responded to 911 calls from residents exposed to the chemicals. This paper presents the findings of the CSB report (U.S. Chemical Safety and Hazard Investigation Board (CSB), Investigation Report: Toxic Chemical Vapor Cloud Release, Report No. 2004-09-I-GA, Washington DC, April 2006) including a discussion on tolling practices; scale-up of batch reaction processes; Process Safety Management (PSM) and Risk Management Plan (RMP) implementation; emergency planning by the company, county and the city; and emergency response and mitigation actions taken during the incident. The reactive chemical testing and atmospheric dispersion modeling conducted by CSB after the incident and recommendations adopted by the Board are also discussed.

Reduction of chemical reaction models

NASA Technical Reports Server (NTRS)

Frenklach, Michael

1991-01-01

An attempt is made to reconcile the different terminologies pertaining to reduction of chemical reaction models. The approaches considered include global modeling, response modeling, detailed reduction, chemical lumping, and statistical lumping. The advantages and drawbacks of each of these methods are pointed out.

Enhancing chemical reactions

DOEpatents

Morrey, John R.

1978-01-01

Methods of enhancing selected chemical reactions. The population of a selected high vibrational energy state of a reactant molecule is increased substantially above its population at thermal equilibrium by directing onto the molecule a beam of radiant energy from a laser having a combination of frequency and intensity selected to pump the selected energy state, and the reaction is carried out with the temperature, pressure, and concentrations of reactants maintained at a combination of values selected to optimize the reaction in preference to thermal degradation by transforming the absorbed energy into translational motion. The reaction temperature is selected to optimize the reaction. Typically a laser and a frequency doubler emit radiant energy at frequencies of .nu. and 2.nu. into an optical dye within an optical cavity capable of being tuned to a wanted frequency .delta. or a parametric oscillator comprising a non-centrosymmetric crystal having two indices of refraction, to emit radiant energy at the frequencies of .nu., 2.nu., and .delta. (and, with a parametric oscillator, also at 2.nu.-.delta.). Each unwanted frequency is filtered out, and each desired frequency is focused to the desired radiation flux within a reaction chamber and is reflected repeatedly through the chamber while reactants are fed into the chamber and reaction products are removed therefrom.

Optimizing Chemical Reactions with Deep Reinforcement Learning.

PubMed

Zhou, Zhenpeng; Li, Xiaocheng; Zare, Richard N

2017-12-27

Deep reinforcement learning was employed to optimize chemical reactions. Our model iteratively records the results of a chemical reaction and chooses new experimental conditions to improve the reaction outcome. This model outperformed a state-of-the-art blackbox optimization algorithm by using 71% fewer steps on both simulations and real reactions. Furthermore, we introduced an efficient exploration strategy by drawing the reaction conditions from certain probability distributions, which resulted in an improvement on regret from 0.062 to 0.039 compared with a deterministic policy. Combining the efficient exploration policy with accelerated microdroplet reactions, optimal reaction conditions were determined in 30 min for the four reactions considered, and a better understanding of the factors that control microdroplet reactions was reached. Moreover, our model showed a better performance after training on reactions with similar or even dissimilar underlying mechanisms, which demonstrates its learning ability.

Silicon-based sleeve devices for chemical reactions

DOEpatents

Northrup, M. Allen; Mariella, Jr., Raymond P.; Carrano, Anthony V.; Balch, Joseph W.

1996-01-01

A silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

Silicon-based sleeve devices for chemical reactions

DOEpatents

Northrup, M.A.; Mariella, R.P. Jr.; Carrano, A.V.; Balch, J.W.

1996-12-31

A silicon-based sleeve type chemical reaction chamber is described that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis. 32 figs.

Binary counting with chemical reactions.

PubMed

Kharam, Aleksandra; Jiang, Hua; Riedel, Marc; Parhi, Keshab

2011-01-01

This paper describes a scheme for implementing a binary counter with chemical reactions. The value of the counter is encoded by logical values of "0" and "1" that correspond to the absence and presence of specific molecular types, respectively. It is incremented when molecules of a trigger type are injected. Synchronization is achieved with reactions that produce a sustained three-phase oscillation. This oscillation plays a role analogous to a clock signal in digital electronics. Quantities are transferred between molecular types in different phases of the oscillation. Unlike all previous schemes for chemical computation, this scheme is dependent only on coarse rate categories for the reactions ("fast" and "slow"). Given such categories, the computation is exact and independent of the specific reaction rates. Although conceptual for the time being, the methodology has potential applications in domains of synthetic biology such as biochemical sensing and drug delivery. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.

Microfabricated electrochemiluminescence cell for chemical reaction detection

DOEpatents

Northrup, M. Allen; Hsueh, Yun-Tai; Smith, Rosemary L.

2003-01-01

A detector cell for a silicon-based or non-silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The detector cell is an electrochemiluminescence cell constructed of layers of silicon with a cover layer of glass, with spaced electrodes located intermediate various layers forming the cell. The cell includes a cavity formed therein and fluid inlets for directing reaction fluid therein. The reaction chamber and detector cell may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The ECL cell may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

Optimizing Chemical Reactions with Deep Reinforcement Learning

PubMed Central

2017-01-01

Deep reinforcement learning was employed to optimize chemical reactions. Our model iteratively records the results of a chemical reaction and chooses new experimental conditions to improve the reaction outcome. This model outperformed a state-of-the-art blackbox optimization algorithm by using 71% fewer steps on both simulations and real reactions. Furthermore, we introduced an efficient exploration strategy by drawing the reaction conditions from certain probability distributions, which resulted in an improvement on regret from 0.062 to 0.039 compared with a deterministic policy. Combining the efficient exploration policy with accelerated microdroplet reactions, optimal reaction conditions were determined in 30 min for the four reactions considered, and a better understanding of the factors that control microdroplet reactions was reached. Moreover, our model showed a better performance after training on reactions with similar or even dissimilar underlying mechanisms, which demonstrates its learning ability. PMID:29296675

Chemical tailoring of teicoplanin with site-selective reactions.

PubMed

Pathak, Tejas P; Miller, Scott J

2013-06-05

Semisynthesis of natural product derivatives combines the power of fermentation with orthogonal chemical reactions. Yet, chemical modification of complex structures represents an unmet challenge, as poor selectivity often undermines efficiency. The complex antibiotic teicoplanin eradicates bacterial infections. However, as resistance emerges, the demand for improved analogues grows. We have discovered chemical reactions that achieve site-selective alteration of teicoplanin. Utilizing peptide-based additives that alter reaction selectivities, certain bromo-teicoplanins are accessible. These new compounds are also scaffolds for selective cross-coupling reactions, enabling further molecular diversification. These studies enable two-step access to glycopeptide analogues not available through either biosynthesis or rapid total chemical synthesis alone. The new compounds exhibit a spectrum of activities, revealing that selective chemical alteration of teicoplanin may lead to analogues with attenuated or enhanced antibacterial properties, in particular against vancomycin- and teicoplanin-resistant strains.

Explorations into Chemical Reactions and Biochemical Pathways.

PubMed

Gasteiger, Johann

2016-12-01

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

Chemical Reactions in Supercritical Carbon Dioxide

NASA Astrophysics Data System (ADS)

Wai, Chien M.; Hunt, Fred; Ji, Min; Chen, Xiaoyuan

1998-12-01

Utilizing supercritical fluids as environmentally benign solvents for chemical synthesis is one of the new approaches in the "greening" of chemistry. Carbon dioxide is the most widely used gas for supercritical fluid studies because of its moderate critical constants, nontoxic nature, and availability in pure form. One unique property of supercritical carbon dioxide (sc-CO2) is its high solubility for fluorinated compounds. Thus sc-CO2 can be used to replace Freons that are conventionally used as solvents for synthesis of perfluoro-polymers. Another property of sc-CO2 is its miscibility with gases such as H2. Heterogeneous reactions involving these gases may become homogeneous reactions in sc-CO2. Reactions in sc-CO2 may offer several advantages including controlling phase behavior and products, increasing speed of reactions, and obtaining specific reaction channels. This paper describes the following nine types of chemical reactions reported in the literature utilizing sc-CO2 as a solvent to illustrate the unique properties of the supercritical fluid reaction systems: (i) hydrogenation and hydroformylation, (ii) synthesis of organometallic compounds, (iii) metal chelation and extraction, (iv) preparation of inorganic nanoparticles, (v) stereo-selectivity of lipase-catalyzed reactions, (vi) asymmetric catalytic hydrogenation, (vii) polymerization, (viii) Diels-Alder reaction, and (ix) free radical reactions.

Taking the plunge: chemical reaction dynamics in liquids.

PubMed

Orr-Ewing, Andrew J

2017-12-11

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

PubMed

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

Modelling Students' Visualisation of Chemical Reaction

ERIC Educational Resources Information Center

Cheng, Maurice M. W.; Gilbert, John K.

2017-01-01

This paper proposes a model-based notion of "submicro representations of chemical reactions". Based on three structural models of matter (the simple particle model, the atomic model and the free electron model of metals), we suggest there are two major models of reaction in school chemistry curricula: (a) reactions that are simple…

Non-equilibrium reaction rates in chemical kinetic equations

NASA Astrophysics Data System (ADS)

Gorbachev, Yuriy

2018-05-01

Within the recently proposed asymptotic method for solving the Boltzmann equation for chemically reacting gas mixture, the chemical kinetic equations has been derived. Corresponding one-temperature non-equilibrium reaction rates are expressed in terms of specific heat capacities of the species participate in the chemical reactions, bracket integrals connected with the internal energy transfer in inelastic non-reactive collisions and energy transfer coefficients. Reactions of dissociation/recombination of homonuclear and heteronuclear diatomic molecules are considered. It is shown that all reaction rates are the complex functions of the species densities, similarly to the unimolecular reaction rates. For determining the rate coefficients it is recommended to tabulate corresponding bracket integrals, additionally to the equilibrium rate constants. Correlation of the obtained results with the irreversible thermodynamics is established.

Electronic energy density in chemical reaction systems

NASA Astrophysics Data System (ADS)

Tachibana, Akitomo

2001-08-01

The energy of chemical reaction is visualized in real space using the electronic energy density nE(r⃗) associated with the electron density n(r⃗). The electronic energy density nE(r⃗) is decomposed into the kinetic energy density nT(r⃗), the external potential energy density nV(r⃗), and the interelectron potential energy density nW(r⃗). Using the electronic energy density nE(r⃗) we can pick up any point in a chemical reaction system and find how the electronic energy E is assigned to the selected point. We can then integrate the electronic energy density nE(r⃗) in any region R surrounding the point and find out the regional electronic energy ER to the global E. The kinetic energy density nT(r⃗) is used to identify the intrinsic shape of the reactants, the electronic transition state, and the reaction products along the course of the chemical reaction coordinate. The intrinsic shape is identified with the electronic interface S that discriminates the region RD of the electronic drop from the region RA of the electronic atmosphere in the density distribution of the electron gas. If the R spans the whole space, then the integral gives the total E. The regional electronic energy ER in thermodynamic ensemble is realized in electrochemistry as the intrinsic Volta electric potential φR and the intrinsic Herring-Nichols work function ΦR. We have picked up first a hydrogen-like atom for which we have analytical exact expressions of the relativistic kinetic energy density nTM(r⃗) and its nonrelativistic version nT(r⃗). These expressions are valid for any excited bound states as well as the ground state. Second, we have selected the following five reaction systems and show the figures of the nT(r⃗) as well as the other energy densities along the intrinsic reaction coordinates: a protonation reaction to He, addition reactions of HF to C2H4 and C2H2, hydrogen abstraction reactions of NH3+ from HF and NH3. Valence electrons possess their unique

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE PAGES

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

2009-01-01

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Mesoscale simulations of shockwave energy dissipation via chemical reactions.

PubMed

Antillon, Edwin; Strachan, Alejandro

2015-02-28

We use a particle-based mesoscale model that incorporates chemical reactions at a coarse-grained level to study the response of materials that undergo volume-reducing chemical reactions under shockwave-loading conditions. We find that such chemical reactions can attenuate the shockwave and characterize how the parameters of the chemical model affect this behavior. The simulations show that the magnitude of the volume collapse and velocity at which the chemistry propagates are critical to weaken the shock, whereas the energetics in the reactions play only a minor role. Shock loading results in transient states where the material is away from local equilibrium and, interestingly, chemical reactions can nucleate under such non-equilibrium states. Thus, the timescales for equilibration between the various degrees of freedom in the material affect the shock-induced chemistry and its ability to attenuate the propagating shock.

Methyl salicylate: a reactive chemical warfare agent surrogate to detect reaction with hypochlorite.

PubMed

Salter, W Bruce; Owens, Jeffery R; Wander, Joseph D

2011-11-01

Methyl salicylate (MeS) has a rich history as an inert physical simulant for the chemical warfare agents sulfur mustard and soman, where it is used extensively for liquid- and vapor-permeation testing. Here we demonstrate possible utility of MeS as a reactivity simulant for chlorine-based decontaminants. In these experiments MeS was reacted with sodium hypochlorite varying stoichiometry, temperature, reaction time, and pH. No colored oxidation products were observed; however, chlorination of the aromatic ring occurred ortho (methyl 3-chlorosalicylate) and para (methyl 5-chlorosalicylate) to the position bearing the -OH group in both the mono- and disubstituted forms. The monosubstituted para product accumulated initially, and the ortho and 3,5-dichloro products formed over the next several hours. Yields from reactions conducted below pH 11 declined rapidly with decreasing pH. Reactions run at 40 °C produced predominantly para substitution, while those run at 0 °C produced lower yields of ortho- and para-substituted products. Reactions were also carried out on textile substrates of cotton, 50/50 nylon-cotton, and a meta aramid. The textile data broadly reproduced reaction times and stoichiometry observed in the liquid phase, but are complicated by physical and possibly chemical interactions with the fabric. These data indicate that, for hypochlorite-containing neutralizing agents operating at strongly alkaline pH, one can expect MeS to react stoichiometrically with the hypochlorite it encounters. This suggests utility of MeS in lieu of such highly hazardous surrogates as monochloroalkyl sulfides as a simulant for threat scenarios involving the stoichiometric decomposition of sulfur mustard. Specifically, the extent of coverage of the simulant on a fabric by the neutralizing agent can be directly measured. Similar reactivity toward other halogen oxidizing agents is likely but remains to be demonstrated.

New Possibilities for Magnetic Control of Chemical and Biochemical Reactions.

PubMed

Buchachenko, Anatoly; Lawler, Ronald G

2017-04-18

Chemistry is controlled by Coulomb energy; magnetic energy is lower by many orders of magnitude and may be confidently ignored in the energy balance of chemical reactions. The situation becomes less clear, however, when reaction rates are considered. In this case, magnetic perturbations of nearly degenerate energy surface crossings may produce observable, and sometimes even dramatic, effects on reactions rates, product yields, and spectroscopic transitions. A case in point that has been studied for nearly five decades is electron spin-selective chemistry via the intermediacy of radical pairs. Magnetic fields, external (permanent or oscillating) and the internal magnetic fields of magnetic nuclei, have been shown to overcome electron spin selection rules for pairs of reactive paramagnetic intermediates, catalyzing or inhibiting chemical reaction pathways. The accelerating effects of magnetic stimulation may therefore be considered to be magnetic catalysis. This type of catalysis is most commonly observed for reactions of a relatively long-lived radical pair containing two weakly interacting electron spins formed by dissociation of molecules or by electron transfer. The pair may exist in singlet (total electron spin is zero) or triplet (total spin is unity) spin states. In virtually all cases, only the singlet state yields stable reaction products. Magnetic interactions with nuclear spins or applied fields may therefore affect the reactivity of radical pairs by changing the angular momentum of the pairs. Magnetic catalysis, first detected via its effect on spin state populations in nuclear and electron spin resonance, has been shown to function in a great variety of well-characterized reactions of organic free radicals. Considerably less well studied are examples suggesting that the basic mechanism may also explain magnetic effects that stimulate ATP synthesis, eliminating ATP deficiency in cardiac diseases, control cell proliferation, killing cancer cells, and

Aerosol simulation including chemical and nuclear reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marwil, E.S.; Lemmon, E.C.

1985-01-01

The numerical simulation of aerosol transport, including the effects of chemical and nuclear reactions presents a challenging dynamic accounting problem. Particles of different sizes agglomerate and settle out due to various mechanisms, such as diffusion, diffusiophoresis, thermophoresis, gravitational settling, turbulent acceleration, and centrifugal acceleration. Particles also change size, due to the condensation and evaporation of materials on the particle. Heterogeneous chemical reactions occur at the interface between a particle and the suspending medium, or a surface and the gas in the aerosol. Homogeneous chemical reactions occur within the aersol suspending medium, within a particle, and on a surface. These reactionsmore » may include a phase change. Nuclear reactions occur in all locations. These spontaneous transmutations from one element form to another occur at greatly varying rates and may result in phase or chemical changes which complicate the accounting process. This paper presents an approach for inclusion of these effects on the transport of aerosols. The accounting system is very complex and results in a large set of stiff ordinary differential equations (ODEs). The techniques for numerical solution of these ODEs require special attention to achieve their solution in an efficient and affordable manner. 4 refs.« less

Isomeric yield ratios of 87m,gY from different nuclear reactions

NASA Astrophysics Data System (ADS)

Naik, H.; Kim, G. N.; Kim, K.; Zaman, M.; Sahid, M.; Yang, S.-C.; Lee, M. W.; Kang, Y. R.; Shin, S. G.; Cho, M.-H.; Goswami, A.; Song, T. Y.

2014-07-01

The independent isomeric yield ratios of 87m,gY produced from the 93Nb( γ, α2n) and natZr( γ, p xn) reactions with the end-point bremsstrahlung energy of 45-70 MeV have been determined by an off-line γ-ray spectrometric technique using 100 MeV electron linac at the Pohang accelerator laboratory, Korea. The isomeric yield ratios of 87m,gY were also determined from the natZr(p, αxn) and the 89Y(p,p2n) reactions with E P = 15-45 MeV as well as those from the 89Y( α, α2n) reaction with E α = 32-43 MeV using the MC-50 cyclotron at the Korea Institute of Radiological and Medical Science, Korea. The isomeric yield ratios of 87m,gY from the present work in the 93Nb( γ, α2n), natZr( γ, p xn), natZr(p, αxn), 89Y(p,p2n), and 89Y( α, α2n) reactions were compared with those of the literature data in the 85Rb( α, 2n), the 86,87,88Sr(d, xn), 89Y(n,3n), and the 89Y( γ, 2n) reactions to examine the role of target, projectiles, and ejectiles through compound nucleus excitation energy and input angular momentum. The isomeric yield ratios of 87m,gY in the above eleven reactions were also calculated using the computer code TALYS 1.4 and compared with the experimental data. The different behaviors between photon- and neutron-induced reactions and charged-particle-induced reactions are discussed from the viewpoint of compound and non-compound (pre-equilibrium) process.

Computed potential energy surfaces for chemical reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Levin, Eugene

1993-01-01

A new global potential energy surface (PES) is being generated for O(P-3) + H2 yields OH + H. This surface is being fit using the rotated Morse oscillator method, which was used to fit the previous POL-CI surface. The new surface is expected to be more accurate and also includes a much more complete sampling of bent geometries. A new study has been undertaken of the reaction N + O2 yields NO + O. The new studies have focused on the region of the surface near a possible minimum corresponding to the peroxy form of NOO. A large portion of the PES for this second reaction has been mapped out. Since state to state cross sections for the reaction are important in the chemistry of high temperature air, these studies will probably be extended to permit generation of a new global potential for reaction.

'GREENER' CHEMICAL SYNTHESES USING ALTERNATE REACTION CONDITIONS

EPA Science Inventory

Microwave (MW) irradiation in conjunction with water as reaction media has proven to be a greener chemical approach for expeditious N-alkylation reactions of amines and hydrazines wherein the reactions under mildly basic conditions afford tertiary amines and double N-alkylation t...

Molecular Dynamics Simulations of Chemical Reactions for Use in Education

ERIC Educational Resources Information Center

Qian Xie; Tinker, Robert

2006-01-01

One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

Chemical mechanisms and reaction rates for the initiation of hot corrosion of IN-738

NASA Technical Reports Server (NTRS)

Fryburg, G. C.; Kohl, F. J.; Stearns, C. A.

1984-01-01

Sodium-sulfate-induced hot corrosion of preoxidized IN-738 was studied at 975 C with special emphasis placed on the processes occurring during the long induction period. Thermogravimetric tests were run for predetermined periods of time, and then one set of specimens was washed with water. Chemical analysis of the wash solutions yielded information about water soluble metal salts and residual sulfate. A second set of samples was cross sectioned dry and polished in a nonaqueous medium. Element distributions within the oxide scale were obtained from electron microprobe X-ray micrographs. Evolution of SO was monitored throughout the thermogravimetric tests. Kinetic rate studies were performed for several pertinent processes; appropriate rate constants were obtained from the following chemical reactions: Cr2O3 + 2 Na2SO4(1) + 3/2 O2 yields 2 Na2CrO4(1) + 2 SO3(g)n TiO2 + Na2SO4(1) yields Na2O(TiO2)n + SO3(g)n TiO2 + Na2CrO4(1) yields Na2O(TiO2)n + CrO3(g).

Chemical reactions simulated by ground-water-quality models

USGS Publications Warehouse

Grove, David B.; Stollenwerk, Kenneth G.

1987-01-01

Recent literature concerning the modeling of chemical reactions during transport in ground water is examined with emphasis on sorption reactions. The theory of transport and reactions in porous media has been well documented. Numerous equations have been developed from this theory, to provide both continuous and sequential or multistep models, with the water phase considered for both mobile and immobile phases. Chemical reactions can be either equilibrium or non-equilibrium, and can be quantified in linear or non-linear mathematical forms. Non-equilibrium reactions can be separated into kinetic and diffusional rate-limiting mechanisms. Solutions to the equations are available by either analytical expressions or numerical techniques. Saturated and unsaturated batch, column, and field studies are discussed with one-dimensional, laboratory-column experiments predominating. A summary table is presented that references the various kinds of models studied and their applications in predicting chemical concentrations in ground waters.

Fission fragment yields from heavy-ion-induced reactions measured with a fragment separator

NASA Astrophysics Data System (ADS)

Tarasov, O. B.; Delaune, O.; Farget, F.; Morrissey, D. J.; Amthor, A. M.; Bastin, B.; Bazin, D.; Blank, B.; Cacéres, L.; Chbihi, A.; Fernández-Dominguez, B.; Grévy, S.; Kamalou, O.; Lukyanov, S. M.; Mittig, W.; Pereira, J.; Perrot, L.; Saint-Laurent, M.-G.; Savajols, H.; Sherrill, B. M.; Stodel, C.; Thomas, J. C.; Villari, A. C.

2018-04-01

The systematic study of fission fragment yields under different initial conditions has provided valuable experimental data for benchmarking models of fission product yields. Nuclear reactions using inverse kinematics coupled to the use of a high-resolution spectrometer with good fragment identification are shown here to be a powerful tool to measure the inclusive isotopic yields of fission fragments. In-flight fusion-fission was used in this work to produce secondary beams of neutron-rich isotopes in the collisions of a 238U beam at 24 MeV/u with 9Be and 12C targets at GANIL using the LISE3 fragment separator. Unique identification of the A, Z, and atomic charge state, q, of fission products was attained with the Δ E- TKE-B ρ- ToF measurement technique. Mass, and atomic number distributions are reported for the two reactions. The results show the importance of different reaction mechanisms in the two cases. The optimal target material for higher yields of neutron-rich high- Z isotopes produced in fusion-fission reactions as a function of projectile energy is discussed.

Chemical Principles Revisited: Annotating Reaction Equations.

ERIC Educational Resources Information Center

Tykodi, R. J.

1987-01-01

Urges chemistry teachers to have students annotate the chemical reactions in aqueous-solutions that they see in their textbooks and witness in the laboratory. Suggests this will help students recognize the reaction type more readily. Examples are given for gas formation, precipitate formation, redox interaction, acid-base interaction, and…

A new type of power energy for accelerating chemical reactions: the nature of a microwave-driving force for accelerating chemical reactions.

PubMed

Zhou, Jicheng; Xu, Wentao; You, Zhimin; Wang, Zhe; Luo, Yushang; Gao, Lingfei; Yin, Cheng; Peng, Renjie; Lan, Lixin

2016-04-27

The use of microwave (MW) irradiation to increase the rate of chemical reactions has attracted much attention recently in nearly all fields of chemistry due to substantial enhancements in reaction rates. However, the intrinsic nature of the effects of MW irradiation on chemical reactions remains unclear. Herein, the highly effective conversion of NO and decomposition of H2S via MW catalysis were investigated. The temperature was decreased by several hundred degrees centigrade. Moreover, the apparent activation energy (Ea') decreased substantially under MW irradiation. Importantly, for the first time, a model of the interactions between microwave electromagnetic waves and molecules is proposed to elucidate the intrinsic reason for the reduction in the Ea' under MW irradiation, and a formula for the quantitative estimation of the decrease in the Ea' was determined. MW irradiation energy was partially transformed to reduce the Ea', and MW irradiation is a new type of power energy for speeding up chemical reactions. The effect of MW irradiation on chemical reactions was determined. Our findings challenge both the classical view of MW irradiation as only a heating method and the controversial MW non-thermal effect and open a promising avenue for the development of novel MW catalytic reaction technology.

A new type of power energy for accelerating chemical reactions: the nature of a microwave-driving force for accelerating chemical reactions

PubMed Central

Zhou, Jicheng; Xu, Wentao; You, Zhimin; Wang, Zhe; Luo, Yushang; Gao, Lingfei; Yin, Cheng; Peng, Renjie; Lan, Lixin

2016-01-01

The use of microwave (MW) irradiation to increase the rate of chemical reactions has attracted much attention recently in nearly all fields of chemistry due to substantial enhancements in reaction rates. However, the intrinsic nature of the effects of MW irradiation on chemical reactions remains unclear. Herein, the highly effective conversion of NO and decomposition of H2S via MW catalysis were investigated. The temperature was decreased by several hundred degrees centigrade. Moreover, the apparent activation energy (Ea’) decreased substantially under MW irradiation. Importantly, for the first time, a model of the interactions between microwave electromagnetic waves and molecules is proposed to elucidate the intrinsic reason for the reduction in the Ea’ under MW irradiation, and a formula for the quantitative estimation of the decrease in the Ea’ was determined. MW irradiation energy was partially transformed to reduce the Ea’, and MW irradiation is a new type of power energy for speeding up chemical reactions. The effect of MW irradiation on chemical reactions was determined. Our findings challenge both the classical view of MW irradiation as only a heating method and the controversial MW non-thermal effect and open a promising avenue for the development of novel MW catalytic reaction technology. PMID:27118640

Target effects in isobaric yield ratio differences between projectile fragmentation reactions

NASA Astrophysics Data System (ADS)

Ma, Chun-Wang; Zhang, Yan-Li; Qiao, Chun-Yuan; Wang, Shan-Shan

2015-01-01

Background: The isobaric yield ratio difference (IBD) between reactions is know to be sensitive to the density difference between projectiles in heavy-ion collisions around the Fermi energy. Purpose: The target effects in the isobaric yield ratio (IYR) and the IBD results have been studied. Methods: The amount of isotopes in the 140 A MeV 48 ,40Ca +181Ta /9Be and 58 ,64Ni +181Ta /9Be reactions have been previously measured with high accuracy. The IYR and IBD results have been obtained from these reactions to study the effects of the light 9Be and heavy 181Ta targets. A ratio (rΔ μ) between the IBD results for the reactions with Ta and Be targets is defined to quantitatively show the target dependence of the IBD results. Results The IYRs for reactions with symmetric projectiles are more easily affected than those for reactions with neutron-rich projectiles. The IBD results are suppressed by using the 181Ta target to different degrees. Conclusions: The IYR and IBD results are influenced by the target used. The IBD for the I =1 isobaric chain is suggested as a probe to study the difference between the neutron and proton densities of the reaction systems.

Chemical computing with reaction-diffusion processes.

PubMed

Gorecki, J; Gizynski, K; Guzowski, J; Gorecka, J N; Garstecki, P; Gruenert, G; Dittrich, P

2015-07-28

Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction-diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Chemical reactions in reverse micelle systems

DOEpatents

Matson, Dean W.; Fulton, John L.; Smith, Richard D.; Consani, Keith A.

1993-08-24

This invention is directed to conducting chemical reactions in reverse micelle or microemulsion systems comprising a substantially discontinuous phase including a polar fluid, typically an aqueous fluid, and a microemulsion promoter, typically a surfactant, for facilitating the formation of reverse micelles in the system. The system further includes a substantially continuous phase including a non-polar or low-polarity fluid material which is a gas under standard temperature and pressure and has a critical density, and which is generally a water-insoluble fluid in a near critical or supercritical state. Thus, the microemulsion system is maintained at a pressure and temperature such that the density of the non-polar or low-polarity fluid exceeds the critical density thereof. The method of carrying out chemical reactions generally comprises forming a first reverse micelle system including an aqueous fluid including reverse micelles in a water-insoluble fluid in the supercritical state. Then, a first reactant is introduced into the first reverse micelle system, and a chemical reaction is carried out with the first reactant to form a reaction product. In general, the first reactant can be incorporated into, and the product formed in, the reverse micelles. A second reactant can also be incorporated in the first reverse micelle system which is capable of reacting with the first reactant to form a product.

Chemical memory reactions induced bursting dynamics in gene expression.

PubMed

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

Entropy Generation in a Chemical Reaction

ERIC Educational Resources Information Center

Miranda, E. N.

2010-01-01

Entropy generation in a chemical reaction is analysed without using the general formalism of non-equilibrium thermodynamics at a level adequate for advanced undergraduates. In a first approach to the problem, the phenomenological kinetic equation of an elementary first-order reaction is used to show that entropy production is always positive. A…

An autonomous organic reaction search engine for chemical reactivity.

PubMed

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

2017-06-09

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.

An autonomous organic reaction search engine for chemical reactivity

NASA Astrophysics Data System (ADS)

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.

An autonomous organic reaction search engine for chemical reactivity

PubMed Central

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

2017-01-01

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. PMID:28598440

Correlations between reaction product yields as a tool for probing heavy-ion reaction scenarios

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gawlikowicz, W.; Heavy-Ion Laboratory, Warsaw University, PL-02-093 Warsaw; Agnihotri, D. K.

2010-01-15

Experimental multidimensional joint distributions of neutrons and charged reaction products were analyzed for {sup 136}Xe + {sup 209}Bi reactions at E/A=28, 40, and 62 MeV and were found to exhibit several different types of prominent correlation patterns. Some of these correlations have a simple explanation in terms of the system excitation energy and pose little challenge to most statistical decay theories. However, several other types of correlation patterns are difficult to reconcile with some, but not other, possible reaction scenarios. In this respect, correlations between the average atomic numbers of intermediate-mass fragments, on the one hand, and light particle multiplicities,more » on the other, are notable. This kind of multiparticle correlation provides a useful tool for probing reaction scenarios, which is different from the traditional approach of interpreting inclusive yields of individual reaction products.« less

Versatile Dual Photoresponsive System for Precise Control of Chemical Reactions.

PubMed

Xu, Can; Bing, Wei; Wang, Faming; Ren, Jinsong; Qu, Xiaogang

2017-08-22

A versatile method for photoregulation of chemical reactions was developed through a combination of near-infrared (NIR) and ultraviolet (UV) light sensitive materials. This regulatory effect was achieved through photoresponsive modulation of reaction temperature and pH values, two prominent factors influencing reaction kinetics. Photothermal nanomaterial graphene oxide (GO) and photobase reagent malachite green carbinol base (MGCB) were selected for temperature and pH regulation, respectively. Using nanocatalyst- and enzyme-mediated chemical reactions as model systems, we demonstrated the feasibility and high efficiency of this method. In addition, a photoresponsive, multifunctional "Band-aid"-like hydrogel platform was presented for programmable wound healing. Overall, this simple, efficient, and reversible system was found to be effective for controlling a wide variety of chemical reactions. Our work may provide a method for remote and sustainable control over chemical reactions for industrial and biomedical applications.

Modelling Chemical Reasoning to Predict and Invent Reactions.

PubMed

Segler, Marwin H S; Waller, Mark P

2017-05-02

The ability to reason beyond established knowledge allows organic chemists to solve synthetic problems and invent novel transformations. Herein, we propose a model that mimics chemical reasoning, and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180 000 randomly selected binary reactions. The data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-)discovering novel transformations (even including transition metal-catalysed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph and because each single reaction prediction is typically achieved in a sub-second time frame, the model can be used as a high-throughput generator of reaction hypotheses for reaction discovery. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Coatings on the Uptake Rate and HONO Yield in Heterogeneous Reaction of Soot with NO2

NASA Astrophysics Data System (ADS)

Cruz-Quiñones, M.; Khalizov, A. F.; Zhang, R.

2009-12-01

Heterogeneous reaction of nitrogen dioxide on carbon soot aerosols has been suggested as a possible source of nighttime nitrous acid (HONO) in atmosphere boundary layer. Available laboratory data show significant variability in the measured reaction probabilities and HONO yields, making it difficult to asses the atmospheric significance of this process. Moreover, little is known of how aging of soot aerosol through internal mixing with other atmospheric trace constituents will affect the heterogeneous reactivity and HONO production. In this work, the heterogeneous reaction of NO2 on fresh and aged soot films leading to HONO formation was studied through a series of kinetic uptake experiments and HONO yield measurements. Soot samples were prepared by incomplete combustion of propane and kerosene fuels under lean and rich flame conditions. Experiments were performed in a low-pressure, fast-flow reactor coupled to a chemical ionization mass spectrometer (CIMS), using atmospheric-level NO2 concentrations. Heterogeneous uptake coefficients, γ(geom) and γ(BET), were calculated using geometric and internal BET soot surface areas, respectively. The uptake coefficient and the HONO yield depend on the type of fuel and combustion regime and are the highest for soot samples prepared using rich kerosene flame. Although, the internal surface area of soot measured by BET method is a factor of 50 to 500 larger than the geometric surface area, only the top soot layers are involved in heterogeneous reaction with NO2 as follows from the observed weak dependence of γ(geom) and decrease in γ(BET) with increasing sample mass. Heating the soot samples before exposure to NO2 increases the BET surface area, the HONO yield, and the NO2 uptake coefficient due to the removal of the organic fraction from the soot backbone that unblocks active sites and makes them accessible for physical adsorption and chemical reactions. Our results support the oxidation-reduction mechanism involving

A network dynamics approach to chemical reaction networks

NASA Astrophysics Data System (ADS)

van der Schaft, A. J.; Rao, S.; Jayawardhana, B.

2016-04-01

A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.

Students' Understandings of Chemical Bonds and the Energetics of Chemical Reactions.

ERIC Educational Resources Information Center

Boo, Hong Kwen

1998-01-01

Investigates Grade 12 students' understandings of the nature of chemical bonds and the energetics elicited across five familiar chemical reactions following a course of instruction. Discusses the many ways in which students can misconstruct concepts and principles. Contains 63 references. (DDR)

Sir John Pople, Gaussian Code, and Complex Chemical Reactions

Science.gov Websites

tool that describes the dance of molecules in chemical reactions ... . Dr. Pople was among the first to colors of light they will absorb or emit, and the pace of chemical reactions. The work culminated in a dropdown arrow Site Map A-Z Index Menu Synopsis Sir John Pople, Gaussian Code, and Complex Chemical

Non-equilibrium effects in high temperature chemical reactions

NASA Technical Reports Server (NTRS)

Johnson, Richard E.

1987-01-01

Reaction rate data were collected for chemical reactions occurring at high temperatures during reentry of space vehicles. The principle of detailed balancing is used in modeling kinetics of chemical reactions at high temperatures. Although this principle does not hold for certain transient or incubation times in the initial phase of the reaction, it does seem to be valid for the rates of internal energy transitions that occur within molecules and atoms. That is, for every rate of transition within the internal energy states of atoms or molecules, there is an inverse rate that is related through an equilibrium expression involving the energy difference of the transition.

The Electronic Flux in Chemical Reactions. Insights on the Mechanism of the Maillard Reaction

NASA Astrophysics Data System (ADS)

Flores, Patricio; Gutiérrez-Oliva, Soledad; Herrera, Bárbara; Silva, Eduardo; Toro-Labbé, Alejandro

2007-11-01

The electronic transfer that occurs during a chemical process is analysed in term of a new concept, the electronic flux, that allows characterizing the regions along the reaction coordinate where electron transfer is actually taking place. The electron flux is quantified through the variation of the electronic chemical potential with respect to the reaction coordinate and is used, together with the reaction force, to shed light on reaction mechanism of the Schiff base formation in the Maillard reaction. By partitioning the reaction coordinate in regions in which different process might be taking place, electronic reordering associated to polarization and transfer has been identified and found to be localized at specific transition state regions where most bond forming and breaking occur.

Modular verification of chemical reaction network encodings via serializability analysis

PubMed Central

Lakin, Matthew R.; Stefanovic, Darko; Phillips, Andrew

2015-01-01

Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a “commit reaction” that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of “extra tolerance”, which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited. PMID:27325906

Chemical Memory Reactions Induced Bursting Dynamics in Gene Expression

PubMed Central

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems. PMID:23349679

Spectroscopy and reactions of molecules important in chemical evolution

NASA Technical Reports Server (NTRS)

Becker, R. S.

1974-01-01

The research includes: (1) hot hydrogen atom reactions in terms of the nature of products produced, mechanism of the reactions and the implication and application of such reactions for molecules existing in interstellar clouds, in planetary atmospheres, and in chemical evolution; (2) photochemical reactions that can lead to molecules important in chemical evolution, interstellar clouds and as constituents in planetary atmospheres; and (3) spectroscopic and theoretical properties of biomolecules and their precursors and where possible, use these to understand their photochemical behavior.

Stochastic thermodynamics and entropy production of chemical reaction systems

NASA Astrophysics Data System (ADS)

Tomé, Tânia; de Oliveira, Mário J.

2018-06-01

We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end, we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of chemical reaction systems based on a master equation defined on the space of microscopic chemical states and on appropriate definitions of entropy and entropy production. The system is in contact with a heat reservoir and is placed out of equilibrium by the contact with particle reservoirs. In our approach, the fluxes of various types, such as the heat and particle fluxes, play a fundamental role in characterizing the nonequilibrium chemical state. We show that the rate of entropy production in the stationary nonequilibrium state is a bilinear form in the affinities and the fluxes of reaction, which are expressed in terms of rate constants and transition rates, respectively. We also show how the description in terms of microscopic states can be reduced to a description in terms of the numbers of particles of each species, from which follows the chemical master equation. As an example, we calculate the rate of entropy production of the first and second Schlögl reaction models.

Particulate representation of a chemical reaction mechanism

NASA Astrophysics Data System (ADS)

Lee, Kam-Wah Lucille

1999-09-01

A growing area of interest in chemical education has been the research associated with conceptual understanding at the particulate level. This study investigated the views of 10 university chemistry lecturers, 85 pre-service chemistry teachers and 23 Secondary 3 (equivalent to Year 9) chemistry students about the particulate level of a chemical reaction, namely the heating of copper (II) carbonate. Four characteristic views were identified on the basis of their diagrammatic representations of particles. These were: (a) formation of intermediates; (b) formation of free particles (e. g., atoms or ions); (c) combination of a and b: formation of free particles (e. g., atoms or ions) first, and then intermediates; (d) no mechanism. Both the majority of the lecturers and the pre-service teachers held an identical view about the reaction mechanism, namely that the decomposition of copper (II) carbonate goes through a transition stage by forming intermediates. In contrast, even though the students were familiar with this reaction, about half of them naïvely believed that copper (II) carbonate broke up on heating and the particles recombined directly to form copper (II) oxide and carbon dioxide, the two observed products. About one-third of the students had neither any notion of how the atoms in the copper (II) carbonate lattice interacted and were rearranged in the reaction nor any concept of bond-breaking and reformation in a chemical reaction.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

Gao, Connie W.; Allen, Joshua W.; Green, William H.; ...

2016-02-24

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involvingmore » carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.« less

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

The Theory of Thermodynamics for Chemical Reactions in Dispersed Heterogeneous Systems

PubMed

Yongqiang; Baojiao; Jianfeng

1997-07-01

In this paper, the expressions of Gibbs energy change, enthalpy change, entropy change, and equilibrium constant for chemical reactions in dispersed heterogeneous systems are derived using classical thermodynamics theory. The thermodynamical relations for the same reaction system between the dispersed and the block state are also derived. The effects of degree of dispersion on thermodynamical properties, reaction directions, and chemical equilibria are discussed. The results show that the present equation of thermodynamics for chemical reactions is only a special case of the above-mentioned formulas and that the effect of the dispersity of a heterogeneous system on the chemical reaction obeys the Le Chatelier principle of movement of equilibria.

Chemical reactions directed Peptide self-assembly.

PubMed

Rasale, Dnyaneshwar B; Das, Apurba K

2015-05-13

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.

Determination of absolute chemiluminescence quantum yields for reactions of bis-(pentachlorophenyl) oxalate, hydrogen peroxide and fluorescent compounds.

PubMed

Catherall, C L; Palmer, T F; Cundall, R B

1989-01-01

Absolute chemiluminescence quantum yields (phi CL) for reactions of bis-(pentachlorophenyl) oxalate (PCPO), hydrogen peroxide (H2O2) and 9:10 diphenyl anthracene (DPA) have been determined. A fully corrected chemiluminescence monitoring spectrometer was calibrated for spectral sensitivity using the chemiluminescence of the bis-(pentachlorophenyl) oxalate system as a liquid light source, the total photon output of which had previously been determined by chemical actinometry. At high (PCPO)/(H2O2) ratios phi CL was found to be independent of PCPO and H2O2 concentrations.

Role of the N*(1535) resonance and the {pi}{sup -}p{yields}KY amplitudes in the OZI forbidden {pi}N{yields}{phi}N reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doering, M.; Oset, E.; Zou, B. S.

2008-08-15

We study the {pi}N{yields}{phi}N reaction close to the {phi}N threshold within the chiral unitary approach, by combining the {pi}{sup -}p{yields}K{sup +}{sigma}{sup -},{pi}{sup -}p{yields}K{sup 0}{sigma}{sup 0}, and {pi}{sup -}p{yields}K{sup 0}{lambda} amplitudes with the coupling of {phi} to the K components of the final states of these reactions via quantum loops. We obtain good agreement with experiment when the dominant {pi}{sup -}p{yields}K{sup 0}{lambda} amplitude is constrained with its experimental cross section. We also evaluate the coupling of N*(1535) to {phi}N and find a moderate coupling as a consequence of partial cancellation of the large KY components of N*(1535). We also show thatmore » the N*(1535) pole approximation is too small to reproduce the measured cross section for the {pi}{sup -}N{yields}{phi}N reaction.« less

Concordant Chemical Reaction Networks and the Species-Reaction Graph

PubMed Central

Shinar, Guy; Feinberg, Martin

2015-01-01

In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class. In particular, multiple equilibria are precluded, as are degenerate positive equilibria. Moreover, under certain circumstances, also related to concordance, all real eigenvalues associated with a positive equilibrium are negative. Although concordance of a reaction network can be decided by readily available computational means, we show here that, when a nondegenerate network’s Species-Reaction Graph satisfies certain mild conditions, concordance and its dynamical consequences are ensured. These conditions are weaker than earlier ones invoked to establish kinetic system injectivity, which, in turn, is just one ramification of network concordance. Because the Species-Reaction Graph resembles pathway depictions often drawn by biochemists, results here expand the possibility of inferring significant dynamical information directly from standard biochemical reaction diagrams. PMID:22940368

Supersonic molecular beam experiments on surface chemical reactions.

PubMed

Okada, Michio

2014-10-01

The interaction of a molecule and a surface is important in various fields, and in particular in complex systems like biomaterials and their related chemistry. However, the detailed understanding of the elementary steps in the surface chemistry, for example, stereodynamics, is still insufficient even for simple model systems. In this Personal Account, I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams demonstrate a significant role of the translational energy of the incident molecules. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths specific for the hyperthermal energy region, and to develop new methods for the fabrication of thin films. On the other hand, oriented molecular beams also demonstrate the possibility of understanding surface chemical reactions in detail by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for finely monitoring the elementary step of the surface chemical reactions and creating new materials on surfaces. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perspective: chemical dynamics simulations of non-statistical reaction dynamics

PubMed Central

Ma, Xinyou; Hase, William L.

2017-01-01

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320906

Lagrangian descriptors of driven chemical reaction manifolds.

PubMed

Craven, Galen T; Junginger, Andrej; Hernandez, Rigoberto

2017-08-01

The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven and R. Hernandez, Phys. Rev. Lett. 115, 148301 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.148301], we obtain this so-called distinguished trajectory and the associated moving reaction manifolds on model energy surfaces subject to various driving and dissipative conditions. In particular, we demonstrate that this is exact for harmonic barriers in one dimension and this verification gives impetus to the application of Lagrangian descriptor-based methods in diverse classes of chemical reactions. The development of these objects is paramount in the theory of reaction dynamics as the transition state structure and its underlying network of manifolds directly dictate reactivity and selectivity.

Limonene ozonolysis in the presence of nitric oxide: Gas-phase reaction products and yields

NASA Astrophysics Data System (ADS)

Ham, Jason E.; Harrison, Joel C.; Jackson, Stephen R.; Wells, J. R.

2016-05-01

The reaction products from limonene ozonolysis were investigated using the new carbonyl derivatization agent, O-tert-butylhydroxylamine hydrochloride (TBOX). With ozone (O3) as the limiting reagent, five carbonyl compounds were detected. The yields of the carbonyl compounds are discussed with and without the presence of a hydroxyl radical (OHrad) scavenger, giving insight into the influence secondary OH radicals have on limonene ozonolysis products. The observed reaction product yields for limonaketone (LimaKet), 7-hydroxyl-6-oxo-3-(prop-1-en-2-yl)heptanal (7H6O), and 2-acetyl-5-oxohexanal (2A5O) were unchanged suggesting OHrad generated by the limonene + O3 reaction does not contribute to their formation. The molar yields of 3-isopropenyl-6-oxo-heptanal (IPOH) and 3-acetyl-6-oxoheptanal (3A6O) decreased by 68% and >95%; respectively, when OHrad was removed. This suggests that OHrad radicals significantly impact the formation of these products. Nitric oxide (NO) did not significantly affect the molar yields of limonaketone or IPOH. However, NO (20 ppb) considerably decreased the molar reaction product yields of 7H6O (62%), 2A5O (63%), and 3A6O (47%), suggesting NO reacted with peroxyl intermediates, generated during limonene ozonolysis, to form other carbonyls (not detected) or organic nitrates. These studies give insight into the transformation of limonene and its reaction products that can lead to indoor exposures.

Ozone deposition velocities, reaction probabilities and product yields for green building materials

NASA Astrophysics Data System (ADS)

Lamble, S. P.; Corsi, R. L.; Morrison, G. C.

2011-12-01

Indoor surfaces can passively remove ozone that enters buildings, reducing occupant exposure without an energy penalty. However, reactions between ozone and building surfaces can generate and release aerosols and irritating and carcinogenic gases. To identify desirable indoor surfaces the deposition velocity, reaction probability and carbonyl product yields of building materials considered green (listed, recycled, sustainable, etc.) were quantified. Nineteen separate floor, wall or ceiling materials were tested in a 10 L, flow-through laboratory reaction chamber. Inlet ozone concentrations were maintained between 150 and 200 ppb (generally much lower in chamber air), relative humidity at 50%, temperature at 25 °C and exposure occurred over 24 h. Deposition velocities ranged from 0.25 m h -1 for a linoleum style flooring up to 8.2 m h -1 for a clay based paint; reaction probabilities ranged from 8.8 × 10 -7 to 6.9 × 10 -5 respectively. For all materials, product yields of C 1 thru C 12 saturated n-aldehydes, plus acetone ranged from undetectable to greater than 0.70 The most promising material was a clay wall plaster which exhibited a high deposition velocity (5.0 m h -1) and a low product yield (

Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Process for preparing a chemical compound enriched in isotope content

DOEpatents

Michaels, Edward D.

1982-01-01

A process to prepare a chemical enriched in isotope content which includes: (a) A chemical exchange reaction between a first and second compound which yields an isotopically enriched first compound and an isotopically depleted second compound; (b) the removal of a portion of the first compound as product and the removal of a portion of the second compound as spent material; (c) the conversion of the remainder of the first compound to the second compound for reflux at the product end of the chemical exchange reaction region; (d) the conversion of the remainder of the second compound to the first compound for reflux at the spent material end of the chemical exchange region; and the cycling of the additional chemicals produced by one conversion reaction to the other conversion reaction, for consumption therein. One of the conversion reactions is an oxidation reaction, and the energy that it yields is used to drive the other conversion reaction, a reduction. The reduction reaction is carried out in a solid polymer electrolyte electrolytic reactor. The overall process is energy efficient and yields no waste by-products.

Suppression of Ostwald Ripening by Chemical Reactions

NASA Astrophysics Data System (ADS)

Zwicker, David; Hyman, Anthony A.; Jülicher, Frank

2015-03-01

Emulsions consisting of droplets immersed in a fluid are typically unstable and coarsen over time. One important coarsening process is Ostwald ripening, which is driven by the surface tension of the droplets. Ostwald ripening must thus be suppressed to stabilize emulsions, e.g. to control the properties of pharmaceuticals, food, or cosmetics. Suppression of Ostwald ripening is also important in biological cells, which contain stable liquid-like compartments, e.g. germ granules, Cajal-bodies, and centrosomes. Such systems are often driven away from equilibrium by chemical reactions and can thus be called active emulsions. Here, we show that non-equilibrium chemical reactions can suppress Ostwald Ripening, leading to stable, monodisperse emulsions. We derive analytical approximations of the typical droplet size, droplet count, and time scale of the dynamics from a coarse-grained description of the droplet dynamics. We also compare these results to numerical simulations of the continuous concentration fields. Generally, we thus show how chemical reactions can be used to stabilize emulsions and to control their properties in technology and nature.

Chemical Reactions Directed Peptide Self-Assembly

PubMed Central

Rasale, Dnyaneshwar B.; Das, Apurba K.

2015-01-01

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly. PMID:25984603

Formation and reactions of negative ions relevant to chemical ionization mass spectrometry. I. Cl mass spectra of organic compounds produced by F− reactions

PubMed Central

Tiernan, T. O.; Chang, C.; Cheng, C. C.

1980-01-01

A systematic study of the negative-ion chemical ionization mass spectra produced by the reaction of F− with a wide variety of organic compounds has been accomplished. A time-of-flight mass spectrometer fitted with a modified high pressure ion source was employed for these experiments. The F− reagent ion was generated from CF3H or NF3, typically at an ion source pressure of 100 μm. In pure NF3, F− is the major ion formed and constitutes more than 90% of the total ion intensity. While F− is also the major primary ion formed in pure CF3H, it undergoes rapid ion-molecule reactions at elevated source pressures, yielding (HF)nF− (n = 1−3) ions, which makes CF3H less suitable as a chemical ionization reagent gas. Among the organic compounds investigated were carboxylic acids, ketones, aldehydes, esters, alcohols, phenols, halides, nitriles, nitrobenzene, ethers, amines and hydrocarbons. An intense (M − 1)− ion was observed in the F− chemical ionization mass spectra of carboxylic acids, ketones, aldehydes and phenols. Alcohols yield only (M + F)− ions upon reaction with F−. A weaker (M + F)− ion was also detected in the F− chemical ionization spectra of carboxylic acids, aldehydes, ketones and nitriles. The F− chemical ionization mass spectra of esters, halides, nitriles, nitrobenzene and ethers are characterized primarily by the ions, RCOO−, X−, CN−, NO2−, and OR−, respectively. In addition, esters show a very weak (M − 1)− ion (except formates). In the F− chemical ionization spectra of some aliphatic alkanes and o-xylene, a very weak (M + F)− ion was observed. Amines and aliphatic alkenes exhibit only insignificant fragment ions under similar conditions, while aromatic hydrocarbons, such as benzene and toluene are not reactive at all with the F− ion. The mechanisms of the various reactions mentioned are discussed, and several experimental complications are noted. In still other studies, the effects of varying several

Precision synthesis of functional materials via RAFT polymerization and click-type chemical reactions

NASA Astrophysics Data System (ADS)

Flores, Joel Diez

2011-12-01

The need to tailor polymeric architectures with specific physico-chemical properties via the simplest, cleanest, and most efficient synthetic route possible has become the ultimate goal in polymer synthesis. Recent progress in macromolecular science, such as the discoveries of controlled/"living" free radical polymerization (CRP) methods, has brought about synthetic capabilities to prepare (co)polymers with advanced topologies, predetermined molecular weights, narrow molecular weight distributions, and precisely located functional groups. In addition, the establishment of click chemistry has redefined the selected few highly efficient chemical reactions that become highly useful in post-polymerization modification strategies. Hence, the ability to make well-defined topologies afforded by controlled polymerization techniques and the facile incorporation of functionalities along the chain via click-type reactions have yielded complex architectures, allowing the investigation of physical phenomena which otherwise could not be studied with systems prepared via conventional methods. The overarching theme of the research work described in this dissertation is the fusion of the excellent attributes of reversible addition-fragmentation chain transfer (RAFT) polymerization method, which is one of the CRP techniques, and click-type chemical reactions in the precision of synthesis of advanced functional materials. Chapter IV is divided into three sections. In Section I, the direct RAFT homopolymerization of 2-(acryloyloxy)ethyl isocyanate (AOI) and subsequent post-polymerization modifications are described. The polymerization conditions were optimized in terms of the choice of RAFT chain transfer agent (CTA), polymerization temperature and the reaction medium. Direct RAFT polymerization of AOI requires a neutral CTA, and relatively low reaction temperature to yield AOI homopolymers with low polydispersities. Efficient side-chain functionalization of PAOI homopolymers was

MRI of chemical reactions and processes.

PubMed

Britton, Melanie M

2017-08-01

As magnetic resonance imaging (MRI) can spatially resolve a wealth of molecular information available from nuclear magnetic resonance (NMR), it is able to non-invasively visualise the composition, properties and reactions of a broad range of spatially-heterogeneous molecular systems. Hence, MRI is increasingly finding applications in the study of chemical reactions and processes in a diverse range of environments and technologies. This article will explain the basic principles of MRI and how it can be used to visualise chemical composition and molecular properties, providing an overview of the variety of information available. Examples are drawn from the disciplines of chemistry, chemical engineering, environmental science, physics, electrochemistry and materials science. The review introduces a range of techniques used to produce image contrast, along with the chemical and molecular insight accessible through them. Methods for mapping the distribution of chemical species, using chemical shift imaging or spatially-resolved spectroscopy, are reviewed, as well as methods for visualising physical state, temperature, current density, flow velocities and molecular diffusion. Strategies for imaging materials with low signal intensity, such as those containing gases or low sensitivity nuclei, using compressed sensing, para-hydrogen or polarisation transfer, are discussed. Systems are presented which encapsulate the diversity of chemical and physical parameters observable by MRI, including one- and two-phase flow in porous media, chemical pattern formation, phase transformations and hydrodynamic (fingering) instabilities. Lastly, the emerging area of electrochemical MRI is discussed, with studies presented on the visualisation of electrochemical deposition and dissolution processes during corrosion and the operation of batteries, supercapacitors and fuel cells. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Linear systems on balancing chemical reaction problem

NASA Astrophysics Data System (ADS)

Kafi, R. A.; Abdillah, B.

2018-01-01

The concept of linear systems appears in a variety of applications. This paper presents a small sample of the wide variety of real-world problems regarding our study of linear systems. We show that the problem in balancing chemical reaction can be described by homogeneous linear systems. The solution of the systems is obtained by performing elementary row operations. The obtained solution represents the finding coefficients of chemical reaction. In addition, we present a computational calculation to show that mathematical software such as Matlab can be used to simplify completion of the systems, instead of manually using row operations.

Communication: Control of chemical reactions using electric field gradients.

PubMed

Deshmukh, Shivaraj D; Tsori, Yoav

2016-05-21

We examine theoretically a new idea for spatial and temporal control of chemical reactions. When chemical reactions take place in a mixture of solvents, an external electric field can alter the local mixture composition, thereby accelerating or decelerating the rate of reaction. The spatial distribution of electric field strength can be non-trivial and depends on the arrangement of the electrodes producing it. In the absence of electric field, the mixture is homogeneous and the reaction takes place uniformly in the reactor volume. When an electric field is applied, the solvents separate and the reactants are concentrated in the same phase or separate to different phases, depending on their relative miscibility in the solvents, and this can have a large effect on the kinetics of the reaction. This method could provide an alternative way to control runaway reactions and to increase the reaction rate without using catalysts.

Evaluation of nanoparticle-immobilized cellulase for improved ethanol yield in simultaneous saccharification and fermentation reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lupoi, Jason; Smith, Emily

2011-12-01

Ethanol yields were 2.1 (P = 0.06) to 2.3 (P = 0.01) times higher in simultaneous saccharification and fermentation (SSF) reactions of microcrystalline cellulose when cellulase was physisorbed on silica nanoparticles compared to enzyme in solution. In SSF reactions, cellulose is hydrolyzed to glucose by cellulase while yeast simultaneously ferments glucose to ethanol. The 35 C temperature and the presence of ethanol in SSF reactions are not optimal conditions for cellulase. Immobilization onto solid supports can stabilize the enzyme and promote activity at non-optimum reaction conditions. Mock SSF reactions that did not contain yeast were used to measure saccharification productsmore » and identify the mechanism for the improved ethanol yield using immobilized cellulase. Cellulase adsorbed to 40 nm silica nanoparticles produced 1.6 times (P = 0.01) more glucose than cellulase in solution in 96 h at pH 4.8 and 35 C. There was no significant accumulation (<250 {mu}g) of soluble cellooligomers in either the solution or immobilized enzyme reactions. This suggests that the mechanism for the immobilized enzyme's improved glucose yield compared to solution enzyme is the increased conversion of insoluble cellulose hydrolysis products to soluble cellooligomers at 35 C and in the presence of ethanol. The results show that silica-immobilized cellulase can be used to produce increased ethanol yields in the conversion of lignocellulosic materials by SSF.« less

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

PubMed Central

2015-01-01

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled. PMID:25516726

Infrared chemiluminescence study of the reaction Cl + HI yielding HCl + I at enhanced collision energies.

NASA Technical Reports Server (NTRS)

Cowley, L. T.; Horne, D. S.; Polanyi, J. C.

1971-01-01

Performed chemiluminescence and beam experiments show a markedly increased efficiency of conversion of the reaction energy into vibration and a markedly enhanced tendency for forward scattering in the reaction Cl + HI yields HCl + I as compared with H + Cl2 yields HCl + Cl. These differences appear to be due predominantly to the difference in the masses involved.

Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

PubMed

Wu, Emilia L

2010-12-01

The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D(2), F+H(2)/D(2)/HD, D(+)+H(2), O+H(2), and He+H(2)(+), have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D(+)+H(2), Ne+H(2)(+), and He+H(2)(+) in both adiabatic and nonadiabatic context. © 2010 Wiley Periodicals, Inc.

Native Chemical Ligation Strategy to Overcome Side Reactions during Fmoc-Based Synthesis of C-Terminal Cysteine-Containing Peptides.

PubMed

Lelièvre, Dominique; Terrier, Victor P; Delmas, Agnès F; Aucagne, Vincent

2016-03-04

The Fmoc-based solid phase synthesis of C-terminal cysteine-containing peptides is problematic, due to side reactions provoked by the pronounced acidity of the Cα proton of cysteine esters. We herein describe a general strategy consisting of the postsynthetic introduction of the C-terminal Cys through a key chemoselective native chemical ligation reaction with N-Hnb-Cys peptide crypto-thioesters. This method was successfully applied to the demanding peptide sequences of two natural products of biological interest, giving remarkably high overall yields compared to that of a state of the art strategy.

Anatomy of an Elementary Chemical Reaction

NASA Astrophysics Data System (ADS)

Alexander, Andrew J.; Zare, Richard N.

1998-09-01

The alchemists of old sought the knowledge to transform one material to another-for example, base metals into gold-as a path to the elixir of life. As chemists have concerned themselves with the transformation from compound to compound, so they have become involved in trying to uncover the structures of molecules and the pathways that reactions follow. Classically, the study of reaction mechanisms in chemistry encompasses reaction kinetics, the study of velocities or rates of reactions, and reaction dynamics, the study of the nanoscopic motion and rearrangement of atoms during a reactive event. An essential aim of this article is to bring the reader to a favorable vantage point with a brief introduction to reactive dynamics, and from there to describe some examples of recent strategies that have been employed to promote a fundamental understanding of the anatomy of elementary chemical reactions. In the final section we ponder future directions for this rapidly evolving field of research.

Non-allergic cutaneous reactions in airborne chemical sensitivity--a population based study.

PubMed

Berg, Nikolaj Drimer; Linneberg, Allan; Thyssen, Jacob Pontoppidan; Dirksen, Asger; Elberling, Jesper

2011-06-01

Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. The aetiology is unknown, but chemical related respiratory symptoms have been found associated with positive patch test. The purpose of this study was to investigate the relationship between cutaneous reactions from patch testing and self-reported severity of chemical sensitivity to common airborne chemicals. A total of 3460 individuals participating in a general health examination, Health 2006, were patch tested with allergens from the European standard series and screened for chemical sensitivity with a standardised questionnaire dividing the participants into four severity groups of chemical sensitivity. Both allergic and non-allergic cutaneous reactions--defined as irritative, follicular, or doubtful allergic reactions--were analysed in relationship with severity of chemical sensitivity. Associations were controlled for the possible confounding effects of sex, age, asthma, eczema, atopic dermatitis, psychological and social factors, and smoking habits. In unadjusted analyses we found associations between allergic and non-allergic cutaneous reactions on patch testing and the two most severe groups of self-reported sensitivity to airborne chemicals. When adjusting for confounding, associations were weakened, and only non-allergic cutaneous reactions were significantly associated with individuals most severely affected by inhalation of airborne chemicals (odds ratio = 2.5, p = 0.006). Our results suggest that individuals with self-reported chemical sensitivity show increased non-allergic cutaneous reactions based on day 2 readings of patch tests. Copyright © 2011 Elsevier GmbH. All rights reserved.

Chemical kinetic reaction mechanism for the combustion of propane

NASA Technical Reports Server (NTRS)

Jachimowski, C. J.

1984-01-01

A detailed chemical kinetic reaction mechanism for the combustion of propane is presented and discussed. The mechanism consists of 27 chemical species and 83 elementary chemical reactions. Ignition and combustion data as determined in shock tube studies were used to evaluate the mechanism. Numerical simulation of the shock tube experiments showed that the kinetic behavior predicted by the mechanism for stoichiometric mixtures is in good agrement with the experimental results over the entire temperature range examined (1150-2600K). Sensitivity and theoretical studies carried out using the mechanism revealed that hydrocarbon reactions which are involved in the formation of the HO2 radical and the H2O2 molecule are very important in the mechanism and that the observed nonlinear behavior of ignition delay time with decreasing temperature can be interpreted in terms of the increased importance of the HO2 and H2O2 reactions at the lower temperatures.

Raman Spectral Determination of Chemical Reaction Rate Characteristics

NASA Astrophysics Data System (ADS)

Balakhnina, I. A.; Brandt, N. N.; Mankova, A. A.; Chikishev, A. Yu.; Shpachenko, I. G.

2017-09-01

The feasibility of using Raman spectroscopy to determine chemical reaction rates and activation energies has been demonstrated for the saponification of ethyl acetate. The temperature dependence of the reaction rate was found in the range from 15 to 45°C.

Computed potential energy surfaces for chemical reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.

1994-01-01

Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

Dynamical coupled-channels study of {pi}N{yields}{pi}{pi}N reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamano, H.; Julia-Diaz, B.; Department d'Estructura i Constituents de la Materia and Institut de Ciencies del Cosmos, Universitat de Barcelona E-08028 Barcelona

As a step toward performing a complete coupled-channels analysis of the world data of {pi}N,{gamma}*N{yields}{pi}N,{eta}N,{pi}{pi}N reactions, the {pi}N{yields}{pi}{pi}N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C 76, 065201 (2007). The channels included are {pi}N,{eta}N, and {pi}{pi}N which has {pi}{delta},{rho}N, and {sigma}N resonant components. The nonresonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16 bare excited nucleon (N*) states that are dressed by the nonresonant interactions as constrained by the unitarity condition. The data of total cross sectionsmore » and {pi}N and {pi}{pi} invariant mass distributions of {pi}{sup +}p{yields}{pi}{sup +}{pi}{sup +}n,{pi}{sup +}{pi}{sup 0}p and {pi}{sup -}p{yields}{pi}{sup +}{pi}{sup -}n,{pi}{sup -}{pi}{sup 0}p,{pi}{sup 0}{pi}{sup 0}n reactions from threshold to the invariant mass W=2 GeV can be described to a very large extent. We show the importance of the coupled-channels effects and the strong interference among the contributions from the {pi}{delta},{sigma}N, and {rho}N channels. The large interference between the resonant and nonresonant amplitudes is also demonstrated. Possible future developments are discussed.« less

Influence of chemical reactions on the nonlinear dynamics of dissipative flows

NASA Astrophysics Data System (ADS)

Karimov, A. R.; Korshunov, A. M.; Beklemishev, V. V.

2015-08-01

The nonlinear dynamics of resistive flow with a chemical reaction is studied. Proceeding from the Lagrangian description, the influence of a chemical reaction on the development of fluid singularities is considered.

Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

PubMed

Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

2014-11-12

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

PubMed Central

Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

2014-01-01

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism. PMID:25387603

An investigation of oxidation products and SOA yields from OH + pesticide reactions

NASA Astrophysics Data System (ADS)

Murschell, T.; Friedman, B.; Link, M.; Farmer, D.

2016-12-01

Pesticides are used globally in agricultural and residential areas. After application and/or volatilization from a surface, these compounds can be transported over long distances in the atmosphere. However, their chemical fate, including oxidation and gas-particle partitioning in the atmosphere, is not well understood. We present gas and particle measurements of oxidation products from pesticide + OH reactions using a dynamic solution injection system coupled to an Oxidative Flow Reactor. Products were detected with a High Resolution Time of Flight Iodide Chemical Mass Spectrometer (HR-ToF-CIMS) and a Size Mobility Particle Scanner (SMPS). The OFR allows pesticides to react with variable OH radical exposures, ranging from the equivalent of one day to a full week of atmospheric oxidative aging. In this work, we explore pesticide oxidation products from reaction with OH and ozone, and compare those products to photolysis reactions. Pesticides of similar chemical structures were explored, including acetochlor / metolachlor and permethrin / cypermethrin, to explore mechanistic differences. We present chemical parameters including average product oxidation state, average oxygen to carbon ratio, and potential secondary organic aerosol formation for each of these compounds.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

DOE PAGES

Kale, Seyit; Sode, Olaseni; Weare, Jonathan; ...

2014-11-07

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum undermore » DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.« less

Chemical reactions at aqueous interfaces

NASA Astrophysics Data System (ADS)

Vecitis, Chad David

2009-12-01

Interfaces or phase boundaries are a unique chemical environment relative to individual gas, liquid, or solid phases. Interfacial reaction mechanisms and kinetics are often at variance with homogeneous chemistry due to mass transfer, molecular orientation, and catalytic effects. Aqueous interfaces are a common subject of environmental science and engineering research, and three environmentally relevant aqueous interfaces are investigated in this thesis: 1) fluorochemical sonochemistry (bubble-water), 2) aqueous aerosol ozonation (gas-water droplet), and 3) electrolytic hydrogen production and simultaneous organic oxidation (water-metal/semiconductor). Direct interfacial analysis under environmentally relevant conditions is difficult, since most surface-specific techniques require relatively `extreme' conditions. Thus, the experimental investigations here focus on the development of chemical reactors and analytical techniques for the completion of time/concentration-dependent measurements of reactants and their products. Kinetic modeling, estimations, and/or correlations were used to extract information on interfacially relevant processes. We found that interfacial chemistry was determined to be the rate-limiting step to a subsequent series of relatively fast homogeneous reactions, for example: 1) Pyrolytic cleavage of the ionic headgroup of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) adsorbed to cavitating bubble-water interfaces during sonolysis was the rate-determining step in transformation to their inorganic constituents carbon monoxide, carbon dioxide, and fluoride; 2) ozone oxidation of aqueous iodide to hypoiodous acid at the aerosol-gas interface is the rate-determining step in the oxidation of bromide and chloride to dihalogens; 3) Electrolytic oxidation of anodic titanol surface groups is rate-limiting for the overall oxidation of organics by the dichloride radical. We also found chemistry unique to the interface, for example: 1

Organic reactions for the electrochemical and photochemical production of chemical fuels from CO2--The reduction chemistry of carboxylic acids and derivatives as bent CO2 surrogates.

PubMed

Luca, Oana R; Fenwick, Aidan Q

2015-11-01

The present review covers organic transformations involved in the reduction of CO2 to chemical fuels. In particular, we focus on reactions of CO2 with organic molecules to yield carboxylic acid derivatives as a first step in CO2 reduction reaction sequences. These biomimetic initial steps create opportunities for tandem electrochemical/chemical reductions. We draw parallels between long-standing knowledge of CO2 reactivity from organic chemistry, organocatalysis, surface science and electrocatalysis. We point out some possible non-faradaic chemical reactions that may contribute to product distributions in the production of solar fuels from CO2. These reactions may be accelerated by thermal effects such as resistive heating and illumination. Copyright © 2015 Elsevier B.V. All rights reserved.

Water catalysis and anticatalysis in photochemical reactions: observation of a delayed threshold effect in the reaction quantum yield.

PubMed

Kramer, Zeb C; Takahashi, Kaito; Skodje, Rex T

2010-11-03

The possible catalysis of photochemical reactions by water molecules is considered. Using theoretical simulations, we investigate the HF-elimination reaction of fluoromethanol in small water clusters initiated by the overtone excitation of the hydroxyl group. The reaction occurs in competition with the process of water evaporation that dissipates the excitation and quenches the reaction. Although the transition state barrier is stabilized by over 20 kcal/mol through hydrogen bonding with water, the quantum yield versus energy shows a pronounced delayed threshold that effectively eliminates the catalytic effect. It is concluded that the quantum chemistry calculations of barrier lowering are not sufficient to infer water catalysis in some photochemical reactions, which instead require dynamical modeling.

Concordant Chemical Reaction Networks

PubMed Central

Shinar, Guy; Feinberg, Martin

2015-01-01

We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with any weakly monotonic kinetics, invariably give rise to kinetic systems that are injective — a quality that, among other things, precludes the possibility of switch-like transitions between distinct positive steady states. We also provide persistence characteristics of concordant networks, instability implications of discordance, and consequences of stronger variants of concordance. Some of our results are in the spirit of recent ones by Banaji and Craciun, but here we do not require that every species suffer a degradation reaction. This is especially important in studying biochemical networks, for which it is rare to have all species degrade. PMID:22659063

Formal modeling of a system of chemical reactions under uncertainty.

PubMed

Ghosh, Krishnendu; Schlipf, John

2014-10-01

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

Computational prediction of chemical reactions: current status and outlook.

PubMed

Engkvist, Ola; Norrby, Per-Ola; Selmi, Nidhal; Lam, Yu-Hong; Peng, Zhengwei; Sherer, Edward C; Amberg, Willi; Erhard, Thomas; Smyth, Lynette A

2018-06-01

Over the past few decades, various computational methods have become increasingly important for discovering and developing novel drugs. Computational prediction of chemical reactions is a key part of an efficient drug discovery process. In this review, we discuss important parts of this field, with a focus on utilizing reaction data to build predictive models, the existing programs for synthesis prediction, and usage of quantum mechanics and molecular mechanics (QM/MM) to explore chemical reactions. We also outline potential future developments with an emphasis on pre-competitive collaboration opportunities. Copyright © 2018 Elsevier Ltd. All rights reserved.

Minimum Energy Pathways for Chemical Reactions

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Computer Animation of a Chemical Reaction.

ERIC Educational Resources Information Center

Eaker, Charles W.; Jacobs, Edwin L.

1982-01-01

Taking a prototype chemical reaction (molecular hydrogen plus hydrogen atom), constructs an accurate semiempirical, generalized diatomics-in-molecules potential energy surface, calculates motions of these atoms on this surface using REACTS trajectory program, and presents results as moving picture on a microcomputer graphics system. Provides…

Non-stationary filtration mode during chemical reactions with the gas phase

NASA Astrophysics Data System (ADS)

Zavialov, Ivan; Konyukhov, Andrey; Negodyaev, Sergey

2015-04-01

An experimental and numerical study of filtration accompanied by chemical reactions between displacing fluid and solid skeleton is considered. Glass balls (400-500 μm in diameter) were placed in 1 cm gap between two glass sheets and were used as model porous medium. The baking soda was added to the glass balls. The 70% solution of acetic acid was used as the displacer. The modeling porous medium was saturated with a mineral oil, and then 70% solution of colored acetic acid was pumped through the medium. The glass balls and a mineral oil have a similar refractive index, so the model porous medium was optically transparent. During the filtration, the gas phase was generated by the chemical reactions between the baking soda and acetic acid, and time-dependent displacement of the chemical reaction front was observed. The front of the chemical reaction was associated with the most intensive gas separation. The front moved, stopped, and then moved again to the area where it had been already. We called this process a secondary oxidation wave. To describe this effect, we added to the balance equations a term associated with the formation and disappearance of phases due to chemical reactions. The equations were supplemented by Darcy's law for multiphase filtration. Nonstationarity front propagation of the chemical reaction in the numerical experiment was observed at Damköhler numbers greater than 100. The mathematical modelling was agreed well with the experimental results.

A laser flash photolysis-resonance fluorescence kinetics study of the reaction Cl/2P/ + CH4 yields CH3 + HCl

NASA Technical Reports Server (NTRS)

Ravishankara, A. R.; Wine, P. H.

1980-01-01

The technique of laser flash photolysis-resonance fluorescence is employed to study the kinetics of the reaction Cl(2P) + CH4 yields CH3 + HCl over the temperature range 221-375 K. At temperatures less than or equal to 241 K the apparent bimolecular rate constant is found to be dependent upon the identity of the chemically inert gases in the reaction mixture. For Cl2/CH4/He reaction mixtures (total pressure = 50 torr) different bimolecular rate constants are measured at low and high methane concentrations. For Cl2/CH4/CCl/He and Cl2/CH4/Ar reaction mixtures, the bimolecular rate constant is independent of methane concentration, being approximately equal to the rate constant measured at low methane concentrations for Cl2/CH4/He mixtures. These rate constants are in good agreement with previous results obtained using the discharge flow-resonance fluorescence and competitive chlorination techniques. At 298 K the measured bimolecular rate constant is independent of the identity of the chemically inert gases in the reaction mixture and in good agreement with all previous investigations. The low-temperature results obtained in this investigation and all previous investigations can be rationalized in terms of a model which assumes that the Cl(2P 1/2) state reacts with CH4 much faster than the Cl(2P 3/2) state. Extrapolation of this model to higher temperatures, however, is not straightforward.

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions.

PubMed

Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B

2007-06-16

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

Nanoparticle-triggered in situ catalytic chemical reactions for tumour-specific therapy.

PubMed

Lin, Han; Chen, Yu; Shi, Jianlin

2018-03-21

Tumour chemotherapy employs highly cytotoxic chemodrugs, which kill both cancer and normal cells by cellular apoptosis or necrosis non-selectively. Catalysing/triggering the specific chemical reactions only inside tumour tissues can generate abundant and special chemicals and products locally to initiate a series of unique biological and pathologic effects, which may enable tumour-specific theranostic effects to combat cancer without bringing about significant side effects on normal tissues. Nevertheless, chemical reaction-initiated selective tumour therapy strongly depends on the advances in chemistry, materials science, nanotechnology and biomedicine. This emerging cross-disciplinary research area is substantially different from conventional cancer-theranostic modalities in clinics. In response to the fast developments in cancer theranostics based on intratumoural catalytic chemical reactions, this tutorial review summarizes the very-recent research progress in the design and synthesis of representative nanoplatforms with intriguing nanostructures, compositions, physiochemical properties and biological behaviours for versatile catalytic chemical reaction-enabled cancer treatments, mainly by either endogenous tumour microenvironment (TME) triggering or exogenous physical irradiation. These unique intratumoural chemical reactions can be used in tumour-starving therapy, chemodynamic therapy, gas therapy, alleviation of tumour hypoxia, TME-responsive diagnostic imaging and stimuli-responsive drug release, and even externally triggered versatile therapeutics. In particular, the challenges and future developments of such a novel type of cancer-theranostic modality are discussed in detail to understand the future developments and prospects in this research area as far as possible. It is highly expected that this kind of unique tumour-specific therapeutics by triggering specific in situ catalytic chemical reactions inside tumours would provide a novel but efficient

Surey of Alternate Stored Chemical Energy Reactions.

DTIC Science & Technology

1985-12-01

Fr., Report No. CEA-N-1293, 36 p. Pilipovich. D.; Rogers, H. H. and Wilson, R. D., 1972, Chlorine trifluoride oxide. II. Photochemical synthesis...some fluorine and chlorine compounds: Zh. Fiz. Khim., V. 43, No. 2, p. 386-9. Rogers, H. H. and Pilipovich, D., 1973, Oxychlorine trifluoride (Patent...chemical energy reactions has been made for purposes of comparison with the lithium- aluminum /water, lithium/sulfur hexafluoride, and other reaction schemes

Sputtering yields and surface chemical modification of tin-doped indium oxide in hydrocarbon-based plasma etching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Hu; Karahashi, Kazuhiro; Hamaguchi, Satoshi, E-mail: hamaguch@ppl.eng.osaka-u.ac.jp

2015-11-15

Sputtering yields and surface chemical compositions of tin-doped indium oxide (or indium tin oxide, ITO) by CH{sup +}, CH{sub 3}{sup +}, and inert-gas ion (He{sup +}, Ne{sup +}, and Ar{sup +}) incidence have been obtained experimentally with the use of a mass-selected ion beam system and in-situ x-ray photoelectron spectroscopy. It has been found that etching of ITO is chemically enhanced by energetic incidence of hydrocarbon (CH{sub x}{sup +}) ions. At high incident energy incidence, it appears that carbon of incident ions predominantly reduce indium (In) of ITO and the ITO sputtering yields by CH{sup +} and CH{sub 3}{sup +}more » ions are found to be essentially equal. At lower incident energy (less than 500 eV or so), however, a hydrogen effect on ITO reduction is more pronounced and the ITO surface is more reduced by CH{sub 3}{sup +} ions than CH{sup +} ions. Although the surface is covered more with metallic In by low-energy incident CH{sub 3}{sup +} ions than CH{sup +} ions and metallic In is in general less resistant against physical sputtering than its oxide, the ITO sputtering yield by incident CH{sub 3}{sup +} ions is found to be lower than that by incident CH{sup +} ions in this energy range. A postulation to account for the relation between the observed sputtering yield and reduction of the ITO surface is also presented. The results presented here offer a better understanding of elementary surface reactions observed in reactive ion etching processes of ITO by hydrocarbon plasmas.« less

Direct single-molecule dynamic detection of chemical reactions.

PubMed

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.

Direct single-molecule dynamic detection of chemical reactions

PubMed Central

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

2018-01-01

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. PMID:29487914

Reduced product yield in chemical processes by second law effects

NASA Technical Reports Server (NTRS)

England, C.; Funk, J. E.

1980-01-01

An analysis of second law effects in chemical processes, where product yield is explicitly related to the individual irreversibilities within the process to indicate a maximum theoretical yield, is presented. Examples are given that indicate differences between first and second law approaches toward process efficiency and process yield. This analysis also expresses production capacity in terms of the heating value of a product. As a result, it is particularly convenient in analyzing fuel conversion plants and their potential for improvement. Relationships are also given for the effects of irreversibilities on requirements for process heat and for feedstocks.

Design criteria for extraction with chemical reaction and liquid membrane permeation

NASA Technical Reports Server (NTRS)

Bart, H. J.; Bauer, A.; Lorbach, D.; Marr, R.

1988-01-01

The design criteria for heterogeneous chemical reactions in liquid/liquid systems formally correspond to those of classical physical extraction. More complex models are presented which describe the material exchange at the individual droplets in an extraction with chemical reaction and in liquid membrane permeation.

Effect of gravity field on the nonequilibrium/nonlinear chemical oscillation reactions

NASA Astrophysics Data System (ADS)

Fujieda, S.; Mori, Y.; Nakazawa, A.; Mogami, Y.

2001-01-01

Biological systems have evolved for a long time under the normal gravity. The Belousov-Zhabotinsky (BZ) reaction is a nonlinear chemical system far from the equilibrium that may be considered as a simplified chemical model of the biological systems so as to study the effect of gravity. The reaction solution is comprised of bromate in sulfuric acid as an oxidizing agent, 1,4-cyclohexanedione as an organic substrate, and ferroin as a metal catalyst. Chemical waves in the BZ reaction-diffusion system are visualized as blue and red patterns of ferriin and ferroin, respectively. After an improvement to the tubular reaction vessels in the experimental setup, the traveling velocity of chemical waves in aqueous solutions was measured in time series under normal gravity, microgravity, hyper-gravity, and normal gravity using the free-fall facility of JAMIC (Japan Microgravity Center), Hokkaido, Japan. Chemical patterns were collected as image data via CCD camera and analyzed by the software of NIH image after digitization. The estimated traveling velocity increased with increasing gravity as expected. It was clear experimentally that the traveling velocity of target patterns in reaction diffusion system was influenced by the effect of convection and correlated closely with the gravity field.

The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van 't Hoff.

PubMed

Yang, Zhongyue; Houk, K N

2018-03-15

Jacobus Henricus van 't Hoff was the first Nobel Laureate in Chemistry. He pioneered in the study of chemical dynamics, which referred at that time to chemical kinetics and thermodynamics. The term has evolved in modern times to refer to the exploration of chemical transformations in a time-resolved fashion. Chemical dynamics has been driven by the development of molecular dynamics trajectory simulations, which provide atomic visualization of chemical processes and illuminate how dynamic effects influence chemical reactivity and selectivity. In homage to the legend of van 't Hoff, we review the development of the chemical dynamics of organic reactions, our area of research. We then discuss our trajectory simulations of pericyclic reactions, and our development of dynamic criteria for concerted and stepwise reaction mechanisms. We also describe a method that we call environment-perturbed transition state sampling, which enables trajectory simulations in condensed-media using quantum mechanics and molecular mechanics (QM/MM). We apply the method to reactions in solvent and in enzyme. Jacobus Henricus van 't Hoff (1852, Rotterdam-1911, Berlin) received the Nobel Prize for Chemistry in 1901 "in recognition of the extraordinary services he has rendered by the discovery of the laws of chemical dynamics and osmotic pressure in solutions". van 't Hoff was born the Netherlands, and earned his doctorate in Utrecht in 1874. In 1896 he moved to Berlin, where he was offered a position with more research and less teaching. van 't Hoff is considered one of the founders of physical chemistry. A key step in establishing this new field was the start of Zeitschrift für Physikalische Chemie in 1887. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions

NASA Astrophysics Data System (ADS)

Molina-Espíritu, M.; Esquivel, R. O.; Dehesa, J. S.

We investigate the complexity of selected elementary chemical reactions (namely, the hydrogenic-abstraction reaction and the identity SN2 exchange reaction) by means of the following single and composite information-theoretic measures: disequilibrium (D), exponential entropy(L), Fisher information (I), power entropy (J), I-D, D-L and I-J planes and Fisher-Shannon (FS) and Lopez-Mancini-Calbet (LMC) shape complexities. These quantities, which are functionals of the one-particle density, are computed in both position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of these reactions can be identified through most of the single information-theoretic measures and the two-component planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures, however for the identity SN2 exchange reaction does not hold a simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.

Solute transport with multiple equilibrium-controlled or kinetically controlled chemical reactions

USGS Publications Warehouse

Friedly, John C.; Rubin, Jacob

1992-01-01

A new approach is applied to the problem of modeling solute transport accompanied by many chemical reactions. The approach, based on concepts of the concentration space and its stoichiometric subspaces, uses elements of the subspaces as primary dependent variables. It is shown that the resulting model equations are compact in form, isolate the chemical reaction expressions from flow expressions, and can be used for either equilibrium or kinetically controlled reactions. The implications of the results on numerical algorithms for solving the equations are discussed. The application of the theory is illustrated throughout with examples involving a simple but broadly representative set of reactions previously considered in the literature. Numerical results are presented for four interconnected reactions: a homogeneous complexation reaction, two sorption reactions, and a dissolution/precipitation reaction. Three cases are considered: (1) four kinetically controlled reactions, (2) four equilibrium-controlled reactions, and (3) a system with two kinetically controlled reactions and two equilibrium-controlled reactions.

High yield neutron generators using the DD reaction

NASA Astrophysics Data System (ADS)

Vainionpaa, J. H.; Harris, J. L.; Piestrup, M. A.; Gary, C. K.; Williams, D. L.; Apodaca, M. D.; Cremer, J. T.; Ji, Qing; Ludewigt, B. A.; Jones, G.

2013-04-01

A product line of high yield neutron generators has been developed at Adelphi technology inc. The generators use the D-D fusion reaction and are driven by an ion beam supplied by a microwave ion source. Yields of up to 5 × 109 n/s have been achieved, which are comparable to those obtained using the more efficient D-T reaction. The microwave-driven plasma uses the electron cyclotron resonance (ECR) to produce a high plasma density for high current and high atomic ion species. These generators have an actively pumped vacuum system that allows operation at reduced pressure in the target chamber, increasing the overall system reliability. Since no radioactive tritium is used, the generators can be easily serviced, and components can be easily replaced, providing essentially an unlimited lifetime. Fast neutron source size can be adjusted by selecting the aperture and target geometries according to customer specifications. Pulsed and continuous operation has been demonstrated. Minimum pulse lengths of 50 μs have been achieved. Since the generators are easily serviceable, they offer a long lifetime neutron generator for laboratories and commercial systems requiring continuous operation. Several of the generators have been enclosed in radiation shielding/moderator structures designed for customer specifications. These generators have been proven to be useful for prompt gamma neutron activation analysis (PGNAA), neutron activation analysis (NAA) and fast neutron radiography. Thus these generators make excellent fast, epithermal and thermal neutron sources for laboratories and industrial applications that require neutrons with safe operation, small footprint, low cost and small regulatory burden.

GREEN CHEMICAL SYNTHESIS THROUGH CATALYSIS AND ALTERNATE REACTION CONDITIONS

EPA Science Inventory

Green chemical synthesis through catalysis and alternate reaction conditions

Encompassing green chemistry techniques and methodologies, we have initiated several projects at the National Risk Management Research laboratory that focus on the design and development of chemic...

Theoretical modeling of yields for proton-induced reactions on natural and enriched molybdenum targets.

PubMed

Celler, A; Hou, X; Bénard, F; Ruth, T

2011-09-07

Recent acute shortage of medical radioisotopes prompted investigations into alternative methods of production and the use of a cyclotron and ¹⁰⁰Mo(p,2n)(99m)Tc reaction has been considered. In this context, the production yields of (99m)Tc and various other radioactive and stable isotopes which will be created in the process have to be investigated, as these may affect the diagnostic outcome and radiation dosimetry in human studies. Reaction conditions (beam and target characteristics, and irradiation and cooling times) need to be optimized in order to maximize the amount of (99m)Tc and minimize impurities. Although ultimately careful experimental verification of these conditions must be performed, theoretical calculations can provide the initial guidance allowing for extensive investigations at little cost. We report the results of theoretically determined reaction yields for (99m)Tc and other radioactive isotopes created when natural and enriched molybdenum targets are irradiated by protons. The cross-section calculations were performed using a computer program EMPIRE for the proton energy range 6-30 MeV. A computer graphical user interface for automatic calculation of production yields taking into account various reaction channels leading to the same final product has been created. The proposed approach allows us to theoretically estimate the amount of (99m)Tc and its ratio relative to (99g)Tc and other radioisotopes which must be considered reaction contaminants, potentially contributing to additional patient dose in diagnostic studies.

Program Helps To Determine Chemical-Reaction Mechanisms

NASA Technical Reports Server (NTRS)

Bittker, D. A.; Radhakrishnan, K.

1995-01-01

General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

Ultrafast Chemical Dynamics of Reactions in Beams

DTIC Science & Technology

1994-04-14

Wave Packet Motion in Dissociative Reactions: Up to 40 Picoseconds. P. Cong, A. Mokhtari , and A. H. Zewail Chem. Phys. Lett., 172.109 (1990) 3. Direct...Femtosecond Mapping of the Trajectories in a Chemical Reaction. A. Mokhtari , P. Cong, J. L. Herek, and A. H. Zewail Nature, 348 225 (1990) 4...to 40 Picoseconds. P. Cong. A. Mokhtari , and A. H. Zewail Chem. Phys. Left., 172. 109 (1990) 8 4. Femtosecond Selective Control of Wave Packet

Functionalization of multi-walled carbon nanotubes with iron phthalocyanine via a liquid chemical reaction for oxygen reduction in alkaline media

NASA Astrophysics Data System (ADS)

Yan, Xiaomei; Xu, Xiao; Liu, Qin; Guo, Jia; Kang, Longtian; Yao, Jiannian

2018-06-01

Iron single-atom catalyst in form of iron-nitrogen-carbon structure possesses the excellent catalytic activity in various chemical reactions. However, exploring a sustainable and stable single-atom metal catalyst still faces a great challenge due to low yield and complicated synthesis. Here, we report a functional multi-wall carbon nanotubes modified with iron phthalocyanine molecules via a liquid chemical reaction and realize the performance of similar single-atom catalysis for oxygen reduction reaction. A serial of characterizations strongly imply the structure change of iron phthalocyanine molecule and its close recombination with multi-wall carbon nanotubes, which are in favor of ORR catalysis. Compared to commercial platinum-carbon catalyst, composites exhibit superior activity for oxygen reduction reaction with higher half-wave potential (0.86 V), lower Tafel slope (38 mV dec-1), higher limiting current density and excellent electrochemical stability. The corresponding Zinc-air battery also presents higher maximum power density and discharge stability. Therefore, these findings provide a facile route to synthesize a highly efficient non-precious metal carbon-based catalyst.

Quantum indistinguishability in chemical reactions.

PubMed

Fisher, Matthew P A; Radzihovsky, Leo

2018-05-15

Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high-temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent, and thus well approximated classically. We explore enzymatic chemical reactions involving small symmetric molecules and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "quantum dynamical selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally nonsymmetric molecular states. As we propose and discuss, the implications of the QDS rule include ( i ) a differential chemical reactivity of para- and orthohydrogen, ( ii ) a mechanism for inducing intermolecular quantum entanglement of nuclear spins, ( iii ) a mass-independent isotope fractionation mechanism, ( iv ) an explanation of the enhanced chemical activity of "reactive oxygen species", ( v ) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, and ( vi ) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.

Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications.

PubMed

Abe, Hiroshi; Kimura, Yasuaki

2018-01-01

Chemical ligation of oligonucleotides (ONs) is the key reaction for various ON-based technologies. We have tried to solve the problems of RNA interference (RNAi) technology by applying ON chemical ligation to RNAi. We designed a new RNAi system, called intracellular buildup RNAi (IBR-RNAi), where the RNA fragments are built up into active small-interference RNA (siRNA) in cells through a chemical ligation reaction. Using the phosphorothioate and iodoacetyl groups as reactive functional groups for the ligation, we achieved RNAi effects without inducing immune responses. Additionally, we developed a new chemical ligation for IBR-RNAi, which affords a more native-like structure in the ligated product. The new ligation method should be useful not only for IBR-RNAi but also for the chemical synthesis of biofunctional ONs.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

An Analysis of the Algebraic Method for Balancing Chemical Reactions.

ERIC Educational Resources Information Center

Olson, John A.

1997-01-01

Analyzes the algebraic method for balancing chemical reactions. Introduces a third general condition that involves a balance between the total amount of oxidation and reduction. Requires the specification of oxidation states for all elements throughout the reaction. Describes the general conditions, the mathematical treatment, redox reactions, and…

Conversion of KCl into KBH4 by Mechano-Chemical Reaction and its Catalytic Decomposition

NASA Astrophysics Data System (ADS)

Bilen, Murat; Gürü, Metin; Çakanyildirim, Çetin

2017-07-01

Production of KBH4, in the presence of KCl, B2O3 and MgH2 by means of a mechanical reaction and a dehydrogenation kinetic, constitute the main parts of this study. Operating time and reactant ratio are considered as two parameters for the mechanical reaction to obtain the maximum yield. The production process was carried out in a ball milling reactor, and the product residue was purified with ethylene diamine (EDA) and subsequently characterized by Fourier Transform Infrared Spectroscopy (FT-IR) and x-ray Diffraction (XRD) analyses. Optimum time for mechano-chemical treatment and reactant ratio (MgH2/KCl) were obtained as 1000 min and 1.0, respectively. Synthesized and commercial KBH4 were compared by hydrolysis tests in the presence of Co1-xNix/Al2O3 heterogeneous catalyst. Hydrogen generation rates, activation energy and order of the KBH4 decomposition reaction were obtained as 1578 {mL}_{{{{H}}2 }} \\min^{ - 1} {g}_{{catalyst}}^{ - 1}, 39.2 kJ mol-1 and zero order, respectively.

[Anaphylactic reactions to low-molecular weight chemicals].

PubMed

Nowak, Daria; Panaszek, Bernard

2015-02-06

Low-molecular weight chemicals (haptens) include a large group of chemical compounds occurring in work environment, items of everyday use (cleaning products, clothing, footwear, gloves, furniture), jewelry (earrings, bracelets), drugs, especially in cosmetics. They cause type IV hypersensitive reactions. During the induction phase of delayed-type hypersensitivity, haptens form complexes with skin proteins. After internalization through antigen presenting cells, they are bound to MHC class II molecules. Next, they are exposed against specific T-lymphocytes, what triggers activation of Th1 cells mainly. After repeating exposition to that hapten, during effector phase, Th1 induce production of cytokines affecting non-specific inflammatory cells. Usually, it causes contact dermatitis. However, occasionally incidence of immediate generalized reactions after contact with some kinds of haptens is noticed. A question arises, how the hapten does induce symptoms which are typical for anaphylaxis, and what contributes to amplification of this mechanism. It seems that this phenomenon arises from pathomechanism occurring in contact urticaria syndrome in which an anaphylactic reaction may be caused either by contact of sensitized skin with protein antigens, high-molecular weight allergens, or haptens. One of the hypotheses indicates the leading role of basophiles in this process. Their contact with haptens, may cause to release mediators of immediate allergic reaction (histamine, eicosanoids) and to produce cytokines corresponding to Th2 cells profile. Furthermore, Th17 lymphocytes secreting pro-inflammatory interleukin-17 might be engaged into amplifying hypersensitivity into immediate reactions and regulatory T-cells may play role in the process, due to insufficient control of the activity of effector cells.

Mapping students' ideas about chemical reactions at different educational levels

NASA Astrophysics Data System (ADS)

Yan, Fan

Understanding chemical reactions is crucial in learning chemistry at all educational levels. Nevertheless, research in science education has revealed that many students struggle to understand chemical processes. Improving teaching and learning about chemical reactions demands that we develop a clearer understanding of student reasoning in this area and of how this reasoning evolves with training in the discipline. Thus, we have carried out a qualitative study using semi-structured interviews as the main data collection tool to explore students reasoning about reaction mechanism and causality. The participants of this study included students at different levels of training in chemistry: general chemistry students (n=22), organic chemistry students (n=16), first year graduate students (n=13) and Ph.D. candidates (n=14). We identified major conceptual modes along critical dimensions of analysis, and illustrated common ways of reasoning using typical cases. Main findings indicate that although significant progress is observed in student reasoning in some areas, major conceptual difficulties seem to persist even at the more advanced educational levels. In addition, our findings suggest that students struggle to integrate important concepts when thinking about mechanism and causality in chemical reactions. The results of our study are relevant to chemistry educators interested in learning progressions, assessment, and conceptual development.

Miscible viscous fingering with chemical reaction involving precipitation.

NASA Astrophysics Data System (ADS)

Bae, Si-Kyun; Nagatsu, Yuichiro; Kato, Yoshihito; Tada, Yutaka

2007-11-01

When a reactive and miscible less-viscous liquid displaces a more-viscous liquid in a Hele-Shaw cell, reactive miscible viscous fingering takes place. The present study has experimentally examined how precipitation produced by chemical reaction affects miscible viscous fingering pattern. A 97 wt % glycerin solution containing iron(III) nitrate (yellow) and a solution containing potassium hexacyano ferrate(II) (colorless) were used as the more- and less-viscous liquids, respectively. In this case, the chemical reaction instantaneously takes place and produces the precipitation being dark blue in color. The experiments were done by varying reactant concentrations, the cell's gap width, and the displacement speed. We compared the patterns involving the precipitation reaction with those in the non-reactive cases. We have found fylfot-like pattern is observed, depending on the experimental condition, which has never been formed in the non-reactive experiments. As the reactant concentrations are increased or the displacement speed is decreased, the effects of the precipitation on the patterns are more pronounced.

Effect of the Gouy phase on the coherent phase control of chemical reactions.

PubMed

Gordon, Robert J; Barge, Vishal J

2007-11-28

We show how the spatial phase of a focused laser beam may be used as a tool for controlling the branching ratio of a chemical reaction. Guoy discovered [Acad. Sci., Paris, C. R. 110, 1250 (1890)] that when an electromagnetic wave passes through a focus its phase increases by pi. In a coherent control scheme involving the absorption of n photons of frequency omega(m) and m photons of frequency omega(n), the overall phase shift produced by the Gouy phase is (n-m)pi. At any given point in space, this phase shift is identical for all reaction products. Nevertheless, if the yields for different reaction channels have different intensity dependencies, the Gouy phase produces a net phase lag between the products that varies with the axial coordinate of the laser focus. We obtain here analytical and numerical values of this phase as the laser focus is scanned across the diameter of the molecular beam, taking into account the Rayleigh range and astigmatism of the laser beam and saturation of the transition. We also show that the modulation depth of the interference pattern may be increased by optimizing the relative intensities of the two fields.

High yield neutron generators using the DD reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vainionpaa, J. H.; Harris, J. L.; Piestrup, M. A.

2013-04-19

A product line of high yield neutron generators has been developed at Adelphi technology inc. The generators use the D-D fusion reaction and are driven by an ion beam supplied by a microwave ion source. Yields of up to 5 Multiplication-Sign 10{sup 9} n/s have been achieved, which are comparable to those obtained using the more efficient D-T reaction. The microwave-driven plasma uses the electron cyclotron resonance (ECR) to produce a high plasma density for high current and high atomic ion species. These generators have an actively pumped vacuum system that allows operation at reduced pressure in the target chamber,more » increasing the overall system reliability. Since no radioactive tritium is used, the generators can be easily serviced, and components can be easily replaced, providing essentially an unlimited lifetime. Fast neutron source size can be adjusted by selecting the aperture and target geometries according to customer specifications. Pulsed and continuous operation has been demonstrated. Minimum pulse lengths of 50 {mu}s have been achieved. Since the generators are easily serviceable, they offer a long lifetime neutron generator for laboratories and commercial systems requiring continuous operation. Several of the generators have been enclosed in radiation shielding/moderator structures designed for customer specifications. These generators have been proven to be useful for prompt gamma neutron activation analysis (PGNAA), neutron activation analysis (NAA) and fast neutron radiography. Thus these generators make excellent fast, epithermal and thermal neutron sources for laboratories and industrial applications that require neutrons with safe operation, small footprint, low cost and small regulatory burden.« less

Physio-chemical reactions in recycle aggregate concrete.

PubMed

Tam, Vivian W Y; Gao, X F; Tam, C M; Ng, K M

2009-04-30

Concrete waste constitutes the major proportion of construction waste at about 50% of the total waste generated. An effective way to reduce concrete waste is to reuse it as recycled aggregate (RA) for the production of recycled aggregate concrete (RAC). This paper studies the physio-chemical reactions of cement paste around aggregate for normal aggregate concrete (NAC) and RAC mixed with normal mixing approach (NMA) and two-stage mixing approach (TSMA) by differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). Four kinds of physio-chemical reactions have been recorded from the concrete samples, including the dehydration of C(3)S(2)H(3), iron-substituted ettringite, dehydroxylation of CH and development of C(6)S(3)H at about 90 degrees C, 135 degrees C, 441 degrees C and 570 degrees C, respectively. From the DSC results, it is confirmed that the concrete samples with RA substitution have generated less amount of strength enhancement chemical products when compared to those without RA substitution. However, the results from the TSMA are found improving the RAC quality. The pre-mix procedure of the TSMA can effectively develop some strength enhancing chemical products including, C(3)S(2)H(3), ettringite, CH and C(6)S(3)H, which shows that RAC made from the TSMA can improve the hydration processes.

Rate constant for the reaction SO + BrO yields SO2 + Br

NASA Technical Reports Server (NTRS)

Brunning, J.; Stief, L.

1986-01-01

The rate of the radical-radical reaction SO + BrO yields SO2 + Br has been determined at 298 K in a discharge flow system near 1 torr pressure with detection of SO and BrO via collision-free sampling mass spectrometry. The rate constant was determined using two different methods: measuring the decay of SO radicals in the presence of an excess of BrO and measuring the decay of BrO radicals in excess SO. The results from the two methods are in reasonable agreement and the simple mean of the two values gives the recommended rate constant at 298 K, k = (5.7 + or - 2.0) x 10 to the -11th cu cm/s. This represents the first determination of this rate constant and it is consistent with a previously derived lower limit based on SO2 formation. Comparison is made with other radical-radical reactions involving SO or BrO. The reaction SO + BrO yields SO2 + Br is of interest for models of the upper atmosphere of the earth and provides a potential coupling between atmospheric sulfur and bromine chemistry.

Stochastic flux analysis of chemical reaction networks

PubMed Central

2013-01-01

Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153

Stochastic flux analysis of chemical reaction networks.

PubMed

Kahramanoğulları, Ozan; Lynch, James F

2013-12-07

Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network.

Method of operating a thermal engine powered by a chemical reaction

DOEpatents

Ross, John; Escher, Claus

1988-01-01

The invention involves a novel method of increasing the efficiency of a thermal engine. Heat is generated by a non-linear chemical reaction of reactants, said heat being transferred to a thermal engine such as Rankine cycle power plant. The novel method includes externally perturbing one or more of the thermodynamic variables of said non-linear chemical reaction.

Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds.

PubMed

Dondi, Daniele; Merli, Daniele; Albini, Angelo; Zeffiro, Alberto; Serpone, Nick

2012-05-01

When a chemical system is submitted to high energy sources (UV, ionizing radiation, plasma sparks, etc.), as is expected to be the case of prebiotic chemistry studies, a plethora of reactive intermediates could form. If oxygen is present in excess, carbon dioxide and water are the major products. More interesting is the case of reducing conditions where synthetic pathways are also possible. This article examines the theoretical modeling of such systems with random-generated chemical networks. Four types of random-generated chemical networks were considered that originated from a combination of two connection topologies (viz., Poisson and scale-free) with reversible and irreversible chemical reactions. The results were analyzed taking into account the number of the most abundant products required for reaching 50% of the total number of moles of compounds at equilibrium, as this may be related to an actual problem of complex mixture analysis. The model accounts for multi-component reaction systems with no a priori knowledge of reacting species and the intermediates involved if system components are sufficiently interconnected. The approach taken is relevant to an earlier study on reactions that may have occurred in prebiotic systems where only a few compounds were detected. A validation of the model was attained on the basis of results of UVC and radiolytic reactions of prebiotic mixtures of low molecular weight compounds likely present on the primeval Earth.

Solid-state reactions to synthesize nanostructured lead selenide semiconductor powders by high-energy milling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rojas-Chavez, H., E-mail: uu_gg_oo@yahoo.com.mx; Reyes-Carmona, F.; Jaramillo-Vigueras, D.

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.more » Therefore an experimental campaign was designed to test the nature of reactions in the PbO-Se system during high-energy milling.« less

Chemical Modification of Cyclodextrin and Amylose by Click Reaction and Its Application to the Synthesis of Poly-alkylamine-Modified Antibacterial Sugars.

PubMed

Yamamura, Hatsuo

2017-01-01

Cyclodextrin (CD) can be chemically modified into desired and sophisticated functional molecules. However, poly-modification often produces complicated mixtures, resulting in a low yield of the desired product. As the most promising procedure to solve such problems and to achieve poly-modification of the CD molecule, we present here the Huisgen 1,3-dipolar cycloaddition, known as a click reaction. This review will describe the results of our microwave-assisted click reaction for the poly-modification of CD and amylose molecules, and its application to the study of synthetic membrane active antibacterial derivatives.

Rate constants for chemical reactions in high-temperature nonequilibrium air

NASA Technical Reports Server (NTRS)

Jaffe, R. L.

1986-01-01

In the nonequilibrium atmospheric chemistry regime that will be encountered by the proposed Aeroassisted Orbital Transfer Vehicle in the upper atmosphere, where air density is too low for thermal and chemical equilibrium to be maintained, the detailed high temperature air chemistry plays a critical role in defining radiative and convective heating loads. Although vibrational and electronic temperatures remain low (less than 15,000 K), rotational and translational temperatures may reach 50,000 K. Attention is presently given to the effects of multiple temperatures on the magnitudes of various chemical reaction rate constants, for the cases of both bimolecular exchange reactions and collisional excitation and dissociation reactions.

Classification of Chemical Reactions: Stages of Expertise

ERIC Educational Resources Information Center

Stains, Marilyne; Talanquer, Vicente

2008-01-01

In this study we explore the strategies that undergraduate and graduate chemistry students use when engaged in classification tasks involving symbolic and microscopic (particulate) representations of different chemical reactions. We were specifically interested in characterizing the basic features to which students pay attention when classifying…

Prediction and Prevention of Chemical Reaction Hazards: Learning by Simulation.

ERIC Educational Resources Information Center

Shacham, Mordechai; Brauner, Neima; Cutlip, Michael B.

2001-01-01

Points out that chemical hazards are the major cause of accidents in chemical industry and describes a safety teaching approach using a simulation. Explains a problem statement on exothermic liquid-phase reactions. (YDS)

Method of operating a thermal engine powered by a chemical reaction

DOEpatents

Ross, J.; Escher, C.

1988-06-07

The invention involves a novel method of increasing the efficiency of a thermal engine. Heat is generated by a non-linear chemical reaction of reactants, said heat being transferred to a thermal engine such as Rankine cycle power plant. The novel method includes externally perturbing one or more of the thermodynamic variables of said non-linear chemical reaction. 7 figs.

Process for preparing a chemical compound enriched in isotope content. [nitrogen 15-enriched nitric acid

DOEpatents

Michaels, E.D.

1981-02-25

A process to prepare a chemical enriched in isotope content includes: a chemical exchange reaction between a first and second compound which yields an isotopically enriched first compound and an isotopically depleted second compound; the removal of a portion of the first compound as product and the removal of a portion of the second compound as spent material; the conversion of the remainder of the first compound to the second compound for reflux at the product end of the chemical exchange reaction region; the conversion of the remainder of the second compound to the first compound for reflux at the spent material end of the chemical exchange region; and the cycling of the additional chemicals produced by one conversion reaction to the other conversion reaction, for consumption therein. One of the conversion reactions is an oxidation reaction, and the energy that it yields is used to drive the other conversion reaction, a reduction. The reduction reaction is carried out in a solid polymer electrolyte electrolytic reactor. The overall process is energy efficient and yields no waste by-products. A particular embodiment of the process in the production of nitrogen-15-enriched nitric acid.

Conditions for extinction events in chemical reaction networks with discrete state spaces.

PubMed

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

2018-05-01

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

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

PubMed

Das, A K; Meuwly, M

2016-01-01

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed. © 2016 Elsevier Inc. All rights reserved.

Characterization of plastic deformation and chemical reaction in titanium-polytetrafluoroethylene mixture

NASA Astrophysics Data System (ADS)

Davis, Jeffery Jon

1998-09-01

The subject of this dissertation is the deformation process of a single metal - polymer system (titanium - polytetrafluoroethylene) and how this process leads to initiation of chemical reaction. Several different kinds of experiments were performed to characterize the behavior of this material to shock and impact. These mechanical conditions induce a rapid plastic deformation of the sample. All of the samples tested had an initial porosity which increased the plastic flow condition. It is currently believed that during the deformation process two important conditions occur: removal of the oxide layer from the metal and decomposition of the polymer. These conditions allow for rapid chemical reaction. The research from this dissertation has provided insight into the complex behavior of plastic deformation and chemical reactions in titanium - polytetrafluoroethylene (PTFE, Teflon). A hydrodynamic computational code was used to model the plastic flow for correlation with the results from the experiments. The results from this work are being used to develop an ignition and growth model for metal/polymer systems. Three sets of experiments were used to examine deformation of the 80% Ti and 20% Teflon materials: drop- weight, gas gun, and split-Hopkinson pressure bar. Recovery studies included post shot analysis of the samples using x-ray diffraction. Lagrangian hydrocode DYNA2D modeling of the drop-weight tests was performed for comparison with experiments. One of the reactions know to occur is Ti + C → TiC (s) which results in an exothermic release. However, the believed initial reactions occur between Ti and fluorine which produces TixFy gases. The thermochemical code CHEETAH was used to investigate the detonation products and concentrations possible during Ti - Teflon reaction. CHEETAH shows that the Ti - fluorine reactions are thermodynamically favorable. This research represents the most comprehensive to date study of deformation induced chemical reaction in metal/polymers.

Chemical intervention in plant sugar signalling increases yield and resilience

NASA Astrophysics Data System (ADS)

Griffiths, Cara A.; Sagar, Ram; Geng, Yiqun; Primavesi, Lucia F.; Patel, Mitul K.; Passarelli, Melissa K.; Gilmore, Ian S.; Steven, Rory T.; Bunch, Josephine; Paul, Matthew J.; Davis, Benjamin G.

2016-12-01

The pressing global issue of food insecurity due to population growth, diminishing land and variable climate can only be addressed in agriculture by improving both maximum crop yield potential and resilience. Genetic modification is one potential solution, but has yet to achieve worldwide acceptance, particularly for crops such as wheat. Trehalose-6-phosphate (T6P), a central sugar signal in plants, regulates sucrose use and allocation, underpinning crop growth and development. Here we show that application of a chemical intervention strategy directly modulates T6P levels in planta. Plant-permeable analogues of T6P were designed and constructed based on a ‘signalling-precursor’ concept for permeability, ready uptake and sunlight-triggered release of T6P in planta. We show that chemical intervention in a potent sugar signal increases grain yield, whereas application to vegetative tissue improves recovery and resurrection from drought. This technology offers a means to combine increases in yield with crop stress resilience. Given the generality of the T6P pathway in plants and other small-molecule signals in biology, these studies suggest that suitable synthetic exogenous small-molecule signal precursors can be used to directly enhance plant performance and perhaps other organism function.

Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

PubMed

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

Heterogeneous reactions of HNO3(g) + NaCl(s) yields HCl(g) + NaNO3(s) and N2O5(g) + NaCl(s) yields ClNO2(g) + NaNO3(s)

NASA Technical Reports Server (NTRS)

Leu, Ming-Taun; Timonen, Raimo S.; Keyser, Leon F.; Yung, Yuk L.

1995-01-01

The heterogeneous reactions of HNO3(g) + NaCl(s) yields HCl(g) + NaNO3(s) (eq 1) and N2O5(g) + NaCl(s) yields ClNO2(g) + NaNO3(S) (eq 2) were investigated over the temperature range 223-296 K in a flow-tube reactor coupled to a quadrupole mass spectrometer. Either a chemical ionization mass spectrometer (CIMS) or an electron-impact ionization mass spectrometer (EIMS) was used to provide suitable detection sensitivity and selectivity. In order to mimic atmospheric conditions, partial pressures of HNO3 and N2O5 in the range 6 x 10(exp -8) - 2 x 10(exp -6) Torr were used. Granule sizes and surface roughness of the solid NaCl substrates were determined by using a scanning electron microscope. For dry NaCl substrates, decay rates of HNO3 were used to obtain gamma(1) = 0.013 +/- 0.004 (1sigma) at 296 K and > 0.008 at 223 K, respectively. The error quoted is the statistical error. After all corrections were made, the overall error, including systematic error, was estimated to be about a factor of 2. HCl was found to be the sole gas-phase product of reaction 1. The mechanism changed from heterogeneous reaction to predominantly physical adsorption when the reactor was cooled from 296 to 223 K. For reaction 2 using dry salts, gamma(2) was found to be less than 1.0 x 10(exp -4) at both 223 and 296 K. The gas-phase reaction product was identified as ClNO2 in previous studies using an infrared spectrometer. An enhancement in reaction probability was observed if water was not completely removed from salt surfaces, probably due to the reaction of N2O5(g) + H2O(s) yields 2HNO3(g). Our results are compared with previous literature values obtained using different experimental techniques and conditions. The implications of the present results for the enhancement of the hydrogen chloride column density in the lower stratosphere after the El Chichon volcanic eruption and for the chemistry of HCl and HNO3 in the marine troposphere are discussed.

2D Lattice Boltzmann Simulation Of Chemical Reactions Within Rayleigh-Bénard And Poiseuille-Bénard Convection Systems

NASA Astrophysics Data System (ADS)

Amaya-Ventura, Gilberto; Rodríguez-Romo, Suemi

2011-09-01

This paper deals with the computational simulation of the reaction-diffusion-advection phenomena emerging in Rayleigh-Bénard (RB) and Poiseuille-Bénard reactive convection systems. We use the Boussinesq's approximation for buoyancy forces and the Lattice Boltzmann method (LBM). The first kinetic mesoscopic model proposed here is based on the discrete Boltzmann equation needed to solve the momentum balance coupled with buoyancy forces. Then, a second lattice Boltzmann algorithm is applied to solve the reaction-diffusion-advection equation to calculate the evolution of the chemical species concentration. We use a reactive system composed by nitrous oxide (so call laughing gas) in air as an example; its spatio-temporal decomposition is calculated. Two cases are considered, a rectangular enclosed cavity and an open channel. The simulations are performed at low Reynolds numbers and in a steady state between the first and second thermo-hydrodynamic instabilities. The results presented here, for the thermo-hydrodynamic behavior, are in good agreement with experimental data; while our| chemical kinetics simulation yields expected results. Some applications of our approach are related to chemical reactors and atmospheric phenomena, among others.

Why Do Lithium-Oxygen Batteries Fail: Parasitic Chemical Reactions and Their Synergistic Effect.

PubMed

Yao, Xiahui; Dong, Qi; Cheng, Qingmei; Wang, Dunwei

2016-09-12

As an electrochemical energy-storage technology with the highest theoretical capacity, lithium-oxygen batteries face critical challenges in terms of poor stabilities and low charge/discharge round-trip efficiencies. It is generally recognized that these issues are connected to the parasitic chemical reactions at the anode, electrolyte, and cathode. While the detailed mechanisms of these reactions have been studied separately, the possible synergistic effects between these reactions remain poorly understood. To fill in the knowledge gap, this Minireview examines literature reports on the parasitic chemical reactions and finds the reactive oxygen species a key chemical mediator that participates in or facilitates nearly all parasitic chemical reactions. Given the ubiquitous presence of oxygen in all test cells, this finding is important. It offers new insights into how to stabilize various components of lithium-oxygen batteries for high-performance operations and how to eventually materialize the full potentials of this promising technology. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Isobaric yield ratio difference and Shannon information entropy

NASA Astrophysics Data System (ADS)

Ma, Chun-Wang; Wei, Hui-Ling; Wang, Shan-Shan; Ma, Yu-Gang; Wada, Ryoichi; Zhang, Yan-Li

2015-03-01

The Shannon information entropy theory is used to explain the recently proposed isobaric yield ratio difference (IBD) probe which aims to determine the nuclear symmetry energy. Theoretically, the difference between the Shannon uncertainties carried by isobars in two different reactions (ΔIn21), is found to be equivalent to the difference between the chemical potentials of protons and neutrons of the reactions [the IBD probe, IB- Δ(βμ)21, with β the reverse temperature]. From the viewpoints of Shannon information entropy, the physical meaning of the above chemical potential difference is interpreted by ΔIn21 as denoting the nuclear symmetry energy or density difference between neutrons and protons in reactions more concisely than from the statistical ablation-abrasion model.

Yields of O2(b 1 Sigma g +) from reactions of HO2. [in planetary atmospheres

NASA Technical Reports Server (NTRS)

Keyser, L. F.; Choo, K. Y.; Leu, M. T.

1985-01-01

The production of O2(b 1 Sigma g +) has been monitored for several reactions of the HO2 radical at 300 K using a discharge-flow apparatus with resonance fluorescence and chemiluminescence detection. In all cases, the resulting quantum efficiencies were found to be less than 0.03. O2(b) was observed when F atoms were added to H2O2 in the gas phase. The signal strengths of O2(b) were proportional to initial concentrations of HO2 formed by the F + H2O2 reaction. Observed /O2(b)/, /HO2/, and /OH/ vs /F/0 were analyzed using a simple three-step mechanism and a more complete computer simulation with 22 reaction steps. The results indicate that the F + HO2 reaction yields O2(b) with an efficiency of (3.6 + or - 1.4) x 10 to the -3rd. Yields from the O + OH2 reaction were less than 0.02, indicating that this reaction cannot be a major source of the O2(b) emission observed in the earth's nightglow.

Measurement of Fluorine Atom Concentrations and Reaction Rates in Chemical Laser Systems.

DTIC Science & Technology

1981-09-01

AD-A1RA 070 AERODYNEERESEARCHUINC BEDFORDM MA F/6_20/5 MEASURE MENT OF FLUORINE ATOM CONCENTRATIONS AND REACTION RATFS -ETC(U) SEP_ A A C STANT ON...0772 LEVELIg 00 ~ARI-RR-272 cO0 MEASUREMENT OF FLUORINE ATOM CONCENTRATIONS AND REACTION RATES IN CHEMICAL LASER SYSTEMS ANNUAL TECHNICAL REPORT by...MEASUREMENT OF FLUORINE ATOM CONCENTRATIONS AND Annual Report REACTION RATES IN CHEMICAL LASER SYSTEMS 23 July 1980 - 23 July 1981 S. PERFORMING ORG. REPORT

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

Chemical properties of colliding sources in 124, 136Xe and 112, 124Sn induced collisions in isobaric yield ratio difference and isoscaling methods

NASA Astrophysics Data System (ADS)

Ma, Chun-Wang; Wang, Shan-Shan; Zhang, Yan-Li; Wei, Hui-Ling

2013-12-01

Isoscaling and isobaric yield ratio difference (IBD) methods are used to study Δμ/T (Δμ being the difference between the chemical potentials of the neutron and proton, and T being the temperature) in the measured 1 A GeV 124Sn + 124Sn, 112Sn + 112Sn, 136Xe + Pb and 124Xe + Pb reactions. The isoscaling phenomena in the 124Sn/112Sn and 136Xe/124Xe reaction pairs are investigated, and the isoscaling parameters α and β are obtained. The Δμ/T determined by the isoscaling method (IS-Δμ/T) and the IBD method (IB-Δμ/T) in the measured Sn and Xe reactions are compared. It is shown that in most fragments, the IS- and IB-Δμ/T are consistent in the Xe reactions, while the IS- and IB-Δμ/T ones are only similar in the less neutron-rich fragments in the Sn reactions. The shell effects in IB-Δμ/T are also discussed.

Multiscale stochastic simulations of chemical reactions with regulated scale separation

NASA Astrophysics Data System (ADS)

Koumoutsakos, Petros; Feigelman, Justin

2013-07-01

We present a coupling of multiscale frameworks with accelerated stochastic simulation algorithms for systems of chemical reactions with disparate propensities. The algorithms regulate the propensities of the fast and slow reactions of the system, using alternating micro and macro sub-steps simulated with accelerated algorithms such as τ and R-leaping. The proposed algorithms are shown to provide significant speedups in simulations of stiff systems of chemical reactions with a trade-off in accuracy as controlled by a regulating parameter. More importantly, the error of the methods exhibits a cutoff phenomenon that allows for optimal parameter choices. Numerical experiments demonstrate that hybrid algorithms involving accelerated stochastic simulations can be, in certain cases, more accurate while faster, than their corresponding stochastic simulation algorithm counterparts.

Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction

NASA Astrophysics Data System (ADS)

Minitti, M. P.; Budarz, J. M.; Kirrander, A.; Robinson, J. S.; Ratner, D.; Lane, T. J.; Zhu, D.; Glownia, J. M.; Kozina, M.; Lemke, H. T.; Sikorski, M.; Feng, Y.; Nelson, S.; Saita, K.; Stankus, B.; Northey, T.; Hastings, J. B.; Weber, P. M.

2015-06-01

Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction.

PubMed

Minitti, M P; Budarz, J M; Kirrander, A; Robinson, J S; Ratner, D; Lane, T J; Zhu, D; Glownia, J M; Kozina, M; Lemke, H T; Sikorski, M; Feng, Y; Nelson, S; Saita, K; Stankus, B; Northey, T; Hastings, J B; Weber, P M

2015-06-26

Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

High-yield production of pure tagatose from fructose by a three-step enzymatic cascade reaction.

PubMed

Lee, Seon-Hwa; Hong, Seung-Hye; Kim, Kyoung-Rok; Oh, Deok-Kun

2017-08-01

To produce tagatose from fructose with a high conversion rate and to establish a high-yield purification method of tagatose from the reaction mixture. Fructose at 1 M (180 g l -1 ) was converted to 0.8 M (144 g l -1 ) tagatose by a three-step enzymatic cascade reaction, involving hexokinase, plus ATP, fructose-1,6-biphosphate aldolase, phytase, over 16 h with a productivity of 9 g l -1 h -1 . No byproducts were detected. Tagatose was recrystallized from ethanol to a purity of 99.9% and a yield of 96.3%. Overall, tagatose at 99.9% purity was obtained from fructose with a yield of 77%. This is the first biotechnological production of tagatose from fructose and the first application of solvent recrystallization for the purification of rare sugars.

High temperature chemical kinetic study of the H2-CO-CO2-NO reaction system

NASA Technical Reports Server (NTRS)

Jachimowski, C. J.

1975-01-01

An experimental study of the kinetics of the H2-CO-CO2-NO reaction system was made behind incident shock waves at temperatures of 2460 and 2950 K. The overall rate of the reaction was measured by monitoring radiation from the CO + O yields CO2 + h upoilon reaction. Correlation of these data with a detailed reaction mechanism showed that the high-temperature rate of the reaction N + OH yields NO + H can be described by the low-temperature (320 K) rate coefficient. Catalytic dissociation of molecular hydrogen was an important reaction under the tests conditions.

Chemical kinetic analysis of hydrogen-air ignition and reaction times

NASA Technical Reports Server (NTRS)

Rogers, R. C.; Schexnayder, C. J., Jr.

1981-01-01

An anaytical study of hydrogen air kinetics was performed. Calculations were made over a range of pressure from 0.2 to 4.0 atm, temperatures from 850 to 2000 K, and mixture equivalence ratios from 0.2 to 2.0. The finite rate chemistry model included 60 reactions in 20 species of the H2-O2-N2 system. The calculations also included an assessment of how small amounts of the chemicals H2O, NOx, H2O2, and O3 in the initial mixture affect ignition and reaction times, and how the variation of the third body efficiency of H2O relative of N2 in certain key reactions may affect reaction time. The results indicate that for mixture equivalence ratios between 0.5 and 1.7, ignition times are nearly constant; however, the presence of H2O and NO can have significant effects on ignition times, depending on the mixture temperature. Reaction time is dominantly influenced by pressure but is nearly independent of initial temperature, equivalence ratio, and the addition of chemicals. Effects of kinetics on reaction at supersonic combustor conditions are discussed.

Chemical yields from low-temperature pyrolysis of CCA-treated wood

Treesearch

Qirong Fu; Dimitris Argyropolous; Lucian Lucia; David Tilotta; Stan Lebow

2009-01-01

Low-temperature pyrolysis offers a feasible option for wood-waste management and the recovery of a variety of useful chemicals. The effect of chromated copper arsenate (CCA) wood preservative on the yield and composition of various pyrolysis products was investigated in the present research. A novel quantitative 31P nuclear magnetic resonance (...

Out-of-equilibrium catalysis of chemical reactions by electronic tunnel currents.

PubMed

Dzhioev, Alan A; Kosov, Daniel S; von Oppen, Felix

2013-04-07

We present an escape rate theory for current-induced chemical reactions. We use Keldysh nonequilibrium Green's functions to derive a Langevin equation for the reaction coordinate. Due to the out of equilibrium electronic degrees of freedom, the friction, noise, and effective temperature in the Langevin equation depend locally on the reaction coordinate. As an example, we consider the dissociation of diatomic molecules induced by the electronic current from a scanning tunnelling microscope tip. In the resonant tunnelling regime, the molecular dissociation involves two processes which are intricately interconnected: a modification of the potential energy barrier and heating of the molecule. The decrease of the molecular barrier (i.e., the current induced catalytic reduction of the barrier) accompanied by the appearance of the effective, reaction-coordinate-dependent temperature is an alternative mechanism for current-induced chemical reactions, which is distinctly different from the usual paradigm of pumping vibrational degrees of freedom.

Finite element modeling of contaminant transport in soils including the effect of chemical reactions.

PubMed

Javadi, A A; Al-Najjar, M M

2007-05-17

The movement of chemicals through soils to the groundwater is a major cause of degradation of water resources. In many cases, serious human and stock health implications are associated with this form of pollution. Recent studies have shown that the current models and methods are not able to adequately describe the leaching of nutrients through soils, often underestimating the risk of groundwater contamination by surface-applied chemicals, and overestimating the concentration of resident solutes. Furthermore, the effect of chemical reactions on the fate and transport of contaminants is not included in many of the existing numerical models for contaminant transport. In this paper a numerical model is presented for simulation of the flow of water and air and contaminant transport through unsaturated soils with the main focus being on the effects of chemical reactions. The governing equations of miscible contaminant transport including advection, dispersion-diffusion and adsorption effects together with the effect of chemical reactions are presented. The mathematical framework and the numerical implementation of the model are described in detail. The model is validated by application to a number of test cases from the literature and is then applied to the simulation of a physical model test involving transport of contaminants in a block of soil with particular reference to the effects of chemical reactions. Comparison of the results of the numerical model with the experimental results shows that the model is capable of predicting the effects of chemical reactions with very high accuracy. The importance of consideration of the effects of chemical reactions is highlighted.

Progression in High School Students' (Aged 16-18) Conceptualizations about Chemical Reactions in Solution.

ERIC Educational Resources Information Center

Boo, Hong-Kwen; Watson, J. R.

2001-01-01

Explores the development over time of students' understandings of the concept of chemical reaction in the context of two familiar reactions in solution. Based on interviews (n=48), results show that students made some progress in their understanding of the concept of chemical reaction but some fundamental misconceptions remained. (Author/MM)

Chemical-Reaction-Controlled Phase Separated Drops: Formation, Size Selection, and Coarsening

NASA Astrophysics Data System (ADS)

Wurtz, Jean David; Lee, Chiu Fan

2018-02-01

Phase separation under nonequilibrium conditions is exploited by biological cells to organize their cytoplasm but remains poorly understood as a physical phenomenon. Here, we study a ternary fluid model in which phase-separating molecules can be converted into soluble molecules, and vice versa, via chemical reactions. We elucidate using analytical and simulation methods how drop size, formation, and coarsening can be controlled by the chemical reaction rates, and categorize the qualitative behavior of the system into distinct regimes. Ostwald ripening arrest occurs above critical reaction rates, demonstrating that this transition belongs entirely to the nonequilibrium regime. Our model is a minimal representation of the cell cytoplasm.

Elementary Chemical Reactions in Surface Photocatalysis

NASA Astrophysics Data System (ADS)

Guo, Qing; Zhou, Chuanyao; Ma, Zhibo; Ren, Zefeng; Fan, Hongjun; Yang, Xueming

2018-04-01

Photocatalytic hydrogen evolution and organic degradation on oxide materials have been extensively investigated in the last two decades. Great efforts have been dedicated to the study of photocatalytic reaction mechanisms of a variety of molecules on TiO2 surfaces by using surface science methods under ultra-high vacuum (UHV) conditions, providing fundamental understanding of surface chemical reactions in photocatalysis. In this review, we summarize the recent progress in the study of photocatalysis of several important species (water, methanol, and aldehydes) on different TiO2 surfaces. The results of these studies have provided us deep insights into the elementary processes of surface photocatalysis and stimulated a new frontier of research in this area. Based on the results of these studies, a new dynamics-based photocatalysis model is also discussed.

Diffusion-controlled reactions modeling in Geant4-DNA

NASA Astrophysics Data System (ADS)

Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.

2014-10-01

Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The

Diffusion-controlled reactions modeling in Geant4-DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karamitros, M., E-mail: matkara@gmail.com; CNRS, INCIA, UMR 5287, F-33400 Talence; Luan, S.

2014-10-01

Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing allmore » the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest

Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications

DOE PAGES

Suleimanov, Yury V.; Aoiz, F. Javier; Guo, Hua

2016-09-14

This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques formore » calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.« less

Vicher: A Virtual Reality Based Educational Module for Chemical Reaction Engineering.

ERIC Educational Resources Information Center

Bell, John T.; Fogler, H. Scott

1996-01-01

A virtual reality application for undergraduate chemical kinetics and reactor design education, Vicher (Virtual Chemical Reaction Model) was originally designed to simulate a portion of a modern chemical plant. Vicher now consists of two programs: Vicher I that models catalyst deactivation and Vicher II that models nonisothermal effects in…

Real time monitoring of accelerated chemical reactions by ultrasonication-assisted spray ionization mass spectrometry.

PubMed

Lin, Shu-Hsuan; Lo, Ta-Ju; Kuo, Fang-Yin; Chen, Yu-Chie

2014-01-01

Ultrasonication has been used to accelerate chemical reactions. It would be ideal if ultrasonication-assisted chemical reactions could be monitored by suitable detection tools such as mass spectrometry in real time. It would be helpful to clarify reaction intermediates/products and to have a better understanding of reaction mechanism. In this work, we developed a system for ultrasonication-assisted spray ionization mass spectrometry (UASI-MS) with an ~1.7 MHz ultrasonic transducer to monitor chemical reactions in real time. We demonstrated that simply depositing a sample solution on the MHz-based ultrasonic transducer, which was placed in front of the orifice of a mass spectrometer, the analyte signals can be readily detected by the mass spectrometer. Singly and multiply charged ions from small and large molecules, respectively, can be observed in the UASI mass spectra. Furthermore, the ultrasonic transducer used in the UASI setup accelerates the chemical reactions while being monitored via UASI-MS. The feasibility of using this approach for real-time acceleration/monitoring of chemical reactions was demonstrated. The reactions of Girard T reagent and hydroxylamine with steroids were used as the model reactions. Upon the deposition of reactant solutions on the ultrasonic transducer, the intermediate/product ions are readily generated and instantaneously monitored using MS within 1 s. Additionally, we also showed the possibility of using this reactive UASI-MS approach to assist the confirmation of trace steroids from complex urine samples by monitoring the generation of the product ions. Copyright © 2014 John Wiley & Sons, Ltd.

Cell-free metabolic engineering: production of chemicals by minimized reaction cascades.

PubMed

Guterl, Jan-Karl; Garbe, Daniel; Carsten, Jörg; Steffler, Fabian; Sommer, Bettina; Reiße, Steven; Philipp, Anja; Haack, Martina; Rühmann, Broder; Koltermann, Andre; Kettling, Ulrich; Brück, Thomas; Sieber, Volker

2012-11-01

The limited supply of fossil resources demands the development of renewable alternatives to petroleum-based products. Here, biobased higher alcohols such as isobutanol are versatile platform molecules for the synthesis of chemical commodities and fuels. Currently, their fermentation-based production is limited by the low tolerance of microbial production systems to the end products and also by the low substrate flux into cell metabolism. We developed an innovative cell-free approach, utilizing an artificial minimized glycolytic reaction cascade that only requires one single coenzyme. Using this toolbox the cell-free production of ethanol and isobutanol from glucose was achieved. We also confirmed that these streamlined cascades functioned under conditions at which microbial production would have ceased. Our system can be extended to an array of industrially-relevant molecules. Application of solvent-tolerant biocatalysts potentially allows for high product yields, which significantly simplifies downstream product recovery. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

ERIC Educational Resources Information Center

Cloonan, Carrie A.; Nichol, Carolyn A.; Hutchinson, John S.

2011-01-01

Chemical reaction kinetics and equilibrium are essential core concepts of chemistry but are challenging topics for many students, both at the high school and undergraduate university level. Visualization at the molecular level is valuable to aid understanding of reaction kinetics and equilibrium. This activity provides a discovery-based method to…

What limits the yield of levoglucosan during fast pyrolysis of cellulose?

NASA Astrophysics Data System (ADS)

Proano-Aviles, Juan

The pyrolysis of cellulose to form levoglucosan is investigated in this study. Although the stoichiometric yield of levoglucosan from the pyrolysis of cellulose is expected to be 100%, only about 60 wt.% yields are reported in the literature. Several possible reasons for this limitation are investigated through experiments in micropyrolyzers and computational studies on the depolymerization of cellulose. Heat and mass transfer limitations in an experimental apparatus is one possible limitation on the yield of levoglucosan. Repolymerization of condensed phase reaction intermediates could prevent the formation and release of volatile levoglucosan. Thermohydrolysis of pyrolyzing cellulose to form non-volatile and thermally unstable glucose has also been proposed as a mechanism that reduces levoglucosan yields. Secondary reactions in the gas phase were also investigated to explain limitations on levoglucosan yields. Population balance models were developed to test ideas on how cellulose depolymerized to form levoglucosan at less than stoichiometric yields. These models were supported with chemical kinetic data obtained from transient pyrolysis experiments. Under carefully controlled experimental conditions, no evidence was found for heat and mass transfer effects limiting levoglucosan yields to 60 wt.% nor do secondary reactions in the condensed- or gas-phases appear to offer a satisfactory explanation. Based on modeling results, it appears levoglucosan-forming reaction rates that decrease as oligosaccharide chain length decreases is the most plausible explanation for limitations on levoglucosan yield from cellulose.

Chemical Reactions in Turbulent Mixing Flows.

DTIC Science & Technology

1986-04-10

fluctuation of the " flame " length of such reactingjeatreent wer copoit sequencd shout tnhawate facility, documented previously’,’ 1 , using laser jets. A...motion film of such a chemically reacting turbulent jet visualized using this technique, is shown in figure 1. In each I. Flame length fluctuations of...acid-base reaction to determine length and time to allow a simultaneous view of mixing in the two scales for the flame length fluctuations of thin

Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior

NASA Astrophysics Data System (ADS)

Lebiedz, Dirk; Brandt-Pollmann, Ulrich

2004-09-01

Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.

Scattering Resonances in the Simplest Chemical Reaction

NASA Astrophysics Data System (ADS)

Fernandez-Alonso, Felix; Zare, Richard N.

2002-10-01

Recent studies of state-resolved angular distributions show the participation of reactive scattering resonances in the simplest chemical reaction. This review is intended for those who wish to learn about the state-of-the-art in the study of the H + H2 reaction family that has made this breakthrough possible. This review is also intended for those who wish to gain insight into the nature of reactive scattering resonances. Following a tour across several fields of physics and chemistry where the concept of resonance has been crucial for the understanding of new phenomena, we offer an operational definition and taxonomy of reactive scattering resonances. We introduce simple intuitive models to illustrate each resonance type. We focus next on the last decade of H + H2 reaction dynamics. Emphasis is placed on the various experimental approaches that have been applied to the search for resonance behavior in the H + H2 reaction family. We conclude by sketching the road ahead in the study of H + H2 reactive scattering resonances.

Process for chemical reaction of amino acids and amides yielding selective conversion products

DOEpatents

Holladay, Jonathan E [Kennewick, WA

2006-05-23

The invention relates to processes for converting amino acids and amides to desirable conversion products including pyrrolidines, pyrrolidinones, and other N-substituted products. L-glutamic acid and L-pyroglutamic acid provide general reaction pathways to numerous and valuable selective conversion products with varied potential industrial uses.

High Performance Computer Cluster for Theoretical Studies of Roaming in Chemical Reactions

DTIC Science & Technology

2016-08-30

High-performance Computer Cluster for Theoretical Studies of Roaming in Chemical Reactions A dedicated high-performance computer cluster was...SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS (ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Computer cluster ...peer-reviewed journals: Final Report: High-performance Computer Cluster for Theoretical Studies of Roaming in Chemical Reactions Report Title A dedicated

Chemical Reaction Engineering: Current Status and Future Directions.

ERIC Educational Resources Information Center

Dudukovic, M. P.

1987-01-01

Describes Chemical Reaction Engineering (CRE) as the discipline that quantifies the interplay of transport phenomena and kinetics in relating reactor performance to operating conditions and input variables. Addresses the current status of CRE in both academic and industrial settings and outlines future trends. (TW)

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

PubMed

Khriachtchev, Leonid; Domanskaya, Alexandra; Marushkevich, Kseniya; Räsänen, Markku; Grigorenko, Bella; Ermilov, Alexander; Andrijchenko, Natalya; Nemukhin, Alexander

2009-07-23

Conformation dictates many physical and chemical properties of molecules. The importance of conformation in the selectivity and function of biologically active molecules is widely accepted. However, clear examples of conformation-dependent bimolecular chemical reactions are lacking. Here we consider a case of formic acid (HCOOH) that is a valuable model system containing the -COOH carboxyl functional group, similar to many biomolecules including the standard amino acids. We have found a strong case of conformation-dependent reaction between formic acid and atomic oxygen obtained in cryogenic matrices. The reaction surprisingly leads to peroxyformic acid only from the ground-state trans conformer of formic acid, and it results in the hydrogen-bonded complex for the higher-energy cis conformer.

Students' Visualisation of Chemical Reactions--Insights into the Particle Model and the Atomic Model

ERIC Educational Resources Information Center

Cheng, Maurice M. W.

2018-01-01

This paper reports on an interview study of 18 Grade 10-12 students' model-based reasoning of a chemical reaction: the reaction of magnesium and oxygen at the submicro level. It has been proposed that chemical reactions can be conceptualised using two models: (i) the "particle model," in which a reaction is regarded as the simple…

A Unified Approach to the Study of Chemical Reactions in Freshman Chemistry.

ERIC Educational Resources Information Center

Cassen, T.; DuBois, Thomas D.

1982-01-01

Provides rationale and objectives for presenting chemical reactions in a unified, logical six-stage approach rather than a piecemeal approach. Stages discussed include: introduction, stable electronic configurations and stable oxidation states, reactions between two free elements, ion transfer/proton transfer reactions, double displacement…

Perspective: Chemical reactions in ionic liquids monitored through the gas (vacuum)/liquid interface.

PubMed

Maier, F; Niedermaier, I; Steinrück, H-P

2017-05-07

This perspective analyzes the potential of X-ray photoelectron spectroscopy under ultrahigh vacuum (UHV) conditions to follow chemical reactions in ionic liquids in situ. Traditionally, only reactions occurring on solid surfaces were investigated by X-ray photoelectron spectroscopy (XPS) in situ. This was due to the high vapor pressures of common liquids or solvents, which are not compatible with the required UHV conditions. It was only recently realized that the situation is very different when studying reactions in Ionic Liquids (ILs), which have an inherently low vapor pressure, and first studies have been performed within the last years. Compared to classical spectroscopy techniques used to monitor chemical reactions, the advantage of XPS is that through the analysis of their core levels all relevant elements can be quantified and their chemical state can be analyzed under well-defined (ultraclean) conditions. In this perspective, we cover six very different reactions which occur in the IL, with the IL, or at an IL/support interface, demonstrating the outstanding potential of in situ XPS to gain insights into liquid phase reactions in the near-surface region.

Understanding chemical binding using the Berlin function and the reaction force

NASA Astrophysics Data System (ADS)

Chakraborty, Debajit; Cárdenas, Carlos; Echegaray, Eleonora; Toro-Labbe, Alejandro; Ayers, Paul W.

2012-06-01

We use the derivative of the electron density with respect to the reaction coordinate, interpreted through the Berlin binding function, to identify portions of the reaction path where chemical bonds are breaking and forming. The results agree with the conventional description for SN2 reactions, but they are much more general and can be used to elucidate other types of reactions also. Our analysis offers support for, and detailed information about, the use of the reaction force profile to separate the reaction coordinates into intervals, each with characteristic extents of geometry change and electronic rearrangement.

Role of the N*(1535) in pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie Jujun; Graduate University of Chinese Academy of Sciences, Beijing 100049; Zou Bingsong

2008-01-15

The near-threshold {phi}-meson production in proton-proton and {pi}{sup -}p collisions is studied with the assumption that the production mechanism is due to the sub-N{phi}-threshold N*(1535) resonance. The {pi}{sup 0}-,{eta}-, and {rho}{sup 0}-meson exchanges for proton-proton collisions are considered. It is shown that the contribution to the pp{yields}pp{phi} reaction from the t-channel {pi}{sup 0}-meson exchange is dominant. With a significant N*(1535)N{phi} coupling [g{sub N*(1535)N{phi}}{sup 2}/4{pi}=0.13], both pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} data are very well reproduced. The significant coupling of the N*(1535) resonance to N{phi} is compatible with previous indications of a large ss component in the quark wave function of themore » N*(1535) resonance and may be the real origin of the significant enhancement of the {phi} production over the naive OZI-rule predictions.« less

Chemical looping coal gasification with calcium ferrite and barium ferrite via solid--solid reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siriwardane, Ranjani; Riley, Jarrett; Tian, Hanjing

Coal gasification to produce synthesis gas by chemical looping was investigated with two oxygen carriers, barium ferrite (BaFe2O4) and calcium ferrite (CaFe2O4). Thermo-gravimetric analysis (TGA) and fixed-bed flow reactor data indicated that a solid–solid interaction occurred between oxygen carriers and coal to produce synthesis gas. Both thermodynamic analysis and experimental data indicated that BaFe2O4 and CaFe2O4 have high reactivity with coal but have a low reactivity with synthesis gas, which makes them very attractive for the coal gasification process. Adding steam increased the production of hydrogen (H2) and carbon monoxide (CO), but carbon dioxide (CO2) remained low because these oxygenmore » carriers have minimal reactivity with H2 and CO. Therefore, the combined steam–oxygen carrier produced the highest quantity of synthesis gas. It appeared that neither the water–gas shift reaction nor the water splitting reaction promoted additional H2 formation with the oxygen carriers when steam was present. Wyodak coal, which is a sub-bituminous coal, had the best gasification yield with oxygen carrier–steam while Illinois #6 coal had the lowest. The rate of gasification and selectivity for synthesis gas production was significantly higher when these oxygen carriers were present during steam gasification of coal. The rates and synthesis gas yields during the temperature ramps of coal–steam with oxygen carriers were better than with gaseous oxygen.« less

Results of the 2010 Survey on Teaching Chemical Reaction Engineering

ERIC Educational Resources Information Center

Silverstein, David L.; Vigeant, Margot A. S.

2012-01-01

A survey of faculty teaching the chemical reaction engineering course or sequence during the 2009-2010 academic year at chemical engineering programs in the United States and Canada reveals change in terms of content, timing, and approaches to teaching. The report consists of two parts: first, a statistical and demographic characterization of the…

A Petri net approach to the study of persistence in chemical reaction networks.

PubMed

Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D

2007-12-01

Persistence is the property, for differential equations in R(n), that solutions starting in the positive orthant do not approach the boundary of the orthant. For chemical reactions and population models, this translates into the non-extinction property: provided that every species is present at the start of the reaction, no species will tend to be eliminated in the course of the reaction. This paper provides checkable conditions for persistence of chemical species in reaction networks, using concepts and tools from Petri net theory, and verifies these conditions on various systems which arise in the modeling of cell signaling pathways.

Nonlinear magnetoacoustic wave propagation with chemical reactions

NASA Astrophysics Data System (ADS)

Margulies, Timothy Scott

2002-11-01

The magnetoacoustic problem with an application to sound wave propagation through electrically conducting fluids such as the ocean in the Earth's magnetic field, liquid metals, or plasmas has been addressed taking into account several simultaneous chemical reactions. Using continuum balance equations for the total mass, linear momentum, energy; as well as Maxwell's electrodynamic equations, a nonlinear beam equation has been developed to generalize the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation for a fluid with linear viscosity but nonlinear and diffraction effects. Thermodynamic parameters are used and not tailored to only an adiabatic fluid case. The chemical kinetic equations build on a relaxing media approach presented, for example, by K. Naugolnukh and L. Ostrovsky [Nonlinear Wave Processes in Acoustics (Cambridge Univ. Press, Cambridge, 1998)] for a linearized single reaction and thermodynamic pressure equation of state. Approximations for large and small relaxation times and for magnetohydrodynamic parameters [Korsunskii, Sov. Phys. Acoust. 36 (1990)] are examined. Additionally, Cattaneo's equation for heat conduction and its generalization for a memory process rather than a Fourier's law are taken into account. It was introduced for the heat flux depends on the temperature gradient at an earlier time to generate heat pulses of finite speed.

Chemical reaction fouling model for single-phase heat transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panchal, C.B.; Watkinson, A.P.

1993-08-01

A fouling model was developed on the premise that the chemical reaction for generation of precursor can take place in the bulk fluid, in the thermalboundary layer, or at the fluid/wall interface, depending upon the interactive effects of flu id dynamics, heat and mass transfer, and the controlling chemical reaction. The analysis was used to examine the experimental data for fouling deposition of polyperoxides produced by autoxidation of indene in kerosene. The effects of fluid and wall temperatures for two flow geometries were analyzed. The results showed that the relative effects of physical parameters on the fouling rate would differmore » for the three fouling mechanisms; therefore, it is important to identify the controlling mechanism in applying the closed-flow-loop data to industrial conditions.« less

Achieving Chemical Equilibrium: The Role of Imposed Conditions in the Ammonia Formation Reaction

ERIC Educational Resources Information Center

Tellinghuisen, Joel

2006-01-01

Under conditions of constant temperature T and pressure P, chemical equilibrium occurs in a closed system (fixed mass) when the Gibbs free energy G of the reaction mixture is minimized. However, when chemical reactions occur under other conditions, other thermodynamic functions are minimized or maximized. For processes at constant T and volume V,…

A versatile method for the determination of photochemical quantum yields via online UV-Vis spectroscopy.

PubMed

Stadler, Eduard; Eibel, Anna; Fast, David; Freißmuth, Hilde; Holly, Christian; Wiech, Mathias; Moszner, Norbert; Gescheidt, Georg

2018-05-16

We have developed a simple method for determining the quantum yields of photo-induced reactions. Our setup features a fibre coupled UV-Vis spectrometer, LED irradiation sources, and a calibrated spectrophotometer for precise measurements of the LED photon flux. The initial slope in time-resolved absorbance profiles provides the quantum yield. We show the feasibility of our methodology for the kinetic analysis of photochemical reactions and quantum yield determination. The typical chemical actinometers, ferrioxalate and ortho-nitrobenzaldehyde, as well as riboflavin, a spiro-compound, phosphorus- and germanium-based photoinitiators for radical polymerizations and the frequently utilized photo-switch azobenzene serve as paradigms. The excellent agreement of our results with published data demonstrates the high potential of the proposed method as a convenient alternative to the time-consuming chemical actinometry.

Role of the N*(1535) in the J/{psi}{yields}p{eta}p and J/{psi}{yields}pK{sup +}{lambda} reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, L. S.; Oset, E.; Zou, B. S.

2009-02-15

We study the J/{psi}{yields}p{eta}p and J/{psi}{yields}pK{sup +}{lambda} reactions with a unitary chiral approach. We find that the unitary chiral approach, which generates the N*(1535) dynamically, can describe the data reasonably well, particularly the ratio of the integrated cross sections. This study provides further support for the unitary chiral description of the N*(1535). We also discuss some subtle differences between the coupling constants determined from the unitary chiral approach and those determined from phenomenological studies.

Universality and chaoticity in ultracold K+KRb chemical reactions

DOE PAGES

Croft, J. F. E.; Makrides, C.; Li, M.; ...

2017-07-19

A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K 2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysismore » of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome.« less

Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks.

PubMed

Koch, Ina

2010-12-17

In this review we introduce and discuss Petri nets - a mathematical formalism to describe and analyze chemical reaction networks. Petri nets were developed to describe concurrency in general systems. We find most applications to technical and financial systems, but since about twenty years also in systems biology to model biochemical systems. This review aims to give a short informal introduction to the basic formalism illustrated by a chemical example, and to discuss possible applications to the analysis of chemical reaction networks, including cheminformatics. We give a short overview about qualitative as well as quantitative modeling Petri net techniques useful in systems biology, summarizing the state-of-the-art in that field and providing the main literature references. Finally, we discuss advantages and limitations of Petri nets and give an outlook to further development. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the Geometry of Chemical Reaction Networks: Lyapunov Function and Large Deviations

NASA Astrophysics Data System (ADS)

Agazzi, A.; Dembo, A.; Eckmann, J.-P.

2018-04-01

In an earlier paper, we proved the validity of large deviations theory for the particle approximation of quite general chemical reaction networks. In this paper, we extend its scope and present a more geometric insight into the mechanism of that proof, exploiting the notion of spherical image of the reaction polytope. This allows to view the asymptotic behavior of the vector field describing the mass-action dynamics of chemical reactions as the result of an interaction between the faces of this polytope in different dimensions. We also illustrate some local aspects of the problem in a discussion of Wentzell-Freidlin theory, together with some examples.

Using Computer-Based "Experiments" in the Analysis of Chemical Reaction Equilibria

ERIC Educational Resources Information Center

Li, Zhao; Corti, David S.

2018-01-01

The application of the Reaction Monte Carlo (RxMC) algorithm to standard textbook problems in chemical reaction equilibria is discussed. The RxMC method is a molecular simulation algorithm for studying the equilibrium properties of reactive systems, and therefore provides the opportunity to develop computer-based "experiments" for the…

Researches on Preliminary Chemical Reactions in Spark-Ignition Engines

NASA Technical Reports Server (NTRS)

Muehlner, E.

1943-01-01

Chemical reactions can demonstrably occur in a fuel-air mixture compressed in the working cylinder of an Otto-cycle (spark ignition) internal-combustion engine even before the charge is ignited by the flame proceeding from the sparking plug. These are the so-called "prelinminary reactions" ("pre-flame" combustion or oxidation), and an exact knowledge of their characteristic development is of great importance for a correct appreciation of the phenomena of engine-knock (detonation), and consequently for its avoidance. Such reactions can be studied either in a working engine cylinder or in a combustion bomb. The first method necessitates a complicated experimental technique, while the second has the disadvantage of enabling only a single reaction to be studied at one time. Consequently, a new series of experiments was inaugurated, conducted in a motored (externally-driven) experimental engine of mixture-compression type, without ignition, the resulting preliminary reactions being detectable and measurable thermometrically.

Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

PubMed

Holliday, Gemma L; Murray-Rust, Peter; Rzepa, Henry S

2006-01-01

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.

Thin layer chromatography coupled with surface-enhanced Raman scattering as a facile method for on-site quantitative monitoring of chemical reactions.

PubMed

Zhang, Zong-Mian; Liu, Jing-Fu; Liu, Rui; Sun, Jie-Fang; Wei, Guo-Hua

2014-08-05

By coupling surface-enhanced Raman spectroscopy (SERS) with thin layer chromatography (TLC), a facile and powerful method was developed for on-site monitoring the process of chemical reactions. Samples were preseparated on a TLC plate following a common TLC procedure, and then determined by SERS after fabricating a large-area, uniform SERS substrate on the TLC plate by spraying gold nanoparticles (AuNPs). Reproducible and strong SERS signals were obtained with substrates prepared by spraying 42-nm AuNPs at a density of 5.54 × 10(10) N/cm(2) on the TLC plate. The capacity of this TLC-SERS method was evaluated by monitoring a typical Suzuki coupling reaction of phenylboronic acid and 2-bromopyridine as a model. Results showed that this proposed method is able to identify reaction product that is invisible to the naked eye, and distinguish the reactant 2-bromopyridine and product 2-phenylpyridine, which showed almost the same retention factors (R(f)). Under the optimized conditions, the peak area of the characteristic Raman band (755 cm(-1)) of the product 2-phenylpyridine showed a good linear correlation with concentration in the range of 2-200 mg/L (R(2) = 0.9741), the estimated detection limit (1 mg/L 2-phenylpyridine) is much lower than the concentration of the chemicals in the common organic synthesis reaction system, and the product yield determined by the proposed TLC-SERS method agreed very well with that by UPLC-MS/MS. In addition, a new byproduct in the reaction system was found and identified through continuous Raman detection from the point of sample to the solvent front. This facile TLC-SERS method is quick, easy to handle, low-cost, sensitive, and can be exploited in on-site monitoring the processes of chemical reactions, as well as environmental and biological processes.

A multi-scaled approach for simulating chemical reaction systems.

PubMed

Burrage, Kevin; Tian, Tianhai; Burrage, Pamela

2004-01-01

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge-Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work. Copyright 2004 Elsevier Ltd.

Upper Limits for Power Yield in Thermal, Chemical, and Electrochemical Systems

NASA Astrophysics Data System (ADS)

Sieniutycz, Stanislaw

2010-03-01

We consider modeling and power optimization of energy converters, such as thermal, solar and chemical engines and fuel cells. Thermodynamic principles lead to expressions for converter's efficiency and generated power. Efficiency equations serve to solve the problems of upgrading or downgrading a resource. Power yield is a cumulative effect in a system consisting of a resource, engines, and an infinite bath. While optimization of steady state systems requires using the differential calculus and Lagrange multipliers, dynamic optimization involves variational calculus and dynamic programming. The primary result of static optimization is the upper limit of power, whereas that of dynamic optimization is a finite-rate counterpart of classical reversible work (exergy). The latter quantity depends on the end state coordinates and a dissipation index, h, which is the Hamiltonian of the problem of minimum entropy production. In reacting systems, an active part of chemical affinity constitutes a major component of the overall efficiency. The theory is also applied to fuel cells regarded as electrochemical flow engines. Enhanced bounds on power yield follow, which are stronger than those predicted by the reversible work potential.

Inflow, Outflow, Yields, and Stellar Population Mixing in Chemical Evolution Models

NASA Astrophysics Data System (ADS)

Andrews, Brett H.; Weinberg, David H.; Schönrich, Ralph; Johnson, Jennifer A.

2017-02-01

Chemical evolution models are powerful tools for interpreting stellar abundance surveys and understanding galaxy evolution. However, their predictions depend heavily on the treatment of inflow, outflow, star formation efficiency (SFE), the stellar initial mass function, the SN Ia delay time distribution, stellar yields, and stellar population mixing. Using flexCE, a flexible one-zone chemical evolution code, we investigate the effects of and trade-offs between parameters. Two critical parameters are SFE and the outflow mass-loading parameter, which shift the knee in [O/Fe]-[Fe/H] and the equilibrium abundances that the simulations asymptotically approach, respectively. One-zone models with simple star formation histories follow narrow tracks in [O/Fe]-[Fe/H] unlike the observed bimodality (separate high-α and low-α sequences) in this plane. A mix of one-zone models with inflow timescale and outflow mass-loading parameter variations, motivated by the inside-out galaxy formation scenario with radial mixing, reproduces the two sequences better than a one-zone model with two infall epochs. We present [X/Fe]-[Fe/H] tracks for 20 elements assuming three different supernova yield models and find some significant discrepancies with solar neighborhood observations, especially for elements with strongly metallicity-dependent yields. We apply principal component abundance analysis to the simulations and existing data to reveal the main correlations among abundances and quantify their contributions to variation in abundance space. For the stellar population mixing scenario, the abundances of α-elements and elements with metallicity-dependent yields dominate the first and second principal components, respectively, and collectively explain 99% of the variance in the model. flexCE is a python package available at https://github.com/bretthandrews/flexCE.

Motivational Factors Contributing to Turkish High School Students' Achievement in Gases and Chemical Reactions

ERIC Educational Resources Information Center

Kadioglu, Cansel; Uzuntiryaki, Esen

2008-01-01

This study aimed to investigate the contribution of motivational factors to 10th grade students' achievement in gases and chemical reactions in chemistry. Three hundred fifty nine 10th grade students participated in the study. The Gases and Chemical Reactions Achievement Test and the Motivated Strategies for Learning Questionnaire were…

Students' Ideas about How and Why Chemical Reactions Happen: Mapping the conceptual landscape

NASA Astrophysics Data System (ADS)

Yan, Fan; Talanquer, Vicente

2015-12-01

Research in science education has revealed that many students struggle to understand chemical reactions. Improving teaching and learning about chemical processes demands that we develop a clearer understanding of student reasoning in this area and of how this reasoning evolves with training in the domain. Thus, we have carried out a qualitative study to explore students reasoning about chemical causality and mechanism. Study participants included individuals at different educational levels, from college to graduate school. We identified diverse conceptual modes expressed by students when engaged in the analysis of different types of reactions. Main findings indicate that student reasoning about chemical reactions is influenced by the nature of the process. More advanced students tended to express conceptual modes that were more normative and had more explanatory power, but major conceptual difficulties persisted in their reasoning. The results of our study are relevant to educators interested in conceptual development, learning progressions, and assessment.

Cross section of α-induced reactions on iridium isotopes obtained from thick target yield measurement for the astrophysical γ process

NASA Astrophysics Data System (ADS)

Szücs, T.; Kiss, G. G.; Gyürky, Gy.; Halász, Z.; Fülöp, Zs.; Rauscher, T.

2018-01-01

The stellar reaction rates of radiative α-capture reactions on heavy isotopes are of crucial importance for the γ process network calculations. These rates are usually derived from statistical model calculations, which need to be validated, but the experimental database is very scarce. This paper presents the results of α-induced reaction cross section measurements on iridium isotopes carried out at first close to the astrophysically relevant energy region. Thick target yields of 191Ir(α,γ)195Au, 191Ir(α,n)194Au, 193Ir(α,n)196mAu, 193Ir(α,n)196Au reactions have been measured with the activation technique between Eα = 13.4 MeV and 17 MeV. For the first time the thick target yield was determined with X-ray counting. This led to a previously unprecedented sensitivity. From the measured thick target yields, reaction cross sections are derived and compared with statistical model calculations. The recently suggested energy-dependent modification of the α + nucleus optical potential gives a good description of the experimental data.

The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled.

PubMed

Göppel, Tobias; Palyulin, Vladimir V; Gerland, Ulrich

2016-07-27

An out-of-equilibrium physical environment can drive chemical reactions into thermodynamically unfavorable regimes. Under prebiotic conditions such a coupling between physical and chemical non-equilibria may have enabled the spontaneous emergence of primitive evolutionary processes. Here, we study the coupling efficiency within a theoretical model that is inspired by recent laboratory experiments, but focuses on generic effects arising whenever reactant and product molecules have different transport coefficients in a flow-through system. In our model, the physical non-equilibrium is represented by a drift-diffusion process, which is a valid coarse-grained description for the interplay between thermophoresis and convection, as well as for many other molecular transport processes. As a simple chemical reaction, we consider a reversible dimerization process, which is coupled to the transport process by different drift velocities for monomers and dimers. Within this minimal model, the coupling efficiency between the non-equilibrium transport process and the chemical reaction can be analyzed in all parameter regimes. The analysis shows that the efficiency depends strongly on the Damköhler number, a parameter that measures the relative timescales associated with the transport and reaction kinetics. Our model and results will be useful for a better understanding of the conditions for which non-equilibrium environments can provide a significant driving force for chemical reactions in a prebiotic setting.

Stability of a laminar premixed supersonic free shear layer with chemical reactions

NASA Technical Reports Server (NTRS)

Menon, S.; Anderson, J. D., Jr.; Pai, S. I.

1984-01-01

The stability of a two-dimensional compressible supersonic flow in the wake of a flat plate is discussed. The fluid is a multi-species mixture which is undergoing finite rate chemical reactions. The spatial stability of an infinitesimal disturbance in the fluid is considered. Numerical solutions of the eigenvalue stability equations for both reactive and nonreactive supersonic flows are presented and discussed. The chemical reactions have significant influence on the stability behavior. For instance, a neutral eigenvalue is observed near the freestream Mach number of 2.375 for the nonreactive case, but disappears when the reaction is turned on. For reactive flows, the eigenvalues are not very dependent on the free stream Mach number.

WATER AS A REACTION MEDIUM FOR CLEAN CHEMICAL PROCESSES.

EPA Science Inventory

Green chemistry is a rapid developing new field that provides us a pro-active avenue for the sustainable development of future science and technologies. When designed properly, clean chemical technology can be developed in water as a reaction media. The technologies generated f...

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

PubMed

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Real-space and real-time observation of a plasmon-induced chemical reaction of a single molecule.

PubMed

Kazuma, Emiko; Jung, Jaehoon; Ueba, Hiromu; Trenary, Michael; Kim, Yousoo

2018-05-04

Plasmon-induced chemical reactions of molecules adsorbed on metal nanostructures are attracting increased attention for photocatalytic reactions. However, the mechanism remains controversial because of the difficulty of direct observation of the chemical reactions in the plasmonic field, which is strongly localized near the metal surface. We used a scanning tunneling microscope (STM) to achieve real-space and real-time observation of a plasmon-induced chemical reaction at the single-molecule level. A single dimethyl disulfide molecule on silver and copper surfaces was dissociated by the optically excited plasmon at the STM junction. The STM study combined with theoretical calculations shows that this plasmon-induced chemical reaction occurred by a direct intramolecular excitation mechanism. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Chemical repair activity of free radical scavenger edaravone: reduction reactions with dGMP hydroxyl radical adducts and suppression of base lesions and AP sites on irradiated plasmid DNA

PubMed Central

Hata, Kuniki; Urushibara, Ayumi; Yamashita, Shinichi; Lin, Mingzhang; Muroya, Yusa; Shikazono, Naoya; Yokoya, Akinari; Fu, Haiying; Katsumura, Yosuke

2015-01-01

Reactions of edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one) with deoxyguanosine monophosphate (dGMP) hydroxyl radical adducts were investigated by pulse radiolysis technique. Edaravone was found to reduce the dGMP hydroxyl radical adducts through electron transfer reactions. The rate constants of the reactions were greater than 4 × 108 dm3 mol−1 s−1 and similar to those of the reactions of ascorbic acid, which is a representative antioxidant. Yields of single-strand breaks, base lesions, and abasic sites produced in pUC18 plasmid DNA by gamma ray irradiation in the presence of low concentrations (10–1000 μmol dm−3) of edaravone were also quantified, and the chemical repair activity of edaravone was estimated by a method recently developed by the authors. By comparing suppression efficiencies to the induction of each DNA lesion, it was found that base lesions and abasic sites were suppressed by the chemical repair activity of edaravone, although the suppression of single-strand breaks was not very effective. This phenomenon was attributed to the chemical repair activity of edaravone toward base lesions and abasic sites. However, the chemical repair activity of edaravone for base lesions was lower than that of ascorbic acid. PMID:25212600

29. NORTHWEST VIEW OF BOILER FEEDWATER CHEMICAL REACTION TANKS, WITH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

29. NORTHWEST VIEW OF BOILER FEEDWATER CHEMICAL REACTION TANKS, WITH FORMER GENERAL OFFICE BUILDING IN BACKGROUND. - U.S. Steel Duquesne Works, Fuel & Utilities Plant, Along Monongahela River, Duquesne, Allegheny County, PA

Evidence of N*(1535) resonance contribution in the pn{yields}d{phi} reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao Xu; Theoretical Physics Center for Sciences Facilities, Chinese Academy of Sciences, Beijing 100049; Graduate University of Chinese Academy of Sciences, Beijing 100049

2009-08-15

The N*(1535) resonance contributions to the pn{yields}d{phi} reaction are evaluated in an effective Lagrangian model. The {pi}-, {eta}-, and {rho}-meson exchange are considered. It is shown that the contributions from {pi}- and {rho}-meson exchange are dominant, while the contribution from {eta}-meson exchange is negligibly small. Our theoretical results reproduce the experimental data of both total cross section and angular distribution well. This is more evidence that the N*(1535) resonance has a large ss component leading to a large coupling to N{phi}, which may be the real origin of the Okubo-Zweig-Iizuka rule violation in the {pi}N and pN reactions.

Chemical reactions in perfume ageing.

PubMed

Blakeway, J M; Frey, M L; Lacroix, S; Salerno, M S

1987-10-01

Summary The interactions between a typical range of perfume materials, alcohol, water, air, elevated temperatures and daylight have been studied. The changes of composition, acidity, peroxide content and the formation of new molecules were followed. The stabilizing effects of UV absorbers, antioxidants and sequestering agents were examined; - the formation of acid reaction products was accelerated by air, temperature, daylight and the presence of natural products; - peroxide formation was accelerated by heat and light and the presence of air; as the acidity increased, the peroxides decomposed; - the acetalization of other aldehydes was accelerated by temperature and daylight and the presence of natural products up to 40% of certain aldehydes may be converted into acetals after 3 months at 37 degrees C; - many stereoisomerizations occur, e.g., transisoeugenol is converted up to 10% into the cis isomer after 3 months at 37 degrees C and 58% in daylight; - evaluation of antioxidants UV absorbers and sequestering agents showed a significant protection against deterioration only by EDTA dipotassium salt; - ethanol was converted into acetaldehyde and its diethylacetal by peroxides present and formed on ageing up to 0.08%. Natural products accelerated this formation; - the reaction between benzoyl peroxide and ethanol was shown to yield up to 63% of acetaldehyde+diethyl acetal whilst di-t-butyl peroxide gave only 23% under the same conditions. These results go some way to explaining odour changes in perfume ageing.

Method and apparatus for controlling gas evolution from chemical reactions

DOEpatents

Skorpik, James R.; Dodson, Michael G.

1999-01-01

The present invention is directed toward monitoring a thermally driven gas evolving chemical reaction with an acoustic apparatus. Signals from the acoustic apparatus are used to control a heater to prevent a run-away condition. A digestion module in combination with a robotic arm further automate physical handling of sample material reaction vessels. The invention is especially useful for carrying out sample procedures defined in EPA Methods SW-846.

Method and apparatus for controlling gas evolution from chemical reactions

DOEpatents

Skorpik, J.R.; Dodson, M.G.

1999-05-25

The present invention is directed toward monitoring a thermally driven gas evolving chemical reaction with an acoustic apparatus. Signals from the acoustic apparatus are used to control a heater to prevent a run-away condition. A digestion module in combination with a robotic arm further automate physical handling of sample material reaction vessels. The invention is especially useful for carrying out sample procedures defined in EPA Methods SW-846. 8 figs.

Ultrafast chemical reactions in shocked nitromethane probed with dynamic ellipsometry and transient absorption spectroscopy.

PubMed

Brown, Kathryn E; McGrane, Shawn D; Bolme, Cynthia A; Moore, David S

2014-04-10

Initiation of the shock driven chemical reactions and detonation of nitromethane (NM) can be sensitized by the addition of a weak base; however, the chemical mechanism by which sensitization occurs remains unclear. We investigated the shock driven chemical reaction in NM and in NM sensitized with diethylenetriamine (DETA), using a sustained 300 ps shock driven by a chirped Ti:sapphire laser. We measured the solutions' visible transient absorption spectra and measured interface particle and shock velocities of the nitromethane solutions using ultrafast dynamic ellipsometry. We found there to be a volume-increasing reaction that takes place around interface particle velocity up = 2.4 km/s and up = 2.2 km/s for neat NM and NM with 5% DETA, respectively. The rate at which transient absorption increases is similar in all mixtures, but with decreasing induction times for solutions with increasing DETA concentrations. This result supports the hypothesis that the chemical reaction mechanisms for shocked NM and NM with DETA are the same. Data from shocked NM are compared to literature experimental and theoretical data.

Theory of rotational transition in atom-diatom chemical reaction

NASA Astrophysics Data System (ADS)

Nakamura, Masato; Nakamura, Hiroki

1989-05-01

Rotational transition in atom-diatom chemical reaction is theoretically studied. A new approximate theory (which we call IOS-DW approximation) is proposed on the basis of the physical idea that rotational transition in reaction is induced by the following two different mechanisms: rotationally inelastic half collision in both initial and final arrangement channels, and coordinate transformation in the reaction zone. This theory gives a fairy compact expression for the state-to-state transition probability. Introducing the additional physically reasonable assumption that reaction (particle rearrangement) takes place in a spatially localized region, we have reduced this expression into a simpler analytical form which can explicitly give overall rotational state distribution in reaction. Numerical application was made to the H+H2 reaction and demonstrated its effectiveness for the simplicity. A further simplified most naive approximation, i.e., independent events approximation was also proposed and demonstrated to work well in the test calculation of H+H2. The overall rotational state distribution is expressed simply by a product sum of the transition probabilities for the three consecutive processes in reaction: inelastic transition in the initial half collision, transition due to particle rearrangement, and inelastic transition in the final half collision.

Chemically Activated Formation of Organic Acids in Reactions of the Criegee Intermediate with Aldehydes and Ketones

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Reactions of the Criegee intermediate (CI, .CH2OO.) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between .CH2OO. and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48–51 kcal mol-1 lower in energy, formed via 1,3- cycloaddition of .CH2OO. across the CQO bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O–O bond to form hydroxyalkyl esters. These hydroxyalkylmore » esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO o CH3CHO o CH3COCH3 (the highest yield being 10-4 times lower than the initial .CH2OO. concentration). At low pressures, chemically activated formation of organic acids (formic acid in the case of HCHO and CH3COCH3, formic and acetic acid in the case of CH3CHO) was found to be the major product channel in agreement with recent direct measurements. Collisional energy transfer parameters and the barrier heights for SOZ reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.« less

Energy partitioning in polyatomic chemical reactions: Quantum state resolved studies of highly exothermic atom abstraction reactions from molecules in the gas phase and at the gas-liquid interface

NASA Astrophysics Data System (ADS)

Zolot, Alexander M.

This thesis recounts a series of experiments that interrogate the dynamics of elementary chemical reactions using quantum state resolved measurements of gas-phase products. The gas-phase reactions F + HCl → HF + Cl and F + H2O → HF + OH are studied using crossed supersonic jets under single collision conditions. Infrared (IR) laser absorption probes HF product with near shot-noise limited sensitivity and high resolution, capable of resolving rovibrational states and Doppler lineshapes. Both reactions yield inverted vibrational populations. For the HCl reaction, strongly bimodal rotational distributions are observed, suggesting microscopic branching of the reaction mechanism. Alternatively, such structure may result from a quantum-resonance mediated reaction similar to those found in the well-characterized F + HD system. For the H2O reaction, a small, but significant, branching into v = 2 is particularly remarkable because this manifold is accessible only via the additional center of mass collision energy in the crossed jets. Rotationally hyperthermal HF is also observed. Ab initio calculations of the transition state geometry suggest mechanisms for both rotational and vibrational excitation. Exothermic chemical reaction dynamics at the gas-liquid interface have been investigated by colliding a supersonic jet of F atoms with liquid squalane (C30H62), a low vapor pressure hydrocarbon compatible with the high vacuum environment. IR spectroscopy provides absolute HF( v,J) product densities and Doppler resolved velocity component distributions perpendicular to the surface normal. Compared to analogous gas-phase F + hydrocarbon reactions, the liquid surface is a more effective "heat sink," yet vibrationally excited populations reveal incomplete thermal accommodation with the surface. Non-Boltzmann J-state populations and hot Doppler lineshapes that broaden with HF excitation indicate two competing scattering mechanisms: (i) a direct reactive scattering channel

Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas.

NASA Astrophysics Data System (ADS)

Hippler, Rainer; Majumdar, Abhijit; Thejaswini, H. C.

Plasma chemical reaction studies with relevance to, e.g., Titan's atmosphere have been per-formed in various laboratory plasmas [1,2]. Chemical reactions in a dielectric barrier discharge at medium pressure of 250-300 mbar have been studied in CH4 /N2 and CH4 /Ar gas mixtures by means of mass spectrometry. The main reaction scheme is production of H2 by fragmenta-tion of CH4 , but also production of larger hydrocarbons like Cn Hm with n up to 10 including formation of different functional CN groups is observed. [1] A. Majumdar and R. Hippler, Development of dielectric barrier discharge plasma processing apparatus for mass spectrometry and thin film deposition, Rev. Sci. Instrum. 78, 075103 (2007) [2] H.T. Do, G. Thieme, M. Frühlich, H. Kersten, and R. Hippler, Ion Molecule and Dust Particle Formation in Ar/CH4 , Ar/C2 H2 and Ar/C3 H6 Radio-frequency Plasmas, Contrib. Plasma Phys. 45, No. 5-6, 378-384 (2005)

Room-temperature and temperature-dependent QSRR modelling for predicting the nitrate radical reaction rate constants of organic chemicals using ensemble learning methods.

PubMed

Gupta, S; Basant, N; Mohan, D; Singh, K P

2016-07-01

Experimental determinations of the rate constants of the reaction of NO3 with a large number of organic chemicals are tedious, and time and resource intensive; and the development of computational methods has widely been advocated. In this study, we have developed room-temperature (298 K) and temperature-dependent quantitative structure-reactivity relationship (QSRR) models based on the ensemble learning approaches (decision tree forest (DTF) and decision treeboost (DTB)) for predicting the rate constant of the reaction of NO3 radicals with diverse organic chemicals, under OECD guidelines. Predictive powers of the developed models were established in terms of statistical coefficients. In the test phase, the QSRR models yielded a correlation (r(2)) of >0.94 between experimental and predicted rate constants. The applicability domains of the constructed models were determined. An attempt has been made to provide the mechanistic interpretation of the selected features for QSRR development. The proposed QSRR models outperformed the previous reports, and the temperature-dependent models offered a much wider applicability domain. This is the first report presenting a temperature-dependent QSRR model for predicting the nitrate radical reaction rate constant at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards NO3 radicals in the atmosphere, hence, their persistence and exposure risk assessment.

Inflow, Outflow, Yields, and Stellar Population Mixing in Chemical Evolution Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrews, Brett H.; Weinberg, David H.; Schönrich, Ralph

Chemical evolution models are powerful tools for interpreting stellar abundance surveys and understanding galaxy evolution. However, their predictions depend heavily on the treatment of inflow, outflow, star formation efficiency (SFE), the stellar initial mass function, the SN Ia delay time distribution, stellar yields, and stellar population mixing. Using flexCE, a flexible one-zone chemical evolution code, we investigate the effects of and trade-offs between parameters. Two critical parameters are SFE and the outflow mass-loading parameter, which shift the knee in [O/Fe]–[Fe/H] and the equilibrium abundances that the simulations asymptotically approach, respectively. One-zone models with simple star formation histories follow narrow tracksmore » in [O/Fe]–[Fe/H] unlike the observed bimodality (separate high- α and low- α sequences) in this plane. A mix of one-zone models with inflow timescale and outflow mass-loading parameter variations, motivated by the inside-out galaxy formation scenario with radial mixing, reproduces the two sequences better than a one-zone model with two infall epochs. We present [X/Fe]–[Fe/H] tracks for 20 elements assuming three different supernova yield models and find some significant discrepancies with solar neighborhood observations, especially for elements with strongly metallicity-dependent yields. We apply principal component abundance analysis to the simulations and existing data to reveal the main correlations among abundances and quantify their contributions to variation in abundance space. For the stellar population mixing scenario, the abundances of α -elements and elements with metallicity-dependent yields dominate the first and second principal components, respectively, and collectively explain 99% of the variance in the model. flexCE is a python package available at https://github.com/bretthandrews/flexCE.« less

Chemical Exchange Saturation Transfer in Chemical Reactions: A Mechanistic Tool for NMR Detection and Characterization of Transient Intermediates.

PubMed

Lokesh, N; Seegerer, Andreas; Hioe, Johnny; Gschwind, Ruth M

2018-02-07

The low sensitivity of NMR and transient key intermediates below detection limit are the central problems studying reaction mechanisms by NMR. Sensitivity can be enhanced by hyperpolarization techniques such as dynamic nuclear polarization or the incorporation/interaction of special hyperpolarized molecules. However, all of these techniques require special equipment, are restricted to selective reactions, or undesirably influence the reaction pathways. Here, we apply the chemical exchange saturation transfer (CEST) technique for the first time to NMR detect and characterize previously unobserved transient reaction intermediates in organocatalysis. The higher sensitivity of CEST and chemical equilibria present in the reaction pathway are exploited to access population and kinetics information on low populated intermediates. The potential of the method is demonstrated on the proline-catalyzed enamine formation for unprecedented in situ detection of a DPU stabilized zwitterionic iminium species, the elusive key intermediate between enamine and oxazolidinones. The quantitative analysis of CEST data at 250 K revealed the population ratio of [Z-iminium]/[exo-oxazolidinone] 0.02, relative free energy +8.1 kJ/mol (calculated +7.3 kJ/mol), and free energy barrier of +45.9 kJ/mol (ΔG ⧧ calc. (268 K) = +42.2 kJ/mol) for Z-iminium → exo-oxazolidinone. The findings underpin the iminium ion participation in enamine formation pathway corroborating our earlier theoretical prediction and help in better understanding. The reliability of CEST is validated using 1D EXSY-build-up techniques at low temperature (213 K). The CEST method thus serves as a new tool for mechanistic investigations in organocatalysis to access key information, such as chemical shifts, populations, and reaction kinetics of intermediates below the standard NMR detection limit.

Balanced Biochemical Reactions: A New Approach to Unify Chemical and Biochemical Thermodynamics

PubMed Central

Sabatini, Antonio; Vacca, Alberto; Iotti, Stefano

2012-01-01

A novel procedure is presented which, by balancing elements and electric charge of biochemical reactions which occur at constant pH and pMg, allows assessing the thermodynamics properties of reaction ΔrG ′0, ΔrH ′0, ΔrS ′0 and the change in binding of hydrogen and magnesium ions of these reactions. This procedure of general applicability avoids the complex calculations required by the use of the Legendre transformed thermodynamic properties of formation ΔfG ′0, ΔfH ′0 and ΔfS ′0 hitherto considered an obligatory prerequisite to deal with the thermodynamics of biochemical reactions. As a consequence, the term “conditional” is proposed in substitution of “Legendre transformed” to indicate these thermodynamics properties. It is also shown that the thermodynamic potential G is fully adequate to give a criterion of spontaneous chemical change for all biochemical reactions and then that the use of the Legendre transformed G′ is unnecessary. The procedure proposed can be applied to any biochemical reaction, making possible to re-unify the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately. PMID:22247780

On the deduction of chemical reaction pathways from measurements of time series of concentrations.

PubMed

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.

Reacting gas mixtures in the state-to-state approach: The chemical reaction rates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kustova, Elena V.; Kremer, Gilberto M.

2014-12-09

In this work chemically reacting mixtures of viscous flows are analyzed within the framework of Boltzmann equation. By applying a modified Chapman-Enskog method to the system of Boltzmann equations general expressions for the rates of chemical reactions and vibrational energy transitions are determined as functions of two thermodynamic forces: the velocity divergence and the affinity. As an application chemically reacting mixtures of N{sub 2} across a shock wave are studied, where the first lowest vibrational states are taken into account. Here we consider only the contributions from the first four single quantum vibrational-translational energy transitions. It is shown that themore » contribution to the chemical reaction rate related to the affinity is much larger than that of the velocity divergence.« less

Organocatalytic sequential α-amination/Corey-Chaykovsky reaction of aldehydes: a high yield synthesis of 4-hydroxypyrazolidine derivatives.

PubMed

Kumar, B Senthil; Venkataramasubramanian, V; Sudalai, Arumugam

2012-05-18

A tandem reaction of in situ generated α-amino aldehydes with dimethyloxosulfonium methylide under Corey-Chaykovsky reaction conditions proceeds efficiently to give 4-hydroxypyrazolidine derivatives in high yields with excellent enantio- and diastereoselectivities. This organocatalytic sequential method provides for the efficient synthesis of anti-1,2-aminoalcohols, structural subunits present in several bioactive molecules as well.

LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

The Role of Electronic Excitations on Chemical Reaction Dynamics at Metal, Semiconductor and Nanoparticle Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tully, John C.

Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opensmore » up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.« less

Thin liquid films with time-dependent chemical reactions sheared by an ambient gas flow

NASA Astrophysics Data System (ADS)

Bender, Achim; Stephan, Peter; Gambaryan-Roisman, Tatiana

2017-08-01

Chemical reactions in thin liquid films are found in many industrial applications, e.g., in combustion chambers of internal combustion engines where a fuel film can develop on pistons or cylinder walls. The reactions within the film and the turbulent outer gas flow influence film stability and lead to film breakup, which in turn can lead to deposit formation. In this work we examine the evolution and stability of a thin liquid film in the presence of a first-order chemical reaction and under the influence of a turbulent gas flow. Long-wave theory with a double perturbation analysis is used to reduce the complexity of the problem and obtain an evolution equation for the film thickness. The chemical reaction is assumed to be slow compared to film evolution and the amount of reactant in the film is limited, which means that the reaction rate decreases with time as the reactant is consumed. A linear stability analysis is performed to identify the influence of reaction parameters, material properties, and environmental conditions on the film stability limits. Results indicate that exothermic reactions have a stabilizing effect whereas endothermic reactions destabilize the film and can lead to rupture. It is shown that an initially unstable film can become stable with time as the reaction rate decreases. The shearing of the film by the external gas flow leads to the appearance of traveling waves. The shear stress magnitude has a nonmonotonic influence on film stability.

THE GAS PHASE REACTION OF OZONE WITH 1,3-BUTADIENE: FORMATION YIELDS OF SOME TOXIC PRODUCTS. (R826236)

EPA Science Inventory

The formation yields of acrolein, 1,2-epoxy-3-butene and OH radicals have been measured from reaction of ozone with 1,3-butadiene at room temperature and atmosphere pressure. 1,3,5-Trimethyl benzene was added to scavenge OH radicals in measurements of product yields. In separa...

Estimating the effective rate of fast chemical reactions with turbulent mixing of reactants

NASA Astrophysics Data System (ADS)

Vorotilin, V. P.; Yanovskii, Yu. G.

2015-07-01

On the basis of representation of a turbulent fluid as an aggregation of independent turbulent particles (vortexes), we derive relations for the effective rate of chemical reactions and obtain a closed system of equations describing reactions with turbulent mixing of reactants. A variant of instantaneous reactions is considered that explains the proposed approach simply. In particular, the turbulent mixing events according to this approach are uniquely related to the acts of chemical interaction, which makes it possible to exclude from consideration the mixing of inert impurities-the most difficult point of the theory formulated using classical notions. The obtained system of equations is closed without introducing arbitrarily adopted correlations, by naturally introducing the concept of effective reaction and writing the equations of conservation for both the concentrations of reactants and their volumes.

The Scales Of Chemical Transport During Dehydration Reactions: The Roles Of Diffusion And Fluid Expulsion

NASA Astrophysics Data System (ADS)

Bedford, J. D.; Wheeler, J.; Fusseis, F.; Leclere, H.; Faulkner, D.

2016-12-01

The growth of new minerals in response to disequilibrium is the most fundamental metamorphic process. However, the kinetics controls on metamorphic reactions, including the transport of chemical components to growing minerals, are poorly understood as direct observation has been impossible both in nature and experiments. Dehydration reactions are common during prograde metamorphism and require both the expulsion of H2O and the transport of solid chemical components to the product mineral(s) in order for reaction to proceed. The expulsion of H2O is particularly important in understanding when fluid overpressures might develop, which can in turn lead to sudden failure (earthquakes) if the fluid is unable to drain. Using time-resolved (4D) synchrotron X-ray microtomography we have imaged a complete dehydration reaction and show how chemical transport of both the solid and fluid phases evolves during reaction. The reaction analysed is the dehydration of gypsum to form bassanite and H2O - an analogue for silicate dehydration but with much faster and controllable reaction rate. Like most dehydration reactions, the breakdown of gypsum is associated with a solid volume reduction which generates pore space. This new porosity wraps around growing bassanite grains, producing fluid-filled moats, across which transport of dissolved solutes to the growing grains occurs via diffusion. As moats grow in width, diffusion and hence reaction rate slow down. Each new grain-moat pair evolves in relative isolation from each other indicating that the chemical transport of solid components occurs over relatively short distances. This is despite the overall pore network becoming connected during the early stages of reaction, thus allowing efficient expulsion of excess H2O. A dehydrating system can therefore act as an open system with respect to the fluid phase and in contrast be restricted to the grain-scale with respect to the dissolved chemicals. This is in accord with observations that

Lattice based Kinetic Monte Carlo Simulations of a complex chemical reaction network

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Savara, Aditya; Hin, Celine

Lattice Kinetic Monte Carlo (KMC) simulations offer a powerful alternative to using ordinary differential equations for the simulation of complex chemical reaction networks. Lattice KMC provides the ability to account for local spatial configurations of species in the reaction network, resulting in a more detailed description of the reaction pathway. In KMC simulations with a large number of reactions, the range of transition probabilities can span many orders of magnitude, creating subsets of processes that occur more frequently or more rarely. Consequently, processes that have a high probability of occurring may be selected repeatedly without actually progressing the system (i.e. the forward and reverse process for the same reaction). In order to avoid the repeated occurrence of fast frivolous processes, it is necessary to throttle the transition probabilities in such a way that avoids altering the overall selectivity. Likewise, as the reaction progresses, new frequently occurring species and reactions may be introduced, making a dynamic throttling algorithm a necessity. We present a dynamic steady-state detection scheme with the goal of accurately throttling rate constants in order to optimize the KMC run time without compromising the selectivity of the reaction network. The algorithm has been applied to a large catalytic chemical reaction network, specifically that of methanol oxidative dehydrogenation, as well as additional pathways on CeO2(111) resulting in formaldehyde, CO, methanol, CO2, H2 and H2O as gas products.

Will water act as a photocatalyst for cluster phase chemical reactions? Vibrational overtone-induced dehydration reaction of methanediol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kramer, Zeb C.; Takahashi, Kaito; Skodje, Rex T.

2012-04-28

The possibility of water catalysis in the vibrational overtone-induced dehydration reaction of methanediol is investigated using ab initio dynamical simulations of small methanediol-water clusters. Quantum chemistry calculations employing clusters with one or two water molecules reveal that the barrier to dehydration is lowered by over 20 kcal/mol because of hydrogen-bonding at the transition state. Nevertheless, the simulations of the reaction dynamics following OH-stretch excitation show little catalytic effect of water and, in some cases, even show an anticatalytic effect. The quantum yield for the dehydration reaction exhibits a delayed threshold effect where reaction does not occur until the photon energymore » is far above the barrier energy. Unlike thermally induced reactions, it is argued that competition between reaction and the irreversible dissipation of photon energy may be expected to raise the dynamical threshold for the reaction above the transition state energy. It is concluded that quantum chemistry calculations showing barrier lowering are not sufficient to infer water catalysis in photochemical reactions, which instead require dynamical modeling.« less

Measurement of Quantum Yield, Quantum Requirement, and Energetic Efficiency of the O2-Evolving System of Photosynthesis by a Simple Dye Reaction

NASA Astrophysics Data System (ADS)

Ros Barcelò, A.; Zapata, J. M.

1996-11-01

Photosynthesis is the conversion of absorbed radiant energy from sunlight into various forms of chemical energy by the chloroplasts of higher green plants. The overall process of photosynthesis consists of the oxidation of water (with the release of O2 as a product) and the reduction of CO2 to form carbohydrates. In the test tube electrons produced by the photolytic cleavage of H2) may be deviated from their true acceptor by inserting a suitable dye in the electron chain; i.e.; 2,6-dichlorophenol indophenol (DCPIP) (E'o = + 0.217 V), which is blue in the oxidized quinone form and which becomes colorless when reduced to the phenolic form. This dye-electrom acceptor also has the advantage that it accepts electroms directly from the quinone (Qa) electron-acceptor of the photosystem II< the reaction center associated with the O2-evolving (or water-slplitting) system. Based in the bleaching of DCPIP by illuminated spinach leaf chloroplasts, a classroom laboratory protocol has been developed to determine the quantum yield (QY = micromol O2 s-1 / micromol photons s-1, the quantum requirement (1/QY) and the energetic efficiency (f = chemical energy stored / light energy supplied) of the O2-evolving system of photosynthesis. Although values for the quantum yield, the quantum requirement and the energetic efficiency calculated in the classroom laboratory differ widely from those expected theoretically, these calculations are useful for illustrating the transformation of light energy into chemical energy by the chloroplasts of green plants.

Chemical and thermal stability of N-heterocyclic ionic liquids in catalytic C-H activation reactions.

PubMed

Chen, Guanyi; Kang, Shujuan; Ma, Qisheng; Chen, Weiqun; Tang, Yongchun

2014-11-01

(1)H-NMR spectrum analyses are applied to study the chemical and thermal stability of selected N-heterocyclic ionic liquids within the reaction system that can highly efficiently activate a C-H bond of methane and convert it into the C-O bond in methanol. Our results indicate that under such reaction conditions involving using a powerful Pt-based catalyst and strong acidic solvent, the aromatic ring of an imidazolium cation becomes unstable generating an ammonium ion (NH(4)(+)). Our results also suggest that the instability of the imidazolium ring is more chemically (participation in reactions) than thermally based. Modifications of the aromatic ring structure such as pyrazolium and triazolium cations can increase the chemical/thermal stability of ionic liquids under these reaction conditions. Copyright © 2014 John Wiley & Sons, Ltd.

Implementation of a vibrationally linked chemical reaction model for DSMC

NASA Technical Reports Server (NTRS)

Carlson, A. B.; Bird, Graeme A.

1994-01-01

A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.

Mapping the dark space of chemical reactions with extended nanomole synthesis and MALDI-TOF MS.

PubMed

Lin, Shishi; Dikler, Sergei; Blincoe, William D; Ferguson, Ronald D; Sheridan, Robert P; Peng, Zhengwei; Conway, Donald V; Zawatzky, Kerstin; Wang, Heather; Cernak, Tim; Davies, Ian W; DiRocco, Daniel A; Sheng, Huaming; Welch, Christopher J; Dreher, Spencer D

2018-05-24

Understanding the practical limitations of chemical reactions is critically important for efficiently planning the synthesis of compounds in pharmaceutical, agrochemical and specialty chemical research and development. However, literature reports of the scope of new reactions are often cursory and biased toward successful results, severely limiting the ability to predict reaction outcomes for untested substrates. We herein illustrate strategies for carrying out large scale surveys of chemical reactivity using a material-sparing nanomole-scale automated synthesis platform with greatly expanded synthetic scope combined with ultra-high throughput (uHT) matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Copyright © 2018, American Association for the Advancement of Science.

High yield of secondary B-side electron transfer in mutant Rhodobacter capsulatus reaction centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kressel, Lucas; Faries, Kaitlyn M.; Wander, Marc J.

2014-08-01

From the crystal structures of reaction centers (RCs) from purple photosynthetic bacteria, two pathways for electron transfer (ET) are apparent but only one pathway (the A side) operates in the native protein-cofactor complex. Partial activation of the B-side pathway has unveiled the true inefficiencies of ET processes on that side in comparison to analogous reactions on the A side. Of significance are the relative rate constants for forward ET and the competing charge recombination reactions. On the B side, these rate constants are nearly equal for the secondary charge-separation step (ET from bacteriopheophytin to quinone), relegating the yield of thismore » process to < 50%. Herein we report efforts to optimize this step. In surveying all possible residues at position 131 in the M subunit, we discovered that when glutamic acid replaces the native valine the efficiency of the secondary ET is nearly two-fold higher than in the wild-type RC. The positive effect of M131 Glu is likely due to formation of a hydrogen bond with the ring V keto group of the B-side bacteriopheophytin leading to stabilization of the charge-separated state involving this cofactor. In conclusion, this change slows charge recombination by roughly a factor of two and affords the improved yield of the desired forward ET to the B-side quinone terminal acceptor.« less

Introducing Stochastic Simulation of Chemical Reactions Using the Gillespie Algorithm and MATLAB: Revisited and Augmented

ERIC Educational Resources Information Center

Argoti, A.; Fan, L. T.; Cruz, J.; Chou, S. T.

2008-01-01

The stochastic simulation of chemical reactions, specifically, a simple reversible chemical reaction obeying the first-order, i.e., linear, rate law, has been presented by Martinez-Urreaga and his collaborators in this journal. The current contribution is intended to complement and augment their work in two aspects. First, the simple reversible…

Mapping Students' Conceptual Modes When Thinking about Chemical Reactions Used to Make a Desired Product

ERIC Educational Resources Information Center

Weinrich, M. L.; Talanquer, V.

2015-01-01

The central goal of this qualitative research study was to uncover major implicit assumptions that students with different levels of training in the discipline apply when thinking and making decisions about chemical reactions used to make a desired product. In particular, we elicited different ways of conceptualizing why chemical reactions happen…

A spectroscopist's view of energy states, energy transfers, and chemical reactions.

PubMed

Moore, C Bradley

2007-01-01

This chapter describes a research career beginning at Berkeley in 1960, shortly after Sputnik and the invention of the laser. Following thesis work on vibrational spectroscopy and the chemical reactivity of small molecules, we studied vibrational energy transfers in my own lab. Collision-induced transfers among vibrations of a single molecule, from one molecule to another, and from vibration to rotation and translation were elucidated. My research group also studied the competition between vibrational relaxation and chemical reaction for potentially reactive collisions with one molecule vibrationally excited. Lasers were used to enrich isotopes by the excitation of a predissociative transition of a selected isotopomer. We also tested the hypotheses of transition-state theory for unimolecular reactions of ketene, formaldehyde, and formyl fluoride by (a) resolving individual molecular eigenstates above a dissociation threshold, (b) locating vibrational levels at the transition state, (c) observing quantum resonances in the barrier region for motion along a reaction coordinate, and (d) studying energy release to fragments.

A Time-Dependent Quantum Dynamics Study of the H2 + CH3 yields H + CH4 Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Kwak, Dochan (Technical Monitor)

2002-01-01

We present a time-dependent wave-packet propagation calculation for the H2 + CH3 yields H + CH4 reaction in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probability for different initial rotational-vibrational states are presented in this study. The cumulative reaction probability (CRP) is obtained by summing over initial-state-selected reaction probability. The energy-shift approximation to account for the contribution of degrees of freedom missing in the 6D calculation is employed to obtain an approximate full-dimensional CRP. Thermal rate constant is compared with different experiment results.

Chemical reaction CO+OH • → CO 2+H • autocatalyzed by carbon dioxide: Quantum chemical study of the potential energy surfaces

DOE PAGES

Masunov, Artem E.; Wait, Elizabeth; Vasu, Subith S.

2016-06-28

The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO 2 molecule. While spectator molecule alter the activation barrier only slightly, the covalent bonding opens a new reaction pathway. The mechanism includes sequential covalent binding of CO 2 to OH radical and CO molecule, hydrogen transfer frommore » oxygen to carbon atoms, and CH bond dissociation. This reduces the activation barrier by 11 kcal/mol at the rate-determining step and is expected to accelerate the reaction rate. The finding of predicted catalytic effect is expected to play an important role not only in combustion but also in a broad array of chemical processes taking place in supercritical CO 2 medium. Furthermore, tt may open a new venue for controlling reaction rates for chemical manufacturing.« less

Inverse electron demand Diels-Alder reactions in chemical biology.

PubMed

Oliveira, B L; Guo, Z; Bernardes, G J L

2017-08-14

The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.

Localized temperature and chemical reaction control in nanoscale space by nanowire array.

PubMed

Jin, C Yan; Li, Zhiyong; Williams, R Stanley; Lee, K-Cheol; Park, Inkyu

2011-11-09

We introduce a novel method for chemical reaction control with nanoscale spatial resolution based on localized heating by using a well-aligned nanowire array. Numerical and experimental analysis shows that each individual nanowire could be selectively and rapidly Joule heated for local and ultrafast temperature modulation in nanoscale space (e.g., maximum temperature gradient 2.2 K/nm at the nanowire edge; heating/cooling time < 2 μs). By taking advantage of this capability, several nanoscale chemical reactions such as polymer decomposition/cross-linking and direct and localized hydrothermal synthesis of metal oxide nanowires were demonstrated.

Non-invasive estimation of dissipation from non-equilibrium fluctuations in chemical reactions.

PubMed

Muy, S; Kundu, A; Lacoste, D

2013-09-28

We show how to extract an estimate of the entropy production from a sufficiently long time series of stationary fluctuations of chemical reactions. This method, which is based on recent work on fluctuation theorems, is direct, non-invasive, does not require any knowledge about the underlying dynamics and is applicable even when only partial information is available. We apply it to simple stochastic models of chemical reactions involving a finite number of states, and for this case, we study how the estimate of dissipation is affected by the degree of coarse-graining present in the input data.

Radiation-Induced Chemical Reactions in Hydrogel of Hydroxypropyl Cellulose (HPC): A Pulse Radiolysis Study.

PubMed

Yamashita, Shinichi; Ma, Jun; Marignier, Jean-Louis; Hiroki, Akihiro; Taguchi, Mitsumasa; Mostafavi, Mehran; Katsumura, Yosuke

2016-12-01

We performed studies on pulse radiolysis of highly transparent and shape-stable hydrogels of hydroxypropyl cellulose (HPC) that were prepared using a radiation-crosslinking technique. Several fundamental aspects of radiation-induced chemical reactions in the hydrogels were investigated. With radiation doses less than 1 kGy, degradation of the HPC matrix was not observed. The rate constants of the HPC composing the matrix, with two water decomposition radicals [hydroxyl radical ( • OH) and hydrated electron ([Formula: see text])] in the gels, were determined to be 4.5 × 10 9 and 1.8 × 10 7 M -1 s -1 , respectively. Direct ionization of HPC in the matrix slightly increased the initial yield of [Formula: see text], but the additionally produced amount of [Formula: see text] disappeared immediately within 200 ps, indicating fast recombination of [Formula: see text] with hole radicals on HPC or on surrounding hydration water molecules. Reactions of [Formula: see text] with nitrous oxide (N 2 O) and nitromethane (CH 3 NO 2 ) were also examined. Decay of [Formula: see text] due to scavenging by N 2 O and CH 3 NO 2 were both slower in hydrogels than in aqueous solutions, showing slower diffusions of the reactants in the gel matrix. The degree of decrease in the decay rate was more effective for N 2 O than for CH 3 NO 2 , revealing lower solubility of N 2 O in gel than in water. It is known that in viscous solvents, such as ethylene glycol, CH 3 NO 2 exhibits a transient effect, which is a fast reaction over the contact distance of reactants and occurs without diffusions of reactants. However, such an effect was not observed in the hydrogel used in the current study. In addition, the initial yield of [Formula: see text], which is affected by the amount of the scavenged precursor of [Formula: see text], in hydrogel containing N 2 O was slightly higher than that in water containing N 2 O, and the same tendency was found for CH 3 NO 2 .

Fission Reaction Event Yield Algorithm FREYA 2.0.2

DOE PAGES

Verbeke, J. M.; Randrup, J.; Vogt, R.

2017-09-01

The purpose of this paper is to present the main differences between FREYA versions 1.0 and 2.0.2. FREYA (Fission Reaction Event Yield Algorithm) is a fission event generator which models complete fission events. As such, it automatically includes fluctuations as well as correlations between observables, resulting from conservation of energy and momentum. The main differences between the two versions are: additional fissionable isotopes, angular momentum conservation, Giant Dipole Resonance form factor for the statistical emission of photons, improved treatment of fission photon emission using RIPL database, and dependence on the incident neutron direction. FREYA 2.0.2 has been integrated into themore » LLNL Fission Library 2.0.2, which has itself been integrated into MCNP6.2, TRIPOLI-4.10, and can be called from Geant4.10.« less

Chemical repair activity of free radical scavenger edaravone: reduction reactions with dGMP hydroxyl radical adducts and suppression of base lesions and AP sites on irradiated plasmid DNA.

PubMed

Hata, Kuniki; Urushibara, Ayumi; Yamashita, Shinichi; Lin, Mingzhang; Muroya, Yusa; Shikazono, Naoya; Yokoya, Akinari; Fu, Haiying; Katsumura, Yosuke

2015-01-01

Reactions of edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one) with deoxyguanosine monophosphate (dGMP) hydroxyl radical adducts were investigated by pulse radiolysis technique. Edaravone was found to reduce the dGMP hydroxyl radical adducts through electron transfer reactions. The rate constants of the reactions were greater than 4 × 10(8) dm(3) mol(-1) s(-1) and similar to those of the reactions of ascorbic acid, which is a representative antioxidant. Yields of single-strand breaks, base lesions, and abasic sites produced in pUC18 plasmid DNA by gamma ray irradiation in the presence of low concentrations (10-1000 μmol dm(-3)) of edaravone were also quantified, and the chemical repair activity of edaravone was estimated by a method recently developed by the authors. By comparing suppression efficiencies to the induction of each DNA lesion, it was found that base lesions and abasic sites were suppressed by the chemical repair activity of edaravone, although the suppression of single-strand breaks was not very effective. This phenomenon was attributed to the chemical repair activity of edaravone toward base lesions and abasic sites. However, the chemical repair activity of edaravone for base lesions was lower than that of ascorbic acid. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Scrap tyre pyrolysis: Modified chemical percolation devolatilization (M-CPD) to describe the influence of pyrolysis conditions on product yields.

PubMed

Tan, Vincent; De Girolamo, Anthony; Hosseini, Tahereh; Alhesan, Jameel Aljariri; Zhang, Lian

2018-03-16

This paper attempts to develop a modified chemical percolation devolatilization (M-CPD) model that can include heat transfer, primary pyrolysis and the secondary cracking reactions of volatiles together to describe the pyrolysis of waste scrap tyre chip, as well as to examine the influence of operating conditions on the scrap tyre pyrolysis product yields. Such a study has yet to be conducted in the past, thereby leading to a large knowledge gap failing to understand the pyrolysis of the coarse feedstock appropriately. To validate the developed model, a number of operating parameters including reactor configurations, carrier gas compositions (argon and argon blended with CO 2 and/or steam), scrap tyre chip size (0.5-15.0 mm), terminal pyrolysis temperature (400-800 °C) and heating rate (10 °C/min and 110 °C/min) were examined in a lab-scale fixed-bed pyrolyser, with a particular focus on the secondary cracking extents of the liquid tar. Through both experimental investigation and modelling approach, it was found that significant secondary cracking extent occurred upon the increase in the feedstock size, heating rate and residence time. Upon the fast pyrolysis, the average temperature gap between the centres of the coarse particle and reactor wall could reach a maximum of 115 °C for the tyre chips of 6-15 mm. Consequently, its primary volatiles underwent the secondary cracking reaction at an overall extent of 17% at a terminal temperature of 600 °C and a fast heating rate of 110 °C/min. Consequently, the yield of light gases including methane was increased remarkably. The flow rate of inert carrier gas was also influential in the secondary cracking, in which a maximum tar yield (54 wt%) was reached at a carrier gas flow rate of 1.5  L/min. This indicates the occurrence of secondary cracking has been largely minimised. At a pyrolysis temperature of 600 °C, the addition of CO 2 in the carrier gas had an insignificant effect on the product

Monitoring chemical reactions by low-field benchtop NMR at 45 MHz: pros and cons.

PubMed

Silva Elipe, Maria Victoria; Milburn, Robert R

2016-06-01

Monitoring chemical reactions is the key to controlling chemical processes where NMR can provide support. High-field NMR gives detailed structural information on chemical compounds and reactions; however, it is expensive and complex to operate. Conversely, low-field NMR instruments are simple and relatively inexpensive alternatives. While low-field NMR does not provide the detailed information as the high-field instruments as a result of their smaller chemical shift dispersion and the complex secondary coupling, it remains of practical value as a process analytical technology (PAT) tool and is complimentary to other established methods, such as ReactIR and Raman spectroscopy. We have tested a picoSpin-45 (currently under ThermoFisher Scientific) benchtop NMR instrument to monitor three types of reactions by 1D (1) H NMR: a Fischer esterification, a Suzuki cross-coupling, and the formation of an oxime. The Fischer esterification is a relatively simple reaction run at high concentration and served as proof of concept. The Suzuki coupling is an example of a more complex, commonly used reaction involving overlapping signals. Finally, the oxime formation involved a reaction in two phases that cannot be monitored by other PAT tools. Here, we discuss the pros and cons of monitoring these reactions at a low-field of 45 MHz by 1D (1) H NMR. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions.

PubMed

Salis, Howard; Kaznessis, Yiannis

2005-02-01

The dynamical solution of a well-mixed, nonlinear stochastic chemical kinetic system, described by the Master equation, may be exactly computed using the stochastic simulation algorithm. However, because the computational cost scales with the number of reaction occurrences, systems with one or more "fast" reactions become costly to simulate. This paper describes a hybrid stochastic method that partitions the system into subsets of fast and slow reactions, approximates the fast reactions as a continuous Markov process, using a chemical Langevin equation, and accurately describes the slow dynamics using the integral form of the "Next Reaction" variant of the stochastic simulation algorithm. The key innovation of this method is its mechanism of efficiently monitoring the occurrences of slow, discrete events while simultaneously simulating the dynamics of a continuous, stochastic or deterministic process. In addition, by introducing an approximation in which multiple slow reactions may occur within a time step of the numerical integration of the chemical Langevin equation, the hybrid stochastic method performs much faster with only a marginal decrease in accuracy. Multiple examples, including a biological pulse generator and a large-scale system benchmark, are simulated using the exact and proposed hybrid methods as well as, for comparison, a previous hybrid stochastic method. Probability distributions of the solutions are compared and the weak errors of the first two moments are computed. In general, these hybrid methods may be applied to the simulation of the dynamics of a system described by stochastic differential, ordinary differential, and Master equations.

Laboratory measurements. [chemical and photochemical data relative to stratospheric modeling

NASA Technical Reports Server (NTRS)

1977-01-01

A compilation of chemical and photochemical data that are relevant to stratospheric modeling is presented. There are three broad categories of data: (1) rate constants for chemical reactions, including temperature and pressure dependencies along with product distributions; (2) absorption cross sections, photodissociation quantum yield, and photolysis; (3) heterogeneous chemical processes.

PDF calculation of scalar mixing layer with simple chemical reactions

NASA Astrophysics Data System (ADS)

Kanzaki, Takao; Pope, Stephen B.

1999-11-01

A joint velocity-composition-turbulent frequency PDF(JPDF) model is used to simulate reactive mixing layer in a grid-generated turbulence with the influence of second-order irreversible chemical reactions. To investigate the effects of molecular mixing, a gas flow and a liquid flow are simulated. For a gas flow, the oxidation reaction (NO+ O3 arrow NO2 +O2 ) between nitricoxide (NO) and ozone (O3 ) is used. For a liquid flow, the saponification reaction(NaOH+HCOOCH3 arrow HCOONa+CH_3OH) between sodiumhydroxide(NaOH) and methylformate(HCOOCH_3) is used. The both cases are moderately fast reactions. Therefore, reactive scalar statistics are affected by turbulent mixing. The results of caliculation are compared with experimental data of Komori et al.(1994) and Bilger et al.(1991)

On-chip isothermal, chemical cycling polymerase chain reaction (ccPCR)

NASA Astrophysics Data System (ADS)

Persat, Alexandre; Santiago, Juan

2008-11-01

We demonstrate a novel ccPCR technique for microfluidic DNA amplification where temperature is held constant in space and time. The polymerase chain reaction is a platform of choice for biological assays and typically based on a three-step thermal cycling: DNA denaturation, primers annealing and extension by an enzyme. We here demonstrate a novel technique where high concentration chemical denaturants (solvents) denature DNA. We leverage the high electrophoretic mobility of DNA and the electrical neutrality of denaturants to achieve chemical cycling. We focus DNA with isotachophoresis (ITP); a robust electrophoretic preconcentration technique which generates strong electric field gradients and protects the sample from dispersion. We apply a pressure-driven flow to balance electromigration velocity and keep the DNA sample stationary in a microchannel. We drive the DNA through a series of high denaturant concentration zones. DNA denatures at high denaturant concentration. At low denaturant concentration, the enzyme creates complementary strands. DNA reaction kinetics are slower than buffer reactions involved in ITP. We demonstrate successful ccPCR amplification for detection of E. Coli. The ccPCR has the potential for simpler chemistry than traditional PCR.

Simulating chemical reactions in ionic liquids using QM/MM methodology.

PubMed

Acevedo, Orlando

2014-12-18

The use of ionic liquids as a reaction medium for chemical reactions has dramatically increased in recent years due in large part to the numerous reported advances in catalysis and organic synthesis. In some extreme cases, ionic liquids have been shown to induce mechanistic changes relative to conventional solvents. Despite the large interest in the solvents, a clear understanding of the molecular factors behind their chemical impact is largely unknown. This feature article reviews our efforts developing and applying mixed quantum and molecular mechanical (QM/MM) methodology to elucidate the microscopic details of how these solvents operate to enhance rates and alter mechanisms for industrially and academically important reactions, e.g., Diels-Alder, Kemp eliminations, nucleophilic aromatic substitutions, and β-eliminations. Explicit solvent representation provided the medium dependence of the activation barriers and atomic-level characterization of the solute-solvent interactions responsible for the experimentally observed "ionic liquid effects". Technical advances are also discussed, including a linear-scaling pairwise electrostatic interaction alternative to Ewald sums, an efficient polynomial fitting method for modeling proton transfers, and the development of a custom ionic liquid OPLS-AA force field.

Monitoring Chemical and Biological Electron Transfer Reactions with a Fluorogenic Vitamin K Analogue Probe.

PubMed

Belzile, Mei-Ni; Godin, Robert; Durantini, Andrés M; Cosa, Gonzalo

2016-12-21

We report herein the design, synthesis, and characterization of a two-segment fluorogenic analogue of vitamin K, B-VK Q , prepared by coupling vitamin K 3 , also known as menadione (a quinone redox center), to a boron-dipyrromethene (BODIPY) fluorophore (a lipophilic reporter segment). Oxidation-reduction reactions, spectroelectrochemical studies, and enzymatic assays conducted in the presence of DT-diaphorase illustrate that the new probe shows reversible redox behavior on par with that of vitamin K, provides a high-sensitivity fluorescence signal, and is compatible with biological conditions, opening the door to monitor remotely (i.e., via imaging) redox processes in real time. In its oxidized form, B-VK Q is non-emissive, while upon reduction to the hydroquinone form, B-VK QH 2 , BODIPY fluorescence is restored, with emission quantum yield values of ca. 0.54 in toluene. Density functional theory studies validate a photoinduced electron transfer intramolecular switching mechanism, active in the non-emissive quinone form and deactivated upon reduction to the emissive dihydroquinone form. Our results highlight the potential of B-VK Q as a fluorogenic probe to study electron transfer and transport in model systems and biological structures with optimal sensitivity and desirable chemical specificity. Use of such a probe may enable a better understanding of the role that vitamin K plays in biological redox reactions ubiquitous in key cellular processes, and help elucidate the mechanism and pathological significance of these reactions in biological systems.

Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

NASA Technical Reports Server (NTRS)

Grodzka, P.; Facemire, B.

1977-01-01

Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

Acid-Base Chemistry According to Robert Boyle: Chemical Reactions in Words as well as Symbols

ERIC Educational Resources Information Center

Goodney, David E.

2006-01-01

Examples of acid-base reactions from Robert Boyle's "The Sceptical Chemist" are used to illustrate the rich information content of chemical equations. Boyle required lengthy passages of florid language to describe the same reaction that can be done quite simply with a chemical equation. Reading or hearing the words, however, enriches the student's…

Time-resolved resonance fluorescence spectroscopy for study of chemical reactions in laser-induced plasmas.

PubMed

Liu, Lei; Deng, Leimin; Fan, Lisha; Huang, Xi; Lu, Yao; Shen, Xiaokang; Jiang, Lan; Silvain, Jean-François; Lu, Yongfeng

2017-10-30

Identification of chemical intermediates and study of chemical reaction pathways and mechanisms in laser-induced plasmas are important for laser-ablated applications. Laser-induced breakdown spectroscopy (LIBS), as a promising spectroscopic technique, is efficient for elemental analyses but can only provide limited information about chemical products in laser-induced plasmas. In this work, time-resolved resonance fluorescence spectroscopy was studied as a promising tool for the study of chemical reactions in laser-induced plasmas. Resonance fluorescence excitation of diatomic aluminum monoxide (AlO) and triatomic dialuminum monoxide (Al 2 O) was used to identify these chemical intermediates. Time-resolved fluorescence spectra of AlO and Al 2 O were used to observe the temporal evolution in laser-induced Al plasmas and to study their formation in the Al-O 2 chemistry in air.

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule.

PubMed

Zheng, Peng; Arantes, Guilherme M; Field, Martin J; Li, Hongbin

2015-06-25

Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule

PubMed Central

Zheng, Peng; Arantes, Guilherme M.; Field, Martin J.; Li, Hongbin

2015-01-01

Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. PMID:26108369

SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents

PubMed Central

Heifets, Abraham; Jurisica, Igor

2012-01-01

The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. We discuss how such information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes. SCRIPDB is available at http://dcv.uhnres.utoronto.ca/SCRIPDB. PMID:22067445

Associated strangeness production in the pp{yields}pK{sup +}K{sup -}p and pp{yields}pK{sup +{pi}0{Sigma}0} reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie Jujun; Department of Physics, Zhengzhou University, Zhengzhou, Henan 450001; Wilkin, Colin

2010-08-15

The total and differential cross sections for associated strangeness production in the pp{yields}pK{sup +}K{sup -}p and pp{yields}pK{sup +{pi}0{Sigma}0} reactions have been studied in a unified approach using an effective Lagrangian model. It is assumed that both the K{sup -}p and {pi}{sup 0{Sigma}0} final states originate from the decay of the {Lambda}(1405) that was formed in the production chain pp{yields}p(N*(1535){yields}K{sup +{Lambda}}(1405)). The available experimental data are well reproduced, especially the ratio of the two total cross sections, which is much less sensitive to the particular model of the entrance channel. The significant coupling of the N*(1535) to {Lambda}(1405)K is further evidencemore » for large ss-bar components in the quark wave function of the N*(1535).« less

Fission fragment yield distribution in the heavy-mass region from the 239Pu (nth,f ) reaction

NASA Astrophysics Data System (ADS)

Gupta, Y. K.; Biswas, D. C.; Serot, O.; Bernard, D.; Litaize, O.; Julien-Laferrière, S.; Chebboubi, A.; Kessedjian, G.; Sage, C.; Blanc, A.; Faust, H.; Köster, U.; Ebran, A.; Mathieu, L.; Letourneau, A.; Materna, T.; Panebianco, S.

2017-07-01

The fission fragment yield distribution has been measured in the 239Pu(nth,f ) reaction in the mass region of A =126 to 150 using the Lohengrin recoil-mass spectrometer. Three independent experimental campaigns were performed, allowing a significant reduction of the uncertainties compared to evaluated nuclear data libraries. The long-standing discrepancy of around 10% for the relative yield of A =134 reported in JEF-2.2 and JEFF-3.1.1 data libraries is finally solved. Moreover, the measured mass distribution in thermal neutron-induced fission does not show any significant dip around the shell closure (A =136 ) as seen in heavy-ion fission data of 208Pb(18O, f ) and 238U(18O, f ) reactions. Lastly, comparisons between our experimental data and the predictions from Monte Carlo codes (gef and fifrelin) are presented and discussed.

Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries.

PubMed

Franzini, Raphael M; Samain, Florent; Abd Elrahman, Maaly; Mikutis, Gediminas; Nauer, Angela; Zimmermann, Mauro; Scheuermann, Jörg; Hall, Jonathan; Neri, Dario

2014-08-20

DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.

Chemical Reactions of Molecules Promoted and Simultaneously Imaged by the Electron Beam in Transmission Electron Microscopy.

PubMed

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

2017-08-15

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

Reaction Paths and Chemical Activation Reactions of 2-Methyl-5-Furanyl Radical with 3O2.

PubMed

Hudzik, Jason M; Bozzelli, Joseph W

2017-10-05

Interest in high-energy substituted furans has been increasing due to their occurrence in biofuel production and their versatility in conversion to other useful products. Methylfurans are the simplest substituted furans and understanding their reaction pathways, thermochemical properties, including intermediate species stability, and chemical kinetics would aid in the study of larger furans. Furan ring C-H bonds have been shown to be extremely strong, approximately 120 kcal mol -1 , due in part to the placement of the oxygen atom and aromatic-like resonance, both within the ring. The thermochemistry and kinetics of the oxidation of 2-methyfuran radical at position 5 of the furan ring, 2-methyl-5-furanyl radical (2MF5j), is analyzed. The resulting chemically activated species, 2MF5OOj radical, has a well depth of 51 kcal mol -1 below the 2MF5j + O 2 reactants; this is 4-5 kcal mol -1 deeper than that of phenyl and vinyl radical plus O 2 , with both of these reactions known to undergo chain branching. Important, low-energy reaction pathways include chain branching dissociations, intramolecular abstractions, group transfers, and radical oxygen additions. Enthalpies of formation, entropies, and heat capacities for the stable molecules, radicals, and transition-state species are analyzed using computational methods. Calculated ΔH ° f 298 values were determined using an isodesmic work reaction from the CBS-QB3 composite method. Elementary rate parameters are from saddle point transition-state structures and compared to variational transition-state analysis for the barrierless reactions. Temperature- and pressure-dependent rate constants which are calculated using QRRK and master equation analysis is used for falloff and stabilization.

Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

PubMed

Suleimanov, Yury V; Green, William H

2015-09-08

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

Chemical Characterization and Reactivity of Fuel-Oxidizer Reaction Product

NASA Technical Reports Server (NTRS)

David, Dennis D.; Dee, Louis A.; Beeson, Harold D.

1997-01-01

Fuel-oxidizer reaction product (FORP), the product of incomplete reaction of monomethylhydrazine and nitrogen tetroxide propellants prepared under laboratory conditions and from firings of Shuttle Reaction Control System thrusters, has been characterized by chemical and thermal analysis. The composition of FORP is variable but falls within a limited range of compositions that depend on three factors: the fuel-oxidizer ratio at the time of formation; whether the composition of the post-formation atmosphere is reducing or oxidizing; and the reaction or post-reaction temperature. A typical composition contains methylhydrazinium nitrate, ammonium nitrate, methylammonium nitrate, and trace amounts of hydrazinium nitrate and 1,1-dimethylhydrazinium nitrate. Thermal decomposition reactions of the FORP compositions used in this study were unremarkable. Neither the various compositions of FORP, the pure major components of FORP, nor mixtures of FORP with propellant system corrosion products showed any unusual thermal activity when decomposed under laboratory conditions. Off-limit thruster operations were simulated by rapid mixing of liquid monomethylhydrazine and liquid nitrogen tetroxide in a confined space. These tests demonstrated that monomethylhydrazine, methylhydrazinium nitrate, ammonium nitrate, or Inconel corrosion products can induce a mixture of monomethylhydrazine and nitrogen tetroxide to produce component-damaging energies. Damaging events required FORP or metal salts to be present at the initial mixing of monomethylhydrazine and nitrogen tetroxide.

Two-Dimensional Resonance Raman Signatures of Vibronic Coherence Transfer in Chemical Reactions.

PubMed

Guo, Zhenkun; Molesky, Brian P; Cheshire, Thomas P; Moran, Andrew M

2017-11-02

Two-dimensional resonance Raman (2DRR) spectroscopy has been developed for studies of photochemical reaction mechanisms and structural heterogeneity in condensed phase systems. 2DRR spectroscopy is motivated by knowledge of non-equilibrium effects that cannot be detected with traditional resonance Raman spectroscopy. For example, 2DRR spectra may reveal correlated distributions of reactant and product geometries in systems that undergo chemical reactions on the femtosecond time scale. Structural heterogeneity in an ensemble may also be reflected in the 2D spectroscopic line shapes of both reactive and non-reactive systems. In this chapter, these capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide. We show that signatures of "vibronic coherence transfer" in the photodissociation process can be targeted with particular 2DRR pulse sequences. Key differences between the signal generation mechanisms for 2DRR and off-resonant 2D Raman spectroscopy techniques are also addressed. Overall, recent experimental developments and applications of the 2DRR method suggest that it will be a valuable tool for elucidating ultrafast chemical reaction mechanisms.

Kinetics of heterogeneous chemical reactions: a theoretical model for the accumulation of pesticides in soil.

PubMed

Lin, S H; Sahai, R; Eyring, H

1971-04-01

A theoretical model for the accumulation of pesticides in soil has been proposed and discussed from the viewpoint of heterogeneous reaction kinetics with a basic aim to understand the complex nature of soil processes relating to the environmental pollution. In the bulk of soil, the pesticide disappears by diffusion and a chemical reaction; the rate processes considered on the surface of soil are diffusion, chemical reaction, vaporization, and regular pesticide application. The differential equations involved have been solved analytically by the Laplace-transform method.

Kinetics of Heterogeneous Chemical Reactions: A Theoretical Model for the Accumulation of Pesticides in Soil

PubMed Central

Lin, S. H.; Sahai, R.; Eyring, H.

1971-01-01

A theoretical model for the accumulation of pesticides in soil has been proposed and discussed from the viewpoint of heterogeneous reaction kinetics with a basic aim to understand the complex nature of soil processes relating to the environmental pollution. In the bulk of soil, the pesticide disappears by diffusion and a chemical reaction; the rate processes considered on the surface of soil are diffusion, chemical reaction, vaporization, and regular pesticide application. The differential equations involved have been solved analytically by the Laplace-transform method. PMID:5279519

Mass Transfer from Gas Bubbles to Impinging Flow of Biological Fluids with Chemical Reaction

PubMed Central

Yang, Wen-Jei; Echigo, R.; Wotton, D. R.; Ou, J. W.; Hwang, J. B.

1972-01-01

The rates of mass transfer from a gas bubble to an impinging flow of a biological fluid such as whole blood and plasma are investigated analytically and experimentally. Gases commonly found dissolved in body fluids are included. Consideration is given to the effects of the chemical reaction between the dissolved gas and the liquid on the rate of mass transfer. Through the application of boundary layer theory the over-all transfer is found to be Sh/(Re)1/2 = 0.845 Sc1/3 in the absence of chemical reaction, and Sh/(Re) 1/2 = F′ (0) in the presence of chemical reaction, where Sh, Re, and Sc are the Sherwood, Reynolds, and Schmidt numbers, respectively, and F′ (0) is a function of Sc and the dimensionless reaction rate constant. Analytical results are also obtained for the bubble lifetime and the bubble radius-time history. These results, which are not incompatible with experimental results, can be applied to predict the dissolution of the entrapped gas emboli in the circulatory system of the human body. PMID:4642218

Modification of apparent fission yields by Chemical Fractionation following Fission (CFF)

NASA Astrophysics Data System (ADS)

Hohenberg, Charles; Meshik, Alex

2008-04-01

Grain-by-grain studies of the 2 billion year old Oklo natural reactor, using laser micro-extraction^1,2, yield detailed information about Oklo, a water-moderated pulsed reactor, cycle times, total neutron fluence and duration, but it also demonstrates Chemical Fractionation following Fission. In the CFF process, members of an isobaric yield chain with long half-lives are subject to migration before decay can occur. Of particular interest is the 129 isobar where 17 million ^129I can migrate out of the host grain before decay, and iodine compounds are water soluble. This is amply demonstated by the variation of Xe spectra between micron-sized uranium-bearing minerals and adjacent uranium-free minerals. Fission 129 yields for the spontaneous fission of ^238U generally come from measured ^129Xe in pitchblend^2, ores emplaced by aqueous activity, and are incorrect due to the CFF process. ^238U yields for the 131 and 129 chains, reported in Hyde^3, as 0.455 +- .02 and < 0.012, respectively, the latter being anomalously low. ^1A Meshik, C Hohenberg and O Pravdivtesva, PRL 93, 182302 (2004); A Meshik Sci. Am. Nov (2005), 55; ^2E K Hyde, Nucl Prop of Heavy Elements III (1964).

Reactions of vitamin A with acceptors of electrons. Interactions with iodine and the formation of iodide

PubMed Central

Lucy, J. A.; Lichti, F. Ulrike

1969-01-01

1. The reactions of retinol and retinoic acid with iodine were investigated since knowledge of the chemical reactions of vitamin A with acceptors of electrons may shed light on its biochemical mode of action. 2. Colloidal retinol, but not retinoic acid, reacts with iodine to yield a blue–green complex that rapidly decomposes, giving iodide and an unknown species with λmax. at 870mμ. 3. In addition, both retinol and retinoic acid reduce iodine to iodide by a reaction that does not involve an intermediate coloured complex; this reaction appears to yield unstable carbonium ion derivatives of the vitamin. 4. The presence of water greatly facilitates the production of iodide from vitamin A and iodine. 5. Possible chemical pathways involved in these reactions are discussed. 6. It is suggested that the chemical properties of retinol and retinoic acid that underlie their biochemical behaviour might be apparent only when the molecules are at a lipid–water interface, and that vitamin A might be expected to react with a number of different electron acceptors in vivo. PMID:5801297

Role of a Streambed's Benthic Biolayer in Enhancing Chemical Reactions in Hyporheic Flow

NASA Astrophysics Data System (ADS)

Harvey, J. W.

2016-12-01

Chemical processing of metals, nutrients, and organic compounds occurs throughout natural waters, however the rate of reactions often is greater at the streambed interface compared with surface water or deeper groundwater. Hydrologic exchange across the sediment interface brings reactive solutes and fine particulate organic matter from surface waters into contact with the streambed biolayer, a zone with algae and other living microflora and fauna, microbial communities, and reactive geochemical coatings on granular sediments. Compared with surface water or deeper hyporheic sediments, the intrinsic rate of reactions may be stimulated in biolayers because of higher rates of metabolic processing and associated redox reactions. Also, hydrologic transport may enhance reaction rates by relieving potential transport limitations through the re-supply of reactive substrates from surface water. As a result the chemical processing that occurs in the biolayer may far exceed processing that occurs in deeper hyporheic flow. Here I highlight new understanding of enhancement of reaction rates and their hydrologic and biogeochemical controls in streambed biolayers compared with hyporheic flow as a whole. The approach distinguishes and quantifies reaction limitation and transport limitation both at the centimeter-scale within the hyporheic zone and at the river network scale where the effect of streambed reactions accumulates and influences downstream water quality.

First-order reactant in homogeneous turbulence before the final period of decay. [contaminant fluctuations in chemical reaction

NASA Technical Reports Server (NTRS)

Kumar, P.; Patel, S. R.

1974-01-01

A method is described for studying theoretically the concentration fluctuations of a dilute contaminate undergoing a first-order chemical reaction. The method is based on Deissler's (1958) theory for homogeneous turbulence for times before the final period, and it follows the approach used by Loeffler and Deissler (1961) to study temperature fluctuations in homogeneous turbulence. Four-point correlation equations are obtained; it is assumed that terms containing fifth-order correlation are very small in comparison with those containing fourth-order correlations, and can therefore be neglected. A spectrum equation is obtained in a form which can be solved numerically, yielding the decay law for the concentration fluctuations in homogeneous turbulence for the period much before the final period of decay.

Nanoscale control of reversible chemical reaction between fullerene C60 molecules using scanning tunneling microscope.

PubMed

Nakaya, Masato; Kuwahara, Yuji; Aono, Masakazu; Nakayama, Tomonobu

2011-04-01

The nanoscale control of reversible chemical reactions, the polymerization and depolymerization between C60 molecules, has been investigated. Using a scanning tunneling microscope (STM), the polymerization and depolymerization can be controlled at designated positions in ultrathin films of C60 molecules. One of the two chemical reactions can be selectively induced by controlling the sample bias voltage (V(s)); the application of negative and positive values of V(s) results in polymerization and depolymerization, respectively. The selectivity between the two chemical reactions becomes extremely high when the thickness of the C60 film increases to more than three molecular layers. We conclude that STM-induced negative and positive electrostatic ionization are responsible for the control of the polymerization and depolymerization, respectively.

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

Measurement of thick target neutron yield from the reaction (p+181 Ta) with projectiles in the range of 6-20 MeV

NASA Astrophysics Data System (ADS)

Paul, Sabyasachi; Sahoo, G. S.; Tripathy, S. P.; Sharma, S. C.; Joshi, D. S.; Bandyopadhyay, T.

2018-02-01

181Ta is a commonly used backing material for many targets in nuclear reaction studies. When the target thickness is less than the range of bombarded projectiles, the interaction via Ta(p,n) reactions in the backing can be a significant source of background. In this study, the neutron spectral yields from the reaction of protons of different energies (between 6 to 20 MeV) with a thick Ta target were determined using CR-39 detectors. The results from this study can be used as a correction factor in such situations. The parameters of registered tracks in CR-39 were analysed using an in-house image analysing program autoTRAK_n and then to derive the associated dose values. The spectral yields obtained experimentally were compared with those obtained from the theoretical calculations. The neutron yield was found to increase with increase in projectile energy mainly due to the opening of reaction channels from (p, n) to (p, 3n).

[Recent results in research on oscillatory chemical reactions].

PubMed

Poros, Eszter; Kurin-Csörgei, Krisztina

2014-01-01

The mechanisms of the complicated periodical phenomenas in the nature (e.g. hearth beat, sleep cycle, circadian rhythms, etc) could be understood with using the laws of nonlinear chemical systems. In this article the newest result in the research of the subfield of nonlinear chemical dynamics aimed at constructing oscillatory chemical reactions, which are novel either in composition or in configuration, are presented. In the introductory part the concept of chemical periodicity is defined, then the forms as it can appear in time and space and the methods of their study are discussed. Detailed description of the experimental work that has resulted in two significant discoveries is provided. A method was developed to design pH-oscillators which are capable of operating under close conditions. The batch pH-oscillators are more convenient to use in some proposed applications than the equivalent CSTR variant. A redox oscillator that is new in composition was found. The permanganate oxidation of some amino acids was shown to take place according to oscillatory kinetics in a narrow range of the experimental parameters. The KMnO4 - glycine - Na2HPO4 system represents the first example in the family of manganese based oscillators where amino acids is involved. In the conclusion formal analogies between the simple chemical and some more complicated biological oscillatory phenomena are mentioned and the possibility of modeling periodic processes with the use of information gained from the studies of chemical oscillations is pointed out.

Fast screening of analytes for chemical reactions by reactive low-temperature plasma ionization mass spectrometry.

PubMed

Zhang, Wei; Huang, Guangming

2015-11-15

Approaches for analyte screening have been used to aid in the fine-tuning of chemical reactions. Herein, we present a simple and straightforward analyte screening method for chemical reactions via reactive low-temperature plasma ionization mass spectrometry (reactive LTP-MS). Solution-phase reagents deposited on sample substrates were desorbed into the vapor phase by action of the LTP and by thermal desorption. Treated with LTP, both reagents reacted through a vapor phase ion/molecule reaction to generate the product. Finally, protonated reagents and products were identified by LTP-MS. Reaction products from imine formation reaction, Eschweiler-Clarke methylation and the Eberlin reaction were detected via reactive LTP-MS. Products from the imine formation reaction with reagents substituted with different functional groups (26 out of 28 trials) were successfully screened in a time of 30 s each. Besides, two short-lived reactive intermediates of Eschweiler-Clarke methylation were also detected. LTP in this study serves both as an ambient ionization source for analyte identification (including reagents, intermediates and products) and as a means to produce reagent ions to assist gas-phase ion/molecule reactions. The present reactive LTP-MS method enables fast screening for several analytes from several chemical reactions, which possesses good reagent compatibility and the potential to perform high-throughput analyte screening. In addition, with the detection of various reactive intermediates (intermediates I and II of Eschweiler-Clarke methylation), the present method would also contribute to revealing and elucidating reaction mechanisms. Copyright © 2015 John Wiley & Sons, Ltd.

Control of femtosecond laser driven retro-Diels-Alder-like reaction of dicyclopentadiene

PubMed Central

Das, Dipak Kumar; Goswami, Tapas; Goswami, Debabrata

2013-01-01

Using femtosecond time resolved degenerate pump-probe mass spectrometry coupled with simple linearly chirped frequency modulated pulse, we elucidate that the dynamics of retro-Diels-Alder-like reaction of diclopentadiene (DCPD) to cyclopentadiene (CPD) in supersonic molecular beam occurs in ultrafast time scale. Negatively chirped pulse enhances the ion yield of CPD, as compared to positively chirped pulse. This indicates that by changing the frequency (chirp) of the laser pulse we can control the ion yield of a chemical reaction. PMID:23814449

In Situ Monitoring of Chemical Reactions at a Solid-Water Interface by Femtosecond Acoustics.

PubMed

Shen, Chih-Chiang; Weng, Meng-Yu; Sheu, Jinn-Kong; Yao, Yi-Ting; Sun, Chi-Kuang

2017-11-02

Chemical reactions at a solid-liquid interface are of fundamental importance. Interfacial chemical reactions occur not only at the very interface but also in the subsurface area, while existing monitoring techniques either provide limited spatial resolution or are applicable only for the outmost atomic layer. Here, with the aid of the time-domain analysis with femtosecond acoustics, we demonstrate a subatomic-level-resolution technique to longitudinally monitor chemical reactions at solid-water interfaces, capable of in situ monitoring even the subsurface area under atmospheric conditions. Our work was proven by monitoring the already-known anode oxidation process occurring during photoelectrochemical water splitting. Furthermore, whenever the oxide layer thickness equals an integer  number of the effective atomic layer thickness, the measured acoustic echo will show higher signal-to-noise ratios with reduced speckle noise, indicating the quantum-like behavior of this coherent-phonon-based technique.

Driving Chemical Reactions in Plasmonic Nanogaps with Electrohydrodynamic Flow.

PubMed

Thrift, William J; Nguyen, Cuong Q; Darvishzadeh-Varcheie, Mahsa; Zare, Siavash; Sharac, Nicholas; Sanderson, Robert N; Dupper, Torin J; Hochbaum, Allon I; Capolino, Filippo; Abdolhosseini Qomi, Mohammad Javad; Ragan, Regina

2017-11-28

Nanoparticles from colloidal solution-with controlled composition, size, and shape-serve as excellent building blocks for plasmonic devices and metasurfaces. However, understanding hierarchical driving forces affecting the geometry of oligomers and interparticle gap spacings is still needed to fabricate high-density architectures over large areas. Here, electrohydrodynamic (EHD) flow is used as a long-range driving force to enable carbodiimide cross-linking between nanospheres and produces oligomers exhibiting sub-nanometer gap spacing over mm 2 areas. Anhydride linkers between nanospheres are observed via surface-enhanced Raman scattering (SERS) spectroscopy. The anhydride linkers are cleavable via nucleophilic substitution and enable placement of nucleophilic molecules in electromagnetic hotspots. Atomistic simulations elucidate that the transient attractive force provided by EHD flow is needed to provide a sufficient residence time for anhydride cross-linking to overcome slow reaction kinetics. This synergistic analysis shows assembly involves an interplay between long-range driving forces increasing nanoparticle-nanoparticle interactions and probability that ligands are in proximity to overcome activation energy barriers associated with short-range chemical reactions. Absorption spectroscopy and electromagnetic full-wave simulations show that variations in nanogap spacing have a greater influence on optical response than variations in close-packed oligomer geometry. The EHD flow-anhydride cross-linking assembly method enables close-packed oligomers with uniform gap spacings that produce uniform SERS enhancement factors. These results demonstrate the efficacy of colloidal driving forces to selectively enable chemical reactions leading to future assembly platforms for large-area nanodevices.

Kinetic calorimetry in the study of the mechanism of low-temperature chemical reactions

NASA Astrophysics Data System (ADS)

Barkalov, I. M.; Kiryukhin, D. P.

Chemical reactions are always followed by a change in the reacting system enthalpy, hence, calorimetry as a method of enthalpy and heat capacity measuring is a universal and, sometimes, even the only possible way of studying chemical reaction kinetics. Throughout its long history, the calorimeter, having preserved the positions of the main method of thermodynamic studies, has conquered a new field of application: that of kinetic study of chemical reactions. The advantages and disadvantages of the kinetic calorimeter are now obvious. First, the advantages are: (1) the possibility of measuring the rate of a chemical reaction without any special requirements being imposed on the reaction medium (solid, viscous, multicomponent systems); (2) the high efficiency: a large volume of kinetic information in one experiment and a non-destructive character of changes; (3) the possibility of measuring directly in the field of ionizing radiation (γ-radiation, accelerated electrons) and light; and (4) recording of the chemical conversion directly at the time of its occurrence. The disadvantages of this method are: (1) the high inertia of standard calorimeter systems (τC⋍102-103S), which restricts the possibilities of studying fast processes; and (2) the complexity of the correct organization of the calorimeter experiment when the parameters of the process are changed (overheating in the sample, conversion of the process to explosive and auto wave regimens). One of the oldest and most universal methods of studying the mechanism of chemical reactions, calorimetry, is now passing through a period of turbulent development due to the advances in electronics and computerization. The wide variety of types of calorimeter set-ups and the large assortment of measurement schemes in the currently described methods complicate the experimental selection of the necessary instrument rather than facilitate it. The basic principles of the method, the types of calorimeters, and the measuring

Ultrahigh-yield growth of GaN via halogen-free vapor-phase epitaxy

NASA Astrophysics Data System (ADS)

Nakamura, Daisuke; Kimura, Taishi

2018-06-01

The material yield of Ga during GaN growth via halogen-free vapor-phase epitaxy (HF-VPE) was systematically investigated and found to be much higher than that obtained using conventional hydride VPE. This is attributed to the much lower process pressure and shorter seed-to-source distance, owing to the inherent chemical reactions and corresponding reactor design used for HF-VPE growth. Ultrahigh-yield GaN growth was demonstrated on a 4-in.-diameter sapphire seed substrate.

Effect of chemical and mechanical weed control on cassava yield, soil quality and erosion under cassava cropping system

NASA Astrophysics Data System (ADS)

Islami, Titiek; Wisnubroto, Erwin; Utomo, Wani

2016-04-01

Three years field experiments were conducted to study the effect of chemical and mechanical weed control on soil quality and erosion under cassava cropping system. The experiment were conducted at University Brawijaya field experimental station, Jatikerto, Malang, Indonesia. The experiments were carried out from 2011 - 2014. The treatments consist of three cropping system (cassava mono culture; cassava + maize intercropping and cassava + peanut intercropping), and two weed control method (chemical and mechanical methods). The experimental result showed that the yield of cassava first year and second year did not influenced by weed control method and cropping system. However, the third year yield of cassava was influence by weed control method and cropping system. The cassava yield planted in cassava + maize intercropping system with chemical weed control methods was only 24 t/ha, which lower compared to other treatments, even with that of the same cropping system used mechanical weed control. The highest cassava yield in third year was obtained by cassava + peanuts cropping system with mechanical weed control method. After three years experiment, the soil of cassava monoculture system with chemical weed control method possessed the lowest soil organic matter, and soil aggregate stability. During three years of cropping soil erosion in chemical weed control method, especially on cassava monoculture, was higher compared to mechanical weed control method. The soil loss from chemical control method were 40 t/ha, 44 t/ha and 54 t/ha for the first, second and third year crop. The soil loss from mechanical weed control method for the same years was: 36 t/ha, 36 t/ha and 38 t/ha. Key words: herbicide, intercropping, soil organic matter, aggregate stability.

On the chemical reaction of matter with antimatter.

PubMed

Lodi Rizzini, Evandro; Venturelli, Luca; Zurlo, Nicola

2007-06-04

A chemical reaction between the building block antiatomic nucleus, the antiproton (p or H- in chemical notation), and the hydrogen molecular ion (H2+) has been observed by the ATHENA collaboration at CERN. The charged pair interact via the long-range Coulomb force in the environment of a Penning trap which is purpose-built to observe antiproton interactions. The net result of the very low energy collision of the pair is the creation of an antiproton-proton bound state, known as protonium (Pn), together with the liberation of a hydrogen atom. The Pn is formed in a highly excited, metastable, state with a lifetime against annihilation of around 1 micros. Effects are observed related to the temperature of the H2+ prior to the interaction, and this is discussed herein.

Chemical research on red pigments after adverse reactions to tattoo.

PubMed

Tammaro, A; Toniolo, C; Giulianelli, V; Serafini, M; Persechino, S

2016-03-01

Currently, the incidence of tattooing is on the rise compared to the past, especially among adolescents, and it leads to the urgency of monitoring the security status of tattooing centers, as well as to inform people about the risks of tattoo practice. In our clinical experience, 20% of tattooed patients presented adverse reactions, like allergic contact dermatitis, psoriasis with Koebner's phenomena and granulomatous reactions, with the latter most prevalent and most often related to red pigment. Adverse reactions to tattoo pigments, especially the red one, are well known and described in literature. Great attention has to be focused on the pigments used, especially for the presence of new substances, often not well known. For this reason, we decided to perform a study on 12 samples of red tattoo ink, obtained by patients affected by different cutaneous reactions in the site of tattoo, to analyze their chemical composition.

Diagnostic Criteria for the Characterization of Electrode Reactions with Chemically Coupled Reactions Preceding the Electron Transfer by Cyclic Square Wave Voltammetry.

PubMed

Helfrick, John C; Mann, Megan A; Bottomley, Lawrence A

2016-08-18

Theory for cyclic square wave voltammetry of electrode reactions with chemical reactions preceding the electron transfer is presented. Theoretical voltammograms were calculated following systematic variation of empirical parameters to assess their impact on the shape of the voltammogram. From the trends obtained, diagnostic criteria for this mechanism were deduced. When properly applied, these criteria will enable non-experts in voltammetry to assign the electrode reaction mechanism and accurately measure reaction kinetics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characteristics of HgS nanoparticles formed in hair by a chemical reaction

NASA Astrophysics Data System (ADS)

Patriarche, G.; Walter, P.; Van Elslande, E.; Ayache, J.; Castaing, J.

2013-01-01

A chemical reaction, derived from an ancient recipe for hair dyeing, is used to precipitate nanoparticles of mercury sulphide in hair by the simple process of immersion in a water solution of Ca(OH)2 and HgO. After several days, HgS nanoparticles appear throughout the hair and are particularly numerous in the various interfaces. The formation of these nanoparticles has been studied by analytical and atomic resolution electron microscopy. High resolution quantitative analysis allowed the determination of two varieties of HgS precipitate crystal structures formed: a hexagonal cinnabar and a cubic metacinnabar structure. This very simple process of a chemical reaction in hair is a particularly inexpensive way to fabricate semiconductor sulphide nanoparticles with specific properties.

Reprint of: A numerical modelling of gas exchange mechanisms between air and turbulent water with an aquarium chemical reaction

NASA Astrophysics Data System (ADS)

Nagaosa, Ryuichi S.

2014-08-01

This paper proposes a new numerical modelling to examine environmental chemodynamics of a gaseous material exchanged between the air and turbulent water phases across a gas-liquid interface, followed by an aquarium chemical reaction. This study uses an extended concept of a two-compartment model, and assumes two physicochemical substeps to approximate the gas exchange processes. The first substep is the gas-liquid equilibrium between the air and water phases, A(g)⇌A(aq), with Henry's law constant H. The second is a first-order irreversible chemical reaction in turbulent water, A(aq)+H2O→B(aq)+H+ with a chemical reaction rate κA. A direct numerical simulation (DNS) technique has been employed to obtain details of the gas exchange mechanisms and the chemical reaction in the water compartment, while zero velocity and uniform concentration of A is considered in the air compartment. The study uses the different Schmidt numbers between 1 and 8, and six nondimensional chemical reaction rates between 10(≈0) to 101 at a fixed Reynolds number. It focuses on the effects of the Schmidt number and the chemical reaction rate on fundamental mechanisms of the gas exchange processes across the interface.

Do high school chemistry examinations inhibit deeper level understanding of dynamic reversible chemical reactions?

NASA Astrophysics Data System (ADS)

Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.

2012-07-01

Background and purpose : Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers require students to use approaches beyond direct application of LCP. Sample : The questionnaire was administered to 162 students studying their first year of advanced chemistry (age 16/17) in three high achieving London high schools. Design and methods : The students' explanations of reversible chemical systems were inductively coded to identify the explanatory approaches used and interviews with 13 students were used to check for consistency. AS level examination questions on reversible reactions were analysed to identify the types of explanations sought and the students' performance in these examinations was compared to questionnaire answers. Results : 19% of students used a holistic explanatory approach: when the rates of forward and reverse reactions are correctly described, recognising their simultaneous and mutually dependent nature. 36% used a mirrored reactions approach when the connected nature of the forward and reverse reactions is identified, but not their mutual dependency. 42% failed to recognize the interdependence of forward and reverse reactions (reactions not connected approach). Only 4% of marks for AS examination questions on reversible chemical systems asked for responses which went beyond either direct application of LCP or recall of equilibrium knowledge. 37% of students attained an A grade in their AS national examinations. Conclusions : Examinations favour the application of LCP making it possible to obtain the highest grade with little understanding of reversible chemical systems beyond a direct application of this algorithm. Therefore students' understanding may be attenuated so that they are

Open-source Framework for Storing and Manipulation of Plasma Chemical Reaction Data

NASA Astrophysics Data System (ADS)

Jenkins, T. G.; Averkin, S. N.; Cary, J. R.; Kruger, S. E.

2017-10-01

We present a new open-source framework for storage and manipulation of plasma chemical reaction data that has emerged from our in-house project MUNCHKIN. This framework consists of python scripts and C + + programs. It stores data in an SQL data base for fast retrieval and manipulation. For example, it is possible to fit cross-section data into most widely used analytical expressions, calculate reaction rates for Maxwellian distribution functions of colliding particles, and fit them into different analytical expressions. Another important feature of this framework is the ability to calculate transport properties based on the cross-section data and supplied distribution functions. In addition, this framework allows the export of chemical reaction descriptions in LaTeX format for ease of inclusion in scientific papers. With the help of this framework it is possible to generate corresponding VSim (Particle-In-Cell simulation code) and USim (unstructured multi-fluid code) input blocks with appropriate cross-sections.

Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces.

PubMed

Gerber, R Benny; Varner, Mychel E; Hammerich, Audrey D; Riikonen, Sampsa; Murdachaew, Garold; Shemesh, Dorit; Finlayson-Pitts, Barbara J

2015-02-17

isolated defects where it involves formation of H3O(+)-acid anion contact ion pairs. This behavior is found in simulations of a model of the ice quasi-liquid layer corresponding to large defect concentrations in crystalline ice. The results are in accord with experiments. (iv) Ionization of acids on wet quartz. A monolayer of water on hydroxylated silica is ordered even at room temperature, but the surface lattice constant differs significantly from that of crystalline ice. The ionization processes of HCl and H2SO4 are of high yield and occur in a few picoseconds. The results are in accord with experimental spectroscopy. (v) Photochemical reactions on water and ice. These simulations require excited state quantum chemical methods. The electronic absorption spectrum of methyl hydroperoxide adsorbed on a large ice cluster is strongly blue-shifted relative to the isolated molecule. The measured and calculated adsorption band low-frequency tails are in agreement. A simple model of photodynamics assumes prompt electronic relaxation of the excited peroxide due to the ice surface. SEMD simulations support this, with the important finding that the photochemistry takes place mainly on the ground state. In conclusion, dynamics simulations using quantum chemical potentials are a useful tool in atmospheric chemistry of water media, capable of comparison with experiment.

Chemical reactions induced by oscillating external fields in weak thermal environments

NASA Astrophysics Data System (ADS)

Craven, Galen T.; Bartsch, Thomas; Hernandez, Rigoberto

2015-02-01

Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally varying external field, the transition state that the reaction must pass through during the transformation from reactant to product is no longer a fixed geometric structure, but is instead time-dependent. For a periodically forced model reaction, we develop a recrossing-free dividing surface that is attached to a transition state trajectory [T. Bartsch, R. Hernandez, and T. Uzer, Phys. Rev. Lett. 95, 058301 (2005)]. We have previously shown that for single-mode sinusoidal driving, the stability of the time-varying transition state directly determines the reaction rate [G. T. Craven, T. Bartsch, and R. Hernandez, J. Chem. Phys. 141, 041106 (2014)]. Here, we extend our previous work to the case of multi-mode driving waveforms. Excellent agreement is observed between the rates predicted by stability analysis and rates obtained through numerical calculation of the reactive flux. We also show that the optimal dividing surface and the resulting reaction rate for a reactive system driven by weak thermal noise can be approximated well using the transition state geometry of the underlying deterministic system. This agreement persists as long as the thermal driving strength is less than the order of that of the periodic driving. The power of this result is its simplicity. The surprising accuracy of the time-dependent noise-free geometry for obtaining transition state theory rates in chemical reactions driven by periodic fields reveals the dynamics without requiring the cost of brute-force calculations.

Boosting Chemical Stability, Catalytic Activity, and Enantioselectivity of Metal-Organic Frameworks for Batch and Flow Reactions.

PubMed

Chen, Xu; Jiang, Hong; Hou, Bang; Gong, Wei; Liu, Yan; Cui, Yong

2017-09-27

A key challenge in heterogeneous catalysis is the design and synthesis of heterogeneous catalysts featuring high catalytic activity, selectivity, and recyclability. Here we demonstrate that high-performance heterogeneous asymmetric catalysts can be engineered from a metal-organic framework (MOF) platform by using a ligand design strategy. Three porous chiral MOFs with the framework formula [Mn 2 L(H 2 O) 2 ] are prepared from enantiopure phosphono-carboxylate ligands of 1,1'-biphenol that are functionalized with 3,5-bis(trifluoromethyl)-, bismethyl-, and bisfluoro-phenyl substituents at the 3,3'-position. For the first time, we show that not only chemical stability but also catalytic activity and stereoselectivity of the MOFs can be tuned by modifying the ligand structures. Particularly, the MOF incorporated with -CF 3 groups on the pore walls exhibits enhanced tolerance to water, weak acid, and base compared with the MOFs with -F and -Me groups. Under both batch and flow reaction systems, the CF 3 -containing MOF demonstrated excellent reactivity, selectivity, and recyclability, affording high yields and enantioselectivities for alkylations of indoles and pyrrole with a range of ketoesters or nitroalkenes. In contrast, the corresponding homogeneous catalysts gave low enantioselectivity in catalyzing the tested reactions.

Spatial relationships among cereal yields and selected soil physical and chemical properties.

PubMed

Lipiec, Jerzy; Usowicz, Bogusław

2018-08-15

Sandy soils occupy large area in Poland (about 50%) and in the world. This study aimed at determining spatial relationships of cereal yields and the selected soil physical and chemical properties in three study years (2001-2003) on low productive sandy Podzol soil (Podlasie, Poland). The yields and soil properties in plough and subsoil layers were determined at 72-150 points. The test crops were: wheat, wheat and barley mixture and oats. To explore the spatial relationship between cereal yields and each soil property spatial statistics was used. The best fitting models were adjusted to empirical semivariance and cross-semivariance, which were used to draw maps using kriging. Majority of the soil properties and crop yields exhibited low and medium variability (coefficient of variation 5-70%). The effective ranges of the spatial dependence (the distance at which data are autocorrelated) for yields and all soil properties were 24.3-58.5m and 10.5-373m, respectively. Nugget to sill ratios showed that crop yields and soil properties were strongly spatially dependent except bulk density. Majority of the pairs in cross-semivariograms exhibited strong spatial interdependence. The ranges of the spatial dependence varied in plough layer between 54.6m for yield×pH up to 2433m for yield×silt content. Corresponding ranges in subsoil were 24.8m for crop yield×clay content in 2003 and 1404m for yield×bulk density. Kriging maps allowed separating sub-field area with the lowest yield and soil cation exchange capacity, organic carbon content and pH. This area had lighter color on the aerial photograph due to high content of the sand and low content of soil organic carbon. The results will help farmers at identifying sub-field areas for applying localized management practices to improve these soil properties and further spatial studies in larger scale. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

The influence of the "cage effect" on the mechanism of reversible bimolecular multistage chemical reactions in solutions.

PubMed

Doktorov, Alexander B

2015-08-21

Manifestations of the "cage effect" at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a "cage complex." Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the "cage effect" leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

Chemical methods and techniques to monitor early Maillard reaction in milk products; A review.

PubMed

Aalaei, Kataneh; Rayner, Marilyn; Sjöholm, Ingegerd

2018-01-23

Maillard reaction is an extensively studied, yet unresolved chemical reaction that occurs as a result of application of the heat and during the storage of foods. The formation of advanced glycation end products (AGEs) has been the focus of several investigations recently. These molecules which are formed at the advanced stage of the Maillard reaction, are suspected to be involved in autoimmune diseases in humans. Therefore, understanding to which extent this reaction occurs in foods, is of vital significance. Because of their composition, milk products are ideal media for this reaction, especially when application of heat and prolonged storage are considered. Thus, in this work several chemical approaches to monitor this reaction in an early stage are reviewed. This is mostly done regarding available lysine blockage which takes place in the very beginning of the reaction. The most popular methods and their applications to various products are reviewed. The methods including their modifications are described in detail and their findings are discussed. The present paper provides an insight into the history of the most frequently-used methods and provides an overview on the indicators of the Maillard reaction in the early stage with its focus on milk products and especially milk powders.

Dominant Overall Chemical Reaction in a Chlorine Trifluoride Silicon Nitrogen System at Atmospheric Pressure

NASA Astrophysics Data System (ADS)

Habuka, Hitoshi; Otsuka, Toru; Qu, Wei-Feng

1999-11-01

This study evaluates the overall chemical reaction in a chlorine trifluoride silicon nitrogen system at atmospheric pressure, based on the observation of the dominant chemical species in the gas phase using a quadrupole mass spectra analyzer coupled with a horizontal cold-wall single-wafer epitaxial reactor. Chlorine trifluoride gas etches the silicon surface, producing two major products, silicon tetrafluoride gas and chlorine gas, at room temperature and 530 K. The production of chlorosilanes was not observed in this study. The results obtained in this study indicate that the dominant overall chemical reaction in a chlorine trifluoride silicon nitrogen system is 3Si + 4ClF3 →3SiF4 ↑+ 2Cl2 ↑.

The reaction of peroxy radicals with OH: rate constants and HO2 yields

NASA Astrophysics Data System (ADS)

Fittschen, C. M.; Assaf, E.; Schoemaecker, C.; Vereecken, L.

2017-12-01

Peroxy radicals, RO2, are key species in the atmosphere. They are formed from a reaction of OH radicals with hydrocarbon: RH + OH + O2 → RO2 + H2O In polluted environments, RO2 radicals react predominantly with NO, leading to formation of NO2 and eventually through photolysis of NO2 to formation of O3. At low NOx concentrations such as in the marine boundary layer or the background troposphere, the lifetime of RO2 radicals increases and other reaction pathways become competitive. Atmospheric chemistry models have considered until recently only the self- and cross reaction with other RO2 radicals or with HO2 radicals as the major fate for RO2 radicals under low NOx conditions. Recently, the rate constants for the reaction of peroxy radicals with OH radicals RO2 + OH → products has been measured for CH3O2 [1, 2] and C2H5O2 [3] and it was shown to become competitive to other sinks [4]. However, in order to evaluate the impact of this so far neglected sink for peroxy radicals on the composition of remote atmospheres, the reaction products must be known. A recently improved experimental set-up combining laser photolysis with two simultaneous cw-CRDS detections in the near IR allowing for a time resolved, absolute quantification of OH and RO2 radicals has been used for a further investigation of this class of reactions. High-repetition rate LIF is used for determining relative OH profiles. For CH3O2 radicals, HO2 has been determined as major product recently [5]. Currently, we study the next larger perxoy, C2H5O2, using different radical precursors (C2H5I, (COCl)2/C2H6, XeF2/C2H6) and also deuterated C2D5I in order to elucidate the product yield. Preliminary results show a much lower HO2 yield for C2H5O2 compared to CH3O2. The most recent results will be presented at the conference. [1] A. Bossolasco, E. Faragó, C. Schoemaecker, and C. Fittschen, CPL, 593, 7, (2014). [2] E. Assaf, B. Song, A. Tomas, C. Schoemaecker, C. Fittschen, JPC A, 120, 8923 (2016) [3] Eszter

Reachability bounds for chemical reaction networks and strand displacement systems.

PubMed

Condon, Anne; Kirkpatrick, Bonnie; Maňuch, Ján

2014-01-01

Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs and DSDs fail to work correctly if the length of the shortest sequence of reactions needed to produce any given molecule exceeds a threshold that grows polynomially with attributes of the system.

Autocatalytic sets and chemical organizations: modeling self-sustaining reaction networks at the origin of life

NASA Astrophysics Data System (ADS)

Hordijk, Wim; Steel, Mike; Dittrich, Peter

2018-01-01

Two related but somewhat different approaches have been proposed to formalize the notion of a self-sustaining chemical reaction network. One is the notion of collectively autocatalytic sets, formalized as RAF theory, and the other is chemical organization theory. Both formalisms have been argued to be relevant to the origin of life. RAF sets and chemical organizations are defined differently, but previously some relationships between the two have been shown. Here, we refine and explore these connections in more detail. In particular, we show that so-called closed RAFs are chemical organizations, but that the converse is not necessarily true. We then introduce and apply a procedure to show how chemical organizations can be used to find all closed RAFs within any chemical reaction system. We end with a discussion of why and how closed RAFs could be important in the context of the origin and early evolution of life.

Kinetics and thermodynamics of chemical reactions in Li/SOCl2 cells

NASA Technical Reports Server (NTRS)

Hansen, Lee D.; Frank, Harvey

1987-01-01

Work is described that was designed to determine the kinetic constants necessary to extrapolate kinetic data on Li/SOCl2 cells over the temperature range from 25 to 75 C. A second objective was to characterize as far as possible the chemical reactions that occur in the cells since these reactions may be important in understanding the potential hazards of these cells. The kinetics of the corrosion processes in undischarged Li/SOCl2 cells were determined and separated according to their occurrence at the anode and cathode; the effects that switching the current on and off has on the corrosion reactions was determined; and the effects of discharge state on the kinetics of the corrosion process were found. A thermodynamic analysis of the current-producing reactions in the cell was done and is included.

Systematization of the yields of products of photonuclear reactions on enriched-tin targets at the bremsstrahlung-photon endpoint energy of 4.5 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balabekyan, A. R., E-mail: balabekyan@ysu.a

2008-11-15

Yields of photonuclear-reaction products formed in targets from separated tin isotopes under the effect of beams of bremsstrahlung photons whose endpoint energy is 4.5 GeV were investigated. The systematization performed on this basis revealed an isoscaling character of the behavior of the production yields for various regions of reaction-product masses.

HCl yield and chemical kinetics study of the reaction of Cl atoms with CH3I at the 298K temperature using the infra-red tunable diode laser absorption spectroscopy.

PubMed

Sharma, R C; Blitz, M; Wada, R; Seakins, P W

2014-07-15

Pulsed ArF excimer laser (193 nm)-CW infrared (IR) tunable diode laser Herriott type absorption spectroscopic technique has been made for the detection of product hydrochloric acid HCl. Absorption spectroscopic technique is used in the reaction chlorine atoms with methyl iodide (Cl+CH3I) to the study of kinetics on reaction Cl+CH3I and the yield of (HCl). The reaction of Cl+CH3I has been studied with the support of the reaction Cl+C4H10 (100% HCl) at temperature 298 K. In the reaction Cl+CH3I, the total pressure of He between 20 and 125 Torr at the constant concentration of [CH3I] 7.0×10(14) molecule cm(-3). In the present work, we estimated adduct formation is very important in the reaction Cl+CH3I and reversible processes as well and CH3I molecule photo-dissociated in the methyl [CH3] radical. The secondary chemistry has been studied as CH3+CH3ICl = product, and CH3I+CH3ICl = product2. The system has been modeled theoretically for secondary chemistry in the present work. The calculated and experimentally HCl yield nearly 65% at the concentration 1.00×10(14) molecule cm(-3) of [CH3I] and 24% at the concentration 4.0×10(15) molecule cm(-3) of [CH3I], at constant concentration 4.85×10(12) molecule cm(-3) of [CH3], and at 7.3×10(12) molecule cm(-3) of [Cl]. The pressure dependent also studied product of HCl at the constant [CH3], [Cl] and [CH3I]. The experimental results are also very good matching with the modelling work at the reaction CH3+CH3ICl = product (k = (2.75±0.35)×10(-10) s(-1)) and CH3I+CH3ICl = product2 (k = 1.90±0.15)×10(-12) s(-1). The rate coefficients of the reaction CH3+CH3ICl and CH3I+CH3ICl has been made in the present work. The experimental results has been studied by two method (1) phase locked and (2) burst mode. Copyright © 2014 Elsevier B.V. All rights reserved.

A transformation theory of stochastic evolution in Red Moon methodology to time evolution of chemical reaction process in the full atomistic system.

PubMed

Suzuki, Yuichi; Nagaoka, Masataka

2017-05-28

Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H 2 + I 2  ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H 2 and I 2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H 2 ] eq and equilibrium constants K eq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H 2 ] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

Reaction of mutualistic and granivorous ants to ulex elaiosome chemicals.

PubMed

Gammans, Nicola; Bullock, James M; Gibbons, Hannah; Schönrogge, Karsten

2006-09-01

It has been proposed that chemicals on plant elaiosomes aid seed detection by seed-dispersing ants. We hypothesized that the chemical interaction between ants and elaiosomes is more intimate than a generic attraction, and that elaiosome chemicals will attract mutualistic but not granivorous ant species. We investigated this by using two gorse species, Ulex minor and U. europaeus, and two associated ant species from European heathlands, the mutualist Myrmica ruginodis and the granivore Tetramorium caespitum. Behavioral studies were conducted with laboratory nests and foraging arenas. Both ants will take Ulex seeds, but while M. ruginodis showed increased antennation toward ether extracts of elaiosome surface chemicals compared with controls, T. caespitum showed no response. Elaiosome extracts were separated into seven lipid fractions. M. ruginodis showed increased antennation only toward the diglyceride fractions of both Ulex species, whereas T. caespitum showed no consistent reaction. This indicates that M. ruginodis can detect the elaiosome by responding to its surface chemicals, but T. caespitum is unresponsive to these chemicals. Responses to surface chemicals could increase the rate of seed detection in the field, and so these results suggest that Ulex elaiosomes produce chemicals that facilitate attraction of mutualistic rather than granivorous ant species. This could reduce seed predation and increase Ulex fitness.

General chemical kinetics computer program for static and flow reactions, with application to combustion and shock-tube kinetics

NASA Technical Reports Server (NTRS)

Bittker, D. A.; Scullin, V. J.

1972-01-01

A general chemical kinetics program is described for complex, homogeneous ideal-gas reactions in any chemical system. Its main features are flexibility and convenience in treating many different reaction conditions. The program solves numerically the differential equations describing complex reaction in either a static system or one-dimensional inviscid flow. Applications include ignition and combustion, shock wave reactions, and general reactions in a flowing or static system. An implicit numerical solution method is used which works efficiently for the extreme conditions of a very slow or a very fast reaction. The theory is described, and the computer program and users' manual are included.

Biochemical methane potential, biodegradability, alkali treatment and influence of chemical composition on methane yield of yard wastes.

PubMed

Gunaseelan, Victor Nallathambi

2016-03-01

In this study, the biochemical CH4 potential, rate, biodegradability, NaOH treatment and the influence of chemical composition on CH4 yield of yard wastes generated from seven trees were examined. All the plant parts were sampled for their chemical composition and subjected to the biochemical CH4 potential assay. The component parts exhibited significant variation in biochemical CH4 potential, which was reflected in their ultimate CH4 yields that ranged from 109 to 382 ml g(-1) volatile solids added and their rate constants that ranged from 0.042 to 0.173 d(-1). The biodegradability of the yard wastes ranged from 0.26 to 0.86. Variation in the biochemical CH4 potential of the yard wastes could be attributed to variation in the chemical composition of the different fractions. In the Thespesia yellow withered leaf, Tamarindus fruit pericarp and Albizia pod husk, NaOH treatment enhanced the ultimate CH4 yields by 17%, 77% and 63%, respectively, and biodegradability by 15%, 77% and 61%, respectively, compared with the untreated samples. The effectiveness of NaOH treatment varied for different yard wastes, depending on the amounts of acid detergent fibre content. Gliricidia petals, Prosopis leaf, inflorescence and immature pod, Tamarindus seeds, Albizia seeds, Cassia seeds and Delonix seeds exhibited CH4 yields higher than 300 ml g(-1) volatile solids added. Multiple linear regression models for predicting the ultimate CH4 yield and biodegradability of yard wastes were designed from the results of this work. © The Author(s) 2016.

Observed secondary organic aerosol (SOA) and organic nitrate yields from NO3 oxidation of isoprene

NASA Astrophysics Data System (ADS)

Rollins, A. W.; Fry, J. L.; Kiendler-Scharr, A.; Wooldridge, P. J.; Brown, S. S.; Fuchs, H.; Dube, W.; Mensah, A.; Tillmann, R.; Dorn, H.; Brauers, T.; Cohen, R. C.

2008-12-01

Formation of organic nitrates and secondary organic aerosol (SOA) from the NO3 oxidation of isoprene has been studied at atmospheric concentrations of VOC (10 ppb) and oxidant (<100 ppt NO3) in the presence of ammonium sulfate seed aerosol in the atmosphere simulation chamber SAPHIR at Forschungszentrum Jülich. Cavity Ringdown (CaRDS) and thermal dissociation - CaRDS measurements of NO3 and N2O5 as well as Thermal Dissociation - Laser Induced Fluorescence (TD-LIF) detection of alkyl nitrates (RONO2) and Aerodyne Aerosol Mass Spectrometer (AMS) measurements of aerosol composition were all used in comparison to a Master Chemical Mechanism (MCM) based chemical kinetics box model to quantify the product yields from two stages in isoprene oxidation. We find significant yields of organic nitrate formation from both the initial isoprene + NO3 reaction (71%) as well as from the reaction of NO3 with the initial oxidation products (30% - 60%). Under these low concentration conditions (~1 μg / m3), measured SOA production was greater than instrument noise only for the second oxidation step. Based on the modeled chemistry, we estimate an SOA mass yield of 10% (relative to isoprene mass reacted) for the reaction of the initial oxidation products with NO3. This yield is found to be consistent with the estimated saturation concentration (C*) of the presumed gas products of the doubly oxidized isoprene, where both oxidations lead to the addition of nitrate, carbonyl, and hydroxyl groups.

Students' Ideas about How and Why Chemical Reactions Happen: Mapping the Conceptual Landscape

ERIC Educational Resources Information Center

Yan, Fan; Talanquer, Vicente

2015-01-01

Research in science education has revealed that many students struggle to understand chemical reactions. Improving teaching and learning about chemical processes demands that we develop a clearer understanding of student reasoning in this area and of how this reasoning evolves with training in the domain. Thus, we have carried out a qualitative…

Chemical reactions studied at ultra-low temperature in liquid helium clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huisken, Friedrich; Krasnokutski, Serge A.

Low-temperature reaction rates are important ingredients for astrophysical reaction networks modeling the formation of interstellar matter in molecular clouds. Unfortunately, such data is difficult to obtain by experimental means. In an attempt to study low-temperature reactions of astrophysical interest, we have investigated relevant reactions at ultralow temperature in liquid helium droplets. Being prepared by supersonic expansion of helium gas at high pressure through a nozzle into a vacuum, large helium clusters in the form of liquid droplets constitute nano-sized reaction vessels for the study of chemical reactions at ultra-low temperature. If the normal isotope {sup 4}He is used, the heliummore » droplets are superfluid and characterized by a constant temperature of 0.37 K. Here we present results obtained for Mg, Al, and Si reacting with O{sub 2}. Mass spectrometry was employed to characterize the reaction products. As it may be difficult to distinguish between reactions occurring in the helium droplets before they are ionized and ion-molecule reactions taking place after the ionization, additional techniques were applied to ensure that the reactions actually occurred in the helium droplets. This information was provided by measuring the chemiluminescence light emitted by the products, the evaporation of helium atoms by the release of the reaction heat, or by laser-spectroscopic identification of the reactants and products.« less

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

NASA Technical Reports Server (NTRS)

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.

Measurement of fission yields and isomeric yield ratios at IGISOL

NASA Astrophysics Data System (ADS)

Pomp, Stephan; Mattera, Andrea; Rakopoulos, Vasileios; Al-Adili, Ali; Lantz, Mattias; Solders, Andreas; Jansson, Kaj; Prokofiev, Alexander V.; Eronen, Tommi; Gorelov, Dimitri; Jokinen, Ari; Kankainen, Anu; Moore, Iain D.; Penttilä, Heikki; Rinta-Antila, Sami

2018-03-01

Data on fission yields and isomeric yield ratios (IYR) are tools to study the fission process, in particular the generation of angular momentum. We use the IGISOL facility with the Penning trap JYFLTRAP in Jyväskylä, Finland, for such measurements on 232Th and natU targets. Previously published fission yield data from IGISOL concern the 232Th(p,f) and 238U(p,f) reactions at 25 and 50 MeV. Recently, a neutron source, using the Be(p,n) reaction, has been developed, installed and tested. We summarize the results for (p,f) focusing on the first measurement of IYR by direct ion counting. We also present first results for IYR and relative yields for Sn and Sb isotopes in the 128-133 mass range from natU(n,f) based on γ-spectrometry. We find a staggering behaviour in the cumulative yields for Sn and a shift in the independent fission yields for Sb as compared to current evaluations. Plans for the future experimental program on fission yields and IYR measurements are discussed.

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

PubMed

Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

2013-10-28

Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

Chemical Reaction Engineering Applications in Non-traditional Technologies. A Textbook Supplement.

ERIC Educational Resources Information Center

Savage, Phillip E.; Blaine, Steven

1991-01-01

A set of educational materials that have been developed which deal with chemical engineering applications in emerging technologies is described. The organization and the content of the supplemental textbook materials and how they can be integrated into an undergraduate reaction engineering course are discussed. (KR)

Chemical equilibrium and reaction modeling of arsenic and selenium in soils

USDA-ARS?s Scientific Manuscript database

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...

Holistic Metrics for Assessment of the Greenness of Chemical Reactions in the Context of Chemical Education

ERIC Educational Resources Information Center

Ribeiro, M. Gabriela T. C.; Machado, Adelio A. S. C.

2013-01-01

Two new semiquantitative green chemistry metrics, the green circle and the green matrix, have been developed for quick assessment of the greenness of a chemical reaction or process, even without performing the experiment from a protocol if enough detail is provided in it. The evaluation is based on the 12 principles of green chemistry. The…

Scaffolding Students' Online Critiquing of Expert- and Peer-generated Molecular Models of Chemical Reactions

NASA Astrophysics Data System (ADS)

Chang, Hsin-Yi; Chang, Hsiang-Chi

2013-08-01

In this study, we developed online critiquing activities using an open-source computer learning environment. We investigated how well the activities scaffolded students to critique molecular models of chemical reactions made by scientists, peers, and a fictitious peer, and whether the activities enhanced the students' understanding of science models and chemical reactions. The activities were implemented in an eighth-grade class with 28 students in a public junior high school in southern Taiwan. The study employed mixed research methods. Data collected included pre- and post-instructional assessments, post-instructional interviews, and students' electronic written responses and oral discussions during the critiquing activities. The results indicated that these activities guided the students to produce overall quality critiques. Also, the students developed a more sophisticated understanding of chemical reactions and scientific models as a result of the intervention. Design considerations for effective model critiquing activities are discussed based on observational results, including the use of peer-generated artefacts for critiquing to promote motivation and collaboration, coupled with critiques of scientific models to enhance students' epistemological understanding of model purpose and communication.

Magnetic isotope effect and theory of atomic orbital hybridization to predict a mechanism of chemical exchange reactions.

PubMed

Epov, Vladimir N

2011-08-07

A novel approach is suggested to investigate the mechanisms of chemical complexation reactions based on the results of Fujii with co-workers; they have experimentally observed that several metals and metalloids demonstrate mass-independent isotope fractionation during the reactions with the DC18C6 crown ether using solvent-solvent extraction. In this manuscript, the isotope fractionation caused by the magnetic isotope effect is used to understand the mechanisms of chemical exchange reactions. Due to the rule that reactions are allowed for certain electron spin states, and forbidden for others, magnetic isotopes show chemical anomalies during these reactions. Mass-independent fractionation is suggested to take place due to the hyperfine interaction of the nuclear spin with the electron spin of the intermediate product. Moreover, the sign of the mass-independent fractionation is found to be dependent on the element and its species, which is also explained by the magnetic isotope effect. For example, highly negative mass-independent isotope fractionation of magnetic isotopes was observed for reactions of DC18C6 with SnCl(2) species and with several Ru(III) chloro-species, and highly positive for reactions of this ether with TeCl(6)(2-), and with several Cd(II) and Pd(II) species. The atomic radius of an element is also a critical parameter for the reaction with crown ether, particularly the element ions with [Kr]4d(n)5s(m) electron shell fits the best with the DC18C6 crown ring. It is demonstrated that the magnetic isotope effect in combination with the theory of orbital hybridization can help to understand the mechanism of complexation reactions. The suggested approach is also applied to explain previously published mass-independent fractionation of Hg isotopes in other types of chemical exchange reactions. This journal is © the Owner Societies 2011

A Study of Interactions between Mixing and Chemical Reaction Using the Rate-Controlled Constrained-Equilibrium Method

NASA Astrophysics Data System (ADS)

Hadi, Fatemeh; Janbozorgi, Mohammad; Sheikhi, M. Reza H.; Metghalchi, Hameed

2016-10-01

The rate-controlled constrained-equilibrium (RCCE) method is employed to study the interactions between mixing and chemical reaction. Considering that mixing can influence the RCCE state, the key objective is to assess the accuracy and numerical performance of the method in simulations involving both reaction and mixing. The RCCE formulation includes rate equations for constraint potentials, density and temperature, which allows taking account of mixing alongside chemical reaction without splitting. The RCCE is a dimension reduction method for chemical kinetics based on thermodynamics laws. It describes the time evolution of reacting systems using a series of constrained-equilibrium states determined by RCCE constraints. The full chemical composition at each state is obtained by maximizing the entropy subject to the instantaneous values of the constraints. The RCCE is applied to a spatially homogeneous constant pressure partially stirred reactor (PaSR) involving methane combustion in oxygen. Simulations are carried out over a wide range of initial temperatures and equivalence ratios. The chemical kinetics, comprised of 29 species and 133 reaction steps, is represented by 12 RCCE constraints. The RCCE predictions are compared with those obtained by direct integration of the same kinetics, termed detailed kinetics model (DKM). The RCCE shows accurate prediction of combustion in PaSR with different mixing intensities. The method also demonstrates reduced numerical stiffness and overall computational cost compared to DKM.

Catalytic Conversion of Renewable Resources into Bulk and Fine Chemicals.

PubMed

de Vries, Johannes G

2016-12-01

Several strategies can be chosen to convert renewable resources into chemicals. In this account, I exemplify the route that starts with so-called platform chemicals; these are relatively simple chemicals that can be produced in high yield, directly from renewable resources, either via fermentation or via chemical routes. They can be converted into the existing bulk chemicals in a very efficient manner using multistep catalytic conversions. Two examples are given of the conversion of sugars into nylon intermediates. 5-Hydroxymethylfurfural (HMF) can be prepared in good yield from fructose. Two hydrogenation steps convert HMF into 1,6-hexanediol. Oppenauer oxidation converts this product into caprolactone, which in the past, has been converted into caprolactam in a large-scale industrial process by reaction with ammonia. An even more interesting platform chemical is levulinic acid (LA), which can be obtained directly from lignocellulose in good yield by treatment with dilute sulfuric acid at 200°C. Hydrogenation converts LA into gamma-valerolactone, which is ring-opened and esterified in a gas-phase process to a mixture of isomeric methyl pentenoates in excellent selectivity. In a remarkable selective palladium-catalysed isomerising methoxycarbonylation, this mixture is converted in to dimethyl adipate, which is finally hydrolysed to adipic acid. Overall selectivities of both processes are extremely high. The conversion of lignin into chemicals is a much more complicated task in view of the complex nature of lignin. It was discovered that breakage of the most prevalent β-O-4 bond in lignin occurs not only via the well-documented C3 pathway, but also via a C2 pathway, leading to the formation of highly reactive phenylacetaldehydes. These compounds went largely unnoticed as they immediately recondense on lignin. We have now found that it is possible to prevent this by converting these aldehydes in a tandem reaction, as they are formed. For this purpose, we have used

Laser-enhanced chemical reactions and the liquid state. II. Possible applications to nuclear fuel reprocessing

DOE Office of Scientific and Technical Information (OSTI.GOV)

DePoorter, G.L.; Rofer-DePoorter, C.K.

1976-01-01

Laser photochemistry is surveyed as a possible improvement upon the Purex process for reprocessing spent nuclear fuel. Most of the components of spent nuclear fuel are photochemically active, and lasers can be used to selectively excite individual chemical species. The great variety of chemical species present and the degree of separation that must be achieved present difficulties in reprocessing. Lasers may be able to improve the necessary separations by photochemical reaction or effects on rates and equilibria of reactions. (auth)

Thermal energy storage. [by means of chemical reactions

NASA Technical Reports Server (NTRS)

Grodzka, P. G.

1975-01-01

The principles involved in thermal energy storage by sensible heat, chemical potential energy, and latent heat of fusion are examined for the purpose of evolving selection criteria for material candidates in the low ( 0 C) and high ( 100 C) temperature ranges. The examination identifies some unresolved theoretical considerations and permits a preliminary formulation of an energy storage theory. A number of candidates in the low and high temperature ranges are presented along with a rating of candidates or potential candidates. A few interesting candidates in the 0 to 100 C region are also included. It is concluded that storage by means of reactions whose reversibility can be controlled either by product removal or by catalytic means appear to offer appreciable advantages over storage with reactions whose reversability cannot be controlled. Among such advantages are listed higher heat storage capacities and more favorable options regarding temperatures of collection, storage, and delivery. Among the disadvantages are lower storage efficiencies.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots.

PubMed

Kazemi, Masoud; Åqvist, Johan

2015-06-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

PubMed Central

Kazemi, Masoud; Åqvist, Johan

2015-01-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies. PMID:26028237

Comparison of designed and randomly generated catalysts for simple chemical reactions.

PubMed

Kipnis, Yakov; Baker, David

2012-09-01

There has been recent success in designing enzymes for simple chemical reactions using a two-step protocol. In the first step, a geometric matching algorithm is used to identify naturally occurring protein scaffolds at which predefined idealized active sites can be realized. In the second step, the residues surrounding the transition state model are optimized to increase transition state binding affinity and to bolster the primary catalytic side chains. To improve the design methodology, we investigated how the set of solutions identified by the design calculations relate to the overall set of solutions for two different chemical reactions. Using a TIM barrel scaffold in which catalytically active Kemp eliminase and retroaldolase designs were obtained previously, we carried out activity screens of random libraries made to be compositionally similar to active designs. A small number of active catalysts were found in screens of 10³ variants for each of the two reactions, which differ from the computational designs in that they reuse charged residues already present in the native scaffold. The results suggest that computational design considerably increases the frequency of catalyst generation for active sites involving newly introduced catalytic residues, highlighting the importance of interaction cooperativity in enzyme active sites. Copyright © 2012 The Protein Society.

The mineralogic evolution of the Martian surface through time: Implications from chemical reaction path modeling studies

NASA Technical Reports Server (NTRS)

Plumlee, G. S.; Ridley, W. I.; Debraal, J. D.; Reed, M. H.

1993-01-01

Chemical reaction path calculations were used to model the minerals that might have formed at or near the Martian surface as a result of volcano or meteorite impact driven hydrothermal systems; weathering at the Martian surface during an early warm, wet climate; and near-zero or sub-zero C brine-regolith reactions in the current cold climate. Although the chemical reaction path calculations carried out do not define the exact mineralogical evolution of the Martian surface over time, they do place valuable geochemical constraints on the types of minerals that formed from an aqueous phase under various surficial and geochemically complex conditions.

Ion-Molecule Reactions and Chemical Composition of Emanated from Herculane Spa Geothermal Sources

PubMed Central

Cosma, Constantin; Suciu, Ioan; Jäntschi, Lorentz; Bolboacă, Sorana D.

2008-01-01

The paper presents a chemical composition analysis of the gases emanated from geothermal sources in the Herculane Spa area (Romania). The upper homologues of methane have been identified in these gases. An ion-molecule reaction mechanism could be implicated in the formation of the upper homologues of methane. The CH4+ ions that appear under the action of radiation are the starting point of these reactions. The presence of hydrogen in the emanated gases may be also a result of these reactions. PMID:19325844

In silico prediction of potential chemical reactions mediated by human enzymes.

PubMed

Yu, Myeong-Sang; Lee, Hyang-Mi; Park, Aaron; Park, Chungoo; Ceong, Hyithaek; Rhee, Ki-Hyeong; Na, Dokyun

2018-06-13

Administered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. However, there are more than thousands of different cellular enzymes that potentially convert administered drug into other forms. We developed an in silico model to predict which of human enzymes including metabolic enzymes as well as CYP450 family can catalyze a given chemical compound. The prediction is based on the chemical and physical similarity between known enzyme substrates and a query chemical compound. Our in silico model was developed using multiple linear regression and the model showed high performance (AUC = 0.896) despite of the large number of enzymes. When evaluated on a test dataset, it also showed significantly high performance (AUC = 0.746). Interestingly, evaluation with literature data showed that our model can be used to predict not only enzymatic reactions but also drug conversion and enzyme inhibition. Our model was able to predict enzymatic reactions of a query molecule with a high accuracy. This may foster to discover new metabolic routes and to accelerate the computational development of drug candidates by enabling the prediction of the potential conversion of administered drugs into active or inactive forms.

Determination of the Rate Coefficients of the SO2 plus O plus M yields SO3 plus M Reaction

NASA Technical Reports Server (NTRS)

Hwang, S. M.; Cooke, J. A.; De Witt, K. J.; Rabinowitz, M. J.

2010-01-01

Rate coefficients of the title reaction R(sub 31) (SO2 +O+M yields SO3 +M) and R(sub 56) (SO2 + HO2 yields SO3 +OH), important in the conversion of S(IV) to S(VI),were obtained at T =970-1150 K and rho (sub ave) = 16.2 micro mol/cubic cm behind reflected shock waves by a perturbation method. Shock-heated H2/ O2/Ar mixtures were perturbed by adding small amounts of SO2 (1%, 2%, and 3%) and the OH temporal profiles were then measured using laser absorption spectroscopy. Reaction rate coefficients were elucidated by matching the characteristic reaction times acquired from the individual experimental absorption profiles via simultaneous optimization of k(sub 31) and k(sub 56) values in the reaction modeling (for satisfactory matches to the observed characteristic times, it was necessary to take into account R(sub 56)). In the experimental conditions of this study, R(sub 31) is in the low-pressure limit. The rate coefficient expressions fitted using the combined data of this study and the previous experimental results are k(sub 31,0)/[Ar] = 2.9 10(exp 35) T(exp ?6.0) exp(?4780 K/T ) + 6.1 10(exp 24) T(exp ?3.0) exp(?1980 K/T ) cm(sup 6) mol(exp ?2)/ s at T = 300-2500 K; k(sub 56) = 1.36 10(exp 11) exp(?3420 K/T ) cm(exp 3)/mol/s at T = 970-1150 K. Computer simulations of typical aircraft engine environments, using the reaction mechanism with the above k(sub 31,0) and k(sub 56) expressions, gave the maximum S(IV) to S(VI) conversion yield of ca. 3.5% and 2.5% for the constant density and constant pressure flow condition, respectively. Moreover, maximum conversions occur at rather higher temperatures (?1200 K) than that where the maximum k(sub 31,0) value is located (approximately 800 K). This is because the conversion yield is dependent upon not only the k(sup 31,0) and k(sup 56) values (production flux) but also the availability of H, O, and HO2 in the system (consumption flux).

Methods and systems for carrying out a pH-influenced chemical and/or biological reaction

DOEpatents

Stern, Michael C.; Simeon, Fritz; Hatton, Trevor Alan

2016-04-05

The present invention generally relates to methods and systems for carrying out a pH-influenced chemical and/or biological reaction. In some embodiments, the pH-influenced reaction involves the conversion of CO.sub.2 to a dissolved species.

Organo- and nano-catalyst in greener reaction medium: Microwave-assisted expedient synthesis of fine chemicals