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Sample records for activated chemical reactions

  1. Force-activated reactivity switch in a bimolecular chemical reaction.

    PubMed

    Garcia-Manyes, Sergi; Liang, Jian; Szoszkiewicz, Robert; Kuo, Tzu-Ling; Fernández, Julio M

    2009-06-01

    The effect of mechanical force on the free-energy surface that governs a chemical reaction is largely unknown. The combination of protein engineering with single-molecule force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by nucleophiles in a bimolecular substitution reaction (S(N)2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity 'switch' at ∼500 pN, after which the accelerating effect of force on the rate of an S(N)2 chemical reaction greatly diminishes. We propose that an abrupt force-induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in S(N)2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule.

  2. Microfluidic chemical reaction circuits

    SciTech Connect

    Lee, Chung-cheng; Sui, Guodong; Elizarov, Arkadij; Kolb, Hartmuth C; Huang, Jiang; Heath, James R; Phelps, Michael E; Quake, Stephen R; Tseng, Hsian-rong; Wyatt, Paul; Daridon, Antoine

    2012-06-26

    New microfluidic devices, useful for carrying out chemical reactions, are provided. The devices are adapted for on-chip solvent exchange, chemical processes requiring multiple chemical reactions, and rapid concentration of reagents.

  3. X-ray imaging of chemically active valence electrons during a pericyclic reaction

    PubMed Central

    Bredtmann, Timm; Ivanov, Misha; Dixit, Gopal

    2014-01-01

    Time-resolved imaging of chemically active valence electron densities is a long-sought goal, as these electrons dictate the course of chemical reactions. However, X-ray scattering is always dominated by the core and inert valence electrons, making time-resolved X-ray imaging of chemically active valence electron densities extremely challenging. Here we demonstrate an effective and robust method, which emphasizes the information encoded in weakly scattered photons, to image chemically active valence electron densities. The degenerate Cope rearrangement of semibullvalene, a pericyclic reaction, is used as an example to visually illustrate our approach. Our work also provides experimental access to the long-standing problem of synchronous versus asynchronous bond formation and breaking during pericyclic reactions. PMID:25424639

  4. Force-activated reactivity switch in a bimolecular chemical reaction at the single molecule level

    NASA Astrophysics Data System (ADS)

    Szoszkiewicz, Robert; Garcia-Manyes, Sergi; Liang, Jian; Kuo, Tzu-Ling; Fernandez, Julio M.

    2009-10-01

    Mechanical force is a distinct and usually less explored way to activate chemical reaction because it can deform the reacting molecules along a well-defined direction of the reaction coordinate. However, the effect of mechanical force on the free- energy surface that governs a chemical reaction is still largely unknown. The combination of protein engineering with single-molecule force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by some reducing agents in a bimolecular substitution reaction (so-called SN2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity ``switch'' at 500 pN, after which the accelerating effect of force on the rate of an SN2 chemical reaction greatly diminishes. We propose that an abrupt force- induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in SN2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule. References: S. Garcia-Manyes, J. Liang, R. Szoszkiewicz, T-L. Kuo and J. M. Fernandez, Nature Chemistry, 1, 236-242, 2009.

  5. Spatiotemporal regulation of chemical reaction kinetics of cell surface molecules by active remodeling of cortical actin

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Bhaswati; Chaudhuri, Abhishek; Gowrishankar, Kripa; Mayor, Satyajit; Rao, Madan

    2010-03-01

    Cell surface proteins such as lipid tethered GPI-anchored proteins and Ras-proteins are distributed as monomers and nanoclusters on the surface of living cells. Recent work from our laboratory suggests that the spatial distribution and dynamics of formation and breakup of these nanoclusters is controlled by the active remodeling dynamics of the underlying cortical actin. To explain these observations, we propose a novel mechanism of nanoclustering, involving the transient binding to and advection along constitutively occuring ``asters'' of cortical actin. Here we study the consequences of such active actin based clustering, in the context of chemical reactions involving conformational changes of cell surface proteins. We find that active remodeling of cortical actin, can give rise to a dramatic increase in the reaction efficiency and output levels. In general, such actin driven clustering of membrane proteins could be a cellular mechanism to spatiotemporally regulate and amplify local chemical reaction rates, in the context of signalling and endocytosis.

  6. Force-activated reactivity switch in a bimolecular chemical reaction at the single molecule level

    NASA Astrophysics Data System (ADS)

    Szoszkiewicz, Robert; Garcia-Manyes, Sergi; Liang, Jian; Kuo, Tzu-Ling; Fernandez, Julio M.

    2010-03-01

    Mechanical force can deform the reacting molecules along a well-defined direction of the reaction coordinate. However, the effect of mechanical force on the free-energy surface that governs a chemical reaction is still largely unknown. The combination of protein engineering with single-molecule AFM force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by some reducing agents in a bimolecular substitution reaction (so-called SN2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity ``switch'' at 500 pN, after which the accelerating effect of force on the rate of an SN2 chemical reaction greatly diminishes. We propose that an abrupt force-induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in SN2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule. References: Sergi Garcia-Manyes, Jian Liang, Robert Szoszkiewicz, Tzu-Ling Kuo and Julio M. Fernandez, Nature Chemistry, 1, 236-242, 2009.

  7. Chemical Reaction Problem Solving.

    ERIC Educational Resources Information Center

    Veal, William

    1999-01-01

    Discusses the role of chemical-equation problem solving in helping students predict reaction products. Methods for helping students learn this process must be taught to students and future teachers by using pedagogical skills within the content of chemistry. Emphasizes that solving chemical reactions should involve creative cognition where…

  8. Time-temperature-transformation curves in chemical reactions regulated by cytoskeletal activity

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Bhaswati; Chaudhuri, Abhishek; Gowrishankar, Kripa; Mayor, Satyajit; Rao, Madan

    2012-02-01

    Efficient and reproducible construction of signaling and sorting complexes, both on the surface and within the living cell, is contingent on local regulation of biochemical reactions by the cellular milieu with active components. We have recently proposed that in many cases this spatiotemporal regulation can be mediated by interaction with components of the dynamic cytoskeleton, where the interplay between active contractility and remodeling of the cytoskeleton results in transient focusing of passive molecules to form clusters, leading to a dramatic increase in the reaction efficiency and output levels. In this presentation, we discuss the implications of actin dynamics by introducing an ``effective temperature,'' which can work as a regulatory parameter for signaling replacing the details of actin dynamics. We show this in time-temperature-transformation plots, with the proposed ``effective temperature'' as a parameter, which paves way for discussion of active chemical thermodynamics.

  9. Translated chemical reaction networks.

    PubMed

    Johnston, Matthew D

    2014-05-01

    Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analyzed via a variety of techniques, including stoichiometric network analysis, deficiency theory, and algebraic techniques (e.g., Gröbner bases). In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a network's capacity to permit a particular class of steady states, called toric steady states, to topological properties of a generalized network called a translated chemical reaction network. These networks share their reaction vectors with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature.

  10. 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…

  11. Heat and Mass Transfer in Unsteady Rotating Fluid Flow with Binary Chemical Reaction and Activation Energy

    PubMed Central

    Awad, Faiz G.; Motsa, Sandile; Khumalo, Melusi

    2014-01-01

    In this study, the Spectral Relaxation Method (SRM) is used to solve the coupled highly nonlinear system of partial differential equations due to an unsteady flow over a stretching surface in an incompressible rotating viscous fluid in presence of binary chemical reaction and Arrhenius activation energy. The velocity, temperature and concentration distributions as well as the skin-friction, heat and mass transfer coefficients have been obtained and discussed for various physical parametric values. The numerical results obtained by (SRM) are then presented graphically and discussed to highlight the physical implications of the simulations. PMID:25250830

  12. Biological and chemical assessment of antioxidant activity of sugar-lysine model maillard reaction products.

    PubMed

    Kitts, David D; Hu, Chun

    2005-06-01

    The antioxidant activity of Maillard reaction products (MRPs) is often associated with increased stability and shelf life of food systems vulnerable to oxidation reactions. In this study, nondialyzed, high-molecular weight (HMW = >3500 Da) MRPs were recovered from three model sugar-lysine (glucose-lysine, Glc-Lys; fructose-lysine, Fru-Lys; and ribose-lysine, Rib-Lys) reactions, heated at 121 degrees C for one hour. Samples were characterized by UV and fluorescence spectra and assessed for antioxidant activity using both standard chemical methods (1,1-diphenyl-2-picryl-hydrazyl [DPPH] and oxygen radical absorbing capacity [ORAC]). In addition, biochemical (e.g., cell culture for intracellular oxidation in RAW264.7 cells and protection against metal ion-induced cytotoxicity in C3H/10T1/2 mouse embryo fibroblast cells) assays were used. Patterns of change for fluorescence and multiple colorimetric parameters corresponded to the recovery yield of HMW MRPs and indicated that Rib was more (P < 0.05) reactive than Glc, which in turn was greater (P < 0.05) than Fru. These characteristics of rate of browning did not parallel the significant (P < 0.05) antioxidant activity noted for different sugar-derived HMW MRPs to scavenge DPPH radical, or exhibit total antioxidant activity using the ORAC (e.g., 800-1000 micromol Trolox/gm MRP) method. Antioxidant activity of Glc-, Fru-, and Rib-Lys HMW-MRPs (50 microg/mL) produced protection (P < 0.05) against both H2O2- and AAPH-induced intracellular oxidation reactions in cultured RAW 264.7 cells. Metal chelating activity of all three sugar-derived HMW MRPs (0.01% w/v) was attributed to similar protection (P < 0.05) against Fe2+ and Cu2+-induced cytotoxicity in cultured mouse embryonic fibroblasts. The reducing activity of all three HMW-MRPs indicated the potential for prooxidant activity that could explain enhanced cytotoxicity of Fe3+ in cultured cells.

  13. Chemical Reactions at Surfaces

    SciTech Connect

    Michael Henderson and Nancy Ryan Gray

    2010-04-14

    Chemical reactions at surfaces underlie some of the most important processes of today, including catalysis, energy conversion, microelectronics, human health and the environment. Understanding surface chemical reactions at a fundamental level is at the core of the field of surface science. The Gordon Research Conference on Chemical Reactions at Surfaces is one of the premiere meetings in the field. The program this year will cover a broad range of topics, including heterogeneous catalysis and surface chemistry, surfaces in environmental chemistry and energy conversion, reactions at the liquid-solid and liquid-gas interface, electronic materials growth and surface modification, biological interfaces, and electrons and photons at surfaces. An exciting program is planned, with contributions from outstanding speakers and discussion leaders from the international scientific community. The conference provides a dynamic environment with ample time for discussion and interaction. Attendees are encouraged to present posters; the poster sessions are historically well attended and stimulate additional discussions. The conference provides an excellent opportunity for junior researchers (e.g. graduate students or postdocs) to present their work and interact with established leaders in the field.

  14. 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.

  15. Chemical Reactions in Clusters

    DTIC Science & Technology

    1992-11-04

    NH 3)n, n _> 4, clusters has been attributed to the (solvated) naphtholate anion.3a A single picosecond decay measurement has been reported which...vibrational energy in the cluster Sl state. The data are summarized in Table I. A model to explain these decay results can be constructed based on a proton...11 TITLE (Include Security Classification) Chemical Reactions in Clusters 12 PERSONAL AUTHOR(S) Elliot R. Bernstein 13a TYPE OF REPORT 13b TIME COVERED

  16. Chemically activated formation of organic acids in reactions of the Criegee intermediate with aldehydes and ketones.

    PubMed

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

    2013-10-21

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

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

    SciTech Connect

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

    2013-08-08

    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 hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO 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.

  18. Chemical Reactions in DSMC

    SciTech Connect

    Bird, G. A.

    2011-05-20

    DSMC simulations of chemically reacting gas flows have generally employed procedures that convert the macroscopic chemical rate equations to reaction cross-sections at the microscopic level. They therefore depend on the availability of experimental data that has been fitted to equations of the Arrhenius form. This paper presents a physical model for dissociation and recombination reactions and a phenomenological model for exchange and chain reactions. These are based on the vibrational states of the colliding molecules and do not require any experimentally-based data. The simplicity of the models allows the corresponding rate equations to be written down and, while these are not required for the implementation of the models, they facilitate their validation. The model is applied to a typical hypersonic atmospheric entry problem and the results are compared with the corresponding results from the traditional method. It is also used to investigate both spontaneous and forced ignition as well as the structure of a deflagration wave in an oxygen-hydrogen mixture.

  19. Chemical Reactions in DSMC

    NASA Astrophysics Data System (ADS)

    Bird, G. A.

    2011-05-01

    DSMC simulations of chemically reacting gas flows have generally employed procedures that convert the macroscopic chemical rate equations to reaction cross-sections at the microscopic level. They therefore depend on the availability of experimental data that has been fitted to equations of the Arrhenius form. This paper presents a physical model for dissociation and recombination reactions and a phenomenological model for exchange and chain reactions. These are based on the vibrational states of the colliding molecules and do not require any experimentally-based data. The simplicity of the models allows the corresponding rate equations to be written down and, while these are not required for the implementation of the models, they facilitate their validation. The model is applied to a typical hypersonic atmospheric entry problem and the results are compared with the corresponding results from the traditional method. It is also used to investigate both spontaneous and forced ignition as well as the structure of a deflagration wave in an oxygen-hydrogen mixture.

  20. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures.

    PubMed

    Tsuruoka, Shuji; Matsumoto, Hidetoshi; Castranova, Vincent; Porter, Dale W; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2015-12-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential.

  1. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures

    PubMed Central

    Castranova, Vincent; Porter, Dale W.; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2016-01-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential. PMID:26783369

  2. 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

  3. Mass Transfer with Chemical Reaction.

    ERIC Educational Resources Information Center

    DeCoursey, W. J.

    1987-01-01

    Describes the organization of a graduate course dealing with mass transfer, particularly as it relates to chemical reactions. Discusses the course outline, including mathematics models of mass transfer, enhancement of mass transfer rates by homogeneous chemical reaction, and gas-liquid systems with chemical reaction. (TW)

  4. Photocatalytic activity of layered perovskite-like oxides in practically valuable chemical reactions

    NASA Astrophysics Data System (ADS)

    Rodionov, I. A.; Zvereva, I. A.

    2016-03-01

    The photocatalytic properties of layered perovskite-like oxides corresponding to the Ruddlesen-Popper, Dion-Jacobson and Aurivillius phases are considered. Of the photocatalytic reactions, the focus is on the reactions of water splitting, hydrogen evolution from aqueous solutions of organic substances and degradation of model organic pollutants. Possibilities to conduct these reactions under UV and visible light in the presence of layered perovskite-like oxides and composite photocatalysts based on them are shown. The specific surface area, band gap energy, particle morphology, cation and anion doping and surface modification are considered as factors that affect the photocatalytic activity. Special attention is paid to the possibilities to enhance the photocatalytic activity by intercalation, ion exchange and exfoliation, which are inherent in this class of compounds. Conclusions are made about the prospects for the use of layered perovskite-like oxides in photocatalysis. The bibliography includes 253 references.

  5. Catalytically active polymers obtained by molecular imprinting and their application in chemical reaction engineering.

    PubMed

    Brüggemann, O

    2001-08-01

    Molecular imprinting is a way of creating polymers bearing artificial receptors. It allows the fabrication of highly selective plastics by polymerizing monomers in the presence of a template. This technique primarily had been developed for the generation of biomimetic materials to be used in chromatographic separation, in extraction approaches and in sensors and assays. Beyond these applications, in the past few years molecular imprinting has become a tool for producing new kinds of catalysts. For catalytic applications, the template must be chosen, so that it is structurally comparable with the transition state (a transition state analogue, TSA) of a reaction, or with the product or substrate. The advantage of using these polymeric catalysts is obvious: the backbone withstands more aggressive conditions than a bio material could ever survive. Results are presented showing the applicability of a molecularly imprinted catalyst in different kinds of chemical reactors. It is demonstrated that the catalysts can be utilized not only in batch but also in continuously driven reactors and that their performance can be improved by means of chemical reaction engineering.

  6. Chemical burn or reaction

    MedlinePlus

    ... different products that contain toxic chemicals such as ammonia and bleach. The mixture can give off hazardous ... chemicals immediately after use. Use paints, petroleum products, ammonia, bleach, and other products that give off fumes ...

  7. More on Chemical Reaction Balancing.

    ERIC Educational Resources Information Center

    Swinehart, D. F.

    1985-01-01

    A previous article stated that only the matrix method was powerful enough to balance a particular chemical equation. Shows how this equation can be balanced without using the matrix method. The approach taken involves writing partial mathematical reactions and redox half-reactions, and combining them to yield the final balanced reaction. (JN)

  8. Impact of active phase chemical composition and dispersity on catalytic behavior in PROX reaction

    NASA Astrophysics Data System (ADS)

    Cherkezova-Zheleva, Z.; Paneva, D.; Todorova, S.; Kolev, H.; Shopska, M.; Yordanova, I.; Mitov, I.

    2014-04-01

    Iron and iron-platinum catalysts supported on activated carbon have been successfully synthesized by wet impregnation method and low-temperature treatment in inert atmosphere. The content of the supported phases corresponds to 10 wt % Fe and 0.5 wt % Pt. Four catalytic samples were synthesized: Sample A—activated carbon impregnated with Fe nitrate; Sample B—activated carbon impregnated with Pt salt; Sample C—activated carbon impregnated consequently with Fe and Pt salts; Sample D—activated carbon impregnated simultaneously with Fe and Pt salts. The as-prepared materials were characterized by Mössbauer spectroscopy, X-ray diffraction, infrared and X-ray photoelectron spectroscopy. The spectra show that the activated carbon support and the preparation procedure give rise to the synthesis of isolated metal Pt ions and ultradispersed Fe and Pt oxide species. Probably the presence of different functional groups of activated carbon gives rise to registered very high dispersion of loaded species on support. The catalytic tests were carried out in PROX reaction. A lower activity of bimetallic Pt-Fe samples was explained with the increase in surface oxygen species as a result of predomination of iron oxide on the support leading to the increase in selectivity to the H2 oxidation. Partial agglomeration of supported iron oxide phase was registered after catalytic tests.

  9. Speeding chemical reactions by focusing.

    PubMed

    Lacasta, A M; Ramírez-Piscina, L; Sancho, J M; Lindenberg, K

    2013-04-14

    We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, and obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate ∼t(-1/2) to very close to the perfect mixing rate, ∼t(-1).

  10. Speeding chemical reactions by focusing

    NASA Astrophysics Data System (ADS)

    Lacasta, A. M.; Ramírez-Piscina, L.; Sancho, J. M.; Lindenberg, K.

    2013-04-01

    We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, and obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate ˜t-1/2 to very close to the perfect mixing rate, ˜t-1.

  11. Singular characteristics and unique chemical bond activation mechanisms of photocatalytic reactions on plasmonic nanostructures.

    PubMed

    Christopher, Phillip; Xin, Hongliang; Marimuthu, Andiappan; Linic, Suljo

    2012-12-01

    The field of heterogeneous photocatalysis has almost exclusively focused on semiconductor photocatalysts. Herein, we show that plasmonic metallic nanostructures represent a new family of photocatalysts. We demonstrate that these photocatalysts exhibit fundamentally different behaviour compared with semiconductors. First, we show that photocatalytic reaction rates on excited plasmonic metallic nanostructures exhibit a super-linear power law dependence on light intensity (rate ∝ intensity(n), with n > 1), at significantly lower intensity than required for super-linear behaviour on extended metal surfaces. We also demonstrate that, in sharp contrast to semiconductor photocatalysts, photocatalytic quantum efficiencies on plasmonic metallic nanostructures increase with light intensity and operating temperature. These unique characteristics of plasmonic metallic nanostructures suggest that this new family of photocatalysts could prove useful for many heterogeneous catalytic processes that cannot be activated using conventional thermal processes on metals or photocatalytic processes on semiconductors.

  12. 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.

  13. Kinematically complete chemical reaction dynamics

    NASA Astrophysics Data System (ADS)

    Trippel, S.; Stei, M.; Otto, R.; Hlavenka, P.; Mikosch, J.; Eichhorn, C.; Lourderaj, U.; Zhang, J. X.; Hase, W. L.; Weidemüller, M.; Wester, R.

    2009-11-01

    Kinematically complete studies of molecular reactions offer an unprecedented level of insight into the dynamics and the different mechanisms by which chemical reactions occur. We have developed a scheme to study ion-molecule reactions by velocity map imaging at very low collision energies. Results for the elementary nucleophilic substitution (SN2) reaction Cl- + CH3I → ClCH3 + I- are presented and compared to high-level direct dynamics trajectory calculations. Furthermore, an improved design of the crossed-beam imaging spectrometer with full three-dimensional measurement capabilities is discussed and characterization measurements using photoionization of NH3 and photodissociation of CH3I are presented.

  14. Chemical characteristics and enhanced hepatoprotective activities of Maillard reaction products derived from milk protein-sugar system.

    PubMed

    Oh, Nam Su; Young Lee, Ji; Lee, Hyun Ah; Joung, Jae Yeon; Shin, Yong Kook; Kim, Sae Hun; Kim, Younghoon; Lee, Kwang Won

    2016-02-01

    The objective of this study was to investigate the characteristics, antioxidative properties, and hepatoprotective effects of Maillard reaction products (MRP) from milk protein reacted with sugars. The MRP were obtained from milk protein, whey protein concentrates and sodium caseinate, using 2 types of sugars, lactose and glucose, by heating the mixture at 55°C for 7d in a sodium phosphate buffer (pH 7.4). Changes in the chemical modification of the milk protein were monitored by measuring the protein-bound carbonyls and PAGE protein profiles. The results showed that the amount of protein-bound carbonyls increased after Maillard reaction (MR). In addition, sodium dodecyl sulfate-PAGE analysis indicated a formation of high-molecular weight complexes through MR. The modification sites induced by MR of milk protein were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of tryptic-digested gel spots of MRP. As a result, modification and their localization in AA sequence of MRP was identified. Also, the MRP showed higher antioxidant activities than the intact milk protein, and they reduced intracellular reactive oxygen species production and inhibited the depletion of the reduced glutathione concentrations in the HepG2 cells. In particular, glucose-sodium caseinate MRP showed the highest biological activities among all MRP. Therefore, these results suggest that the MRP from milk protein reacting with sugars possess effective antioxidant activity and have a protective ability against oxidative damage.

  15. Chemical reactions confined within carbon nanotubes.

    PubMed

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

    2016-08-22

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

  16. A continuous sirtuin activity assay without any coupling to enzymatic or chemical reactions

    PubMed Central

    Schuster, Sabine; Roessler, Claudia; Meleshin, Marat; Zimmermann, Philipp; Simic, Zeljko; Kambach, Christian; Schiene-Fischer, Cordelia; Steegborn, Clemens; Hottiger, Michael O.; Schutkowski, Mike

    2016-01-01

    Sirtuins are NAD+ dependent lysine deacylases involved in many regulatory processes such as control of metabolic pathways, DNA repair and stress response. Modulators of sirtuin activity are required as tools for uncovering the biological function of these enzymes and as potential therapeutic agents. Systematic discovery of such modulators is hampered by the lack of direct and continuous activity assays. The present study describes a novel continuous assay based on the increase of a fluorescence signal subsequent to sirtuin mediated removal of a fluorescent acyl chain from a modified TNFα-derived peptide. This substrate is well recognized by human sirtuins 1–6 and represents the best sirtuin 2 substrate described so far with a kcat/KM-value of 176 000 M−1s−1. These extraordinary substrate properties allow the first determination of Ki-values for the specific Sirt2 inhibitory peptide S2iL5 (600 nM) and for the quasi-universal sirtuin inhibitor peptide thioxo myristoyl TNFα (80 nM). PMID:26940860

  17. Artificial Chemical Reporter Targeting Strategy Using Bioorthogonal Click Reaction for Improving Active-Targeting Efficiency of Tumor.

    PubMed

    Yoon, Hong Yeol; Shin, Min Lee; Shim, Man Kyu; Lee, Sangmin; Na, Jin Hee; Koo, Heebeom; Lee, Hyukjin; Kim, Jong-Ho; Lee, Kuen Yong; Kim, Kwangmeyung; Kwon, Ick Chan

    2017-03-15

    Biological ligands such as aptamer, antibody, glucose, and peptide have been widely used to bind specific surface molecules or receptors in tumor cells or subcellular structures to improve tumor-targeting efficiency of nanoparticles. However, this active-targeting strategy has limitations for tumor targeting due to inter- and intraheterogeneity of tumors. In this study, we demonstrated an alternative active-targeting strategy using metabolic engineering and bioorthogonal click reaction to improve tumor-targeting efficiency of nanoparticles. We observed that azide-containing chemical reporters were successfully generated onto surface glycans of various tumor cells such as lung cancer (A549), brain cancer (U87), and breast cancer (BT-474, MDA-MB231, MCF-7) via metabolic engineering in vitro. In addition, we compared tumor targeting of artificial azide reporter with bicyclononyne (BCN)-conjugated glycol chitosan nanoparticles (BCN-CNPs) and integrin αvβ3 with cyclic RGD-conjugated CNPs (cRGD-CNPs) in vitro and in vivo. Fluorescence intensity of azide-reporter-targeted BCN-CNPs in tumor tissues was 1.6-fold higher and with a more uniform distribution compared to that of cRGD-CNPs. Moreover, even in the isolated heterogeneous U87 cells, BCN-CNPs could bind artificial azide reporters on tumor cells more uniformly (∼92.9%) compared to cRGD-CNPs. Therefore, the artificial azide-reporter-targeting strategy can be utilized for targeting heterogeneous tumor cells via bioorthogonal click reaction and may provide an alternative method of tumor targeting for further investigation in cancer therapy.

  18. 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

  19. 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

  20. 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

  1. Chemical reactions in endoreversible thermodynamics

    NASA Astrophysics Data System (ADS)

    Wagner, Katharina; Hoffmann, Karl Heinz

    2016-01-01

    Endoreversible thermodynamics is a theory for the (approximate) description of thermodynamic non-equilibrium systems, which allows us to capture the ever present irreversibilities of real processes. For instance in heat engines the dissipation due to finite heat transport capabilities, as well as the resulting limitations in the energy fluxes, can be incorporated into the theory. It has thus been very successful in closing the gap between observed and theoretically predicted efficiencies. Here an extension of the theory is provided, with which chemical reactions can be included in the formalism. This opens up a wide field of applications for endoreversible modeling and the investigation of dissipative processes, for instance in fuel cells or batteries.

  2. 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.

  3. 2005 Chemical Reactions at Surfaces

    SciTech Connect

    Cynthia M. Friend

    2006-03-14

    The Gordon Research Conference (GRC) on 2005 Chemical Reactions at Surfaces was held at Ventura Beach Marriott, Ventura California from February 13, 2005 through February 18, 2005. The Conference was well-attended with 124 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, 'free time' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

  4. Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions

    ERIC Educational Resources Information Center

    Schultz, Emeric

    2008-01-01

    A highly flexible learning tool, referred to as a dynamic reaction figure, is described. Application of these figures can (i) yield the correct chemical equation by simply following a set of menu driven directions; (ii) present the underlying "mechanism" in chemical reactions; and (iii) help to solve quantitative problems in a number of different…

  5. Analytic study of the chain dark decomposition reaction of iodides - atomic iodine donors - in the active medium of a pulsed chemical oxygen-iodine laser: 2. Limiting parameters of the branching chain dark decomposition reaction of iodides

    SciTech Connect

    Andreeva, Tamara L; Kuznetsova, S V; Maslov, Aleksandr I; Sorokin, Vadim N

    2009-08-31

    The final stages in the development of a branching chain decomposition reaction of iodide in the active medium of a pulsed chemical oxygen-iodine laser (COIL) are analysed. Approximate expressions are derived to calculate the limiting parameters of the chain reaction: the final degree of iodide decomposition, the maximum concentration of excited iodine atoms, the time of its achievement, and concentrations of singlet oxygen and iodide at that moment. The limiting parameters, calculated by using these expressions for a typical composition of the active medium of a pulsed COIL, well coincide with the results of numerical calculations. (active media)

  6. 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.

  7. Quantum-Chemical Study of the Discrimination against dNTP in the Nucleotide Addition Reaction in the Active Site of RNA Polymerase II.

    PubMed

    Roßbach, Sven; Ochsenfeld, Christian

    2017-04-11

    Eukaryotic RNA polymerase II catalyzes the transcription of DNA into mRNA very efficiently and with an extremely low error rate with regard to matching base and sugar moiety. Despite its importance, little is known about how it discriminates against 2'-deoxy NTPs during the chemical reaction. To investigate the differences in the addition reactions of ATP and dATP, we used FF-MD and QM/MM calculations within a nudged elastic band approach, which allowed us to find the energetically accessible reaction coordinates. By converging the QM size, we found that 800 QM atoms are necessary to properly describe the active site. We show how the absence of a single hydrogen bond between the enzyme and the NTP 2'-OH group leads to an increase of the reaction barrier by 16 kcal/mol and therefore conclude that Arg446 is the key residue in the discrimination process.

  8. Chemical reactions in shear-free turbulence

    NASA Astrophysics Data System (ADS)

    de Bruyn Kops, Stephen M.; Riley, James J.

    2000-11-01

    Understanding and predicting the reaction of chemical species in shear-free turbulence is important in research addressing natural as well as technological problems. In the configuration considered here, two initially separated species mix and react downstream of a turbulence-generating grid in a wind tunnel. Results are reported from high resolution, direct numerical simulations in which the evolution of the conserved scalar field accurately matches that of the temperature field in existing laboratory experiments. Superimposed on the flow are passive, single-step, temperature-dependent reactions with a wide range of activation energies and stoichiometric ratios. Several aspects of the flow are investigated here with the conclusions that (1) reactions in which r ne 1 are more accurately modeled by frozen and equilibrium chemistry limits than are reactions in which r=1; (2) an existing definition of a reduced Damköhler number that includes temperature and stoichiometry effects is a very good measure of reaction rate; and (3) existing theoretical models for the coherence and phase of fuel-oxidizer cross-spectra and the spectrum of the equilibrium fuel mass fraction when r=1 yield accurate predictions. (Supported by NSF and AFOSR.)

  9. 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.

  10. 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.

  11. '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...

  12. 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.

  13. Vibrational Participation in Chemical Reactions.

    DTIC Science & Technology

    1986-08-22

    Cesaro Xue-Feng Yang .. V-. V 8. IV. BIBLIOGRAPHY, AFOSR-SPONSORED RESEARCH, 1981 - 1984 1981 Vibrational Excitation of Ozone and Molecular Fluorine...Phys. Chem. 87, 2142 (1983). G.C. Pimentel, S.N. Cesaro and H. Frei. 11. Selective Vibronic Excitation of Singlet Oxygen-Furan Reactions in Cryogenic

  14. Modeling of turbulent chemical reaction

    NASA Technical Reports Server (NTRS)

    Chen, J.-Y.

    1995-01-01

    Viewgraphs are presented on modeling turbulent reacting flows, regimes of turbulent combustion, regimes of premixed and regimes of non-premixed turbulent combustion, chemical closure models, flamelet model, conditional moment closure (CMC), NO(x) emissions from turbulent H2 jet flames, probability density function (PDF), departures from chemical equilibrium, mixing models for PDF methods, comparison of predicted and measured H2O mass fractions in turbulent nonpremixed jet flames, experimental evidence of preferential diffusion in turbulent jet flames, and computation of turbulent reacting flows.

  15. 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.

  16. Chemical Reactions at Surfaces. Final Progress Report

    SciTech Connect

    2003-02-21

    The Gordon Research Conference (GRC) on Chemical Reactions at Surfaces was held at Holiday Inn, Ventura, California, 2/16-21/03. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  17. Chemically activated reactions on the C7H5 energy surface: propargyl + diacetylene, i-C5H3 + acetylene, and n-C5H3 + acetylene.

    PubMed

    da Silva, Gabriel; Trevitt, Adam J

    2011-05-21

    This study uses computational chemistry and statistical reaction rate theory to investigate the chemically activated reaction of diacetylene (butadiyne, C(4)H(2)) with the propargyl radical (C˙H(2)CCH) and the reaction of acetylene (C(2)H(2)) with the i-C(5)H(3) (CH(2)CCCC˙H) and n-C(5)H(3) (CHCC˙HCCH) radicals. A detailed G3SX-level C(7)H(5) energy surface demonstrates that the C(3)H(3) + C(4)H(2) and C(5)H(3) + C(2)H(2) addition reactions proceed with moderate barriers, on the order of 10 to 15 kcal mol(-1), and form activated open-chain C(7)H(5) species that can isomerize to the fulvenallenyl radical with the highest barrier still significantly below the entrance channel energy. Higher-energy pathways are available leading to other C(7)H(5) isomers and to a number of C(7)H(4) species + H. Rate constants in the large multiple-well (15) multiple-channel (30) chemically activated system are obtained from a stochastic solution of the one-dimensional master equation, with RRKM theory for microcanonical rate constants. The dominant products of the C(4)H(2) + C(3)H(3) reaction at combustion-relevant temperatures and pressures are i-C(5)H(3) + C(2)H(2) and CH(2)CCHCCCCH + H, along with several quenched C(7)H(5) intermediate species below 1500 K. The major products in the n-C(5)H(3) + C(2)H(2) reaction are i-C(5)H(3) + C(2)H(2) and a number of C(7)H(4) species + H, with C(7)H(5) radical stabilization at lower temperatures. The i-C(5)H(3) + C(2)H(2) reaction predominantly leads to C(7)H(4) + H and to stabilized C(7)H(5) products. The title reactions may play an important role in polycyclic aromatic hydrocarbon (PAH) formation in combustion systems. The C(7)H(5) potential energy surface developed here also provides insight into several other important reacting gas-phase systems relevant to combustion and astrochemistry, including C(2)H + the C(3)H(4) isomers propyne and allene, benzyne + CH, benzene + C((3)P), and C(7)H(5) radical decomposition, for which some

  18. Chemical Reactions in Turbulent Mixing Flows

    DTIC Science & Technology

    1993-07-15

    investigations of turbulent mixing, chemical reaction and combustion processes in turbulent, subsonic and supersonic flows. The program was comprised of...34) n•4I Abstract The purpose of this research is to conduct fundamental investigations of tur- bulent mixing, chemical reaction and combustion processes ...Another issue to consider is that different data- processing used on the different sets of data might result in differences between sets of data. To this end

  19. 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.

  20. Kinetic studies of elementary chemical reactions

    SciTech Connect

    Durant, J.L. Jr.

    1993-12-01

    This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

  1. 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…

  2. The quantum dynamics of chemical reactions

    NASA Astrophysics Data System (ADS)

    Kuppermann, A.

    1983-03-01

    In this project, we developed accurate and approximate methods for calculating cross sections of elementary reactions. These methods were applied to systems of importance for the fundamental aspects of chemical dynamics and for advanced technologies of interest to the United States Air Force. The application included calculations of three-atom exchange reactions, break-up and three-body recombination collisions and vibrational quenching by reaction. These calculations improved our understanding of such processes and permitted an assessment of some approximate methods.

  3. Ultrafast Dynamics of Chemical Reactions.

    DTIC Science & Technology

    2007-11-02

    Michael R. Berman 11 SUPPLEMENTARY NOTES 12a D!STRIBUTION AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE 13 Ap’-,T,,,ACT `’,Ii "•--200words) The research and...Caltech), Professor K. Wilson (UC, San Diego), and Professor J. Polanyi (Toronto). 3 6. Publications (1995/1996) Books Collected Works (up to 1994...1995) Direct Observation of The Transition State J. C. Polanyi and A. H. Zewail Accounts of Chemical Research (Holy-Grail Special Issue), 28,119 (1995

  4. 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.

  5. Effects of Chemical versus Electrochemical Delithiation on the Oxygen Evolution Reaction Activity of Nickel-Rich Layered LiMO2.

    PubMed

    Augustyn, Veronica; Manthiram, Arumugam

    2015-10-01

    Nickel-rich layered LiMO2 (M = transition metal) oxides doped with iron exhibit high oxygen evolution reaction (OER) activity in alkaline electrolytes. The LiMO2 oxides offer the possibility of investigating the influence of the number of d electrons on OER by tuning the oxidation state of M via chemical or electrochemical delithiation. Accordingly, we investigate here the electrocatalytic behavior of LiNi0.7Co0.3O2 and LiNi0.7Co0.2Fe0.1O2 before and after chemical delithiation. In addition to varying the oxidation state of the transition-metal ions, we find that chemical delithiation also affects the local chemical environment and morphology. The electrochemical response differs depending on whether the delithiation occurred ex situ chemically or in situ during the electrocatalysis. The results point to the important role of in situ transformation in LiMO2 in alkaline electrolytes during electrocatalytic cycling.

  6. 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…

  7. 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).

  8. Gas-phase reactions of doubly charged actinide cations with alkanes and alkenes--probing the chemical activity of 5f electrons from Th to Cm.

    PubMed

    Marçalo, Joaquim; Santos, Marta; Gibson, John K

    2011-11-07

    Small alkanes (methane, ethane, propane, n-butane) and alkenes (ethene, propene, 1-butene) were used to probe the gas-phase reactivity of doubly charged actinide cations, An(2+) (An = Th, Pa, U, Np, Pu, Am, Cm), by means of Fourier transform ion cyclotron resonance mass spectrometry. Different combinations of doubly and singly charged ions were observed as reaction products, comprising species formed via metal-ion induced eliminations of small molecules, simple adducts and ions resulting from electron, hydride or methide transfer channels. Th(2+), Pa(2+), U(2+) and Np(2+) preferentially yielded doubly charged products of hydrocarbon activation, while Pu(2+), Am(2+) and Cm(2+) reacted mainly through transfer channels. Cm(2+) was also capable of forming doubly charged products with some of the hydrocarbons whereas Pu(2+) and Am(2+) were not, these latter two ions conversely being the only for which adduct formation was observed. The product distributions and the reaction efficiencies are discussed in relation to the electronic configurations of the metal ions, the energetics of the reactions and similar studies previously performed with doubly charged lanthanide and transition metal cations. The conditions for hydrocarbon activation to occur as related to the accessibility of electronic configurations with one or two 5f and/or 6d unpaired electrons are examined and the possible chemical activity of the 5f electrons in these early actinide ions, particularly Pa(2+), is considered.

  9. Aerosol simulation including chemical and nuclear reactions

    SciTech Connect

    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 reactions 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.

  10. Theoretical study of chemical reactions in solution

    SciTech Connect

    Yokogawa, D.

    2015-12-31

    Quantum chemical calculations in solution are becoming more and more important in chemistry. Reference interaction site model self-consistent field (RISM-SCF) is one of the powerful approaches to perform quantum chemical calculations in solution. In this work, we developed a new generation of RISM-SCF, where a robust fitting method was newly introduced. We applied the new method to tautomerization reaction of cytosine in aqueous phase. Our calculation reproduced experimentally obtained relative stabilities and relative free energies correctly.

  11. Parameter Sensitivity Study of the Unreacted-Core Shrinking Model: A Computer Activity for Chemical Reaction Engineering Courses

    ERIC Educational Resources Information Center

    Tudela, Ignacio; Bonete, Pedro; Fullana, Andres; Conesa, Juan Antonio

    2011-01-01

    The unreacted-core shrinking (UCS) model is employed to characterize fluid-particle reactions that are important in industry and research. An approach to understand the UCS model by numerical methods is presented, which helps the visualization of the influence of the variables that control the overall heterogeneous process. Use of this approach in…

  12. Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory.

    PubMed

    Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G

    2016-03-02

    Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition state theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional-potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.

  13. Chemical Demonstrations with Consumer Chemicals: The Black and White Reaction

    NASA Astrophysics Data System (ADS)

    Wright, Stephen W.

    2002-01-01

    A color-change reaction is described in which two colorless solutions are combined to afford a black mixture. Two more colorless solutions are combined to afford a white mixture. The black and white mixtures are then combined to afford a clear, colorless solution. The reaction uses chemicals that are readily available on the retail market: vitamin C, tincture of iodine, vinegar, ammonia, bleach, Epsom salt, and laundry starch.

  14. 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…

  15. Chemical Reactions in Turbulent Mixing Flows

    DTIC Science & Technology

    1989-10-15

    example, Levenspiel (1962). Eq. 27 would be necessary. A first guess is that it might scale with 6/z as it does for subsonic flow. i.e. -(r, s; M., -0 ) -(r...France), 45-63. KELLER. J. 0. and DAILY. J. W. (1985] "The Effect of Highly Exothermic Chemical Reaction on a Two-Dimensional Mixing Layer", LEVENSPIEL

  16. Documentation of Chemical Reactions. I. A Faceted Classification

    ERIC Educational Resources Information Center

    Osinga, M.; Verrijn Stuart, A. A.

    1973-01-01

    Existing methods for coding chemical compounds are discussed and evaluated as to their suitability for documentation of chemical reactions, a new classification for chemical reactions is presented, and possibilities of automatic encoding are studied. (24 references) (Author)

  17. 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.

  18. Uncertainty Quantification for Nonlinear Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Srinivasan, G.; Robinson, B. A.; Aceves, A. B.; Tartakovsky, D. M.

    2006-12-01

    Systems of coupled chemical reactions are greatly affected by the inherent uncertainties in natural phenomena. These uncertainties can be parametric in nature due to measurement errors or insufficient data. Modeling uncertainties also arise at the molecular level when determining what fraction of the population of each chemical species participates in a chemical reaction at any given time. We present different methods used to quantify both modeling and parametric uncertainties. The application we focus on is that of chemical reactions in the subsurface that greatly affect the transport of contaminants in groundwater. The example considered here is the sorption of Neptunium Np-237 through a competitive ion exchange process. Np-237 is a key radio-nuclide of concern for the Yucca Mountain High Level Waste storage site due to its relatively long half-life, high solubility and low sorption properties. By quantifying the effects of modeling and parametric uncertainties, we can estimate the error associated with Np-237 sorptivity and hence its transport.

  19. Concordant chemical reaction networks and the Species-Reaction Graph.

    PubMed

    Shinar, Guy; Feinberg, Martin

    2013-01-01

    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.

  20. 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

  1. Theoretical studies of chemical reaction dynamics

    SciTech Connect

    Schatz, G.C.

    1993-12-01

    This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

  2. 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.

  3. Quantum Theory of Fast Chemical Reactions

    SciTech Connect

    Light, John C

    2007-07-30

    The aims of the research under this grant were to develop a theoretical understanding and predictive abiility for a variety of processes occurring in the gas phase. These included bimolecular chemical exchange reactions, photodissociation, predissociation resonances, unimolecular reactions and recombination reactions. In general we assumed a knowledge, from quantum chemistry, of the interactions of the atoms and molecular fragments involved. Our focus was primarily on the accurate (quantum) dynamics of small molecular systems. This has been important for many reactions related to combustion and atmospheric chemistry involving light atom transfer reactions and, for example, resonances in dissociation and recombination reactions. The rates of such reactions, as functions of temperature, internal states, and radiation (light), are fundamental for generating models of overall combustion processes. A number of new approaches to these problems were developed inclluding the use of discrete variable representations (DVR's) for evaluating rate constants with the flux-flux correlation approach, finite range approaches to exact quantum scattering calculations, energy selected basis representations, transition state wave packet approaches and improved semiclassical approaches. These (and others) were applied to a number of reactive systems and molecular systems of interest including (many years ago) the isotopic H + H2 exchange reactions, the H2 + OH (and H + H2O) systems, Ozone resonances, van der Waals molecule reactions, etc. A total of 7 graduate students, and 5 post-doctoral Research Associates were supported, at least in part, under this grant and seven papers were published with a total of 10 external collaborators. The majority of the 36 publications under this grant were supported entirely by DOE.

  4. 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

  5. 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.

  6. Steric Control of Complex Chemical Reactions

    DTIC Science & Technology

    2014-05-31

    new light onto the mode- and bond-selective chemistry . We envision that the mode- and bond-selectivity are intimately related to the stereo...of a reaction, as demonstrated in our 2012 Nature Chemistry paper. The detailed methodology is described in the 2014 Journal Chemical Physics paper...13). The most significant contributions during this period are the two papers published in Science 331, 900-903 (2011) and Nature Chemistry 4

  7. Correlating the chemical composition and size of various metal oxide substrates with the catalytic activity and stability of as-deposited Pt nanoparticles for the methanol oxidation reaction

    DOE PAGES

    Megan E. Scofield; Wong, Stanislaus S.; Koenigsmann, Christopher; ...

    2015-12-09

    The performance of electrode materials in conventional direct alcohol fuel cells (DAFC) is constrained by (i) the low activity of the catalyst materials relative to their overall cost, (ii) the poisoning of the active sites due to the presence of partially oxidized carbon species (such as but not limited to CO, formate, and acetate) produced during small molecule oxidation, and (iii) the lack of catalytic stability and durability on the underlying commercial carbon support. Therefore, as a viable alternative, we have synthesized various metal oxide and perovskite materials of different sizes and chemical compositions as supports for Pt nanoparticles (NPs).more » Our results including unique mechanistic studies demonstrate that the SrRuO3 substrate with immobilized Pt NPs at its surface evinces the best methanol oxidation performance as compared with all of the other substrate materials tested herein, including commercial carbon itself. In addition, data from electron energy loss spectroscopy (EELS) and X-ray photoelectron spectroscopy (XPS) confirmed the presence of electron transfer from bound Pt NPs to surface Ru species within the SrRuO3 substrate itself, thereby suggesting that favorable metal support interactions are responsible for the increased methanol oxidation reaction (MOR) activity of Pt species with respect to the underlying SrRuO3 composite catalyst material.« less

  8. Correlating the chemical composition and size of various metal oxide substrates with the catalytic activity and stability of as-deposited Pt nanoparticles for the methanol oxidation reaction

    SciTech Connect

    Megan E. Scofield; Wong, Stanislaus S.; Koenigsmann, Christopher; Bobb-Semple, Dara; Tao, Jing; Tong, Xiao; Wang, Lei; Lewis, Crystal S.; Vuklmirovic, Miomir; Zhu, Yimei; Adzic, Radoslav R.

    2015-12-09

    The performance of electrode materials in conventional direct alcohol fuel cells (DAFC) is constrained by (i) the low activity of the catalyst materials relative to their overall cost, (ii) the poisoning of the active sites due to the presence of partially oxidized carbon species (such as but not limited to CO, formate, and acetate) produced during small molecule oxidation, and (iii) the lack of catalytic stability and durability on the underlying commercial carbon support. Therefore, as a viable alternative, we have synthesized various metal oxide and perovskite materials of different sizes and chemical compositions as supports for Pt nanoparticles (NPs). Our results including unique mechanistic studies demonstrate that the SrRuO3 substrate with immobilized Pt NPs at its surface evinces the best methanol oxidation performance as compared with all of the other substrate materials tested herein, including commercial carbon itself. In addition, data from electron energy loss spectroscopy (EELS) and X-ray photoelectron spectroscopy (XPS) confirmed the presence of electron transfer from bound Pt NPs to surface Ru species within the SrRuO3 substrate itself, thereby suggesting that favorable metal support interactions are responsible for the increased methanol oxidation reaction (MOR) activity of Pt species with respect to the underlying SrRuO3 composite catalyst material.

  9. Chemical Reaction Networks for Computing Polynomials.

    PubMed

    Salehi, Sayed Ahmad; Parhi, Keshab K; Riedel, Marc D

    2017-01-20

    Chemical reaction networks (CRNs) provide a fundamental model in the study of molecular systems. Widely used as formalism for the analysis of chemical and biochemical systems, CRNs have received renewed attention as a model for molecular computation. This paper demonstrates that, with a new encoding, CRNs can compute any set of polynomial functions subject only to the limitation that these functions must map the unit interval to itself. These polynomials can be expressed as linear combinations of Bernstein basis polynomials with positive coefficients less than or equal to 1. In the proposed encoding approach, each variable is represented using two molecular types: a type-0 and a type-1. The value is the ratio of the concentration of type-1 molecules to the sum of the concentrations of type-0 and type-1 molecules. The proposed encoding naturally exploits the expansion of a power-form polynomial into a Bernstein polynomial. Molecular encoders for converting any input in a standard representation to the fractional representation as well as decoders for converting the computed output from the fractional to a standard representation are presented. The method is illustrated first for generic CRNs; then chemical reactions designed for an example are mapped to DNA strand-displacement reactions.

  10. Novel tubing microreactor for monitoring chemical reactions.

    PubMed

    Nielsen, Charles A; Chrisman, Ray W; LaPointe, Robert E; Miller, Theodore E

    2002-07-01

    There is an expanding interest in small-scale methods to evaluate catalysts and chemical reactions at a variety of conditions, ranging up to 6.9 MPa (1000 psig) and 300 degrees C. Multiwell parallel batch techniques are most commonly applied in high-throughput screening systems. In contrast, we describe here a rapid, serial, highly controllable method based on LC-type steel tubing rated for high pressures. The tube, containing a variety of flowing ingredients, such as carrier solvents, catalyst formulations, and reactants, is self-heated ohmically using electrical current from a power supply monitored and regulated with a precision of 0.01%. An array of voltage taps arranged along its length serves to sense the real-time temperature profile of the tube. Reactions are seen as temperature pulses progressing through the reactor, in zones of 200 microL each, and tracked with a temperature precision of 0.1 degrees C. A unique pressure controller was devised to maintain constant reactor pressures despite effluent viscosity fluctuations due to polymerization. Several chemical reaction systems have been characterized to date, including decomposition reactions of di-tert-butyl peroxide, polymerizations of styrene, formation of polyethylene from ethylene, and copolymerization of ethylene with 1-octene. For ethylene polymerization, the amount of mass of polymer formed is proportional to the responses observed.

  11. Stochastic thermodynamics of chemical reaction networks.

    PubMed

    Schmiedl, Tim; Seifert, Udo

    2007-01-28

    For chemical reaction networks in a dilute solution described by a master equation, the authors define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy, applied (chemical) work, and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the entropy of the network itself and the entropy of the medium. The latter is given by the exchanged heat identified through the first law. Total entropy production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem for networks in the steady state. Further exact relations such as a generalized Jarzynski relation and a generalized Clausius inequality are discussed. The authors illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different steady states.

  12. 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...

  13. Role of chemical composition in the enhanced catalytic activity of Pt-based alloyed ultrathin nanowires for the hydrogen oxidation reaction under alkaline conditions

    SciTech Connect

    Megan E. Scofield; Wong, Stanislaus S.; Zhou, Yuchen; Yue, Shiyu; Wang, Lei; Su, Dong; Tong, Xiao; Vukmirovic, Miomir B.; Adzic, Radoslav R.

    2016-05-11

    With the increased interest in the development of hydrogen fuel cells as a plausible alternative to internal combustion engines, recent work has focused on creating alkaline fuel cells (AFC), which employ an alkaline environment. Working in alkaline as opposed to acidic media yields a number of tangible benefits, including (i) the ability to use cheaper and plentiful precious-metal-free catalysts, due to their increased stability, (ii) a reduction in the amount of degradation and corrosion of Pt-based catalysts, and (iii) a longer operational lifetime for the overall fuel cell configuration. However, in the absence of Pt, no catalyst has achieved activities similar to those of Pt. Herein, we have synthesized a number of crystalline ultrathin PtM alloy nanowires (NWs) (M = Fe, Co, Ru, Cu, Au) in order to replace a portion of the costly Pt metal without compromising on activity while simultaneously adding in metals known to exhibit favorable synergistic ligand and strain effects with respect to the host lattice. In fact, our experiments confirm theoretical insights about a clear and correlative dependence between measured activity and chemical composition. We have conclusively demonstrated that our as-synthesized alloy NW catalysts yield improved hydrogen oxidation reaction (HOR) activities as compared with a commercial Pt standard as well as with our as-synthesized Pt NWs. The Pt7Ru3 NW system, in particular, quantitatively achieved an exchange current density of 0.493 mA/cm2, which is higher than the corresponding data for Pt NWs alone. In addition, the HOR activities follow the same expected trend as their calculated hydrogen binding energy (HBE) values, thereby confirming the critical importance and correlation of HBE with the observed activities.

  14. Chemical Reactions in a Sonoluminescing Bubble

    NASA Astrophysics Data System (ADS)

    Yasui, Kyuichi

    1997-09-01

    Rates of chemical reactions in an air bubble are calculatednumerically under a condition of the single-bubble sonoluminescence(SBSL) and that of non-light-emission. In the calculations, effect of non-equilibrium evaporation and condensationof water vapor at the bubble wall andthat of thermal conduction both inside and outside the bubbleare taken into account.Numerical calculations reveal that appreciable amounts of OH, H2O2, HO2, O3, H2, H, and O moleculesare created in a bubble under the condition of SBSL.The amounts of chemical products containing nitrogen such as NOx, NHx, and HNOx are much less than those of the above products at least in the first few acoustic cycles.Numerical calculations also reveal that no chemical reactionstake place under a condition of non-light-emission.Connection with sonoluminescence is also discussed.

  15. 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.

  16. Role of chemical composition in the enhanced catalytic activity of Pt-based alloyed ultrathin nanowires for the hydrogen oxidation reaction under alkaline conditions

    DOE PAGES

    Megan E. Scofield; Wong, Stanislaus S.; Zhou, Yuchen; ...

    2016-05-11

    With the increased interest in the development of hydrogen fuel cells as a plausible alternative to internal combustion engines, recent work has focused on creating alkaline fuel cells (AFC), which employ an alkaline environment. Working in alkaline as opposed to acidic media yields a number of tangible benefits, including (i) the ability to use cheaper and plentiful precious-metal-free catalysts, due to their increased stability, (ii) a reduction in the amount of degradation and corrosion of Pt-based catalysts, and (iii) a longer operational lifetime for the overall fuel cell configuration. However, in the absence of Pt, no catalyst has achieved activitiesmore » similar to those of Pt. Herein, we have synthesized a number of crystalline ultrathin PtM alloy nanowires (NWs) (M = Fe, Co, Ru, Cu, Au) in order to replace a portion of the costly Pt metal without compromising on activity while simultaneously adding in metals known to exhibit favorable synergistic ligand and strain effects with respect to the host lattice. In fact, our experiments confirm theoretical insights about a clear and correlative dependence between measured activity and chemical composition. We have conclusively demonstrated that our as-synthesized alloy NW catalysts yield improved hydrogen oxidation reaction (HOR) activities as compared with a commercial Pt standard as well as with our as-synthesized Pt NWs. The Pt7Ru3 NW system, in particular, quantitatively achieved an exchange current density of 0.493 mA/cm2, which is higher than the corresponding data for Pt NWs alone. In addition, the HOR activities follow the same expected trend as their calculated hydrogen binding energy (HBE) values, thereby confirming the critical importance and correlation of HBE with the observed activities.« less

  17. The smallest chemical reaction system with bistability

    PubMed Central

    Wilhelm, Thomas

    2009-01-01

    Background Bistability underlies basic biological phenomena, such as cell division, differentiation, cancer onset, and apoptosis. So far biologists identified two necessary conditions for bistability: positive feedback and ultrasensitivity. Results Biological systems are based upon elementary mono- and bimolecular chemical reactions. In order to definitely clarify all necessary conditions for bistability we here present the corresponding minimal system. According to our definition, it contains the minimal number of (i) reactants, (ii) reactions, and (iii) terms in the corresponding ordinary differential equations (decreasing importance from i-iii). The minimal bistable system contains two reactants and four irreversible reactions (three bimolecular, one monomolecular). We discuss the roles of the reactions with respect to the necessary conditions for bistability: two reactions comprise the positive feedback loop, a third reaction filters out small stimuli thus enabling a stable 'off' state, and the fourth reaction prevents explosions. We argue that prevention of explosion is a third general necessary condition for bistability, which is so far lacking discussion in the literature. Moreover, in addition to proving that in two-component systems three steady states are necessary for bistability (five for tristability, etc.), we also present a simple general method to design such systems: one just needs one production and three different degradation mechanisms (one production, five degradations for tristability, etc.). This helps modelling multistable systems and it is important for corresponding synthetic biology projects. Conclusion The presented minimal bistable system finally clarifies the often discussed question for the necessary conditions for bistability. The three necessary conditions are: positive feedback, a mechanism to filter out small stimuli and a mechanism to prevent explosions. This is important for modelling bistability with simple systems and for

  18. Quantum dynamics of fast chemical reactions

    SciTech Connect

    Light, J.C.

    1993-12-01

    The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.

  19. Law of Localization in Chemical Reaction Networks

    NASA Astrophysics Data System (ADS)

    Okada, Takashi; Mochizuki, Atsushi

    2016-07-01

    In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g., metabolic pathways. Here we developed a theory to predict the sensitivity, i.e., the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone. Nonzero response patterns turn out to exhibit two characteristic features, localization and hierarchy. We present a general theorem connecting sensitivity with network topology that explains these characteristic patterns. Our results imply that network topology is an origin of biological robustness. Finally, we suggest a strategy to determine real networks from experimental measurements.

  20. Chemical reactions in viscous liquids under space conditions

    NASA Astrophysics Data System (ADS)

    Kondyurin, A.; Lauke, B.; Richter, E.

    A long-term human flight needs a large-size space ships with artificial self-regulating ecological life-support system. The best way for creation of large-size space ship is a synthesis of light construction on Earth orbit, that does not need a high energy transportation carriers from Earth surface. The construction can be created by the way of chemical polymerisation reaction under space environment. But the space conditions are very specific for chemical reactions. A high vacuum, high energy particles, X-rays, UV- and VUV-irradiations, atomic oxygen, microgravity have a significant influence on chemical reactions. Polymerisation reactions in liquid active mixture were studied in simulated space environment. The epoxy resins based on Bisphenol A and amine curing agents were investigated under vacuum, microwave plasma discharge and ion beam. An acceleration of polymerisation reaction with free radicals formation was observed. The polymerisation reaction can be carried out under space environment. The study was supported by Alexander von Humboldt Foundation (A. Kondyurin) and European Space Agency, ESTEC (contract 17083/03/NL/Sfe "Space Environmental Effects on the Polymerisation of Composite Structures").

  1. Strategies for chemical reaction searching in SciFinder

    PubMed

    Ridley

    2000-09-01

    The bibliographic, chemical structure, and chemical reaction databases produced by Chemical Abstracts Service allow a number of possibilities for chemical reaction searching. While these same databases may be searched through the STN network, many end-users find the intuitive software interface SciFinder simpler, but there still are issues to address. Searching may be performed through keywords, chemical structures, or chemical reactions, and the answers may vary with respect to precision and comprehension. Often combinations of search options may be needed to best solve the problem. Retrosynthetic analyses are easily performed in the chemical reaction database and can give unique insights into synthetic alternatives.

  2. 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…

  3. The role of chemical reactions in the Chernobyl accident

    SciTech Connect

    Grishanin, E. I.

    2010-12-15

    It is shown that chemical reactions played an essential role in the Chernobyl accident at all of its stages. It is important that the reactor before the explosion was at maximal xenon poisoning, and its reactivity, apparently, was not destroyed by the explosion. The reactivity release due to decay of Xe-235 on the second day after the explosion led to a reactor power of 80-110 MW. Owing to this power, the chemical reactions of reduction of uranium, plutonium, and other metals at a temperature of about 2000 Degree-Sign C occurred in the core. The yield of fission products thus sharply increased. Uranium and other metals flew down in the bottom water communications and rooms. After reduction of the uranium and its separation from the graphite, the chain reaction stopped, the temperature of the core decreased, and the activity yield stopped.

  4. 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.

  5. Chemical Potentials and Activities: An Electrochemical Introduction.

    ERIC Educational Resources Information Center

    Wetzel, T. L.; And Others

    1986-01-01

    Describes a laboratory experiment which explores the effects of adding inert salts to electrolytic cells and demonstrates the difference between concentration and chemical activity. Examines chemical potentials as the driving force of reactions. Provides five examples of cell potential and concentration change. (JM)

  6. Quantum theory of chemical reaction rates

    SciTech Connect

    Miller, W.H. |

    1994-10-01

    If one wishes to describe a chemical reaction at the most detailed level possible, i.e., its state-to-state differential scattering cross section, then it is necessary to solve the Schroedinger equation to obtain the S-matrix as a function of total energy E and total angular momentum J, in terms of which the cross sections can be calculated as given by equation (1) in the paper. All other physically observable attributes of the reaction can be derived from the cross sections. Often, in fact, one is primarily interested in the least detailed quantity which characterizes the reaction, namely its thermal rate constant, which is obtained by integrating Eq. (1) over all scattering angles, summing over all product quantum states, and Boltzmann-averaging over all initial quantum states of reactants. With the proper weighting factors, all of these averages are conveniently contained in the cumulative reaction probability (CRP), which is defined by equation (2) and in terms of which the thermal rate constant is given by equation (3). Thus, having carried out a full state-to-state scattering calculation to obtain the S-matrix, one can obtain the CRP from Eq. (2), and then rate constant from Eq. (3), but this seems like ``overkill``; i.e., if one only wants the rate constant, it would clearly be desirable to have a theory that allows one to calculate it, or the CRP, more directly than via Eq. (2), yet also correctly, i.e., without inherent approximations. Such a theory is the subject of this paper.

  7. Modelling of chemical reactions in plasma

    NASA Astrophysics Data System (ADS)

    Aktaev, N. E.; Remnev, G. E.; Yalovets, A. P.

    2017-01-01

    The paper is devoted to theoretical investigation of interaction of pulsed high current electron beam with gas substance. As a result of the interaction the formation of chemical active plasma can be observed. One of the key parameter for theoretical analyze of the process is the electron distribution function. Within the framework of the Boltzmann approach we obtained the dynamical equation for electron distribution function depending on the electron energy, coordinate and time.

  8. 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.

  9. 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.

  10. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models.

    PubMed

    Liberman, M A; Kiverin, A D; Ivanov, M F

    2012-05-01

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  11. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models

    NASA Astrophysics Data System (ADS)

    Liberman, M. A.; Kiverin, A. D.; Ivanov, M. F.

    2012-05-01

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  12. Advanced chemical heat pumps using liquid-vapor reactions

    NASA Astrophysics Data System (ADS)

    Kirol, L.

    Chemical heat pumps utilizing liquid-vapor reactions can be configured in forms analogous to electric drive vapor-compression heat pumps and heat activated absorption heat pumps. Basic thermodynamic considerations eliminate some heat pumps and place restrictive working fluid requirements on others, but two thermodynamically feasible systems have significant potential advantage over conventional technology. An electric drive reactive heat pump can use smaller heat exchangers and compressor than a vapor-compression machine, and have more flexible operating characteristics. A waste heat driven heat pump (temperature amplifier) using liquid-vapor chemical reactions can operate with higher coefficient of performance and smaller heat exchangers than an absorption temperature amplifying heat pump. Higher temperatures and larger temperature lifts should also be possible.

  13. Plasmon-driven sequential chemical reactions in an aqueous environment

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  14. 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.

  15. Chemical reactions driven by concentrated solar energy

    NASA Astrophysics Data System (ADS)

    Levy, Moshe

    Solar energy can be used for driving endothermic reactions, either photochemically or thermally. The fraction of the solar spectrum that can be photochemically active is quite small. Therefore, it is desirable to be able to combine photochemical and thermal processes in order to increase the overall efficiency. Two thermally driven reactions are being studied: oil shale gasification and methane reforming. In both cases, the major part of the work was done in opaque metal reactors where photochemical reactions cannot take place. We then proceeded working in transparent quartz reactors. The results are preliminary, but they seem to indicate that there may be some photochemical enhancement. The experimental solar facilities used for this work include the 30 kW Schaeffer Solar Furnace and the 3 MW Solar Central Receiver in operation at the Weizmann Institute. The furnace consists of a 96 sq. m flat heliostat, that follows the sun by computer control. It reflects the solar radiation onto a spherical concentrator, 7.3 m in diameter, with a rim angle of 65 degrees. The furnace was characterized by radiometric and calorimetric measurements to show a solar concentration ratio of over 10,000 suns. The central receiver consists of 64 concave heliostats, 54 sq. m each, arranged in a north field and facing a 52 m high tower. The tower has five target levels that can be used simultaneously. The experiments with the shale gasification were carried out at the lowest level, 20 m above ground, which has the lowest solar efficiency and is assigned for low power experiments. We used secondary concentrators to boost the solar flux.

  16. Heterogeneous chemical reactions: Preparation of monodisperse latexes

    NASA Technical Reports Server (NTRS)

    Vanderhoff, J. W.; Micale, F. J.; El-Aasser, M. S.; Sterk, A. A.; Bethke, G. W.

    1977-01-01

    It is demonstrated that a photoinitiated emulsion polymerization can be carried out to a significant conversion in a SPAR rocket prototype polymerization vessel within the six minutes allowed for the experiment. The percentage of conversion was determined by both dilatometry and gravimetric methods with good agreement. The experimental results lead to the following conclusions: (1) emulsion polymerizations can be carried out to conversions as high as 75%, using a stable micellized styrene-SLS system plus photoinitiator; (2) dilatometry can be used to accurately determine both the rate and conversion of polymerization; (3) thermal expansion due to the light source and heat of reaction is small and can be corrected for if necessary; (4) although seeded emulsion polymerizations are unfavorable in photoinitiation, as opposed to chemical initiation, polymerizations can be carried out to at least 15% conversion using 7940A seed particles, with 0.05% solids; and (5) photoinitiation should be used to initiate polymerization in the SPAR rocket experiments because of the mechanical simplicity of the experiment.

  17. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    PubMed

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

    2014-03-11

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

  18. 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.

  19. Shaking Catalysts Accelerating Chemical Reaction in Micro Reactors

    NASA Astrophysics Data System (ADS)

    Suzumori, Koichi; Nagata, Takashi; Kanda, Takefumi; Sakata, Yusaku; Muto, Akinori

    Efficient uniform mixing is an essential process for chemical reaction. However, it is difficult to fabricate many tiny stirrers on reactor chips. This paper shows a new method promoting high-efficient chemical reaction in micro chamber. To stir chemicals and to accelerate reaction catalytic particles are driven electrostatically in micro chamber. Two driving methods have been evaluated; AC drive and DC drive. Evaluation of chemical reactions revealed the effect of this developed devices. In addition conveyance system of catalytic particles is necessary for particles exchange.

  20. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    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.

  1. 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.

  2. 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...

  3. 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)

  4. Classification of chemical reactions and chemoinformatic processing of enzymatic transformations.

    PubMed

    Latino, Diogo A R S; Aires-de-Sousa, João

    2011-01-01

    The automatic perception of chemical similarities between chemical reactions is required for a variety of applications in chemistry and connected fields, namely with databases of metabolic reactions. Classification of enzymatic reactions is required, e.g., for genome-scale reconstruction (or comparison) of metabolic pathways, computer-aided validation of classification systems, or comparison of enzymatic mechanisms. This chapter presents different current approaches for the representation of chemical reactions enabling automatic reaction classification. Representations based on the encoding of the reaction center are illustrated, which use physicochemical features, Reaction Classification (RC) numbers, or Condensed Reaction Graphs (CRG). Representation of differences between the structures of products and reactants include reaction signatures, fingerprint differences, and the MOLMAP approach. The approaches are illustrated with applications to real datasets.

  5. Structure-activity relationships for chemical and glutathione S-transferase-catalysed glutathione conjugation reactions of a series of 2-substituted 1-chloro-4-nitrobenzenes.

    PubMed Central

    Van der Aar, E M; Bouwman, T; Commandeur, J N; Vermeulen, N P

    1996-01-01

    Glutathione S-transferases (GSTs) constitute an important class of phase II (de)toxifying enzymes, catalysing the conjugation of glutathione (GSH) with electrophilic compounds. In the present study, Km, kcat and kcat/Km values for the rat GST 1-1-, 3-3-, 4-4- and 7-7-catalysed conjugation reactions between GSH and a series of 10 different 2-substituted 1-chloro-4-nitrobenzenes, and the second-order rate constants (ks) of the corresponding base-catalysed reactions, were correlated with nine classical physicochemical parameters (electronic, steric and lipophilic) of the substituents and with 16 computer-calculated molecular parameters of the substrates and of the corresponding Meisenheimer complexes with MeS- as a model nucleophile for GS- (charge distributions and several energy values), giving structure-activity relationships. On the basis of an identical dependence of the base-catalysed as well as the GST 1-1- and GST 7-7-catalysed reactions on electronic parameters (among others, Hammett substituent constant sigma p and charge on p-nitro substituents), and the finding that the corresponding reactions catalysed by GSTs 3-3 and 4-4 depend to a significantly lesser extent on these parameters, it was concluded that the Mu-class GST isoenzymes have a rate-determining transition state in the conjugation reaction between 2-substituted 1-chloro-4-nitrobenzenes and GSH which is different from that of the other two GSTs. Several alternative rate-limiting transition states for GST 3-3 and 4-4 are discussed. Furthermore, based on the obtained structure-activity relationships, it was possible to predict the kcat/Km values of the four GST isoenzymes and the ks of the base-catalysed GSH conjugation of 1-chloro-4-nitrobenzene. PMID:8973562

  6. Semiclassical methods in chemical reaction dynamics

    SciTech Connect

    Keshavamurthy, Srihari

    1994-12-01

    Semiclassical approximations, simple as well as rigorous, are formulated in order to be able to describe gas phase chemical reactions in large systems. We formulate a simple but accurate semiclassical model for incorporating multidimensional tunneling in classical trajectory simulations. This model is based on the existence of locally conserved actions around the saddle point region on a multidimensional potential energy surface. Using classical perturbation theory and monitoring the imaginary action as a function of time along a classical trajectory we calculate state-specific unimolecular decay rates for a model two dimensional potential with coupling. Results are in good comparison with exact quantum results for the potential over a wide range of coupling constants. We propose a new semiclassical hybrid method to calculate state-to-state S-matrix elements for bimolecular reactive scattering. The accuracy of the Van Vleck-Gutzwiller propagator and the short time dynamics of the system make this method self-consistent and accurate. We also go beyond the stationary phase approximation by doing the resulting integrals exactly (numerically). As a result, classically forbidden probabilties are calculated with purely real time classical trajectories within this approach. Application to the one dimensional Eckart barrier demonstrates the accuracy of this approach. Successful application of the semiclassical hybrid approach to collinear reactive scattering is prevented by the phenomenon of chaotic scattering. The modified Filinov approach to evaluating the integrals is discussed, but application to collinear systems requires a more careful analysis. In three and higher dimensional scattering systems, chaotic scattering is suppressed and hence the accuracy and usefulness of the semiclassical method should be tested for such systems.

  7. Incidents of chemical reactions in cell equipment

    SciTech Connect

    Baldwin, N.M.; Barlow, C.R.

    1991-12-31

    Strongly exothermic reactions can occur between equipment structural components and process gases under certain accident conditions in the diffusion enrichment cascades. This paper describes the conditions required for initiation of these reactions, and describes the range of such reactions experienced over nearly 50 years of equipment operation in the US uranium enrichment program. Factors are cited which can promote or limit the destructive extent of these reactions, and process operations are described which are designed to control the reactions to minimize equipment damage, downtime, and the possibility of material releases.

  8. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1990-01-01

    The objective was to obtain accurate potential energy surfaces (PES's) for a number of reactions which are important in the H/N/O combustion process. The interest in this is centered around the design of the SCRAM jet engine for the National Aerospace Plane (NASP), which was envisioned as an air-breathing hydrogen-burning vehicle capable of reaching velocities as large as Mach 25. Preliminary studies indicated that the supersonic flow in the combustor region of the scram jet engine required accurate reaction rate data for reactions in the H/N/O system, some of which was not readily available from experiment. The most important class of combustion reactions from the standpoint of the NASP project are radical recombinaton reactions, since these reactions result in most of the heat release in the combustion process. Theoretical characterizations of the potential energy surfaces for these reactions are presented and discussed.

  9. Self-diffusiophoresis of chemically active colloids

    NASA Astrophysics Data System (ADS)

    Popescu, Mihail N.; Uspal, William E.; Dietrich, Siegfried

    2016-11-01

    Chemically active colloids locally change the chemical composition of their solvent via catalytic reactions which occur on parts of their surface. They achieve motility by converting the released chemical free energy into mechanical work through various mechanisms, such as phoresis. Here we discuss the theoretical aspects of self-diffusiophoresis, which - despite being one of the simplest motility mechanisms - captures many of the general features characterizing self-phoresis, such as self-generated and maintained hydrodynamic flows "driven" by surface activity induced inhomogeneities in solution. By studying simple examples, which provide physical insight, we highlight the complex phenomenology which can emerge from self-diffusiophoresis.

  10. Chemical Looping Combustion Reactions and Systems

    SciTech Connect

    Sarofim, Adel; Lighty, JoAnn; Smith, Philip; Whitty, Kevin; Eyring, Edward; Sahir, Asad; Alvarez, Milo; Hradisky, Michael; Clayton, Chris; Konya, Gabor; Baracki, Richard; Kelly, Kerry

    2014-03-01

    , they performed a sensitivity analysis for velocity, height and polydispersity and compared results against literature data for experimental studies of CLC beds with no reaction. Finally, they present an optimization space using simple non-reactive configurations. In Subtask 5.3, through a series of experimental studies, behavior of a variety of oxygen carriers with different loadings and manufacturing techniques was evaluated under both oxidizing and reducing conditions. The influences of temperature, degree of carrier conversion and thermodynamic driving force resulting from the difference between equilibrium and system O{sub 2} partial pressures were evaluated through several experimental campaigns, and generalized models accounting for these influences were developed to describe oxidation and oxygen release. Conversion of three solid fuels with widely ranging reactivities was studied in a small fluidized bed system, and all but the least reactive fuel (petcoke) were rapidly converted by oxygen liberated from the CLOU carrier. Attrition propensity of a variety of carriers was also studied, and the carriers produced by freeze granulation or impregnation of preformed substrates displayed the lowest rates of attrition. Subtask 5.4 focused on gathering kinetic data for a copper-based oxygen carrier to assist with modeling of a functioning chemical looping reactor. The kinetics team was also responsible for the development and analysis of supported copper oxygen carrier material.

  11. Metabolic activation and inactivation of chemical carcinogens

    SciTech Connect

    Pelkonen, O.; Vaehaekangas, K.

    1980-09-01

    Chemical carcinogens are metabolized by numerous pathways catalyzed by enzymes in endoplasmic reticulum and other parts of the cell. Reactions in which functional groups are created are especially important in the activation of polycyclic hydrocarbon carcinogens to ultimate carcinogenic forms, although other enzymes may also participate in the activation of other chemical carcinogens. The reasons why carcinogens act on specific target tissues are incompletely understood, although differences in enzyme profiles between tissues certainly contribute to the target tissue variability. The concept of metabolic activation of carcinogens by body's own enzymes has led to the development of short-term assay systems, which essentially measure the production of biologically active metabolites from potential carcinogens.

  12. Chemical Demonstrations with Consumer Chemicals: The Black and White Reaction.

    ERIC Educational Resources Information Center

    Wright, Stephen W.

    2002-01-01

    Describes a dramatic chemical demonstration in which chemicals that are black and white combine to produce a colorless liquid. Reactants include tincture of iodine, bleach, white vinegar, Epsom salt, vitamin C tablets, and liquid laundry starch. (DDR)

  13. Stereodynamics: From elementary processes to macroscopic chemical reactions

    SciTech Connect

    Kasai, Toshio; Che, Dock-Chil; Tsai, Po-Yu; Lin, King-Chuen; Palazzetti, Federico; Aquilanti, Vincenzo

    2015-12-31

    This paper aims at discussing new facets on stereodynamical behaviors in chemical reactions, i.e. the effects of molecular orientation and alignment on reactive processes. Further topics on macroscopic processes involving deviations from Arrhenius behavior in the temperature dependence of chemical reactions and chirality effects in collisions are also discussed.

  14. Chemical kinetics computer program for static and flow reactions

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

    General chemical kinetics computer program for complex gas mixtures has been developed. Program can be used for any homogeneous reaction in either one dimensional flow or static system. It is flexible, accurate, and easy to use. It can be used for any chemical system for which species thermodynamic data and reaction rate constant data are known.

  15. Negative Temperature Coefficient in Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Leenson, I. A.; Sergeev, Gleb B.

    1984-05-01

    A systematic analysis of reactions whose rate decreases with increase of temperature is presented. The possibility of a negative temperature coefficient in the elementary reactions is examined from the standpoint of the transition state theory and of collision theory. The mechanisms of complex reactions in which the temperature dependence of the rate is anomalous are discussed, and possible reasons for the anomaly are examined. The bibliography contains 175 references.

  16. Confinement effects on chemical reactions in nanostructured carbon materials

    NASA Astrophysics Data System (ADS)

    George, Aaron; Kostov, Milen; Buongiorno Nardelli, Marco

    2005-03-01

    Chemical reactions are frequently carried out in nano-structured media, such as micellar or colloidal solutions, nano-porous media, hydrogels or organogels, or in systems involving nano-particles. Nanostructured environments have been shown to enhance reaction rates through a variety of catalytic effects, such as high surface area, interactions with the nano-structure or confinement. In this work, we have used state-of-the-art electronic structure techniques to study the prototypical example of the hydrogen-producing reaction of formaldehyde dissociation (H2CO -> H2 + CO) within various configurations of a graphitic pore. Using the Nudged Elastic Band (NEB) method for transition states analysis, we have found that the activation energy of the dissociation can be influenced by the presence of a graphitic pore. In particular, while a graphene surface reduces the activation barrier for the reaction, this catalytic effect is enhanced by the presence of two planar sheets, which mimic the geometry of a nano-pore. These findings will be discussed in terms of the charge transfer and/or polarization mechanism associated with the catalytic process.

  17. Chemical and genomic evolution of enzyme-catalyzed reaction networks.

    PubMed

    Kanehisa, Minoru

    2013-09-02

    There is a tendency that a unit of enzyme genes in an operon-like structure in the prokaryotic genome encodes enzymes that catalyze a series of consecutive reactions in a metabolic pathway. Our recent analysis shows that this and other genomic units correspond to chemical units reflecting chemical logic of organic reactions. From all known metabolic pathways in the KEGG database we identified chemical units, called reaction modules, as the conserved sequences of chemical structure transformation patterns of small molecules. The extracted patterns suggest co-evolution of genomic units and chemical units. While the core of the metabolic network may have evolved with mechanisms involving individual enzymes and reactions, its extension may have been driven by modular units of enzymes and reactions.

  18. 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.

  19. Chemical redox reactions in ES-MS: Study of electrode reactions

    SciTech Connect

    Zhou, Feimeng; VAn Berkel, G.J.

    1995-12-31

    The authors previously demonstrated that chemical redox reactions can be used to ionize neutral commpounds for electrospray mass spectrometric (ES-MS) detection. Two different compounds, viz, C{sub 60}F{sub 48} and {beta}-carotene were used to demonstrate the utility of chemical redox reactions with on-line ES-MS for the elucidation of mechanisms of complicated electron transfer reactions and for the kinetic study of electrode reactions in which relatively short-lived intermediates are involved.

  20. 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…

  1. 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.

  2. Chemical reaction optimization for solving shortest common supersequence problem.

    PubMed

    Khaled Saifullah, C M; Rafiqul Islam, Md

    2016-10-01

    Shortest common supersequence (SCS) is a classical NP-hard problem, where a string to be constructed that is the supersequence of a given string set. The SCS problem has an enormous application of data compression, query optimization in the database and different bioinformatics activities. Due to NP-hardness, the exact algorithms fail to compute SCS for larger instances. Many heuristics and meta-heuristics approaches were proposed to solve this problem. In this paper, we propose a meta-heuristics approach based on chemical reaction optimization, CRO_SCS that is designed inspired by the nature of the chemical reactions. For different optimization problems like 0-1 knapsack, quadratic assignment, global numeric optimization problems CRO algorithm shows very good performance. We have redesigned the reaction operators and a new reform function to solve the SCS problem. The outcomes of the proposed CRO_SCS algorithm are compared with those of the enhanced beam search (IBS_SCS), deposition and reduction (DR), ant colony optimization (ACO) and artificial bee colony (ABC) algorithms. The length of supersequence, execution time and standard deviation of all related algorithms show that CRO_SCS gives better results on the average than all other algorithms.

  3. FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    The chemical research in the late 1990's witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into the atmo...

  4. The How and Why of Chemical Reactions

    ERIC Educational Resources Information Center

    Schubert, Leo

    1970-01-01

    Presents a discussion of some of the fundamental concepts in thermodynamics and quantum mechanics including entropy, enthalpy, free energy, the partition function, chemical kinetics, transition state theory, the making and breaking of chemical bonds, electronegativity, ion sizes, intermolecular energies and of their role in explaining the nature…

  5. Modular verification of chemical reaction network encodings via serializability analysis.

    PubMed

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

    2016-06-13

    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.

  6. Chemical Reaction Experiment for the Undergraduate Laboratory.

    ERIC Educational Resources Information Center

    Kwon, K. C.; And Others

    1987-01-01

    Provides an overview of an experiment on reaction kinetics of the anthracene-hydrogen system. Includes a description of the laboratory equipment, procedures, and data analysis requirements. Points out the advantages of the recommended technique. (ML)

  7. 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.

  8. Kinetics of Chemical Reactions in Flames

    NASA Technical Reports Server (NTRS)

    Zeldovich, Y.; Semenov, N.

    1946-01-01

    In part I of the paper the theory of flame propagation is developed along the lines followed by Frank-Kamenetsky and one of the writers. The development of chain processes in flames is considered. A basis is given for the application of the method of stationary concentrations to reactions in flames; reactions with branching chains are analyzed. The case of a diffusion coefficient different from the coefficient of temperature conductivity is considered.

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

    PubMed

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

    2016-01-22

    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.

  10. On the mechanism of effective chemical reactions with turbulent mixing of reactants and finite rate of molecular reactions

    NASA Astrophysics Data System (ADS)

    Vorotilin, V. P.

    2017-01-01

    A generalization of the theory of chemical transformation processes under turbulent mixing of reactants and arbitrary values of the rate of molecular reactions is presented that was previously developed for the variant of an instantaneous reaction [13]. The use of the features of instantaneous reactions when considering the general case, namely, the introduction of the concept of effective reaction for the reactant volumes and writing a closing conservation equation for these volumes, became possible due to the partition of the whole amount of reactants into "active" and "passive" classes; the reactants of the first class are not mixed and react by the mechanism of instantaneous reactions, while the reactants of the second class approach each other only through molecular diffusion, and therefore their contribution to the reaction process can be neglected. The physical mechanism of reaction for the limit regime of an ideal mixing reactor (IMR) is revealed and described. Although formally the reaction rate in this regime depends on the concentration of passive fractions of the reactants, according to the theory presented, the true (hidden) mechanism of the reaction is associated only with the reaction of the active fractions of the reactants with vanishingly small concentration in the volume of the reactor. It is shown that the rate constant of fast chemical reactions can be evaluated when the mixing intensity of reactants is much less than that needed to reach the mixing conditions in an IMR.

  11. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Heinemann, K.; Walch, Stephen P.

    1992-01-01

    The work on the NH + NO system which was described in the last progress report was written up and a draft of the manuscript is included in the appendix. The appendix also contains a draft of a manuscript on an Ar + H + H surface. New work which was completed in the last six months includes the following: (1) calculations on the (1)CH2 + H2O, H2 + HCOH, and H2 + H2CO product channels in the CH3 + OH reaction; (2) calculations for the NH2 + O reaction; (3) calculations for the CH3 + O2 reaction; and (4) calculations for CH3O and the two decomposition channels--CH2OH and H + H2CO. Detailed descriptions of this work will be given in manuscripts; however, brief descriptions of the CH3 + OH and CH3 + O2 projects are given.

  12. 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.

  13. 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.

  14. Steric Control of Complex Chemical Reactions - 1

    DTIC Science & Technology

    2011-12-26

    their contrasting behaviors upon vibrational and translational excitations can serve as benchmark for gaining deeper insights into polyatomic reaction...equipped with a uniquely designed ion velocity map imaging detector capable of measuring the product pair correlation. The ultrafast femtosecond laser...From A + BC to Polyatomic Systems” K. Liu, Adv. in Chem. Phys. 149, (in press). Invited Review Invited talks at Conferences (* denoting

  15. Developing Secondary Students' Conceptions of Chemical Reactions: The Introduction of Chemical Equilibrium.

    ERIC Educational Resources Information Center

    Van Driel, Jan H.; De Vos, Wobbe; Verloop, Nico; Dekkers, Hetty

    1998-01-01

    Describes an empirical study concerning the introduction of the concept of chemical equilibrium in chemistry classrooms in a way which challenges students' initial conceptions of chemical reactions. Contains 23 references. (DDR)

  16. Femtosecond Diffraction and Spectroscopy of Chemical Reactions

    DTIC Science & Technology

    2008-03-31

    bifurcation into phytical and chemical channels, redefines structural dynamics of the energy landscape in radiationless processes. Paper 6. In this... acid bilayers. In 4DUEM we are now able, using timed single-electron packets, to image nano-to-micro scale structures of materials and biological

  17. Computed Potential Energy Surfaces for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Heinemann, K.; Walch, Stephen P.; Levin, Eugene

    1993-01-01

    A manuscript describing the calculations on the (1)CH2 + H2O, H2 + HCOH, and H2 + H2CO product channels in the CH3 + OH reaction, which were described in the last progress report, has been accepted for publication in J. Chem. Phys., and a copy of the manuscript is included in the appendix. The production of (1)CH2 in this reaction is important in hydrocarbon combustion since (1)CH2 is highly reactive and would be expected to insert into N2, possibly leading to a new source for prompt NO(x) (vide infra). During the last six months new calculations have been carried out for the NH2 + NO system, which is important in the thermal de-NO(x) process.

  18. 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

  19. 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.

  20. Chemical reactions of organic compounds on clay surfaces.

    PubMed Central

    Soma, Y; Soma, M

    1989-01-01

    Chemical reactions of organic compounds including pesticides at the interlayer and exterior surfaces of clay minerals and with soil organic matter are reviewed. Representative reactions under moderate conditions possibly occurring in natural soils are described. Attempts have been made to clarify the importance of the chemical nature of molecules, their structures and their functional groups, and the Brönsted or Lewis acidity of clay minerals. PMID:2533556

  1. Ultrafast Chemical Dynamics of Reactions in Beams

    DTIC Science & Technology

    1989-10-31

    sensitive probe of the transition-state(s) region. The so-called femtosecond transition-state spectroscopy FTS method [M. Dantus, M. Rosker, and A. Zewail, J...Femtosecond Clocking of the Chemical Bond Mark J. Rosker, Marcos Dantus, and Ahmed H. Zewail BY Science 241, 1200 (1988) Dilrbtyon/ 5. Femtosecond Spectroscopy ...Potential from Femtosecond Transition-State Spectroscopy Experiments. 5 Richard B. Bernstein and Ahmed H. Zewail J. Chem. Phys. 90,829 (1989) 5

  2. Coherent Radiative Control of Chemical Reactions

    DTIC Science & Technology

    1992-01-01

    effective were determined and successful control was displayed using a model of Stilbene isomerization. F. Control over Chemically Distinct Products...than, the stilbene molecule for which Si(t>to) = Ia(to)Il14ru-(I’ f = 1, II11 (3) there is a vast array of data available art for which...mechanical o calculation of ground and first excited electronic potential surfaces _o for trans- and cis- stilbene . To minimize computational cost we 0

  3. Phase Waves in Oscillatory Chemical Reactions.

    DTIC Science & Technology

    number of waves emitted from a center of heterogeneous catalysis , the rate of wave emission. the lifetime of each wave, the asymptotic wave pattern, the...A theory is presented for the effect of heterogeneity on an oscillatory chemically reactive system in a stable limit cycle such as in heterogeneous ... catalysis . A perturbation technique is developed free of secular behavior for the solution of the non-linear partial differential equations. The

  4. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    SciTech Connect

    Rodriguez, J.A.; Barrio, L.; Kubacka, A.; Zhou, G.; Estrella, M.; Martınez-Arias, A.; Hanson, J.C.; Fernandez-Garcıa, M.

    2010-07-29

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni?O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate?carbonate route is operative for the production of hydrogen.

  5. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    SciTech Connect

    Barrio, L.; Kubacka, A; Zhou, G; Estrella, M; Martinez-Arias, A; Hanson, J; Fernandez-Garcia, M; Rodriguez, J

    2010-01-01

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni-O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate-carbonate route is operative for the production of hydrogen.

  6. Quantifying chemical reactions by using mixing analysis.

    PubMed

    Jurado, Anna; Vázquez-Suñé, Enric; Carrera, Jesús; Tubau, Isabel; Pujades, Estanislao

    2015-01-01

    This work is motivated by a sound understanding of the chemical processes that affect the organic pollutants in an urban aquifer. We propose an approach to quantify such processes using mixing calculations. The methodology consists of the following steps: (1) identification of the recharge sources (end-members) and selection of the species (conservative and non-conservative) to be used, (2) identification of the chemical processes and (3) evaluation of mixing ratios including the chemical processes. This methodology has been applied in the Besòs River Delta (NE Barcelona, Spain), where the River Besòs is the main aquifer recharge source. A total number of 51 groundwater samples were collected from July 2007 to May 2010 during four field campaigns. Three river end-members were necessary to explain the temporal variability of the River Besòs: one river end-member is from the wet periods (W1) and two are from dry periods (D1 and D2). This methodology has proved to be useful not only to compute the mixing ratios but also to quantify processes such as calcite and magnesite dissolution, aerobic respiration and denitrification undergone at each observation point.

  7. 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

  8. 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.

  9. Accelerated Chemical Reactions and Organic Synthesis in Leidenfrost Droplets.

    PubMed

    Bain, Ryan M; Pulliam, Christopher J; Thery, Fabien; Cooks, R Graham

    2016-08-22

    Leidenfrost levitated droplets can be used to accelerate chemical reactions in processes that appear similar to reaction acceleration in charged microdroplets produced by electrospray ionization. Reaction acceleration in Leidenfrost droplets is demonstrated for a base-catalyzed Claisen-Schmidt condensation, hydrazone formation from precharged and neutral ketones, and for the Katritzky pyrylium into pyridinium conversion under various reaction conditions. Comparisons with bulk reactions gave intermediate acceleration factors (2-50). By keeping the volume of the Leidenfrost droplets constant, it was shown that interfacial effects contribute to acceleration; this was confirmed by decreased reaction rates in the presence of a surfactant. The ability to multiplex Leidenfrost microreactors, to extract product into an immiscible solvent during reaction, and to use Leidenfrost droplets as reaction vessels to synthesize milligram quantities of product is also demonstrated.

  10. Chemical Reactions in Turbulent Mixing Flows.

    DTIC Science & Technology

    1987-06-01

    soot particles are also often formed at the reaction interface, so the feasibility study was intenced to determine whether the two sources of particles...buoyancy effects (i.e. gravity is ipored). it can be shown that the disturbance eigentunction , satisfies the equation .0 .....o ... P I ./Pl...34 * (o’’o) *’t [a" U L" + I ’ U’/g ""* where ( )’ corresponds to d/dy. The equation * above reduces to the Rayleigh equation when the -4.0 d ensity is

  11. Laser cutting with chemical reaction assist

    DOEpatents

    Gettemy, Donald J.

    1992-01-01

    A method for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation.

  12. Laser cutting with chemical reaction assist

    DOEpatents

    Gettemy, D.J.

    1992-11-17

    A method is described for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation. 1 figure.

  13. Colloidal Assemblies Effect on Chemical Reactions.

    DTIC Science & Technology

    1986-07-01

    carried out mainly with TiO2 as photocatalyst . I.I. Phenol A typical experiment of phenol photocatalytic degradation is reported in Figure 2 where also...It may be safely assumed that in the alkaline slurgy the surface of TiO2 is fully covered with water molecules and with OH- groups; in a somewhat...concentrations on the TiO2 sur- face were practically zero. By calculating the ratio bet- ween the maximum mass transfer rate and the reaction rate, it comes

  14. Colloidal Assemblies Effect on Chemical Reactions

    DTIC Science & Technology

    1988-12-01

    mainly with TiO 2 as photocatalyst . 1.1. Phenol A typical experiment of phenol photocatalytic degradation is reported in Figure 2 where also the...therefore state that the photodegradation reaction occurs between the reactants both adsorbed on the TiO2 sur- face. These adsorbed species as well as others...electrons and holes which must be trapped to avoid recombination (charge separation): TiO 2 + hv - TiO2 + e(cb) + h(vb) (1) It is widely accepted that the

  15. Is the simplest chemical reaction really so simple?

    PubMed

    Jankunas, Justin; Sneha, Mahima; Zare, Richard N; Bouakline, Foudhil; Althorpe, Stuart C; Herráez-Aguilar, Diego; Aoiz, F Javier

    2014-01-07

    Modern computational methods have become so powerful for predicting the outcome for the H + H2 → H2 + H bimolecular exchange reaction that it might seem further experiments are not needed. Nevertheless, experiments have led the way to cause theorists to look more deeply into this simplest of all chemical reactions. The findings are less simple.

  16. Is the simplest chemical reaction really so simple?

    PubMed Central

    Jankunas, Justin; Sneha, Mahima; Zare, Richard N.; Bouakline, Foudhil; Althorpe, Stuart C.; Herráez-Aguilar, Diego; Aoiz, F. Javier

    2014-01-01

    Modern computational methods have become so powerful for predicting the outcome for the H + H2 → H2 + H bimolecular exchange reaction that it might seem further experiments are not needed. Nevertheless, experiments have led the way to cause theorists to look more deeply into this simplest of all chemical reactions. The findings are less simple. PMID:24367084

  17. Plasmonic smart dust for probing local chemical reactions.

    PubMed

    Tittl, Andreas; Yin, Xinghui; Giessen, Harald; Tian, Xiang-Dong; Tian, Zhong-Qun; Kremers, Christian; Chigrin, Dmitry N; Liu, Na

    2013-04-10

    Locally probing chemical reactions or catalytic processes on surfaces under realistic reaction conditions has remained one of the main challenges in materials science and heterogeneous catalysis. Where conventional surface interrogation techniques usually require high-vacuum conditions or ensemble average measurements, plasmonic nanoparticles excel in extreme light focusing and can produce highly confined electromagnetic fields in subwavelength volumes without the need for complex near-field microscopes. Here, we demonstrate an all-optical probing technique based on plasmonic smart dust for monitoring local chemical reactions in real time. The silica shell-isolated gold nanoparticles that form the smart dust can work as strong light concentrators and optically report subtle environmental changes at their pinning sites on the probed surface during reaction processes. As a model system, we investigate the hydrogen dissociation and subsequent uptake trajectory in palladium with both "dust-on-film" and "film-on-dust" platforms. Using time-resolved single particle measurements, we demonstrate that our technique can in situ encode chemical reaction information as optical signals for a variety of surface morphologies. The presented technique offers a unique scheme for real-time, label-free, and high-resolution probing of local reaction kinetics in a plethora of important chemical reactions on surfaces, paving the way toward the development of inexpensive and high-output reaction sensors for real-world applications.

  18. Modelling Chemical Reasoning to Predict and Invent Reactions.

    PubMed

    Segler, Marwin H S; Waller, Mark P

    2016-11-11

    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.

  19. 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…

  20. Chemical reactions on solid surfaces using molecular beam techniques

    NASA Astrophysics Data System (ADS)

    Palmer, R. L.

    1980-07-01

    Thermal energy molecular beams have been used to study chemical interactions with metal surfaces. Chemisorption of simple molecules such as H2, O2, CH4, C2Hx and CO was investigated on single and polycrystalline surfaces of Pt, Ni, Co, and Ag. Kinetic parameters and reaction mechanisms were determined for model catalytic reactions including CO and C2Hx oxidation and methanation from H2/CO mixtures. Chemical reactions of NOx with CO and D2 on Pt(111) and other surfaces have been surveyed and the kinetics of NO and O2 chemisorption have been measured. The theory of adsorption/desorption kinetics is reviewed and certain deficiencies identified.

  1. 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.

  2. 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.

  3. 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 .

  4. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    PubMed

    Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

    2014-06-25

    Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.

  5. Chemical Strategies for Enhancing Activity and Charge Transfer in Ultrathin Pt Nanowires Immobilized onto Nanotube Supports for the Oxygen Reduction Reaction

    DOE PAGES

    Li, Luyao; Liu, Haiqing; Wang, Lei; ...

    2016-12-12

    Multiwalled carbon nanotubes (MWNTs) represent a promising support medium for electrocatalysts, especially Pt nanoparticles (NPs). The advantages of using MWNTs include their large surface area, high conductivity, as well as long-term stability. Surface functionalization of MWNTs with various terminal groups, such as -COOH, -SH, and -NH2, allows for rational electronic tuning of catalyst–support interactions. But, several issues still need to be addressed for such systems. Over the course of an electrochemical run, catalyst durability can decrease, due in part to metal NP dissolution, a process facilitated by the inherently high surface defect concentration within the support. Second, the covalent functionalizationmore » treatment of MWNTs adopted by most groups tends to lead to a loss of structural integrity of the nanotubes (NTs). In order to mitigate for all of these issues, we have utilized two different attachment approaches (i.e., covalent versus noncovalent) to functionalize the outer walls of pristine MWNTs and compared the catalytic performance of as-deposited ultrathin (<2 nm) 1D Pt nanowires with that of conventional Pt NPs toward the oxygen reduction reaction (ORR). Our results demonstrated that the electrochemical activity of Pt nanostructures immobilized onto functionalized carbon nanotube (CNT) supports could be dramatically improved by using ultrathin Pt nanowires (instead of NPs) with noncovalently (as opposed to covalently) functionalized CNT supports. Spectroscopic evidence corroborated the definitive presence of charge transfer between the metal catalysts and the underlying NT support, whose direction and magnitude are a direct function of (i) the terminal chemistry as well as (ii) the attachment methodology, both of which simultaneously impact upon the observed electrocatalytic performance. Specifically, the use of a noncovalent π–π stacking method coupled with a -COOH terminal moiety yielded the highest performance results, reported to

  6. Chemical Strategies for Enhancing Activity and Charge Transfer in Ultrathin Pt Nanowires Immobilized onto Nanotube Supports for the Oxygen Reduction Reaction

    SciTech Connect

    Li, Luyao; Liu, Haiqing; Wang, Lei; Yue, Shiyu; Tong, Xiao; Zaliznyak, Tatiana; Taylor, Gordon T.; Wong, Stanislaus S.

    2016-12-12

    Multiwalled carbon nanotubes (MWNTs) represent a promising support medium for electrocatalysts, especially Pt nanoparticles (NPs). The advantages of using MWNTs include their large surface area, high conductivity, as well as long-term stability. Surface functionalization of MWNTs with various terminal groups, such as -COOH, -SH, and -NH2, allows for rational electronic tuning of catalyst–support interactions. But, several issues still need to be addressed for such systems. Over the course of an electrochemical run, catalyst durability can decrease, due in part to metal NP dissolution, a process facilitated by the inherently high surface defect concentration within the support. Second, the covalent functionalization treatment of MWNTs adopted by most groups tends to lead to a loss of structural integrity of the nanotubes (NTs). In order to mitigate for all of these issues, we have utilized two different attachment approaches (i.e., covalent versus noncovalent) to functionalize the outer walls of pristine MWNTs and compared the catalytic performance of as-deposited ultrathin (<2 nm) 1D Pt nanowires with that of conventional Pt NPs toward the oxygen reduction reaction (ORR). Our results demonstrated that the electrochemical activity of Pt nanostructures immobilized onto functionalized carbon nanotube (CNT) supports could be dramatically improved by using ultrathin Pt nanowires (instead of NPs) with noncovalently (as opposed to covalently) functionalized CNT supports. Spectroscopic evidence corroborated the definitive presence of charge transfer between the metal catalysts and the underlying NT support, whose direction and magnitude are a direct function of (i) the terminal chemistry as well as (ii) the attachment methodology, both of which simultaneously impact upon the observed electrocatalytic performance. Specifically, the use of a noncovalent π–π stacking method coupled with a -COOH terminal moiety yielded the highest performance results, reported

  7. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1988-01-01

    The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.

  8. A Light-Activated Reaction Manifold.

    PubMed

    Hiltebrandt, Kai; Elies, Katharina; D'hooge, Dagmar R; Blinco, James P; Barner-Kowollik, Christopher

    2016-06-08

    We introduce an efficient reaction manifold where the rate of a thermally induced ligation can be controlled by a photonic field via two competing reaction channels. The effectiveness of the reaction manifold is evidenced by following the transformations of macromolecular chain termini via high-resolution mass spectrometry and subsequently by selective block copolymer formation. The light-controlled reaction manifold consists of a so-called o-quinodimethane species, a photocaged diene, that reacts in the presence of light with suitable enes in a Diels-Alder reaction and undergoes a transformation into imines with amines in the absence of light. The chemical selectivity of the manifold is controlled by the amount of ene present in the reaction and can be adjusted from 100% imine formation (0% photo product) to 5% imine formation (95% photo product). The reported light-controlled reaction manifold is highly attractive because a simple external field is used to switch the selectivity of specific reaction channels.

  9. Chemical Looping Combustion Reactions and Systems

    SciTech Connect

    Sarofim, Adel; Lighty, JoAnn; Smith, Philip; Whitty, Kevin; Eyring, Edward; Sahir, Asad; Alvarez, Milo; Hradisky, Michael; Clayton, Chris; Konya, Gabor; Baracki, Richard; Kelly, Kerry

    2011-07-01

    Chemical Looping Combustion (CLC) is one promising fuel-combustion technology, which can facilitate economic CO2 capture in coal-fired power plants. It employs the oxidation/reduction characteristics of a metal, or oxygen carrier, and its oxide, the oxidizing gas (typically air) and the fuel source may be kept separate. This work focused on two classes of oxygen carrier, one that merely undergoes a change in oxidation state, such as Fe3O4/Fe2O3 and one that is converted from its higher to its lower oxidation state by the release of oxygen on heating, i.e., CuO/Cu2O. This topical report discusses the results of four complementary efforts: (1) the development of process and economic models to optimize important design considerations, such as oxygen carrier circulation rate, temperature, residence time; (2) the development of high-performance simulation capabilities for fluidized beds and the collection, parameter identification, and preliminary verification/uncertainty quantification (3) the exploration of operating characteristics in the laboratory-scale bubbling bed reactor, with a focus on the oxygen carrier performance, including reactivity, oxygen carrying capacity, attrition resistance, resistance to deactivation, cost and availability (4) the identification of mechanisms and rates for the copper, cuprous oxide, and cupric oxide system using thermogravimetric analysis.

  10. Functionalization of Hydrogenated Chemical Vapour Deposition-Grown Graphene by On-Surface Chemical Reactions.

    PubMed

    Drogowska, Karolina; Kovaříček, Petr; Kalbáč, Martin

    2017-03-23

    The reactivity of hydrogenated graphene when treated with oxidising agents, KMnO4 and KIO4 , as well as alkylated with benzyl bromide (BnBr) was studied. The probed reactions are strictly limited to the partly hydrogenated form of graphene in which most of the hydrogen atoms are located in activated benzylic/allylic positions. This, in turn, clearly demonstrates the presence of hydrogen attached to the graphene lattice. Attachment of the benzyl group was also unequivocally demonstrated by characteristic vibrations recorded in the surface-enhanced Raman spectra, and all reactions were shown to proceed solely on hydrogenated graphene as evidenced by the comparison with pristine chemical vapour deposition-grown graphene.

  11. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    PubMed

    Latino, Diogo A R S; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

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

    PubMed

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

    2016-10-03

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

  13. Asymmetric chemical reactions by polarized quantum beams

    NASA Astrophysics Data System (ADS)

    Takahashi, Jun-Ichi; Kobayashi, Kensei

    One of the most attractive hypothesis for the origin of homochirality in terrestrial bio-organic compounds (L-amino acid and D-sugar dominant) is nominated as "Cosmic Scenario"; a chiral impulse from asymmetric excitation sources in space triggered asymmetric reactions on the surfaces of such space materials as meteorites or interstellar dusts prior to the existence of terrestrial life. 1) Effective asymmetric excitation sources in space are proposed as polarized quantum beams, such as circularly polarized light and spin polarized electrons. Circularly polarized light is emitted as synchrotron radiation from tightly captured electrons by intense magnetic field around neutron stars. In this case, either left-or right-handed polarized light can be observed depending on the direction of observation. On the other hand, spin polarized electrons is emitted as beta-ray in beta decay from radioactive nuclei or neutron fireballs in supernova explosion. 2) The spin of beta-ray electrons is longitudinally polarized due to parity non-conservation in the weak interaction. The helicity (the the projection of the spin onto the direction of kinetic momentum) of beta-ray electrons is universally negative (left-handed). For the purpose of verifying the asymmetric structure emergence in bio-organic compounds by polarized quantum beams, we are now carrying out laboratory simulations using circularly polarized light from synchrotron radiation facility or spin polarized electron beam from beta-ray radiation source. 3,4) The target samples are solid film or aqueous solution of racemic amino acids. 1) K.Kobayashi, K.Kaneko, J.Takahashi, Y.Takano, in Astrobiology: from simple molecules to primitive life; Ed. V.Basiuk; American Scientific Publisher: Valencia, 2008. 2) G.A.Gusev, T.Saito, V.A.Tsarev, A.V.Uryson, Origins Life Evol. Biosphere. 37, 259 (2007). 3) J.Takahashi, H.Shinojima, M.Seyama, Y.Ueno, T.Kaneko, K.Kobayashi, H.Mita, M.Adachi, M.Hosaka, M.Katoh, Int. J. Mol. Sci. 10, 3044

  14. An Efficient Chemical Reaction Optimization Algorithm for Multiobjective Optimization.

    PubMed

    Bechikh, Slim; Chaabani, Abir; Ben Said, Lamjed

    2015-10-01

    Recently, a new metaheuristic called chemical reaction optimization was proposed. This search algorithm, inspired by chemical reactions launched during collisions, inherits several features from other metaheuristics such as simulated annealing and particle swarm optimization. This fact has made it, nowadays, one of the most powerful search algorithms in solving mono-objective optimization problems. In this paper, we propose a multiobjective variant of chemical reaction optimization, called nondominated sorting chemical reaction optimization, in an attempt to exploit chemical reaction optimization features in tackling problems involving multiple conflicting criteria. Since our approach is based on nondominated sorting, one of the main contributions of this paper is the proposal of a new quasi-linear average time complexity quick nondominated sorting algorithm; thereby making our multiobjective algorithm efficient from a computational cost viewpoint. The experimental comparisons against several other multiobjective algorithms on a variety of benchmark problems involving various difficulties show the effectiveness and the efficiency of this multiobjective version in providing a well-converged and well-diversified approximation of the Pareto front.

  15. Matrix isolation as a tool for studying interstellar chemical reactions

    NASA Technical Reports Server (NTRS)

    Ball, David W.; Ortman, Bryan J.; Hauge, Robert H.; Margrave, John L.

    1989-01-01

    Since the identification of the OH radical as an interstellar species, over 50 molecular species were identified as interstellar denizens. While identification of new species appears straightforward, an explanation for their mechanisms of formation is not. Most astronomers concede that large bodies like interstellar dust grains are necessary for adsorption of molecules and their energies of reactions, but many of the mechanistic steps are unknown and speculative. It is proposed that data from matrix isolation experiments involving the reactions of refractory materials (especially C, Si, and Fe atoms and clusters) with small molecules (mainly H2, H2O, CO, CO2) are particularly applicable to explaining mechanistic details of likely interstellar chemical reactions. In many cases, matrix isolation techniques are the sole method of studying such reactions; also in many cases, complexations and bond rearrangements yield molecules never before observed. The study of these reactions thus provides a logical basis for the mechanisms of interstellar reactions. A list of reactions is presented that would simulate interstellar chemical reactions. These reactions were studied using FTIR-matrix isolation techniques.

  16. Incorporation of Chemical Reactions into Building-scale Flow

    SciTech Connect

    Humphreys, T D; Jayaweera, T M; Lee, R L

    2003-10-30

    Many hazardous atmospheric releases involve chemical reactions that occur within a few kilometers of the source. Reactions with commonly occurring atmospheric compounds such as the OH radical, can transform and potentially neutralize original release compounds. Especially in these cases, accurately resolving flow around nearby structures and over surrounding topography can be critical to correctly predicting material dispersion, and thus, the extent of any hazard. Accurate prediction of material dispersion around complex geometries near the source of an atmospheric release requires high-resolution computation. Further complications arise if the compounds released undergo chemical reactions which could alter the extent of the main plume. The reaction products form dispersion patterns separate from, and often more complicated than, the original plume. Directions for future work include expanding the library of chemical reaction mechanisms, adding capabilities for aqueous and heterogeneous reactions, and integrating this model within larger-scale models. We plan that the larger-scale models will provide meteorological and chemical boundary conditions, and that this model could provide a source term in larger-scale models, both for momentum and for dispersed compounds.

  17. 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.

  18. Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction.

    PubMed

    Schenk, Gerhard; Mitić, Nataša; Gahan, Lawrence R; Ollis, David L; McGeary, Ross P; Guddat, Luke W

    2012-09-18

    Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear

  19. Structural simplification of chemical reaction networks in partial steady states.

    PubMed

    Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa

    2016-11-01

    We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology.

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  3. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

    SciTech Connect

    Kale, Seyit; Sode, Olaseni; Weare, Jonathan; Dinner, Aaron R.

    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 under DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.

  4. 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

  5. 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

  6. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis

    NASA Astrophysics Data System (ADS)

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-10-01

    The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

  7. 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

  8. Maximum Probability Reaction Sequences in Stochastic Chemical Kinetic Systems

    PubMed Central

    Salehi, Maryam; Perkins, Theodore J.

    2010-01-01

    The detailed behavior of many molecular processes in the cell, such as protein folding, protein complex assembly, and gene regulation, transcription and translation, can often be accurately captured by stochastic chemical kinetic models. We investigate a novel computational problem involving these models – that of finding the most-probable sequence of reactions that connects two or more states of the system observed at different times. We describe an efficient method for computing the probability of a given reaction sequence, but argue that computing most-probable reaction sequences is EXPSPACE-hard. We develop exact (exhaustive) and approximate algorithms for finding most-probable reaction sequences. We evaluate these methods on test problems relating to a recently-proposed stochastic model of folding of the Trp-cage peptide. Our results provide new computational tools for analyzing stochastic chemical models, and demonstrate their utility in illuminating the behavior of real-world systems. PMID:21629860

  9. 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.

  10. 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.

  11. Mianserin affects alarm reaction to conspecific chemical alarm cues in Nile tilapia.

    PubMed

    Barreto, Rodrigo Egydio

    2017-02-01

    In this study, I show that mianserin, a chemical with serotonin and adrenoceptor antagonist activities, increases fish vulnerability to a potential predator threat, when prey fish must deal with this threat based on conspecific chemical alarm cues. For that, I evaluated whether mianserin, diluted in the water, influences the behavioral responses of Nile tilapia (Oreochromis niloticus) to conspecific skin extract (chemical alarm cues). I found that, while mianserin did not abolished antipredator responses, this drug mitigates some components of this defensive reaction. Thus, a potential decrease in serotonin and adrenergic activities reduces the ability of dealing with predators when perceiving conspecific chemical alarm cues.

  12. Equilibriumlike behavior in chemical reaction networks far from equilibrium.

    PubMed

    Lubensky, David K

    2010-06-01

    In an equilibrium chemical reaction mixture, the number of molecules present obeys a Poisson distribution. We report that, surprisingly, the same is true of a large class of nonequilibrium reaction networks. In particular, we show that certain topological features imply a Poisson distribution, whatever the reaction rates. Such driven systems also obey an analog of the fluctuation-dissipation theorem. Our results shed light on the fundamental question of when equilibrium concepts might apply to nonequilibrium systems and may have applications to models of noise in biochemical networks.

  13. Femtosecond activation of reactions and the concept of nonergodic molecules

    PubMed

    Diau; Herek; Kim; Zewail

    1998-02-06

    The description of chemical reaction dynamics often assumes that vibrational modes are well coupled (ergodic) and redistribute energy rapidly with respect to the course of the reaction. To experimentally probe nonergodic, nonstatistical behavior, studies of a series of reactions induced by femtosecond activation for molecules of varying size but having the same reaction coordinates [CH2 - (CH2)n-2 - C = Odagger --> products, with n = 4, 5, 6, and 10] were performed. Comparison of the experimental results with theoretical electronic structure and rate calculations showed a two to four orders of magnitude difference, indicating that the basic assumption of statistical energy redistribution is invalid. These results suggest that chemical selectivity can be achieved with femtosecond activation even at very high energies.

  14. Uncertainty quantification for quantum chemical models of complex reaction networks.

    PubMed

    Proppe, Jonny; Husch, Tamara; Simm, Gregor N; Reiher, Markus

    2016-12-22

    For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

  15. Modeling Second-Order Chemical Reactions using Cellular Automata

    NASA Astrophysics Data System (ADS)

    Hunter, N. E.; Barton, C. C.; Seybold, P. G.; Rizki, M. M.

    2012-12-01

    Cellular automata (CA) are discrete, agent-based, dynamic, iterated, mathematical computational models used to describe complex physical, biological, and chemical systems. Unlike the more computationally demanding molecular dynamics and Monte Carlo approaches, which use "force fields" to model molecular interactions, CA models employ a set of local rules. The traditional approach for modeling chemical reactions is to solve a set of simultaneous differential rate equations to give deterministic outcomes. CA models yield statistical outcomes for a finite number of ingredients. The deterministic solutions appear as limiting cases for conditions such as a large number of ingredients or a finite number of ingredients and many trials. Here we present a 2-dimensional, probabilistic CA model of a second-order gas phase reaction A + B → C, using a MATLAB basis. Beginning with a random distribution of ingredients A and B, formation of C emerges as the system evolves. The reaction rate can be varied based on the probability of favorable collisions of the reagents A and B. The model permits visualization of the conversion of reagents to products, and allows one to plot concentration vs. time for A, B and C. We test hypothetical reaction conditions such as: limiting reagents, the effects of reaction probabilities, and reagent concentrations on the reaction kinetics. The deterministic solutions of the reactions emerge as statistical averages in the limit of the large number of cells in the array. Modeling results for dynamic processes in the atmosphere will be presented.

  16. 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.

  17. Chemical pathways in ultracold reactions of SrF molecules

    SciTech Connect

    Meyer, Edmund R.; Bohn, John L.

    2011-03-15

    We present a theoretical investigation of the chemical reaction SrF + SrF {yields} products, focusing on reactions at ultralow temperatures. We find that bond swapping SrF + SrF {yields} Sr{sub 2} + F{sub 2} is energetically forbidden at these temperatures. Rather, the only energetically allowed reaction is SrF + SrF {yields} SrF{sub 2} + Sr, and even then only singlet states of the SrF{sub 2} trimer can form. A calculation along a reduced reaction path demonstrates that this abstraction reaction is barrierless and proceeds by one SrF molecule ''handing off'' a fluorine atom to the other molecule.

  18. Reduction of chemical reaction networks through delay distributions

    NASA Astrophysics Data System (ADS)

    Barrio, Manuel; Leier, André; Marquez-Lago, Tatiana T.

    2013-03-01

    Accurate modelling and simulation of dynamic cellular events require two main ingredients: an adequate description of key chemical reactions and simulation of such chemical events in reasonable time spans. Quite logically, posing the right model is a crucial step for any endeavour in Computational Biology. However, more often than not, it is the associated computational costs which actually limit our capabilities of representing complex cellular behaviour. In this paper, we propose a methodology aimed at representing chains of chemical reactions by much simpler, reduced models. The abridgement is achieved by generation of model-specific delay distribution functions, consecutively fed to a delay stochastic simulation algorithm. We show how such delay distributions can be analytically described whenever the system is solely composed of consecutive first-order reactions, with or without additional "backward" bypass reactions, yielding an exact reduction. For models including other types of monomolecular reactions (constitutive synthesis, degradation, or "forward" bypass reactions), we discuss why one must adopt a numerical approach for its accurate stochastic representation, and propose two alternatives for this. In these cases, the accuracy depends on the respective numerical sample size. Our model reduction methodology yields significantly lower computational costs while retaining accuracy. Quite naturally, computational costs increase alongside network size and separation of time scales. Thus, we expect our model reduction methodologies to significantly decrease computational costs in these instances. We anticipate the use of delays in model reduction will greatly alleviate some of the current restrictions in simulating large sets of chemical reactions, largely applicable in pharmaceutical and biological research.

  19. Reaction Hamiltonian and state-to-state description of chemical reactions

    SciTech Connect

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

    1985-08-01

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

  20. Effects of incomplete mixing on chemical reactions under flow heterogeneities.

    NASA Astrophysics Data System (ADS)

    Perez, Lazaro; Hidalgo, Juan J.; Dentz, Marco

    2016-04-01

    Evaluation of the mixing process in aquifers is of primary importance when assessing attenuation of pollutants. In aquifers different hydraulic and chemical properties can increase mixing and spreading of the transported species. Mixing processes control biogeochemical transformations such as precipitation/dissolution reactions or degradation reactions that are fast compared to mass transfer processes. Reactions are local phenomena that fluctuate at the pore scale, but predictions are often made at much larger scales. However, aquifer heterogeities are found at all scales and generates flow heterogeneities which creates complex concentration distributions that enhances mixing. In order to assess the impact of spatial flow heterogeneities at pore scale we study concentration profiles, gradients and reaction rates using a random walk particle tracking (RWPT) method and kernel density estimators to reconstruct concentrations and gradients in two setups. First, we focus on a irreversible bimolecular reaction A+B → C under homogeneous flow to distinguish phenomena of incomplete mixing of reactants from finite-size sampling effects. Second, we analise a fast reversible bimolecular chemical reaction A+B rightleftharpoons C in a laminar Poiseuille flow reactor to determine the difference between local and global reaction rates caused by the incomplete mixing under flow heterogeneities. Simulation results for the first setup differ from the analytical solution of the continuum scale advection-dispersion-reaction equation studied by Gramling et al. (2002), which results in an overstimation quantity of reaction product (C). In the second setup, results show that actual reaction rates are bigger than the obtained from artificially mixing the system by averaging the concentration vertically. - LITERATURE Gramling, C. M.,Harvey, C. F., Meigs, and L. C., (2002). Reactive transport in porous media: A comparison of model prediction with laboratory visualization, Environ. Sci

  1. 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.

  2. Perspective: chemical dynamics simulations of non-statistical reaction dynamics.

    PubMed

    Ma, Xinyou; Hase, William L

    2017-04-28

    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'.

  3. Molecular codes in biological and chemical reaction networks.

    PubMed

    Görlich, Dennis; Dittrich, Peter

    2013-01-01

    Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

  4. 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.

  5. 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)

  6. Quantum and semiclassical theories of chemical reaction rates

    SciTech Connect

    Miller, W.H. |

    1995-09-01

    A rigorous quantum mechanical theory (and a semiclassical approximation thereto) is described for calculating chemical reaction rates ``directly``, i.e., without having to solve the complete state-to-state reactive scattering problem. The approach has many vestiges of transition state theory, for which it may be thought of as the rigorous generalization.

  7. 2011 Chemical Reactions at Surfaces Gordon Research Conference

    SciTech Connect

    Peter Stair

    2011-02-11

    The Gordon Research Conference on Chemical Reactions at Surfaces is dedicated to promoting and advancing the fundamental science of interfacial chemistry and physics by providing surface scientists with the foremost venue for presentation and discussion of research occurring at the frontiers of their fields.

  8. 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.

  9. Prediction of Rate Constants for Catalytic Reactions with Chemical Accuracy.

    PubMed

    Catlow, C Richard A

    2016-08-01

    Ex machina: A computational method for predicting rate constants for reactions within microporous zeolite catalysts with chemical accuracy has recently been reported. A key feature of this method is a stepwise QM/MM approach that allows accuracy to be achieved while using realistic models with accessible computer resources.

  10. Stabilization of miscible viscous fingering by chemical reaction decreasing viscosity

    NASA Astrophysics Data System (ADS)

    Arai, Shuntaro; Nagatsu, Yuichiro; Shukla, Priyanka; de Wit, Anne

    2016-11-01

    Viscous fingering (VF) occurs when a more viscous fluid is displaced by a less viscous one in porous media or Hele-Shaw cells. In this study, experiment on miscible VF with chemical reaction is conducted by using a Hele-Shaw cell. Here, the chemical reaction takes place between a polymer dissolved in the more viscous solution and hydrochloric acid (HCl) dissolved in the less viscous one in the miscible interface region. The reaction decreases the viscosity of the polymer solution. The experiment shows that the reaction stabilizes VF when the flow rate is small. In the present study, the corresponding numerical simulation is also conducted. The simulation is able to reproduce the experimental results mentioned above when different diffusion coefficients are considered meaning that HCl diffuses faster than the polymer. However, the stabilization cannot be found under conditions of the same diffusivity of the reactants. These numerical results show that the different diffusivity is responsible for the stabilization of miscible VF by the chemical reaction decreasing viscosity.

  11. 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.

  12. Mixing, chemical reaction and flow field development in ducted rockets

    SciTech Connect

    Vanka, S.P.; Craig, R.R.; Stull, F.D.

    1984-09-01

    Calculations have been made of the three-dimensional mixing, chemical reaction, and flow field development in a typical ducted rocket configuration. The governing partial differential equations are numerically solved by an iterative finite-difference solution procedure. The physical models include the k approx. epsilon turbulence model, one-step reaction, and mixing controlled chemical reaction rate. Radiation is neglected. The mean flow structure, fuel dispersal patterns, and temperature field are presented in detail for a base configuration with 0.058 m (2 in.) dome height, 45/sup 0/ side arm inclination, and with gaseous ethylene injected from the dome plate at an eccentric location. In addition, the influences of the geometrical parameters such as dome height, inclination of the side arms, and location of the fuel injector are studied.

  13. 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.

  14. 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.

  15. 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.

  16. Interplay between chemical reactions and transport in structured spaces

    NASA Astrophysics Data System (ADS)

    Konkoli, Zoran

    2005-07-01

    The main motivation behind this study is to understand the interplay between the reactions and transport in a geometries that are not compact. Typical examples of compact geometries are a box or a sphere. A network made of containers C1,C2,…,CN and tubes is an example of the space that is structured and noncompact. In containers, particles react with the rate λ . Tubes connecting containers allow for the exchange of chemicals with the transport rate D . A situation is considered where a number of reactants is small and kinetics is noise dominated. A method is presented that can be used to calculate the average and higher moments of the reaction time. A number of different chemical reactions are studied and their performance compared in various ways. Two schemes are discussed in general, the reaction on a fixed geometry ensemble (ROGE) and the geometry on a fixed reaction ensemble, examples are given in the ROGE case. The most important findings are as follows. (i) There is a large number of reactions that run faster in a networklike geometry. Such reactions contain antagonistic catalytic influences in the intermediate stages of a reaction scheme that are best dealt with in a networklike structure. (ii) Antagonistic catalytic influences are hard to identify since they are strongly connected to the pattern of injected molecules (inject pattern) and depend on the choice of molecules that have to be synthesized at the end (task pattern). (iii) The reaction time depends strongly on the details of the inject and task patterns.

  17. Density functional study of chemical reaction equilibrium for dimerization reactions in slit and cylindrical nanopores

    NASA Astrophysics Data System (ADS)

    Malijevský, Alexandr; Lísal, Martin

    2009-04-01

    We present a theoretical study of the effects of confinement on chemical reaction equilibrium in slit and cylindrical nanopores. We use a density functional theory (DFT) to investigate the effects of temperature, pore geometry, bulk pressure, transition layering, and capillary condensation on a dimerization reaction that mimics the nitric oxide dimerization reaction, 2NO⇌(NO)2, in carbonlike slit and cylindrical nanopores in equilibrium with a vapor reservoir. In addition to the DFT calculations, we also utilize the reaction ensemble Monte Carlo method to supplement the DFT results for reaction conversion. This work is an extension of the previous DFT study by Tripathi and Chapman [J. Chem. Phys. 118, 7993 (2003)] on the dimerization reactions confined in the planar slits.

  18. Development of a chemical oxygen - iodine laser with production of atomic iodine in a chemical reaction

    SciTech Connect

    Censky, M; Spalek, O; Jirasek, V; Kodymova, J; Jakubec, I

    2009-11-30

    The alternative method of atomic iodine generation for a chemical oxygen - iodine laser (COIL) in chemical reactions with gaseous reactants is investigated experimentally. The influence of the configuration of iodine atom injection into the laser cavity on the efficiency of the atomic iodine generation and small-signal gain is studied. (lasers)

  19. 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)

  20. 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)

  1. 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.

  2. Exact Analytic Solution of the Non-Markovian Chemical Reaction Process Via Time-Subordination

    NASA Astrophysics Data System (ADS)

    Benson, D. A.

    2015-12-01

    Perfectly-mixed reactions are Markovian, because the advance of the state depends only on the current state. Poor mixing (or the partner process of upscaling over heterogeneous concentrations) renders the process non-Markovian because of memory of the chemical structure. In other words, a particle takes some time to reach a suitable reaction site. The time depends on structure, and the structure changes over time. For purely diffusive transport, a calculation of the random time to reach the edges of ``islands'' allows a solution of the non-Markovian reaction rates that evolve (decrease) over time. This randomization of the active (operational) reaction time leads to non-Markovian reactions and an integro-differential governing equation of chemical evolution. Implications for more complex (advection/diffusion) environments are discussed.

  3. Deblocking reaction of chemically amplified ArF positive resists

    NASA Astrophysics Data System (ADS)

    Yamana, Mitsuharu; Itani, Toshiro; Yoshino, Hiroshi; Hashimoto, Shuichi; Tanabe, Hiroyoshi; Kasama, Kunihiko

    1998-06-01

    Deblocking reaction mechanisms and lithographic performance in chemically amplified positive ArF resists were investigated by analyzing acid concentration and blocking level. The resists consisted of triphenylsulfonium triflate as a acid generator and either the copolymer, poly(carboxy- tetracyclododecyl methacrylate70-co- tetrahydropyranylcarboxy-tetracyclododecyl methacrylate30) or the terpolymer, poly(tricyclodecylacrylate60- co-tetrahydropyranylmethacrylate20-co-methacrylic acid20). The deblocking reaction mechanisms were evaluated from Arrhenius plots of the deblocking reaction rate constant. It was found that the deblocking reaction of both resists is ruled by two rate-determining steps, i.e., reaction-controlled in the low-temperature region and acid- diffusion-controlled in the high-temperature region. Furthermore, the copolymer resist had better post-exposure- delay (PED) stability. To clarify this result, acid loss caused by air-born contamination effect on deblocking reaction was investigated. The change of amount of blocking group by acid loss was small for the copolymer. Therefore the copolymer resist had better PED stability. Furthermore, the post-exposure bake (PEB) sensitivity of linewidth of the copolymer resist was smaller than that of the terpolymer resist. Both deblocking reaction rate constant and reverse reaction rate constant of the copolymer resist increased with PEB temperature. As a result, equilibrium constant of the copolymer was not valuable with temperature. This is the reason why the copolymer resist has low PEB sensitivity. It is concluded that small acid loss effect on deblocking reaction induces better PED stability. A resist with reverse reaction has an advantage for PEB temperature sensitivity.

  4. Photo-induced chemical reaction of trans-resveratrol.

    PubMed

    Zhao, Yue; Shi, Meng; Ye, Jian-Hui; Zheng, Xin-Qiang; Lu, Jian-Liang; Liang, Yue-Rong

    2015-03-15

    Photo-induced chemical reaction of trans-resveratrol has been studied. UV B, liquid state and sufficient exposure time are essential conditions to the photochemical change of trans-resveratrol. Three principal compounds, cis-resveratrol, 2,4,6-phenanthrenetriol and 2-(4-hydroxyphenyl)-5,6-benzofurandione, were successively generated in the reaction solution of trans-resveratrol (0.25 mM, 100% ethanol) under 100 μW cm(-2) UV B radiation for 4h. cis-Resveratrol, originated from isomerization of trans-resveratrol, resulted in 2,4,6-phenanthrenetriol through photocyclisation reaction meanwhile loss of 2 H. 2,4,6-Phenanthrenetriol played a role of photosensitizer producing singlet oxygen in the reaction pathway. The singlet oxygen triggered [4+2] cycloaddition reaction of trans-resveratrol, and then resulted in the generation of 2-(4-hydroxyphenyl)-5,6-benzofurandione through photorearrangement and oxidation reaction. The singlet oxygen reaction was closely related to the substrate concentration of trans-resveratrol in solution.

  5. A chemical reaction network solver for the astrophysics code NIRVANA

    NASA Astrophysics Data System (ADS)

    Ziegler, U.

    2016-02-01

    Context. Chemistry often plays an important role in astrophysical gases. It regulates thermal properties by changing species abundances and via ionization processes. This way, time-dependent cooling mechanisms and other chemistry-related energy sources can have a profound influence on the dynamical evolution of an astrophysical system. Modeling those effects with the underlying chemical kinetics in realistic magneto-gasdynamical simulations provide the basis for a better link to observations. Aims: The present work describes the implementation of a chemical reaction network solver into the magneto-gasdynamical code NIRVANA. For this purpose a multispecies structure is installed, and a new module for evolving the rate equations of chemical kinetics is developed and coupled to the dynamical part of the code. A small chemical network for a hydrogen-helium plasma was constructed including associated thermal processes which is used in test problems. Methods: Evolving a chemical network within time-dependent simulations requires the additional solution of a set of coupled advection-reaction equations for species and gas temperature. Second-order Strang-splitting is used to separate the advection part from the reaction part. The ordinary differential equation (ODE) system representing the reaction part is solved with a fourth-order generalized Runge-Kutta method applicable for stiff systems inherent to astrochemistry. Results: A series of tests was performed in order to check the correctness of numerical and technical implementation. Tests include well-known stiff ODE problems from the mathematical literature in order to confirm accuracy properties of the solver used as well as problems combining gasdynamics and chemistry. Overall, very satisfactory results are achieved. Conclusions: The NIRVANA code is now ready to handle astrochemical processes in time-dependent simulations. An easy-to-use interface allows implementation of complex networks including thermal processes

  6. 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.

  7. Active Chemical Thermodynamics promoted by activity of cortical actin

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Bhaswati; Chaudhuri, Abhishek; Gowrishankar, Kripa; Rao, Madan

    2011-03-01

    The spatial distribution and dynamics of formation and breakup of the nanoclusters of cell surface proteins is controlled by the active remodeling dynamics of the underlying cortical actin. To explain these observations, we have proposed a novel mechanism of nanoclustering, involving the transient binding to and advection along constitutively occuring ``asters'' of cortical actin. We study the consequences of such active actin-based clustering, in the context of chemical reactions involving conformational changes of cell surface proteins. We find that the active remodeling of cortical actin, can give rise to a dramatic increase in efficiency and extent of conformational spread, even at low levels of expression at the cell surface. We define a activity temperature (τa) arising due to actin activities which can be used to describe chemical thermodynamics of the system. We plot TTT (time-temparature-transformation) curves and compute the Arrhenius factors which depend on τa . With this, the active asters can be treated as enzymes whose enzymatic reaction rate can be related to the activity.

  8. Internal Active Thermal Control System (IATCS) Sodium Bicarbonate/Carbonate Buffer in an Open Aqueous Carbon Dioxide System and Corollary Electrochemical/Chemical Reactions Relative to System pH Changes

    NASA Technical Reports Server (NTRS)

    Stegman, Thomas W.; Wilson, Mark E.; Glasscock, Brad; Holt, Mike

    2014-01-01

    The International Space Station (ISS) Internal Active Thermal Control System (IATCS) experienced a number of chemical changes driven by system absorption of CO2 which altered the coolant’s pH. The natural effects of the decrease in pH from approximately 9.2 to less than 8.4 had immediate consequences on system corrosion rates and corrosion product interactions with specified coolant constituents. The alkalinity of the system was increased through the development and implementation of a carbonate/bicarbonate buffer that would increase coolant pH to 9.0 – 10.0 and maintain pH above 9.0 in the presence of ISS cabin concentrations of CO2 up to twenty times higher than ground concentrations. This paper defines how a carbonate/bicarbonate buffer works in an open carbon dioxide system and summarizes the analyses performed on the buffer for safe and effective application in the on-orbit system. The importance of the relationship between the cabin environment and the IATCS is demonstrated as the dominant factor in understanding the system chemistry and pH trends before and after addition of the carbonate/bicarbonate buffer. The paper also documents the corollary electrochemical and chemical reactions the system has experienced and the rationale for remediation of these effects with the addition of the carbonate/bicarbonate buffer.

  9. 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 (Ea), 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. Ea, 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.

  10. Laser studies of chemical reaction and collision processes

    SciTech Connect

    Flynn, G.

    1993-12-01

    This work has concentrated on several interrelated projects in the area of laser photochemistry and photophysics which impinge on a variety of questions in combustion chemistry and general chemical kinetics. Infrared diode laser probes of the quenching of molecules with {open_quotes}chemically significant{close_quotes} amounts of energy in which the energy transferred to the quencher has, for the first time, been separated into its vibrational, rotational, and translational components. Probes of quantum state distributions and velocity profiles for atomic fragments produced in photodissociation reactions have been explored for iodine chloride.

  11. Chemical reaction fouling model for single-phase heat transfer

    SciTech Connect

    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 differ for the three fouling mechanisms; therefore, it is important to identify the controlling mechanism in applying the closed-flow-loop data to industrial conditions.

  12. Crossed molecular beam studies of atmospheric chemical reaction dynamics

    SciTech Connect

    Zhang, Jingsong

    1993-04-01

    The dynamics of several elementary chemical reactions that are important in atmospheric chemistry are investigated. The reactive scattering of ground state chlorine or bromine atoms with ozone molecules and ground state chlorine atoms with nitrogen dioxide molecules is studied using a crossed molecular beams apparatus with a rotatable mass spectrometer detector. The Cl + O3 → ClO + O2 reaction has been studied at four collision energies ranging from 6 kcal/mole to 32 kcal/mole. The derived product center-of-mass angular and translational energy distributions show that the reaction has a direct reaction mechanism and that there is a strong repulsion on the exit channel. The ClO product is sideways and forward scattered with respect to the Cl atom, and the translational energy release is large. The Cl atom is most likely to attack the terminal oxygen atom of the ozone molecule. The Br + O3 → ClO + O2 reaction has been studied at five collision energies ranging from 5 kcal/mole to 26 kcal/mole. The derived product center-of-mass angular and translational energy distributions are quite similar to those in the Cl + O3 reaction. The Br + O3 reaction has a direct reaction mechanism similar to that of the Cl + O3 reaction. The electronic structure of the ozone molecule seems to play the central role in determining the reaction mechanism in atomic radical reactions with the ozone molecule. The Cl + NO2 → ClO + NO reaction has been studied at three collision energies ranging from 10.6 kcal/mole to 22.4 kcal/mole. The center-of-mass angular distribution has some forward-backward symmetry, and the product translational energy release is quite large. The reaction proceeds through a short-lived complex whose lifetime is less than one rotational period. The experimental results seem to show that the Cl atom mainly attacks the oxygen atom instead of the nitrogen atom of the NO2

  13. 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.

  14. A microvascular system for chemical reactions using surface waste heat.

    PubMed

    Nguyen, Du Thai; Esser-Kahn, Aaron P

    2013-12-16

    Coffee-powered chemistry: Low-grade waste heat on surfaces can be used to drive chemical reactions, including the regeneration of a CO2 capture solution. Flowing two-phase heat transfer has been implemented within microvascular systems. This stripping system can be adapted to pre-fabricated surfaces, as demonstrated by a coffee mug containing a 1.2 m long microchannel. MEA=monoethanolamine.

  15. Stochastic Generator of Chemical Structure. 3. Reaction Network Generation

    SciTech Connect

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

    A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.

  16. Shock-Induced Chemical Reactions in Condensed Matter.

    DTIC Science & Technology

    1982-08-01

    Technical, 4/1/78 - 6/30/82 Matter 6. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(s) S. CONTRACT OR GRANT NUMUER(e) George E. Duvall, Principal Investigator...CHEMICAL REACTIONS IN CONDENSED MATTER George E. Duvall, Principal Investigator Stephen A. Sheffield* Kendal M. OgilvieT 4 C. Robert Wilson Paul...Temperture," in Sixth Symposium (International on Detonation (Office of Naval Research, Arlington, 1976), ACR-Z21, p. 36. 24. G. Gamow , "Tentative

  17. Kinetics with chemical reactions and nonequilibrium structures in open systems

    NASA Astrophysics Data System (ADS)

    Aristov, Vladimir; Frolova, Anna; Zabelok, Sergei

    2013-10-01

    Simulations of flows on the basis of kinetic equations for mixtures with chemical reactions are performed. The Nonuniform Relaxation Problems (NRP) are formulated and solved. The Unified Flow Solver (UFS) is used for 1D and 2D NRP. The nonequilibrium kinetics can provide results outside the traditional theory of macroscopic phenomena based on the Navier-Stokes equations. Nonequilibrium flows with different properties in relaxation zones are described.

  18. Separation of the isotopes of boron by chemical exchange reactions

    DOEpatents

    McCandless, Frank P.; Herbst, Ronald S.

    1995-01-01

    The isotopes of boron, .sup.10 B and .sup.11 B, are separated by means of a gas-liquid chemical exchange reaction involving the isotopic equilibrium between gaseous BF.sub.3 and a liquid BF.sub.3 . donor molecular addition complex formed between BF.sub.3 gas and a donor chosen from the group consisting of: nitromethane, acetone, methyl isobutyl ketone, or diisobutyl ketone.

  19. Separation of the isotopes of boron by chemical exchange reactions

    DOEpatents

    McCandless, F.P.; Herbst, R.S.

    1995-05-30

    The isotopes of boron, {sup 10}B and {sup 11}B, are separated by means of a gas-liquid chemical exchange reaction involving the isotopic equilibrium between gaseous BF{sub 3} and a liquid BF{sub 3} donor molecular addition complex formed between BF{sub 3} gas and a donor chosen from the group consisting of: nitromethane, acetone, methyl isobutyl ketone, or diisobutyl ketone. 1 Fig.

  20. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks.

    PubMed

    Smadbeck, Patrick; Kaznessis, Yiannis N

    2014-08-01

    Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized.

  1. Nitrosonium cation in chemical and biochemical reactions: achievements and prospects

    NASA Astrophysics Data System (ADS)

    Borodkin, G. I.; Shubin, V. G.

    2017-01-01

    Data on the reactivity of nitrosonium cation in chemical reactions are systematized and integrated. The review demonstrates the structural diversity of nitrosonium complexes resulting from the specific features of the electronic structure of NO+. The use of nitrosonium salts in the synthesis of heterocyclic compounds and for the preparation of modern materials, including nanomaterials, is considered. The participation of NO+ in oxidative, catalytic and biochemical processes is discussed. The bibliography includes 332 references.

  2. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

    PubMed Central

    Smadbeck, Patrick; Kaznessis, Yiannis N.

    2014-01-01

    Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized. PMID:25215268

  3. Nanochemistry - Chemical Reactions of Iron and Benzene Within Molecular Clusters

    NASA Astrophysics Data System (ADS)

    Feigerle, C. S.; Bililign, S.; Miller, John C.

    2000-06-01

    Molecular clusters represent a nanoscale test tube where chemical reactions can be examined in a unique way for the effects of the local environment and the possibility of size-dependent reactions. Previous experiments have shown that the ionization/dissociation of iron pentacarbonyl clusters can lead to the formation of iron ions and iron cluster ions and that these species can further react with dopant molecules to yield chemically rearranged products. The present experiments characterize similar reactions with benzene molecules and clusters. Heteroclusters of the form [Fe(CO)5]m(C6H6)nArp are created in an expanding supersonic jet of the component molecules. Following ionization by a 30 ps, 266 nm laser pulse, extensive dissociation, aggregation, and chemical rearrangement occurs leading to ionic products which are characterized by mass spectrometry. Cluster ions of the type Fem(C6H6)n + are observed as products. The stability of the sandwich form of the ion, Fe(benzene)2 +, is inferred from the data. Evidence for a similar special stability for the double-decker, Fe2(benzene)3 +, is presented.

  4. Chemically activated manganese dioxide for dry batteries

    NASA Astrophysics Data System (ADS)

    Askar, M.; Abbas, H.

    1994-10-01

    The present investigation has enabled us to convert inactive beta-manganese dioxide to high electrochemically active types by chemical processes. Natural and chemically prepared beta-manganese dioxides were roasted at 1050 C to form Mn3O4. This compound was subjected to activation treatment using hydrochloric and sulfuric acid under various reaction conditions. The manganese dioxide so obtained was examined by x-ray diffraction, thermogravimetric, differential thermal, and chemical analyses. The structure of the dioxide obtained was found to be greatly dependent on the origin of MnO2 and type of acid used. Treatment with hydrochloric acid yielded the so-called gamma-variety while sulfuric acid tended to produce gamma- or alpha-MnO2. In addition, waste manganese sulfate obtained as by-product from sulfuric acid digestion treatment was recycled and electrolytically oxidized to gamma-MnO2. The discharge performance of the above-mentioned MnO2 samples as battery cathodic active material was evaluated and compared with the ordinary battery grade.

  5. The nature of chemical reaction-driven tip-streaming

    NASA Astrophysics Data System (ADS)

    Mayer, H. C.; Krechetnikov, R.

    2013-05-01

    The discovery of chemical reaction-driven tip-streaming (also known as "an amazing drop") was made about a decade ago during measurements of the dynamic interfacial tension of a water-alkali pendant droplet immersed in oil-linoleic acid. A plausible explanation for this self-sustained ejection of micron sized droplets from the tip of the macroscopic pendant drop was offered at that time and attributed to Marangoni stresses driving the reaction-produced surfactant along the interface. Later, asymptotic theory based on the analysis of a complete fluid dynamical formulation supported this hypothesis. As this discovery promised a way of microdroplet generation without the need for complex microchannel geometries or externally imposed flow or electric fields, we were recently motivated to study the influence of the reagent concentrations and reaction rate on the droplet generation. However, in an attempt to recreate the original experiments, we revealed that the cause for tip-streaming is not what it originally seemed to be. This led to a series of experiments clarifying the role of the Marangoni stresses and the crucial differences from similar phenomena. As the mechanism by which the phenomenon was originally thought to operate was supported by recent theoretical studies, the present work leads to new intriguing questions of existence and conditions under which a chemical reaction alone can drive Marangoni stresses capable of self-sustaining the process of tip-streaming.

  6. Effect of aspect ratio on chemical reactions on microchip.

    PubMed

    Shimizu, Takahiro; Masaki, Hiroyuki; Korenaga, Takashi

    2006-01-01

    Parallel two-phase laminar flow, which is formed when two solutions flow in microchannels, has been developed and has advanced unique research in the area of microchip analysis. In two-phase laminar flow, channel size has a significant effect on the efficiency of chemical reactions. However, the sizes of microchannels vary greatly in many studies. In this paper, we report on the effect of microchannel size on chemical reactions on a microchip. Aspect ratio is defined as the ratio of depth to width of a microchannel. Five microchips with different aspect ratios (from 0.50 to 2.00) were fabricated by mechanical machining. The reaction of nitrous acid and Saltzman reagent was carried out on these microchips and the absorbance was measured on-line in a capillary tube, which was attached to the outlet on the microchip. The results showed that the color reaction occurred more efficiently as the aspect ratio increased. This result is expected to be useful when determining the size of microchannels.

  7. Laser-initiated chemical reactions in carbon suspensions.

    SciTech Connect

    McGrath, T. E.; Diebold, G. J.; Bartels, D. M.; Crowell, R. A.; Chemistry; Brown Univ.

    2002-10-31

    We report on laser-initiated chemical reactions in colloidal carbon suspensions. Irradiation of carbon particles ranging in size from 13 to 75 nm in diameter suspended in water, toluene, and benzene with high power nanosecond, picosecond, and femtosecond laser pulses leads to the formation of a number of gaseous hydrocarbons as well as a series of liquid-phase products. In the product gas above irradiated carbon suspensions in water, H{sub 2} and CO, the main reaction products of the carbon-steam reaction, and numerous hydrocarbons ranging from C{sub 1}-C{sub 4} were detected. Irradiation of particulate carbon in toluene and benzene gave H{sub 2} as the main gas product with small amounts of C{sub 1}-C{sub 3} hydrocarbons. Bibenzyl and biphenyl were found as the main liquid products produced in toluene and benzene suspensions, respectively, but with numerous polycyclic aromatic hydrocarbons in smaller concentrations. The amount of products generated by pulsed laser irradiation is shown to depend on particle size and concentration, as well as the laser fluence and pulse width. The chemical reactions reported take place under conditions characterized by extremely high temperatures and pressures of short duration.

  8. Phase and chemical equilibria in multicomponent fluid systems with a chemical reaction

    NASA Astrophysics Data System (ADS)

    Toikka, A. M.; Samarov, A. A.; Toikka, M. A.

    2015-04-01

    Studies of the phase and chemical equilibria in the systems with chemical reaction cover a wide range of problems related to both experimental determination of physicochemical characteristics of these systems and various aspects of thermodynamic analysis of the phase and chemical processes occurring there. The main goal of this review consists in systematization and analysis of available experimental data concerning the vapour-liquid and liquid-liquid equilibria in multicomponent systems where chemical reactions occur. The studies considered here have been mainly published in recent years, and they include rather detailed data on physicochemical properties, phase transitions and chemical processes in fluid systems, i.e., the data which are essential for thermodynamic analysis. Available approaches to the thermodynamic analysis of heterogeneous systems with chemical reactions are also discussed. Particular attention is paid to the studies of the simultaneous phase and chemical equilibria. We hope that this review could be useful both for fundamental studies of heterogeneous reactive systems and for solving applied problems on the design of combined reactive and mass-transfer processes. The bibliography includes 79 references.

  9. Surface-Activated Coupling Reactions Confined on a Surface.

    PubMed

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

    2015-10-20

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

  10. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    SciTech Connect

    Gray, S.K.

    1993-12-01

    A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.

  11. [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.

  12. 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.

  13. Reversible chemical reactions for single-color multiplexing microscopy.

    PubMed

    Brox, Dominik; Schwering, Michael; Engelhardt, Johann; Herten, Dirk-Peter

    2014-08-04

    Recent developments in biology demand an increasing number of simultaneously imaged structures with standard fluorescence microscopy. However, the number of multiplexed channels is limited for most multiplexing modalities, such as spectral multiplexing or fluorescence-lifetime imaging. We propose extending the number of imaging channels by using chemical reactions, controlling the emissive state of fluorescent dyes. As proof of concept, we reversibly switch a fluorescent copper sensor to enable successive imaging of two different structures in the same spectral channel. We also show that this chemical multiplexing is orthogonal to existing methods. By using two different dyes, we combine chemical with spectral multiplexing for the simultaneous imaging of four different structures with only two spectrally different channels. We characterize and discuss the approach and provide perspectives for extending imaging modalities in stimulated emission depletion microscopy, for which spectral multiplexing is technically demanding.

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

    SciTech Connect

    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 to 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.

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

    SciTech Connect

    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 to 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.

  16. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

    PubMed

    Bloudoff, Kristjan; Alonzo, Diego A; Schmeing, T Martin

    2016-03-17

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.

  17. Compare and contrast the reaction coordinate diagrams for chemical reactions and cytoskeletal force generators

    PubMed Central

    Scholey, Jonathan M.

    2013-01-01

    Reaction coordinate diagrams are used to relate the free energy changes that occur during the progress of chemical processes to the rate and equilibrium constants of the process. Here I briefly review the application of these diagrams to the thermodynamics and kinetics of the generation of force and motion by cytoskeletal motors and polymer ratchets as they mediate intracellular transport, organelle dynamics, cell locomotion, and cell division. To provide a familiar biochemical context for discussing these subcellular force generators, I first review the application of reaction coordinate diagrams to the mechanisms of simple chemical and enzyme-catalyzed reactions. My description of reaction coordinate diagrams of motors and polymer ratchets is simplified relative to the rigorous biophysical treatment found in many of the references that I use and cite, but I hope that the essay provides a valuable qualitative representation of the physical chemical parameters that underlie the generation of force and motility at molecular scales. In any case, I have found that this approach represents a useful interdisciplinary framework for understanding, researching, and teaching the basic molecular mechanisms by which motors contribute to fundamental cell biological processes. PMID:23408787

  18. Current Chemical Risk Reduction Activities

    EPA Pesticide Factsheets

    EPA's existing chemicals programs address pollution prevention, risk assessment, hazard and exposure assessment and/or characterization, and risk management for chemicals substances in commercial use.

  19. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: hidden intermediates and hidden transition States.

    PubMed

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

    Computational approaches to understanding chemical reaction mechanisms generally begin by establishing the relative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening species via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by-step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an efficient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mechanism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. In this Account, we examine mechanistic analysis with URVA in detail, focusing on recent theoretical insights (with a variety of reaction types) from our laboratories. Through the utilization of the concept of localized adiabatic vibrational modes that are associated with the internal coordinates, q(n)(s), of the reaction complex, the chemical character of each reaction phase can be identified via the adiabatic curvature coupling coefficients, A(n,s)(s). These quantities reveal whether a local adiabatic vibrational mode supports (A(n,s) > 0) or resists

  20. Chemical activation through super energy transfer collisions.

    PubMed

    Smith, Jonathan M; Nikow, Matthew; Ma, Jianqiang; Wilhelm, Michael J; Han, Yong-Chang; Sharma, Amit R; Bowman, Joel M; Dai, Hai-Lung

    2014-02-05

    Can a molecule be efficiently activated with a large amount of energy in a single collision with a fast atom? If so, this type of collision will greatly affect molecular reactivity and equilibrium in systems where abundant hot atoms exist. Conventional expectation of molecular energy transfer (ET) is that the probability decreases exponentially with the amount of energy transferred, hence the probability of what we label "super energy transfer" is negligible. We show, however, that in collisions between an atom and a molecule for which chemical reactions may occur, such as those between a translationally hot H atom and an ambient acetylene (HCCH) or sulfur dioxide, ET of chemically significant amounts of energy commences with surprisingly high efficiency through chemical complex formation. Time-resolved infrared emission observations are supported by quasi-classical trajectory calculations on a global ab initio potential energy surface. Results show that ∼10% of collisions between H atoms moving with ∼60 kcal/mol energy and HCCH result in transfer of up to 70% of this energy to activate internal degrees of freedom.

  1. Chemical reaction network approaches to Biochemical Systems Theory.

    PubMed

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R

    2015-11-01

    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed.

  2. Determination of caffeine using oscillating chemical reaction in a CSTR.

    PubMed

    Gao, Jinzhang; Ren, Jie; Yang, Wu; Liu, XiuHui; Yang, Hua

    2003-07-14

    A new analytical method for the determination of caffeine by the sequential perturbation caused by different amounts of caffeine on the oscillating chemical system involving the manganese(II)-catalyzed reaction between potassium bromate and tyrosine in acidic medium in a CSTR was proposed. The method exposed for the first time in this work. It relies on the relationship between the changes in the oscillation amplitude of the chemical system and the concentration of caffeine. The calibration curve fits a second-order polynomial equation very well when the concentration of caffeine over the range 4.0 x 10(-6) - 1.2 x 10(-4) M (r = 0.9968). The effect of influential variables, such as the concentration of reaction components, injection point, temperature, flow rate and stirring rate were studied. Some aspects of the potential mechanism of action of caffeine on the chemical oscillating system were also discussed. A real sample was determined and the result was satisfactory.

  3. 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.

  4. 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…

  5. Chemical characteristics of mineral trioxide aggregate and its hydration reaction

    PubMed Central

    2012-01-01

    Mineral trioxide aggregate (MTA) was developed in early 1990s and has been successfully used for root perforation repair, root end filling, and one-visit apexification. MTA is composed mainly of tricalcium silicate and dicalcium silicate. When MTA is hydrated, calcium silicate hydrate (CSH) and calcium hydroxide is formed. Formed calcium hydroxide interacts with the phosphate ion in body fluid and form amorphous calcium phosphate (ACP) which finally transforms into calcium deficient hydroxyapatite (CDHA). These mineral precipitate were reported to form the MTA-dentin interfacial layer which enhances the sealing ability of MTA. Clinically, the use of zinc oxide euginol (ZOE) based materials may retard the setting of MTA. Also, the use of acids or contact with excessive blood should be avoided before complete set of MTA, because these conditions could adversely affect the hydration reaction of MTA. Further studies on the chemical nature of MTA hydration reaction are needed. PMID:23429542

  6. 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.

  7. Nature of the chemical reaction for furfural modified asphalt

    SciTech Connect

    Memon, G.M.; Chollar, B.H.

    1994-12-31

    Three of the most serious problems of asphalt pavements today are rutting, cracking, and susceptibility to moisture damage (stripping). Asphalt manufacturers have been mixing asphalts with polymers to produce polymer-modified asphalts with improved rheological properties. However, the costs for these improved polymer-modified asphalts are almost double that of regular asphalts. FHWA researchers have found that asphalt modified by the chemical, furfural (which is prepared by simple elimination reaction of aldopentoses obtained from oat hulls), exhibited better stripping properties and was less temperature susceptible than the virgin asphalt while costing less than polymer-modified asphalts. This paper discusses the possible structure of the furfural-modified asphalt, data for the virgin and furfural-modified asphalts and their Corbett fractions, data from a model reaction between phenol and furfural, and a possible explanation of this structure based on these data.

  8. Method for detecting pollutants. [through chemical reactions and heat treatment

    NASA Technical Reports Server (NTRS)

    Rogowski, R. S.; Richards, R. R.; Conway, E. J. (Inventor)

    1976-01-01

    A method is described for detecting and measuring trace amounts of pollutants of the group consisting of ozone, nitrogen dioxide, and carbon monoxide in a gaseous environment. A sample organic solid material that will undergo a chemical reaction with the test pollutant is exposed to the test environment and thereafter, when heated in the temperature range of 100-200 C., undergoes chemiluminescence that is measured and recorded as a function of concentration of the test pollutant. The chemiluminescence of the solid organic material is specific to the pollutant being tested.

  9. Interaction between measurement time and observed Hugoniot cusp due to chemical reactions

    NASA Astrophysics Data System (ADS)

    McGrane, S. D.; Brown, K. E.; Bolme, C. A.; Moore, D. S.

    2017-01-01

    Chemistry occurring on picosecond timescales can be observed through ultrafast laser shock drive experiments that measure Hugoniot data and transient absorption. The shock stress needed to induce chemical reactions on picosecond time scales is significantly larger than the stress needed to induce reactions on nanosecond time scales typical of gas gun and explosively driven plate impact experiments. This discrepancy is consistent with the explanation that increased shock stress leads to increased temperature, which drives thermally activated processes at a faster rate. While the data are qualitatively consistent with the interpretation of thermally dominated reactions, they are not a critical test of this interpretation. In this paper, we review data from several shocked liquids that illustrate a Hugoniot cusp due to volume changing reactions that occurs at higher shock stress states in picosecond experiments than in nanosecond to microsecond experiments. We also correlate the observed Hugoniot cusp states with transient absorption changes that occur due to the buildup of reaction products.

  10. Spatially resolved chemical reaction monitoring using magnetic resonance imaging.

    PubMed

    Feindel, Kirk W

    2016-06-01

    Over the previous three decades, the use of MRI for studying dynamic physical and chemical processes of materials systems has grown significantly. This mini-review provides a brief introduction to relevant principles of MRI, including methods of spatial localization, factors contributing to image contrast, and chemical shift imaging. A few historical examples of (1) H MRI for reaction monitoring will be presented, followed by a review of recent research including (1) H MRI studies of gelation and biofilms, (1) H, (7) Li, and (11) B MRI studies of electrochemical systems, in vivo glucose metabolism monitored with (19) F MRI, and in situ temperature monitoring with (27) Al MRI. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Chemical Kinetic Reaction Mechanisms for Combustion of Hydrocarbon and Other Types of Chemical Fuels

    DOE Data Explorer

    The central feature of the Combustion Chemistry project at LLNL is the development, validation, and application of detailed chemical kinetic reaction mechanisms for the combustion of hydrocarbon and other types of chemical fuels. For the past 30 years, LLNL's Chemical Sciences Division has built hydrocarbon mechanisms for fuels from hydrogen and methane through much larger fuels including heptanes and octanes. Other classes of fuels for which models have been developed include flame suppressants such as halons and organophosphates, and air pollutants such as soot and oxides of nitrogen and sulfur. Reaction mechanisms have been tested and validated extensively through comparisons between computed results and measured data from laboratory experiments (e.g., shock tubes, laminar flames, rapid compression machines, flow reactors, stirred reactors) and from practical systems (e.g., diesel engines, spark-ignition engines, homogeneous charge, compression ignition (HCCI) engines). These kinetic models are used to examine a wide range of combustion systems.

  12. A stronger necessary condition for the multistationarity of chemical reaction networks.

    PubMed

    Soliman, Sylvain

    2013-11-01

    Biochemical reaction networks grow bigger and bigger, fed by the high-throughput data provided by biologists and bred in open repositories of models allowing merging and evolution. Nevertheless, since the available data is still very far from permitting the identification of the increasing number of kinetic parameters of such models, the necessity of structural analyses for describing the dynamics of chemical networks appears stronger every day. Using the structural information, notably from the stoichiometric matrix, of a biochemical reaction system, we state a more strict version of the famous Thomas' necessary condition for multistationarity. In particular, the obvious cases where Thomas' condition was trivially satisfied, mutual inhibition due to a multimolecular reaction and mutual activation due to a reversible reaction, can now easily be ruled out. This more strict condition shall not be seen as some version of Thomas' circuit functionality for the continuous case but rather as related and complementary to the whole domain of the structural analysis of (bio)chemical reaction systems, as pioneered by the chemical reaction network theory.

  13. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions.

    PubMed

    Cheng, Gui-Juan; Zhang, Xinhao; Chung, Lung Wa; Xu, Liping; Wu, Yun-Dong

    2015-02-11

    Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

  14. KINETICS: A computer program to analyze chemical reaction data. Revision 2

    SciTech Connect

    Braun, R.L.; Burnham, A.K.

    1994-09-01

    KINETICS (Version 3.2) is a copyrighted, user-friendly kinetics analysis computer program designed for reactions such-as kerogen or polymer decomposition. It can fit rate parameters to chemical reaction data (rate or cumulative reacted) measured at a series of constant temperatures, constant heating rates, or arbitrary thermal histories. The program uses two models with conversion-dependent Azrhenius parameters and two models with activation energy distributions. The discrete distribution model fits an average frequency factor and relative fractions and activation energies for up to 25 parallel, fast-order reactions. The Gaussian distribution model fits a frequency factor, activation energy, Gaussian distribution parameter, and reaction order for up to 3 parallel reactions. For both distribution models, if the experiments are at a series of constant heating rates, the program uses a very fast approximate fitting procedure to determine possible initial parameter-estimates for the subsequent nonlinear regression analysis. This increases the probability that the regression analysis will properly. converge with a minimum of computer time. Once convergence is reached by the discrete model, the parameter space is further systematically searched to achieve global convergence. With the Gaussian model, the calculated rates or integrals can be convoluted with an experimental tracer signal during the nonlinear regression to account for dispersion effects often found in real chemical reaction data. KINETICS can also be used in an application mode to calculate reaction rates and integrals for previously determined Gaussian or discrete, parameters, using an arbitrary thermal history. Four additional models have been incorporated for the kinetics analysis of polymers and other materials, including some kerogens, which have a reaction-rate profile that is narrower than that for a single first-order reaction.

  15. Single-collision studies of energy transfer and chemical reaction

    SciTech Connect

    Valentini, J.J.

    1993-12-01

    The research focus in this group is state-to-state dynamics of reaction and energy transfer in collisions of free radicals such as H, OH, and CH{sub 3} with H{sub 2}, alkanes, alcohols and other hydrogen-containing molecules. The motivation for the work is the desire to provide a detailed understanding of the chemical dynamics of prototype reactions that are important in the production and utilization of energy sources, most importantly in combustion. The work is primarily experimental, but with an important and growing theoretical/computational component. The focus of this research program is now on reactions in which at least one of the reactants and one of the products is polyatomic. The objective is to determine how the high dimensionality of the reactants and products differentiates such reactions from atom + diatom reactions of the same kinematics and energetics. The experiments use highly time-resolved laser spectroscopic methods to prepare reactant states and analyze the states of the products on a single-collision time scale. The primary spectroscopic tool for product state analysis is coherent anti-Stokes Raman scattering (CARS) spectroscopy. CARS is used because of its generality and because the extraction of quantum state populations from CARS spectra is straightforward. The combination of the generality and easy analysis of CARS makes possible absolute cross section measurements (both state-to-state and total), a particularly valuable capability for characterizing reactive and inelastic collisions. Reactant free radicals are produced by laser photolysis of appropriate precursors. For reactant vibrational excitation stimulated Raman techniques are being developed and implemented.

  16. Community Detection Using Dual-Representation Chemical Reaction Optimization.

    PubMed

    Chang, Honghao; Feng, Zuren; Ren, Zhigang

    2016-09-23

    Many complex networks have been shown to have community structures. Detecting those structures is very important for understanding the organization and function of networks. Because this problem is NP-hard, it is appropriate to resort to evolutionary algorithms. Chemical reaction optimization (CRO) is a novel evolutionary algorithm inspired by the interactions among molecules during chemical reactions. In this paper, we propose a CRO variant named dual-representation CRO (DCRO) to address the community detection problem. DCRO encodes a solution in two representations: one is locus-based and the other is vector-based. The former representation can ensure the validity of a solution and fits for diversification search, and the latter is convenient for intensification search. We thus design two operators for CRO based on these two representations. Their cooperation enables DCRO to achieve a good balance between exploration and exploitation. Experimental results on synthetic and real-life networks show that DCRO can find community structures close to the actual ones and is capable of achieving solutions comparable to several state-of-the-art methods.

  17. Dynamics of self-propelled nanomotors in chemically active media

    NASA Astrophysics Data System (ADS)

    Thakur, Snigdha; Kapral, Raymond

    2011-07-01

    Synthetic chemically powered nanomotors often rely on the environment for their fuel supply. The propulsion properties of such motors can be altered if the environment in which they move is chemically active. The dynamical properties of sphere dimer motors, composed of linked catalytic and noncatalytic monomers, are investigated in active media. Chemical reactions occur at the catalytic monomer and the reactant or product of this reaction is involved in cubic autocatalytic or linear reactions that take place in the bulk phase environment. For these reactions, as the bulk phase reaction rates increase, the motor propulsion velocity decreases. For the cubic autocatalytic reaction, this net effect arises from a competition between a reduction of the nonequilibrium concentration gradient that leads to smaller velocity and the generation of fuel in the environment that tends to increase the motor propulsion. The role played by detailed balance in determining the form of the concentration gradient in the motor vicinity in the active medium is studied. Simulations are carried out using reactive multiparticle collision dynamics and compared with theoretical models to obtain further insight into sphere dimer dynamics in active media.

  18. New Possibilities for Magnetic Control of Chemical and Biochemical Reactions.

    PubMed

    Buchachenko, Anatoly; Lawler, Ronald G

    2017-02-20

    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

  19. Ligand reorganization and activation energies in nonadiabatic electron transfer reactions

    NASA Astrophysics Data System (ADS)

    Zhu, Jianjun; Wang, Jianji; Stell, George

    2006-10-01

    The activation energy and ligand reorganization energy for nonadiabatic electron transfer reactions in chemical and biological systems are investigated in this paper. The free energy surfaces and the activation energy are derived exactly in the general case in which the ligand vibration frequencies are not equal. The activation energy is derived by free energy minimization at the transition state. Our formulation leads to the Marcus-Hush [J. Chem. Phys. 24, 979 (1956); 98, 7170 (1994); 28, 962 (1958)] results in the equal-frequency limit and also generalizes the Marcus-Sumi [J. Chem. Phys. 84, 4894 (1986)] model in the context of studying the solvent dynamic effect on electron transfer reactions. It is found that when the ligand vibration frequencies are different, the activation energy derived from the Marcus-Hush formula deviates by 5%-10% from the exact value. If the reduced reorganization energy approximation is introduced in the Marcus-Hush formula, the result is almost exact.

  20. Inorganic chemically active adsorbents (ICAAs)

    SciTech Connect

    Ally, M.R.; Tavlarides, L.

    1997-10-01

    Oak Ridge National Laboratory (ORNL) researchers are developing a technology that combines metal chelation extraction technology and synthesis chemistry. They begin with a ceramic substrate such as alumina, titanium oxide or silica gel because they provide high surface area, high mechanical strength, and radiolytic stability. One preparation method involves silylation to hydrophobize the surface, followed by chemisorption of a suitable chelation agent using vapor deposition. Another route attaches newly designed chelating agents through covalent bonding by the use of coupling agents. These approaches provide stable and selective, inorganic chemically active adsorbents (ICAAs) tailored for removal of metals. The technology has the following advantages over ion exchange: (1) higher mechanical strength, (2) higher resistance to radiation fields, (3) higher selectivity for the desired metal ion, (4) no cation exchange, (5) reduced or no interference from accompanying anions, (6) faster kinetics, and (7) easy and selective regeneration. Target waste streams include metal-containing groundwater/process wastewater at ORNL`s Y-12 Plant (multiple metals), Savannah River Site (SRS), Rocky Flats (multiple metals), and Hanford; aqueous mixed wastes at Idaho National Engineering Laboratory (INEL); and scrubber water generated at SRS and INEL. Focus Areas that will benefit from this research include Mixed Waste, and Subsurface Contaminants.

  1. The quantum dynamics of electronically nonadiabatic chemical reactions

    NASA Technical Reports Server (NTRS)

    Truhlar, Donald G.

    1993-01-01

    Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally

  2. Raman spectroscopic studies of gas/aerosol chemical reactions

    SciTech Connect

    Aardahl, C.L.; Davis, E.J.

    1995-12-31

    Reactions between sorbent particles and SO{sub 2} can be used to reduce atmospheric pollution either by {open_quotes}dry scrubbing{close_quotes} or {open_quotes}wet scrubbing{close_quotes} processes. This paper reports Raman spectroscopy results for single electrodynamically levitated droplets of NaOH reacting with SO{sub 2} and studies of the dehydration reactions of some hygroscopic salt species. The NaOH/SO{sub 2} reaction products and the liquid or solid state of the products are shown to depend on the gas phase SO{sub 2} concentration. Deliquesced particles of NaOH exhibit enhanced light scattering intensities associated with morphological resonances of the incident laser light, but crystalline materials show no such resonances. Raman-active hygroscopic salts exhibit bond frequencies characteristic of the stretching vibrations of the anionic group, but these frequencies are different in the presence of water because hydrogen bonding changes the bond force. This allows efficient tracking of the dehydration reactions in hygroscopic aerosols by Raman spectroscopy as the intensities of the two different modes are related to the degree of dehydration in the particle.

  3. Solar photo-thermal catalytic reactions to produce high value chemicals

    SciTech Connect

    Prengle, Jr, H W; Wentworth, W E

    1992-04-01

    This report presents a summary of the research work accomplished to date on the utilization of solar photo-thermal energy to convert low cost chemical feedstocks into high $-value chemical products. The rationale is that the solar IR-VIS-UV spectrum is unique, supplying endothermic reaction energy as well as VIS-UV for photochemical activation. Chemical market analysis and product price distribution focused attention on speciality chemicals with prices >$1.00/lb, and a synthesis sequence of n-paraffins to aromatics to partial oxidized products. The experimental work has demonstrated that enhanced reaction effects result from VIS-UV irradiation of catalytically active V2O5/SiO2. Experiments of the past year have been on dehydrogenation and dehydrocyclization of n-paraffins to olefins and aromatics with preference for the latter. Recent results using n-hexane produced 95% conversion with 56% benzene; it is speculated that aromatic yield should reach {approximately}70% by further optimization. Pilot- and commercial-scale reactor configurations have been examined; the odds-on-favorite being a shallow fluid-bed of catalyst with incident radiation from the top. Sequencing for maximum cost effectiveness would be day-time endothermic followed by night-time exothermic reactions to produce the products.

  4. Miscible viscous fingering involving production of gel by chemical reactions

    NASA Astrophysics Data System (ADS)

    Nagatsu, Yuichiro; Hoshino, Kenichi

    2015-11-01

    We have experimentally investigated miscible viscous fingering with chemical reactions producing gel. Here, two systems were employed. In one system, sodium polyacrylate (SPA) solution and aluminum ion (Al3 +) solution were used as the more and less viscous liquids, respectively. In another system, SPA solution and ferric ion (Fe3 +) solution were used as the more and less viscous liquids, respectively. In the case of Al3 +, displacement efficiency was smaller than that in the non-reactive case, whereas in the case of Fe3 +, the displacement efficiency was larger. We consider that the difference in change of the patterns in the two systems will be caused by the difference in the properties of the gels. Therefore, we have measured the rheological properties of the gels by means of a rheometer. We discuss relationship between the VF patterns and the rheological measurement.

  5. Chemical Reactions in the Processing of Mosi2 + Carbon Compacts

    NASA Technical Reports Server (NTRS)

    Jacobson, Nathan S.; Lee, Kang N.; Maloy, Stuart A.; Heuer, Arthur H.

    1993-01-01

    Hot-pressing of MoSi2 powders with carbon at high temperatures reduces the siliceous grain boundary phase in the resultant compact. The chemical reactions in this process were examined using the Knudsen cell technique. A 2.3 wt pct oxygen MoSi2 powder and a 0.59 wt pct oxygen MoSi2 powder, both with additions of 2 wt pct carbon, were examined. The reduction of the siliceous grain boundary phase was examined at 1350 K and the resultant P(SiO)/P(CO) ratios interpreted in terms of the SiO(g) and CO(g) isobars on the Si-C-O predominance diagram. The MoSi2 + carbon mixtures were then heated at the hot-pressing temperature of 2100 K. Large weight losses were observed and could be correlated with the formation of a low-melting eutectic and the formation and vaporization of SiC.

  6. Waste Heat Recovery from Blast Furnace Slag by Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Qin, Yuelin; Lv, Xuewei; Bai, Chenguang; Qiu, Guibao; Chen, Pan

    2012-08-01

    Blast furnace (BF) slag, which is the main byproduct in the ironmaking process, contains large amounts of sensible heat. To recover the heat, a new waste heat-recovery system—granulating molten BF slag by rotary multinozzles cup atomizer and pyrolyzing printed circuited board with obtained hot BF slag particle—was proposed in this study. The feasibility of the waste heat-recovery system was verified by dry granulation and pyrolyzation experiments. The energy of hot BF slag could be converted to chemical energy through the pyrolysis reaction, and a large amount of combustible gas like CO, H2, C m H n , and CH4 can be generated during the process.

  7. The effect of heat conduction on the rate of chemical reaction in dilute gases

    NASA Astrophysics Data System (ADS)

    Fort, J.; Cukrowski, A. S.

    1997-09-01

    Information statistical theory is used to obtain the second-order terms (similar to those analyzed in the Burnett approximation to the solution of the Boltzmann equation) in the expansion of the nonequilibrium velocity distribution function. These terms are used for the evaluation of the effect of the heat flux on the rate of bimolecular chemical reactions. This effect is shown to be important for reactions characterized by high values of the activation energy. However, very large values of the heat flux would be necessary. The results are compared with those obtained earlier from the square terms calculated from the linearized Boltzmann equation and with recent results due to Nettleton.

  8. A new mathematical solution for predicting char activation reactions

    USGS Publications Warehouse

    Rafsanjani, H.H.; Jamshidi, E.; Rostam-Abadi, M.

    2002-01-01

    The differential conservation equations that describe typical gas-solid reactions, such as activation of coal chars, yield a set of coupled second-order partial differential equations. The solution of these coupled equations by exact analytical methods is impossible. In addition, an approximate or exact solution only provides predictions for either reaction- or diffusion-controlling cases. A new mathematical solution, the quantize method (QM), was applied to predict the gasification rates of coal char when both chemical reaction and diffusion through the porous char are present. Carbon conversion rates predicted by the QM were in closer agreement with the experimental data than those predicted by the random pore model and the simple particle model. ?? 2002 Elsevier Science Ltd. All rights reserved.

  9. Importance of cytochromes in cyclization reactions: quantum chemical study on a model reaction of proguanil to cycloguanil.

    PubMed

    Arfeen, Minhajul; Patel, Dhilon S; Abbat, Sheenu; Taxak, Nikhil; Bharatam, Prasad V

    2014-10-30

    Proguanil, an anti-malarial prodrug, undergoes cytochrome P450 catalyzed biotransformation to the pharmacologically active triazine metabolite (cycloguanil), which inhibits plasmodial dihydrofolate reductase. This cyclization is catalyzed by CYP2C19 and many anti-malarial lead compounds are being designed and synthesized to exploit this pathway. Quantum chemical calculations were performed using the model species (Cpd I for active species of cytochrome and N4-isopropyl-N6-methylbiguanide for proguanil) to elucidate the mechanism of the cyclization pathway. The overall reaction involves the loss of a water molecule, and is exothermic by approximately 55 kcal/mol, and involves a barrier of approximately 17 kcal/mol. The plausible reaction pathway involves the initial H-radical abstraction from the isopropyl group by Cpd I, followed by two alternative paths- (i) oxygen rebound to provide hydroxyl derivative and (ii) loss of additional H-radical to yield 1,3,5-triazatriene, which undergoes cyclization. This study helped in understanding the role of the active species of cytochromes in this important cyclization reaction.

  10. Electrokinetics for control of on-chip chemical reactions.

    NASA Astrophysics Data System (ADS)

    Erickson, David; Venditti, Roberto

    2005-03-01

    It is well known that electrokinetics affords precise control over flow and species transport in microfluidic systems through simple manipulation of externally applied electric potentials. In this work it is demonstrated how electrokinetic effects can be extended to provide simultaneous control over on-chip chemical reactions through manipulation of the local thermal (ohmic/joule heating), shear (electroosmosis) and electrical (electrophoresis) energies at the reaction site. The coupling of the electrical, flow and ``whole-chip'' thermal effects in both the fluidic and substrate domains are investigated through extensive finite element simulations and experimentally validated using microscale fluorescence thermometry. The simulations reveal changes in viscosity and local conductivity on the order of 50% induced by changes in the fluidic geometry. General chip design guidelines for maximizing or minimizing these effects will also be discussed. The degree of precision available and clinical utility of the technique is demonstrated through the detection of a single base pair mutation (single nucleotide polymorphism) in a DNA microarray integrated into a PDMS/glass microfluidic chip.

  11. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    SciTech Connect

    Ziaul Huque

    2007-08-31

    This is the final technical report for the project titled 'Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks'. The aim of the project was to develop an efficient chemistry model for combustion simulations. The reduced chemistry model was developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) was used via a new network topology known as Non-linear Principal Components Analysis (NPCA). A commonly used Multilayer Perceptron Neural Network (MLP-NN) was modified to implement NPCA-NN. The training rate of NPCA-NN was improved with the GEneralized Regression Neural Network (GRNN) based on kernel smoothing techniques. Kernel smoothing provides a simple way of finding structure in data set without the imposition of a parametric model. The trajectory data of the reaction mechanism was generated based on the optimization techniques of genetic algorithm (GA). The NPCA-NN algorithm was then used for the reduction of Dimethyl Ether (DME) mechanism. DME is a recently discovered fuel made from natural gas, (and other feedstock such as coal, biomass, and urban wastes) which can be used in compression ignition engines as a substitute for diesel. An in-house two-dimensional Computational Fluid Dynamics (CFD) code was developed based on Meshfree technique and time marching solution algorithm. The project also provided valuable research experience to two graduate students.

  12. Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics

    NASA Astrophysics Data System (ADS)

    Rao, Riccardo; Esposito, Massimiliano

    2016-10-01

    We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations with mass action kinetics. Our most general framework considers open networks driven by time-dependent chemostats. The energy and entropy balances are established and a nonequilibrium Gibbs free energy is introduced. The difference between this latter and its equilibrium form represents the minimal work done by the chemostats to bring the network to its nonequilibrium state. It is minimized in nondriven detailed-balanced networks (i.e., networks that relax to equilibrium states) and has an interesting information-theoretic interpretation. We further show that the entropy production of complex-balanced networks (i.e., networks that relax to special kinds of nonequilibrium steady states) splits into two non-negative contributions: one characterizing the dissipation of the nonequilibrium steady state and the other the transients due to relaxation and driving. Our theory lays the path to study time-dependent energy and information transduction in biochemical networks.

  13. Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation.

    PubMed

    Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca

    2016-10-28

    Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species. We present an approximate model checking algorithm based on the Linear Noise Approximation (LNA) of the CME, whose computational complexity is independent of the population size of each species and polynomial in the number of different species. The algorithm requires the solution of first order polynomial differential equations. We prove that our approach is valid for any CRN close enough to the thermodynamical limit. However, we show on four case studies that it can still provide good approximation even for low molecule counts. Our approach enables rigorous analysis of CRNs that are not analyzable by solving the CME, but are far from the deterministic limit. Moreover, it can be used for a fast approximate stochastic characterization of a CRN.

  14. Stochastic analysis of Chemical Reaction Networks using Linear Noise Approximation.

    PubMed

    Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca

    2016-11-01

    Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analyzed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species. We present an approximate model checking algorithm based on the Linear Noise Approximation (LNA) of the CME, whose computational complexity is independent of the population size of each species and polynomial in the number of different species. The algorithm requires the solution of first order polynomial differential equations. We prove that our approach is valid for any CRN close enough to the thermodynamical limit. However, we show on four case studies that it can still provide good approximation even for low molecule counts. Our approach enables rigorous analysis of CRNs that are not analyzable by solving the CME, but are far from the deterministic limit. Moreover, it can be used for a fast approximate stochastic characterization of a CRN.

  15. Chemical Reaction and Flow Modeling in Fullerene and Nanotube Production

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Farhat, Samir; Greendyke, Robert B.

    2004-01-01

    The development of processes to produce fullerenes and carbon nanotubes has largely been empirical. Fullerenes were first discovered in the soot produced by laser ablation of graphite [1]and then in the soot of electric arc evaporated carbon. Techniques and conditions for producing larger and larger quantities of fullerenes depended mainly on trial and error empirical variations of these processes, with attempts to scale them up by using larger electrodes and targets and higher power. Various concepts of how fullerenes and carbon nanotubes were formed were put forth, but very little was done based on chemical kinetics of the reactions. This was mainly due to the complex mixture of species and complex nature of conditions in the reactors. Temperatures in the reactors varied from several thousand degrees Kelvin down to near room temperature. There are hundreds of species possible, ranging from atomic carbon to large clusters of carbonaceous soot, and metallic catalyst atoms to metal clusters, to complexes of metals and carbon. Most of the chemical kinetics of the reactions and the thermodynamic properties of clusters and complexes have only been approximated. In addition, flow conditions in the reactors are transient or unsteady, and three dimensional, with steep spatial gradients of temperature and species concentrations. All these factors make computational simulations of reactors very complex and challenging. This article addresses the development of the chemical reaction involved in fullerene production and extends this to production of carbon nanotubes by the laser ablation/oven process and by the electric arc evaporation process. In addition, the high-pressure carbon monoxide (HiPco) process is discussed. The article is in several parts. The first one addresses the thermochemical aspects of modeling; and considers the development of chemical rate equations, estimates of reaction rates, and thermodynamic properties where they are available. The second part

  16. Electronically excited molecules: Reaction kinetics and emission of light: Nanosecond infrared spectroscopy, electronic emission from chemical reactions

    NASA Astrophysics Data System (ADS)

    Moore, C. B.

    1992-02-01

    A time-resolved IR absorption spectrometer capable of detecting chemical transients on the nanosecond timescale was designed, constructed, and successfully implemented. The spectrometer was used to characterize the vibrational relaxation of an open shell radical species, CF3, produced with excess energy from the photolysis of the parent CF3I compound. The effects of vibrational excitation in the CF3 radical on the reaction CF3 + Br2 yields CF3Br + Br were measured. Broadband data collection techniques were used to monitor the reactive and relaxation pathways simultaneously. The energetic radicals react no faster than the thermalized CF3 and may actually have a lower cross section for reaction. The spectrometer was also used to detect the gas phase absorption spectra of the polyatomic radicals. A thorough investigation into ozone-olefin reactions in a cryogenic matrix environment was completed. It was possible to complex ozone with various olefinic partners through careful control of the matrix deposition process, despite the very low (1-5 kcal/mole) activation energies for the ozonolysis reactions. The ground state complexes were observed to form a charge-transfer (CT) complex upon excitation.

  17. Inorganic chemicals in an effluent-dominated stream as indicators for chemical reactions and streamflows

    NASA Astrophysics Data System (ADS)

    Kim, Kangjoo; Lee, Ji Sun; Oh, Chang-Whan; Hwang, Gab-Soo; Kim, Jinsam; Yeo, Sungku; Kim, Yeongkyoo; Park, Seongmin

    2002-07-01

    The chemical behavior of major inorganic ions in the streams of the Mankyung River area (South Korea) was investigated. Mixing with effluent from the Jeonju STP (a municipal sewage treatment plant in Jeonju City) was the most important process in regulating the water chemistry of the streams. The effluent was chemically distinct relative to the stream waters in inorganic composition. Behavior of various ions was evaluated by comparing their concentrations with the concentration of chloride, a conservative chemical species. It was revealed that concentrations of chloride and sulfate, the total concentration of major cations, and electrical conductivity in the stream were controlled only by mixing, indicating their conservative behavior similar to chloride. Alkalinity and concentration of nitrate, however, were regulated by various reactions such as mixing, photosynthesis, respiration, and decomposition of organic matter. Streamflows were estimated by observing chemical composition of the effluent and those of up/downstream waters. Estimated flows based on the conservative chemical parameters were nearly the same as those directly measured using an area-velocity method, indicating the validity of the chemistry-based method.

  18. Active colloids in the context of chemical kinetics

    NASA Astrophysics Data System (ADS)

    Oshanin, G.; Popescu, M. N.; Dietrich, S.

    2017-03-01

    We study a mesoscopic model of a chemically active colloidal particle which on certain parts of its surface promotes chemical reactions in the surrounding solution. For reasons of simplicity and conceptual clarity, we focus on the case in which only electrically neutral species are present in the solution and on chemical reactions which are described by first order kinetics. Within a self-consistent approach we explicitly determine the steady state product and reactant number density fields around the colloid as functionals of the interaction potentials of the various molecular species in solution with the colloid. By using a reciprocal theorem, this allows us to compute and to interpret—in a transparent way in terms of the classical Smoluchowski theory of chemical kinetics—the external force needed to keep such a catalytically active colloid at rest (stall force) or, equivalently, the corresponding velocity of the colloid if it is free to move. We use the particular case of triangular-well interaction potentials as a benchmark example for applying the general theoretical framework developed here. For this latter case, we derive explicit expressions for the dependences of the quantities of interest on the diffusion coefficients of the chemical species, the reaction rate constant, the coverage by catalyst, the size of the colloid, as well as on the parameters of the interaction potentials. These expressions provide a detailed picture of the phenomenology associated with catalytically-active colloids and self-diffusiophoresis.

  19. CH 1 Introduction to Chemistry. Study Guide to Minicourse I - 13 Chemical Reaction Principles.

    ERIC Educational Resources Information Center

    Schlenker, Richard

    Provided is a study guide for an introductory minicourse to the principles of chemical reactions. This written text is designed to accompany a series of audio tapes and 35mm slides which the student studies at his own pace. The course presents chemical kinetics, reaction mechanisms, reaction rates, and equilibrium. (SL)

  20. 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)

  1. Transport Properties of a Kinetic Model for Chemical Reactions without Barriers

    SciTech Connect

    Alves, Giselle M.; Kremer, Gilberto M.; Soares, Ana Jacinta

    2011-05-20

    A kinetic model of the Boltzmann equation for chemical reactions without energy barrier is considered here with the aim of evaluating the reaction rate and characterizing the transport coefficient of shear viscosity for the reactive system. The Chapman-Enskog solution of the Boltzmann equation is used to compute the chemical reaction effects, in a flow regime for which the reaction process is close to the final equilibrium state. Some numerical results are provided illustrating that the considered chemical reaction without energy barrier can induce an appreciable influence on the reaction rate and on the transport coefficient of shear viscosity.

  2. An approach for modeling surface reaction kinetics in chemical vapor deposition processes

    SciTech Connect

    Wang, Y.F.; Pollard, R.

    1995-05-01

    A methodology is presented for determining the rate constants of elementary surface reactions that can take place in chemical vapor deposition (CVD) processes. The calculations consider well-defined surfaces that can have one or more dangling bonds at a given site and adsorbates that can take up one or more different bonding configurations. Rate constants for each reaction are obtained independently of any process data using statistical mechanics, transition state theory, and bond dissociation energies. Specifically, the reactions are divided in transition state structures and determine preexponential factors, and the requirement of thermodynamic consistency is used to estimate activation energies. The level of sophistication of the calculations is suitable for treating the large number of plausible steps that could take place in a practical CVD system. Incorporation of the calculated rate constants into a reactor model that includes the effects of fluid flow, transport phenomena, and reactions in the gas and at the growing surface enables dominant reaction pathways and rate-limiting steps to be identified. Moreover, the dependence of growth rate and species compositions on operating conditions can be predicted without fitting any parameters. The utility of the approach is illustrated by modeling low pressure deposition of tungsten from tungsten hexafluoride and silane. This model treats 35 reactions in the gas and 213 reactions at the growing surface. Results are compared with available experimental data and sensitivity studies are used to assess the limitations of the approach.

  3. Grazing-activated chemical defence in a unicellular marine alga

    NASA Astrophysics Data System (ADS)

    Wolfe, Gordon V.; Steinke, Michael; Kirst, Gunter O.

    1997-06-01

    Marine plankton use a variety of defences against predators, some of which affect trophic structure and biogeochemistry. We have previously shown that, during grazing by the protozoan Oxyrrhis marina on the alga Emiliania huxleyi, dimethylsulphoniopropionate (DMSP) from the prey is converted to dimethyl sulphide (DMS) when lysis of ingested prey cells initiates mixing of algal DMSP and the enzyme DMSP lyase. Such a mechanism is similar to macrophyte defence reactions,. Here we show that this reaction deters protozoan herbivores, presumably through the production of highly concentrated acrylate, which has antimicrobial activity. Protozoan predators differ in their ability to ingest and survive on prey with high-activity DMSP lyase, but all grazers preferentially select strains with low enzyme activity when offered prey mixtures. This defence system involves investment in a chemical precursor, DMSP, which is not self-toxic and has other useful metabolic functions. We believe this is the first report of grazing-activated chemical defence in unicellular microorganisms.

  4. The effect of chemical and physiological factors on the kinetics for product formation as it relates to enzyme activity and concentration, reaction time and to substrate adsorption and affinity.

    PubMed

    Chrastil, J; Wilson, J T

    1982-01-01

    1. The dependency of product formation on reaction time and on enzyme concentration was studied with certain purified enzymes and liver microsomal mixed-function oxidase system. 2. The product-formation-time relation was estimated with different enzyme and/or substrate concentrations for the reactions limited by diffusion. 3. The kinetic constants of the product-time relations in these diffusion systems have been verified experimentally to give a more specific and detailed characterization of an enzyme system under a variety of physiologic and reaction conditions. 4. The influence of inhibitors and activators in vitro, the effect of enzyme preparation technic, aging, starvation, pretreatment with somatotropic hormone, phenobarbital or 3-methylcholanthrene, and the effect of a tumor were studied. 5. The influence of vitamin C deficiency in guinea pig was also studied.

  5. Valence-bond description of chemical reactions on Born-Oppenheimer molecular dynamics trajectories

    NASA Astrophysics Data System (ADS)

    Noguchi, Nao; Nakano, Haruyuki

    2009-04-01

    The nature of chemical bonds on dynamic paths was investigated using the complete active space valence-bond (CASVB) method and the Born-Oppenheimer dynamics. To extract the chemical bond picture during reactions, a scheme to collect contributions from several VB (resonance) structures into a small numbers of indices was introduced. In this scheme, a tree diagram for the VB structures is constructed with the numbers of the ionic bonds treated as generation. A pair of VB structures is related to each other if one VB structure is transferred into the other by changing a covalent bond to an ionic bond. The former and latter VB structures are named parent and child structures, respectively. The weights of the bond pictures are computed as the sum of the CASVB occupation numbers running from the top generation to the bottom along the descent of the VB structures. Thus, a number of CASVB occupation numbers are collected into a small number of indices, and a clear bond picture may be obtained from the CASVB wave function. The scheme was applied to the hydrogen exchange reaction H2+F→H+HF and the Diels-Alder reaction C5H6(cyclopentadiene)+CH2=CH2(ethylene)→C7H10(norbornene). In both the reactions, the scheme gave a clear picture for the Born-Oppenheimer dynamics trajectories. The reconstruction of the bonds during reactions was well described by following the temporal changes in weight.

  6. 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.

  7. Chemical activation by mechanochemical mixing, microwave, and ultrasonic irradiation

    EPA Science Inventory

    The use of emerging MW-assisted chemistry techniques in conjunction with benign reaction media is dramatically reducing chemical waste ad reaction times in several organic syntheses and chemical transformations. This editorial comments on the recent developments in mechanochemica...

  8. A Case Study in Chemical Kinetics: The OH + CO Reaction.

    ERIC Educational Resources Information Center

    Weston, Ralph E., Jr.

    1988-01-01

    Reviews some important properties of the bimolecular reaction between the hydroxyl radical and carbon monoxide. Investigates the kinetics of the reaction, the temperature and pressure dependence of the rate constant, the state-to-state dynamics of the reaction, and the reverse reaction. (MVL)

  9. Oxygen reduction reaction over silver particles with various morphologies and surface chemical states

    NASA Astrophysics Data System (ADS)

    Ohyama, Junya; Okata, Yui; Watabe, Noriyuki; Katagiri, Makoto; Nakamura, Ayaka; Arikawa, Hidekazu; Shimizu, Ken-ichi; Takeguchi, Tatsuya; Ueda, Wataru; Satsuma, Atsushi

    2014-01-01

    The oxygen reduction reaction (ORR) in an alkaline solution was carried out using Ag powders having various particle morphologies and surface chemical states (Size: ca. 40-110 nm in crystalline size. Shape: spherical, worm like, and angular. Surface: smooth with easily reduced AgOx, defective with AgOx, and Ag2CO3 surface layer). The various Ag powders were well characterized by X-ray diffraction, X-ray photoelectron spectroscopy, N2 adsorption, scanning electron microscopy, Raman spectroscopy, cyclic voltammetry, and stripping voltammetry of underpotential-deposited lead. Defective and oxidized surfaces enhanced the Ag active surface area during the ORR. The ORR activity was affected by the morphology and surface chemical state: Ag particles with defective and angular surfaces showed smaller electron exchange number between three and four but showed higher specific activity compared to Ag particles with smooth surfaces.

  10. Science Activities in Energy: Chemical Energy.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Presented is a science activities in energy package which includes 15 activities relating to chemical energy. Activities are simple, concrete experiments for fourth, fifth and sixth grades which illustrate principles and problems relating to energy. Each activity is outlined on a single card which is introduced by a question. A teacher's…

  11. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    SciTech Connect

    Nelson Butuk

    2005-12-01

    This is an annual technical report for the work done over the last year (period ending 9/30/2005) on the project titled ''Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks''. The aim of the project is to develop an efficient chemistry model for combustion simulations. The reduced chemistry model will be developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) will be used via a new network topology know as Non-linear Principal Components Analysis (NPCA). We report on the development of a novel procedure to speed up the training of NPCA. The same procedure termed L{sub 2}Boost can be used to increase the order of approximation of the Generalized Regression Neural Network (GRNN). It is pointed out that GRNN is a basic procedure for the emerging mesh free CFD. Also reported is an efficient simple approach of computing the derivatives of GRNN function approximation using complex variables or the Complex Step Method (CSM). The results presented demonstrate the significance of the methods developed and will be useful in many areas of applied science and engineering.

  12. Capillary Action may Cool Systems and Precisely balance Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Kriske, Richard

    2011-10-01

    It is well known that it takes no work for Water to rise in a Capillary tube against the force of Gravity. There is a precise balance in this system that resembles Robert Millikan's ``Oil Drop'' experiment, where mass was balanced against the electrostatic force. If at the top of the capillary tube there is evaporation, one can see that the system is cooled as another water molecule has room to move up the column. Furthermore, if the evaporation process can be controlled one photon at a time, a precise balance is created between a photon, and the height/mass of the column. If other molecules are place in the column, they can be moved up and down the column, in a chromatograph way, in a fairly precise manner, by controlling evaporation and molecular weight. If in addition to all of this, the interface of the solution against the walls of the column have Fermi levels, it can be seen as a very precise Electrochemical Device. In the situation of nanotubes, as opposed to trees and plants, these properties can be used to create measure environmental properties and to Balance Chemical Reactions. Forests, and Plants may cool themselves and their environment using this process, and using this process coupled with more energetic photons through photosynthesis.

  13. Detailed Chemical Kinetic Reaction Mechanism for Biodiesel Components Methyl Stearate and Methyl Oleate

    SciTech Connect

    Naik, C; Westbrook, C K; Herbinet, O; Pitz, W J; Mehl, M

    2010-01-22

    New chemical kinetic reaction mechanisms are developed for two of the five major components of biodiesel fuel, methyl stearate and methyl oleate. The mechanisms are produced using existing reaction classes and rules for reaction rates, with additional reaction classes to describe other reactions unique to methyl ester species. Mechanism capabilities were examined by computing fuel/air autoignition delay times and comparing the results with more conventional hydrocarbon fuels for which experimental results are available. Additional comparisons were carried out with measured results taken from jet-stirred reactor experiments for rapeseed methyl ester fuels. In both sets of computational tests, methyl oleate was found to be slightly less reactive than methyl stearate, and an explanation of this observation is made showing that the double bond in methyl oleate inhibits certain low temperature chain branching reaction pathways important in methyl stearate. The resulting detailed chemical kinetic reaction mechanism includes more approximately 3500 chemical species and more than 17,000 chemical reactions.

  14. Chemical wave propagation preserved on an inhibitory field in the ruthenium-catalyzed Belousov-Zhabotinsky reaction.

    PubMed

    Nakata, Satoshi; Ezaki, Takato; Ikura, Yumihiko S; Kitahata, Hiroyuki

    2013-10-17

    The propagation of a chemical wave on an inhibitory field, which was wedged between two excitable fields, was investigated for the photosensitive Belousov-Zhabotinsky (BZ) reaction. With an increase in the width of the inhibitory field between the excitable fields (W), the chemical wave divided into two waves at W = Wα. The divided chemical waves then coalesced at W = Wβ with a decrease in W. Wα was larger than Wβ, i.e., hysteresis on the width of the inhibitory field was observed between the division and coalescence of the chemical wave. The experimental results were qualitatively reproduced by a numerical calculation based on a three-variable Oregonator model modified for the photosensitive BZ reaction. These results suggest that the chemical wave may be preserved on the inhibitory field due to an activator supplied from a chemical wave on the excitable field.

  15. Influence of nonlinear chemical reactions on the transport coefficients in oscillatory Couette flow

    NASA Astrophysics Data System (ADS)

    Barik, Swarup; Dalal, D. C.

    2016-10-01

    A multiple-scale method of averaging is applied to the study of transport of a chemical species in oscillatory Couette flow where the species may undergoes a reversible phase exchange with the boundary wall and nonlinear chemical reactions both within the fluid and at the boundary wall. Analytical expressions are obtained for transport coefficients. The results shows how the transport coefficients are influenced by the reversible phase exchange reaction kinetics and the rate and degree of the nonlinear decay chemical reaction.

  16. Chemical reactions between Venus' surface and atmosphere - An update. (Invited)

    NASA Astrophysics Data System (ADS)

    Treiman, A. H.

    2013-12-01

    The surface of Venus, at ~740K, is hot enough to allow relatively rapid chemical reactions between it and the atmosphere, i.e. weathering. Venus chemical weathering has been explored in detail [1], to the limits of available data. New data from Venus Express (VEx) and new ideas from exoplanets have sparked a modest renewal of interest in Venus weathering. Venus' surface cannot be observed in visible light, but there are several NIR ';windows' through its atmosphere that allow surface imaging. The VIRTIS spectrometer on VEx viewed the surface through one window [2]; emissivity variations among lava flows on Imdr and Themis Regios have been explained as varying degrees of weathering, and thus age [3]. The VMC camera on VEx also provides images through a NIR window, which suggest variable degrees of weathering on some basaltic plains [4]. Indirect evidence for weathering may come from varying SO2 abundance at Venus' cloud tops; repeated rapid increases and gradual declines may represent volcanic eruptions followed by weathering to form sulfate minerals [5]. Continued geochemical modeling relevant to Venus weathering is motivated by expolanet studies [6]. Models have been extended to hypothetical exo-Venuses of different temperatures and surface compositions [7]. The idea that Venus' atmosphere composition can be buffered by reaction with its surface was explored in detail, and the derived constraint extended to other types of planets [8]. Several laboratories are investigating Venus weathering, motivated in part by the hope that they can provide real constraints on timescales of Venus volcanism [3]. Aveline et al. [9] are extending early studies [10] by reacting rocks and minerals with concentrated SO2 (to accelerate reaction rates to allow detectability of products). Kohler et al. [11] are investigating the stability of metals and chalcogenides as possible causes of the low-emissivity surfaces at high elevations. Berger and Aigouy [12] studied rock alteration on a

  17. Total chemical synthesis of a thermostable enzyme capable of polymerase chain reaction.

    PubMed

    Xu, Weiliang; Jiang, Wenjun; Wang, Jiaxing; Yu, Linping; Chen, Ji; Liu, Xianyu; Liu, Lei; Zhu, Ting F

    2017-01-01

    Polymerase chain reaction (PCR) has been a defining tool in modern biology. Towards realizing mirror-image PCR, we have designed and chemically synthesized a mutant version of the 352-residue thermostable Sulfolobus solfataricus P2 DNA polymerase IV with l-amino acids and tested its PCR activity biochemically. To the best of our knowledge, this enzyme is the largest chemically synthesized protein reported to date. We show that with optimization of PCR conditions, the fully synthetic polymerase is capable of amplifying template sequences of up to 1.5 kb. The establishment of this synthetic route for chemically synthesizing DNA polymerase IV is a stepping stone towards building a d-enzyme system for mirror-image PCR, which may open up an avenue for the creation of many mirror-image molecular tools such as mirror-image systematic evolution of ligands by exponential enrichment.

  18. Total chemical synthesis of a thermostable enzyme capable of polymerase chain reaction

    PubMed Central

    Xu, Weiliang; Jiang, Wenjun; Wang, Jiaxing; Yu, Linping; Chen, Ji; Liu, Xianyu; Liu, Lei; Zhu, Ting F

    2017-01-01

    Polymerase chain reaction (PCR) has been a defining tool in modern biology. Towards realizing mirror-image PCR, we have designed and chemically synthesized a mutant version of the 352-residue thermostable Sulfolobus solfataricus P2 DNA polymerase IV with l-amino acids and tested its PCR activity biochemically. To the best of our knowledge, this enzyme is the largest chemically synthesized protein reported to date. We show that with optimization of PCR conditions, the fully synthetic polymerase is capable of amplifying template sequences of up to 1.5 kb. The establishment of this synthetic route for chemically synthesizing DNA polymerase IV is a stepping stone towards building a d-enzyme system for mirror-image PCR, which may open up an avenue for the creation of many mirror-image molecular tools such as mirror-image systematic evolution of ligands by exponential enrichment. PMID:28265464

  19. Plasmon-assisted chemical reactions revealed by high-vacuum tip-enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Lu, Shuaicheng; Sheng, Shaoxiang; Zhang, Zhenglong; Xu, Hongxing; Zheng, Hairong

    2014-08-01

    Tip-enhanced Raman spectroscopy (TERS) is the technique that combines the nanoscale spatial resolution of a scanning probe microscope and the highly sensitive Raman spectroscopy enhanced by the surface plasmons. It is suitable for chemical analysis at nanometer scale. Recently, TERS exhibited powerful potential in analyzing the chemical reactions at nanoscale. The high sensitivity and spatial resolution of TERS enable us to learn the reaction processes more clearly. More importantly, the chemical reaction in TERS is assisted by surface plasmons, which provides us an optical method to manipulate the chemical reactions at nanoscale. Here using our home-built high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup, we successfully observed the plasmon-assisted molecule dimerization and dissociation reactions. In HV-TERS system, under laser illumination, 4-nitrobenzenethiol (4NBT) molecules can be dimerized to p,p'-dimercaptoazobenzene (DMAB), and dissociation reaction occurs for malachite green (MG) molecules. Using our HV-TERS setup, the dynamic processes of the reactions are clearly revealed. The chemical reactions can be manipulated by controlling the plasmon intensity through changing the power of the incident laser, the tunneling current and the bias voltage. We also investigated the role of plasmonic thermal effect in the reactions by measuring both the Stokes and anti- Stokes Raman peaks. Our findings extend the applications of TERS, which can help to study the chemical reactions and understand the dynamic processes at single molecular level, and even design molecules by the plasmon-assisted chemical reactions.

  20. Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks.

    PubMed

    Hartenfeller, Markus; Eberle, Martin; Meier, Peter; Nieto-Oberhuber, Cristina; Altmann, Karl-Heinz; Schneider, Gisbert; Jacoby, Edgar; Renner, Steffen

    2012-05-25

    In the search for new bioactive compounds, there is a trend toward increasingly complex compound libraries aiming to target the demanding targets of the future. In contrast, medicinal chemistry and traditional library design rely mainly on a small set of highly established and robust reactions. Here, we probe a set of 58 such reactions for their ability to sample the chemical space of known bioactive molecules, and the potential to create new scaffolds. Combined with ~26,000 common available building blocks, the reactions retrieve around 9% of a scaffold-diverse set of compounds active on human target proteins covering all major pharmaceutical target classes. Almost 80% of generated scaffolds from virtual one-step synthesis products are not present in a large set of known bioactive molecules for human targets, indicating potential for new discoveries. The results suggest that established synthesis resources are well suited to cover the known bioactivity-relevant chemical space and that there are plenty of unexplored regions accessible by these reactions, possibly providing valuable "low-hanging fruit" for hit discovery.

  1. 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.

  2. Computational Analyses of Complex Flows with Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Bae, Kang-Sik

    The heat and mass transfer phenomena in micro-scale for the mass transfer phenomena on drug in cylindrical matrix system, the simulation of oxygen/drug diffusion in a three dimensional capillary network, and a reduced chemical kinetic modeling of gas turbine combustion for Jet propellant-10 have been studied numerically. For the numerical analysis of the mass transfer phenomena on drug in cylindrical matrix system, the governing equations are derived from the cylindrical matrix systems, Krogh cylinder model, which modeling system is comprised of a capillary to a surrounding cylinder tissue along with the arterial distance to veins. ADI (Alternative Direction Implicit) scheme and Thomas algorithm are applied to solve the nonlinear partial differential equations (PDEs). This study shows that the important factors which have an effect on the drug penetration depth to the tissue are the mass diffusivity and the consumption of relevant species during the time allowed for diffusion to the brain tissue. Also, a computational fluid dynamics (CFD) model has been developed to simulate the blood flow and oxygen/drug diffusion in a three dimensional capillary network, which are satisfied in the physiological range of a typical capillary. A three dimensional geometry has been constructed to replicate the one studied by Secomb et al. (2000), and the computational framework features a non-Newtonian viscosity model for blood, the oxygen transport model including in oxygen-hemoglobin dissociation and wall flux due to tissue absorption, as well as an ability to study the diffusion of drugs and other materials in the capillary streams. Finally, a chemical kinetic mechanism of JP-10 has been compiled and validated for a wide range of combustion regimes, covering pressures of 1atm to 40atm with temperature ranges of 1,200 K--1,700 K, which is being studied as a possible Jet propellant for the Pulse Detonation Engine (PDE) and other high-speed flight applications such as hypersonic

  3. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  4. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical `atomistic' molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  5. Response of a chemical wave to local pulse irradiation in the ruthenium-catalyzed Belousov-Zhabotinsky reaction.

    PubMed

    Nakata, Satoshi; Suzuki, Shogo; Ezaki, Takato; Kitahata, Hiroyuki; Nishi, Kei; Nishiura, Yasumasa

    2015-04-14

    The photo-sensitive Belousov-Zhabotinsky (BZ) reaction system was investigated to understand the response of wave propagation to local pulse stimulation in an excitable field. When the chemical wave was irradiated with a bright pulse or a dark pulse, the speed of wave propagation decreased or increased. The timing of pulse irradiation that significantly affected the speed of chemical wave propagation was different with the bright and dark pulses. That is, there is a sensitive point in the chemical wave. The experimental results were qualitatively reproduced by a numerical calculation based on a three-variable Oregonator model that was modified for the photosensitive BZ reaction. These results suggest that the chemical wave is sensitive to the timing of pulse irradiation due to the rates of production of an activator and an inhibitor in the photochemical reaction.

  6. An Activation Energy Experiment for a Second-Order Reaction in a Single Laboratory Period.

    ERIC Educational Resources Information Center

    Barile, Raymond C.; Michiels, Leo P.

    1983-01-01

    Describes modification of a chemical reaction to a single 4 1/2-hour laboratory period. Reaction kinetics between 2, 4-initrochlorobenzene and piperidine to form 2, 4-dinitrophenyl-piperidine and piperidinium hydrochloride are followed conductometrically at three temperatures to obtain data to calculate activation parameters. (Author/JN)

  7. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    SciTech Connect

    Nelson Butuk

    2006-09-21

    This is an annual technical report for the work done over the last year (period ending 9/30/2005) on the project titled ''Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks''. The aim of the project is to develop an efficient chemistry model for combustion simulations. The reduced chemistry model will be developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) will be used via a new network topology know as Non-linear Principal Components Analysis (NPCA). We report on the significant development made in developing a truly meshfree computational fluid dynamics (CFD) flow solver to be coupled to NPCA. First, the procedure of obtaining nearly analytic accurate first order derivatives using the complex step method (CSM) is extended to include computation of accurate meshfree second order derivatives via a theorem described in this report. Next, boosted generalized regression neural network (BGRNN), described in our previous report is combined with CSM and used to obtain complete solution of a hard to solve wave dominated sample second order partial differential equation (PDE): the cubic Schrodinger equation. The resulting algorithm is a significant improvement of the meshfree technique of smooth particle hydrodynamics method (SPH). It is suggested that the demonstrated meshfree technique be termed boosted smooth particle hydrodynamics method (BSPH). Some of the advantages of BSPH over other meshfree methods include; it is of higher order accuracy than SPH; compared to other meshfree methods, it is completely meshfree and does not require any background meshes; It does not involve any construction of shape function with their associated solution of possibly ill conditioned matrix equations; compared to some SPH techniques, no equation for the smoothing parameter is required; finally it is easy to program.

  8. CHEMICAL SYNTHESIS USING 'GREENER' ALTERNATIVE REACTION CONDITIONS AND MEDIA

    EPA Science Inventory

    The chemical research during the last decade has witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into ...

  9. SUBSTITUTION REACTIONS FOR THE DETOXIFICATION OF HAZARDOUS CHEMICALS

    EPA Science Inventory

    Chemical Treatment is one of several treatment techniques used for the remediation of toxic and hazardous chemicals. Chemical treatment in this report is defined as substitution of halogens by hydrogens for the conversion of halogenated organic toxicant into its native hydrocarb...

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Cordes, Thorben; Blum, Suzanne A.

    2013-12-01

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

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

    PubMed

    Cordes, Thorben; Blum, Suzanne A

    2013-12-01

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

  13. Mixing and chemical reaction in sheared and nonsheared homogeneous turbulence

    NASA Technical Reports Server (NTRS)

    Leonard, Andy D.; Hill, James C.

    1992-01-01

    Direct numerical simulations were made to examine the local structure of the reaction zone for a moderately fast reaction between unmixed species in decaying, homogeneous turbulence and in a homogeneous turbulent shear flow. Pseudospectral techniques were used in domains of 64 exp 3 and higher wavenumbers. A finite-rate, single step reaction between non-premixed reactants was considered, and in one case temperature-dependent Arrhenius kinetics was assumed. Locally intense reaction rates that tend to persist throughout the simulations occur in locations where the reactant concentration gradients are large and are amplified by the local rate of strain. The reaction zones are more organized in the case of a uniform mean shear than in isotropic turbulence, and regions of intense reaction rate appear to be associated with vortex structures such as horseshoe vortices and fingers seen in mixing layers. Concentration gradients tend to align with the direction of the most compressive principal strain rate, more so in the isotropic case.

  14. 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…

  15. 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…

  16. 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.

  17. 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…

  18. 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.

  19. 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…

  20. 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,…

  1. 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.

  2. Facile Synthesis of Single Crystal Vanadium Disulfide Nanosheets by Chemical Vapor Deposition for Efficient Hydrogen Evolution Reaction.

    PubMed

    Yuan, Jiangtan; Wu, Jingjie; Hardy, Will J; Loya, Philip; Lou, Minhan; Yang, Yingchao; Najmaei, Sina; Jiang, Menglei; Qin, Fan; Keyshar, Kunttal; Ji, Heng; Gao, Weilu; Bao, Jiming; Kono, Junichiro; Natelson, Douglas; Ajayan, Pulickel M; Lou, Jun

    2015-10-07

    A facile chemical vapor deposition method to prepare single-crystalline VS2 nanosheets for the hydrogen evolution reaction is reported. The electrocatalytic hydrogen evolution reaction (HER) activities of VS2 show an extremely low overpotential of -68 mV at 10 mA cm(-2), small Tafel slopes of ≈34 mV decade(-1), as well as high stability, demonstrating its potential as a candidate non-noble-metal catalyst for the HER.

  3. The Chemical Composition of the Active Stars

    NASA Astrophysics Data System (ADS)

    Glazunova, L. V.

    The comparison of the results of the studies of the active stars' chemical composition obtained by different authors has been performed. It was concluded that the difference between the abundances of some elements in active and inactive stars becomes significant (> 3σ) only for the active stars with high chromospheric activity (lgR'HK > -4). This is the case primarily for the light elements, namely Li, Na and Al, as well as heavy elements with Z > 30.

  4. Theoretical research program to study chemical reactions in AOTV bow shock tubes

    NASA Technical Reports Server (NTRS)

    Taylor, P.

    1986-01-01

    Progress in the development of computational methods for the characterization of chemical reactions in aerobraking orbit transfer vehicle (AOTV) propulsive flows is reported. Two main areas of code development were undertaken: (1) the implementation of CASSCF (complete active space self-consistent field) and SCF (self-consistent field) analytical first derivatives on the CRAY X-MP; and (2) the installation of the complete set of electronic structure codes on the CRAY 2. In the area of application calculations the main effort was devoted to performing full configuration-interaction calculations and using these results to benchmark other methods. Preprints describing some of the systems studied are included.

  5. Quantum chemical analysis of reaction paths in chorismate mutase: Conformational effects and electrostatic stabilization

    NASA Astrophysics Data System (ADS)

    Szefczyk, Borys; Claeyssens, Frederik; Mulholland, Adrian J.; Sokalski, W. Andrzej

    We have performed a detailed, quantum chemical, decomposition analysis of the physical nature of key interactions in the model enzyme chorismate mutase (CM), for several active conformations produced by high level combined quantum mechanics/molecular mechanics (QM/MM) modeling. In opposition to our previous study, interactions between selected residues in the active site of CM were analysed along the whole reaction path, for several paths. The interaction energy is calculated up to Møller-Plesset second order level of theory and decomposed into physically meaningful components (electrostatic, exchange, delocalization, and electron correlation). This analysis shows, that the dominant interaction is differential stabilization by Arg90: this residue significantly stabilizes the transition state (TS) relative to the substrate in all the paths studied. Interactions in the active site of CM are dominated by the electrostatic component, whereas other components, for example electron correlation, are constant during reaction. Electrostatic effects alone are found to be responsible for lowering the barrier for reaction at the active site. Analysis of four reaction paths derived from QM/MM modeling shows that differences in the height of the barrier are due to differences in the electrostatic interactions of several weakly interacting residues. The influence of conformational effects, such as hydroxyl group rotation in the chorismate/TS, and the distance between Arg90 and the reacting chorismate, have also been analysed. The results show that specific conformations provide better activation barrier lowering. Even small changes in the conformation, like rotation of the hydroxyl group in chorismate (substrate), can significantly alter the activation barrier.0

  6. Phase and chemical equilibria in the transesterification reaction of vegetable oils with supercritical lower alcohols

    NASA Astrophysics Data System (ADS)

    Anikeev, V. I.; Stepanov, D. A.; Ermakova, A.

    2011-08-01

    Calculations of thermodynamic data are performed for fatty acid triglycerides, free fatty acids, and fatty acid methyl esters, participants of the transesterification reaction of vegetable oils that occurs in methanol. Using the obtained thermodynamic parameters, the phase diagrams for the reaction mixture are constructed, and the chemical equilibria of the esterification reaction of free fatty acids and the transesterification reaction of fatty acid triglycerides attained upon treatment with supercritical methanol are determined. Relying on our analysis of the obtained equilibria for the esterification reaction of fatty acids and the transesterification reaction of triglycerides attained upon treatment with lower alcohols, we select the optimum conditions for performing the reaction in practice.

  7. The canonical and other mechanisms of elementary chemical reactions.

    PubMed

    Aldegunde, Jesús; Aoiz, F Javier; Sáez-Rábanos, Vicente; Kendrick, Brian K; de Miranda, Marcelo P

    2007-11-21

    This article introduces a definition of the concept of elementary reaction mechanism that, while conforming to the traditional view of reaction mechanisms as dynamical processes whereby reagents are transformed into products, sharpens it by requiring reagent and product states to be completely specified and fully correlated. This leads to well-defined mathematical requirements for classification of a dynamical process as a reaction mechanism and also to a straightforward mathematical procedure for the determination of a special class of independent collision mechanisms that are dubbed "canonical". Canonical mechanisms result from an exact decomposition of the differential cross section of the reaction and form a complete orthogonal basis in terms of which all reaction mechanisms can be described. Examples involving the benchmark F + H2 and D + H2 reactions at energies ranging from ultralow to hyperthermal illustrate how canonical and other reaction mechanisms can be visualised and also how analysis of a reaction in terms of its canonical mechanisms can provide insight into its dynamics.

  8. Chemical Synthesis Accelerated by Paper Spray: The Haloform Reaction

    ERIC Educational Resources Information Center

    Bain, Ryan M.; Pulliam, Christopher J.; Raab, Shannon A.; Cooks, R. Graham

    2016-01-01

    In this laboratory, students perform a synthetic reaction in two ways: (i) by traditional bulk-phase reaction and (ii) in the course of reactive paper spray ionization. Mass spectrometry (MS) is used both as an analytical method and a means of accelerating organic syntheses. The main focus of this laboratory exercise is that the same ionization…

  9. Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry (Briefing Charts)

    DTIC Science & Technology

    2015-06-28

    Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...Unlimited. 13. SUPPLEMENTARY NOTES Briefing Charts presented at 9th Int. Conf. Chemical Kinetics; Ghent, Belgium; 28 Jun 2015. PA#15351. 14. ABSTRACT...ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A

  10. A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure.

    PubMed

    Cammi, Roberto

    2015-11-15

    A quantum chemical method for studying potential energy surfaces of reactive molecular systems at extreme high pressures is presented. The method is an extension of the standard Polarizable Continuum Model that is usually used for Quantum Chemical study of chemical reactions at a standard condition of pressure. The physical basis of the method and the corresponding computational protocol are described in necessary detail, and an application of the method to the dimerization of cyclopentadiene (up to 20 GPa) is reported.

  11. Aerosols formed from the chemical reaction of monoterpenes and ozone

    NASA Astrophysics Data System (ADS)

    Yokouchi, Y.; Ambe, Y.

    Chamber experiments were conducted to study the aerosol products from the ozonolysis of the major atmospheric monoterpenes; α-pinene, β-pinene and limonene. It was found that the α-pinene-O 3 reaction produced mainly 2', 2'-dimethyl-3'-acetyl cyclobutyl ethanal (pinonaldehyde), the β-pinene-O 3 reaction, mainly 6,6-dimethyl-bicyclo [3.1.1] heptan-2-one and the limonene-O 3 reaction, several unidentified products. These products were sought in forest aerosols and pinonaldehyde was detected in the atmosphere.

  12. Aerosols formed from the chemical reaction of monoterpenes and ozone

    NASA Astrophysics Data System (ADS)

    Yokouchi, Y.; Ambe, Y.

    Chamber experiments were conducted to study the aerosol products from the ozonolysis of the major atmospheric monoterpenes; α-pinene, β-pinene and limonene. It was found that the α-pinend-O 3 reaction produced mainly 2'. 2'-dimethyl-3'-acetyl cyclobutyl ethanal (pinonaldehyde), the β-pinene-O 3 reaction, mainly 6,6-dimethyl-bicyclo [3.1.1] heptan-2-one and the limonene-O 3 reaction, several unidentified products. These products were sought in forest aerosols and pinonaldehyde was detected in the atmosphere.

  13. Ultrafast infrared studies of chemical reaction dynamics in room-temperature liquids

    SciTech Connect

    Yang, Haw

    1999-11-01

    Femtosecond infrared spectroscopy provides sufficient spectral and temporal resolution to support a detailed investigation of the early events of a photochemical reaction. Previously unreported transient species that arise as intermediates during the course of a reaction may have lifetimes that are too short for conventional characterization. For these species, quantum-mechanical (density functional theoretical and ab initio) electronic structure calculations provide invaluable insight into chemical properties including molecular structure and energetic. With the combination of experimental and theoretical results, it is possible to assemble a comprehensive picture of the reaction dynamics of a system that is intricately influenced by the surrounding solvent molecules. The mechanisms of several important organometallic reactions, such as alkane C– H bond activation by η3-Tp*Rh(CO), silane Si–H bond activation by η5-CpMn(CO)2 and η5-CpRe(CO)2, as well as chlorinated methane C–Cl bond cleavage by the Re(CO)5 radical are elucidated. The results demonstrate the importance of molecular morphology change (C–H and Si–H act ivat ion), solvent rearrangement (Si–H activation), intersystem crossing (Si–H activation), and solvent caging (C–Cl cleavage) in understanding the reactivity of the organometallic species, The nature of the apparent free-energy barrier for C–H, Si–H, and C–Cl bond activation reaction is found to be- cleavage of an alkane C–H bond, rearrangement of a silane molecule HSiR3 (R = alkyl group) from a nonreactive alkyl site to the reactive Si–H bond, and Cl atom transfer from a chlorinated methane molecule to Re(CO)5, respectively. These results support previous d initio calculations for C–H and Si–H bond activation reaction profiles which suggest that cleavage of an alkane C–H bond by a transition metal center, unlike that of a silane

  14. 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…

  15. Identification of 4-(3-Pyridyl)-4-oxobutyl-2'-deoxycytidine Adducts Formed in the Reaction of DNA with 4-(Acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone: A Chemically Activated Form of Tobacco-Specific Carcinogens.

    PubMed

    Michel, Anna K; Zarth, Adam T; Upadhyaya, Pramod; Hecht, Stephen S

    2017-03-31

    Metabolic activation of the carcinogenic tobacco-specific nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1) and N'-nitrosonornicotine (NNN, 2) results in the formation of 4-(3-pyridyl)-4-oxobutyl (POB)-DNA adducts, several of which have been previously identified both in vitro and in tissues of laboratory animals treated with NNK or NNN. However, 2'-deoxycytidine adducts formed in this process have been incompletely examined in previous studies. Therefore, in this study we prepared characterized standards for the identification of previously unknown 2'-deoxycytidine and 2'-deoxyuridine adducts that could be produced in these reactions. The formation of these products in reactions of 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKOAc, 3), a model 4-(3-pyridyl)-4-oxobutylating agent, with DNA was investigated. The major 2'-deoxycytidine adduct, identified as its stable cytosine analogue O(2)-[4-(3-pyridyl)-4-oxobut-1-yl]-cytosine (12), was O(2)-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxycytidine (13), whereas lesser amounts of 3-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxycytidine (14) and N(4)-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxycytidine (15) were also observed. The potential conversion of relatively unstable 2'-deoxycytidine adducts to stable 2'-deoxyuridine adducts by treatment of the adducted DNA with bisulfite was also investigated, but the harsh conditions associated with this approach prevented quantitation. The results of this study provide new validated standards for the study of 4-(3-pyridyl)-4-oxobutylation of DNA, a critical reaction in the carcinogenesis by 1 and 2, and demonstrate the presence of previously unidentified 2'-deoxycytidine adducts in this DNA.

  16. Identification of 4-(3-Pyridyl)-4-oxobutyl-2′-deoxycytidine Adducts Formed in the Reaction of DNA with 4-(Acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone: A Chemically Activated Form of Tobacco-Specific Carcinogens

    PubMed Central

    2017-01-01

    Metabolic activation of the carcinogenic tobacco-specific nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1) and N′-nitrosonornicotine (NNN, 2) results in the formation of 4-(3-pyridyl)-4-oxobutyl (POB)-DNA adducts, several of which have been previously identified both in vitro and in tissues of laboratory animals treated with NNK or NNN. However, 2′-deoxycytidine adducts formed in this process have been incompletely examined in previous studies. Therefore, in this study we prepared characterized standards for the identification of previously unknown 2′-deoxycytidine and 2′-deoxyuridine adducts that could be produced in these reactions. The formation of these products in reactions of 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKOAc, 3), a model 4-(3-pyridyl)-4-oxobutylating agent, with DNA was investigated. The major 2′-deoxycytidine adduct, identified as its stable cytosine analogue O2-[4-(3-pyridyl)-4-oxobut-1-yl]-cytosine (12), was O2-[4-(3-pyridyl)-4-oxobut-1-yl]-2′-deoxycytidine (13), whereas lesser amounts of 3-[4-(3-pyridyl)-4-oxobut-1-yl]-2′-deoxycytidine (14) and N4-[4-(3-pyridyl)-4-oxobut-1-yl]-2′-deoxycytidine (15) were also observed. The potential conversion of relatively unstable 2′-deoxycytidine adducts to stable 2′-deoxyuridine adducts by treatment of the adducted DNA with bisulfite was also investigated, but the harsh conditions associated with this approach prevented quantitation. The results of this study provide new validated standards for the study of 4-(3-pyridyl)-4-oxobutylation of DNA, a critical reaction in the carcinogenesis by 1 and 2, and demonstrate the presence of previously unidentified 2′-deoxycytidine adducts in this DNA. PMID:28393135

  17. Chemical Reactions Impacting the Potential of Planetary Habitability

    NASA Astrophysics Data System (ADS)

    Kamakolanu, U. G.

    2017-02-01

    The formation of building blocks of life might have been a two-step process. 1) Acid catalyzed cyclization reaction, resulting in the formation of substituted pyran moiety, and 2) ring opening of pyran resulting in chiral prebiotic precursor molecule.

  18. Noble metal-free hydrazine fuel cell catalysts: EPOC effect in competing chemical and electrochemical reaction pathways.

    PubMed

    Sanabria-Chinchilla, Jean; Asazawa, Koichiro; Sakamoto, Tomokazu; Yamada, Koji; Tanaka, Hirohisa; Strasser, Peter

    2011-04-13

    We report the discovery of a highly active Ni-Co alloy electrocatalyst for the oxidation of hydrazine (N(2)H(4)) and provide evidence for competing electrochemical (faradaic) and chemical (nonfaradaic) reaction pathways. The electrochemical conversion of hydrazine on catalytic surfaces in fuel cells is of great scientific and technological interest, because it offers multiple redox states, complex reaction pathways, and significantly more favorable energy and power densities compared to hydrogen fuel. Structure-reactivity relations of a Ni(60)Co(40) alloy electrocatalyst are presented with a 6-fold increase in catalytic N(2)H(4) oxidation activity over today's benchmark catalysts. We further study the mechanistic pathways of the catalytic N(2)H(4) conversion as function of the applied electrode potential using differentially pumped electrochemical mass spectrometry (DEMS). At positive overpotentials, N(2)H(4) is electrooxidized into nitrogen consuming hydroxide ions, which is the fuel cell-relevant faradaic reaction pathway. In parallel, N(2)H(4) decomposes chemically into molecular nitrogen and hydrogen over a broad range of electrode potentials. The electroless chemical decomposition rate was controlled by the electrode potential, suggesting a rare example of a liquid-phase electrochemical promotion effect of a chemical catalytic reaction ("EPOC"). The coexisting electrocatalytic (faradaic) and heterogeneous catalytic (electroless, nonfaradaic) reaction pathways have important implications for the efficiency of hydrazine fuel cells.

  19. Self-Organized Stationary Patterns in Networks of Bistable Chemical Reactions.

    PubMed

    Kouvaris, Nikos E; Sebek, Michael; Mikhailov, Alexander S; Kiss, István Z

    2016-10-10

    Experiments with networks of discrete reactive bistable electrochemical elements organized in regular and nonregular tree networks are presented to confirm an alternative to the Turing mechanism for the formation of self-organized stationary patterns. The results show that the pattern formation can be described by the identification of domains that can be activated individually or in combinations. The method also enabled the localization of chemical reactions to network substructures and the identification of critical sites whose activation results in complete activation of the system. Although the experiments were performed with a specific nickel electrodissolution system, they reproduced all the salient dynamic behavior of a general network model with a single nonlinearity parameter. Thus, the considered pattern-formation mechanism is very robust, and similar behavior can be expected in other natural or engineered networked systems that exhibit, at least locally, a treelike structure.

  20. Numerical investigation of oscillatory multiphase flow in porous medium with chemically active skeleton

    NASA Astrophysics Data System (ADS)

    Konyukhov, A. V.; Zavialov, I. N.

    2016-11-01

    Self-oscillating mode of reaction front propagation in multiphase flow in the porous medium with chemically active skeleton is investigated numerically. The considered flow represents an immiscible displacement process, such that the displacing fluid and the skeleton of the porous medium have chemically active components which react with production of gaseous phase. The calculations have demonstrated strong influence of the reaction kinetics on stability of the reactive flow. The presence of a time delay between the change of concentration of the reactants and the change of the reaction rate is shown to stimulate transition of the reaction front propagation to the oscillatory mode.

  1. Chemical Reaction CO+OH(•) → CO2+H(•) Autocatalyzed by Carbon Dioxide: Quantum Chemical Study of the Potential Energy Surfaces.

    PubMed

    Masunov, Artëm E; Wait, Elizabeth; Vasu, Subith S

    2016-08-04

    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 CO2 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 CO2 to OH radical and CO molecule, hydrogen transfer from 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 CO2 medium. It may open a new venue for controlling reaction rates for chemical manufacturing.

  2. Chemical reaction CO+OH • → CO2+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 CO2 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 CO2 to OH radical and CO molecule, hydrogen transfer from oxygen tomore » 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 CO2 medium. Furthermore, tt may open a new venue for controlling reaction rates for chemical manufacturing.« less

  3. Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas

    SciTech Connect

    Sakai, Osamu Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide

    2015-10-15

    Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH{sub 3} in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.

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

    PubMed Central

    Yao, Xiahui; Dong, Qi; Cheng, Qingmei

    2016-01-01

    Abstract 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. PMID:27381169

  5. 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.

  6. A constrained reduced-dimensionality search algorithm to follow chemical reactions on potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Lankau, Timm; Yu, Chin-Hui

    2013-06-01

    A constrained reduced-dimensionality algorithm can be used to efficiently locate transition states and products in reactions involving conformational changes. The search path (SP) is constructed stepwise from linear combinations of a small set of manually chosen internal coordinates, namely the predictors. The majority of the internal coordinates, the correctors, are optimized at every step of the SP to minimize the total energy of the system so that the path becomes a minimum energy path connecting products and transition states with the reactants. Problems arise when the set of predictors needs to include weak coordinates, for example, dihedral angles, as well as strong ones such as bond distances. Two principal constraining methods for the weak coordinates are proposed to mend this situation: static and dynamic constraints. Dynamic constraints are automatically activated and revoked depending on the state of the weak coordinates among the predictors, while static ones require preset control factors and act permanently. All these methods enable the successful application (4 reactions are presented involving cyclohexane, alanine dipeptide, trimethylsulfonium chloride, and azafulvene) of the reduced dimensionality method to reactions where the reaction path covers large conformational changes in addition to the formation/breaking of chemical bonds. Dynamic constraints are found to be the most efficient method as they require neither additional information about the geometry of the transition state nor fine tuning of control parameters.

  7. Modeling the Influence of Transport on Chemical Reactivity in Microbial Membranes: Mineral Precipitation/Dissolution Reactions.

    NASA Astrophysics Data System (ADS)

    Felmy, A. R.; Liu, C.; Clark, S.; Straatsma, T.; Rustad, J.

    2003-12-01

    It has long been known that microorganisms can alter the chemical composition of their immediate surroundings and influence such processes as ion uptake or adsorption and mineral precipitation dissolution. However, only recently have molecular imaging and molecular modeling capabilities been developed that begin to shed light on the nature of these processes at the nm to um scale at the surface of bacterial membranes. In this presentation we will show the results of recent molecular simulations of microbial surface reactions and describe our efforts to develop accurate non-equilibrium thermodynamic models for the microbial surface that can describe ion uptake and surface induced mineral precipitation. The thermodynamic models include the influence of the bacterial electrical double layer on the uptake of ions from solution and the removal, or exclusion, of ions from the surface of the cell, non-equilibrium diffusion and chemical reaction within the membrane, as well as a new thermodynamic approach to representing ion activities within the microbial membrane. In the latter case, the variability in the water content within the microbial membrane has a significant influence on the calculated mineral saturation indices. In such cases, we will propose the use of recently developed mixed solvent-electrolyte formalisms. Recent experimental data for mixed-solvent electrolyte systems will also be presented to demonstrate the potential impact of the variable water content on calculated ion activities within the membrane.

  8. Cutaneous reactions in nuclear, biological and chemical warfare.

    PubMed

    Arora, Sandeep

    2005-01-01

    Nuclear, biological and chemical warfare have in recent times been responsible for an increasing number of otherwise rare dermatoses. Many nations are now maintaining overt and clandestine stockpiles of such arsenal. With increasing terrorist threats, these agents of mass destruction pose a risk to the civilian population. Nuclear and chemical attacks manifest immediately while biological attacks manifest later. Chemical and biological attacks pose a significant risk to the attending medical personnel. The large scale of anticipated casualties in the event of such an occurrence would need the expertise of all physicians, including dermatologists, both military and civilian. Dermatologists are uniquely qualified in this respect. This article aims at presenting a review of the cutaneous manifestations in nuclear, chemical and biological warfare and their management.

  9. 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.

  10. Molecule-based approach for computing chemical-reaction rates in upper atmosphere hypersonic flows.

    SciTech Connect

    Gallis, Michail A.; Bond, Ryan Bomar; Torczynski, John Robert

    2009-08-01

    This report summarizes the work completed during FY2009 for the LDRD project 09-1332 'Molecule-Based Approach for Computing Chemical-Reaction Rates in Upper-Atmosphere Hypersonic Flows'. The goal of this project was to apply a recently proposed approach for the Direct Simulation Monte Carlo (DSMC) method to calculate chemical-reaction rates for high-temperature atmospheric species. The new DSMC model reproduces measured equilibrium reaction rates without using any macroscopic reaction-rate information. Since it uses only molecular properties, the new model is inherently able to predict reaction rates for arbitrary nonequilibrium conditions. DSMC non-equilibrium reaction rates are compared to Park's phenomenological non-equilibrium reaction-rate model, the predominant model for hypersonic-flow-field calculations. For near-equilibrium conditions, Park's model is in good agreement with the DSMC-calculated reaction rates. For far-from-equilibrium conditions, corresponding to a typical shock layer, the difference between the two models can exceed 10 orders of magnitude. The DSMC predictions are also found to be in very good agreement with measured and calculated non-equilibrium reaction rates. Extensions of the model to reactions typically found in combustion flows and ionizing reactions are also found to be in very good agreement with available measurements, offering strong evidence that this is a viable and reliable technique to predict chemical reaction rates.

  11. 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.

  12. Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

    NASA Astrophysics Data System (ADS)

    Fernandez, Julio M.

    2008-03-01

    The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule

  13. Chemical and mathematical modeling of asphaltene reaction pathways

    SciTech Connect

    Salvage, P.E.

    1986-01-01

    Precipitated asphaltene was subjected to pyrolysis and hydropyrolysis, both neat and in solvents, and catalytic hydroprocessing. A solvent extraction procedure defined gas, maltene, asphaltene, and coke product fractions. The apparent first order rate constant for asphaltene conversion at 400/sup 0/C was relatively insensitive to the particular reaction scheme. The yield of gases likewise showed little variation and was always less than 10%. On the other hand, the maltene and coke yields were about 20% and 60%, respectively, from neat pyrolysis, and about 60% and less than 5%, respectively, from catalytic reactions. The temporal variations of the product fractions allowed discernment of asphaltene reaction pathways. The primary reaction of asphaltene was to residual asphaltene, maltenes, and gases. The residual asphaltene reacted thermally to coke and catalytically to maltenes at the expense of coke. Secondary degradation of these primary products led to lighter compounds. Reaction mechanism for pyrolysis of asphaltene model compounds and alkylaromstics were determined. The model compound kinetics results were combined with a stochastic description of asphaltene structure in a mathematical model of asphaltene pyrolysis. Individual molecular product were assigned to either the gas, maltene, asphaltene, or coke product fractions, and summation of the weights of each constituted the model's predictions. The temporal variation of the product fractions from simulated asphaltene pyrolysis compared favorably with experimental results.

  14. Chemical activation of carbon mesophase pitches.

    PubMed

    Mora, E; Blanco, C; Pajares, J A; Santamaría, R; Menéndez, R

    2006-06-01

    This paper studies the chemical activation of mesophase pitches of different origins in order to obtain activated carbons suitable for use as electrodes in supercapacitors. The effect that the activating agent (NaOH, LiOH, and KOH), the alkaline hydroxide/pitch ratio, and the activation temperature had on the characteristics of the resultant activated carbons was studied. LiOH was found to be a noneffective activating agent, while activation with NaOH and KOH yielded activated carbons with high apparent surface areas and pore volumes. The increase of the KOH/pitch ratio caused an increase of the chemical attack on the carbon, producing higher burnoffs and development of porosity. Extremely high apparent surface areas were obtained when the petroleum pitch was activated with 5:1 KOH/carbon ratio. The increase of the activation temperature caused an increase of the burnoff, although the differences were not as significant as those derived from the use of different proportions of activating agent.

  15. Activated coconut shell charcoal carbon using chemical-physical activation

    NASA Astrophysics Data System (ADS)

    Budi, Esmar; Umiatin, Nasbey, Hadi; Bintoro, Ridho Akbar; Wulandari, Futri; Erlina

    2016-02-01

    The use of activated carbon from natural material such as coconut shell charcoal as metal absorbance of the wastewater is a new trend. The activation of coconut shell charcoal carbon by using chemical-physical activation has been investigated. Coconut shell was pyrolized in kiln at temperature about 75 - 150 °C for about 6 hours in producing charcoal. The charcoal as the sample was shieved into milimeter sized granule particle and chemically activated by immersing in various concentration of HCl, H3PO4, KOH and NaOH solutions. The samples then was physically activated using horizontal furnace at 400°C for 1 hours in argon gas environment with flow rate of 200 kg/m3. The surface morphology and carbon content of activated carbon were characterized by using SEM/EDS. The result shows that the pores of activated carbon are openned wider as the chemical activator concentration is increased due to an excessive chemical attack. However, the pores tend to be closed as further increasing in chemical activator concentration due to carbon collapsing.

  16. Predicting rare events in chemical reactions: Application to skin cell proliferation.

    PubMed

    Lee, Chiu Fan

    2010-08-01

    In a well-stirred system undergoing chemical reactions, fluctuations in the reaction propensities are approximately captured by the corresponding chemical Langevin equation. Within this context, we discuss in this work how the Kramers escape theory can be used to predict rare events in chemical reactions. As an example, we apply our approach to a recently proposed model on cell proliferation with relevance to skin cancer [P. B. Warren, Phys. Rev. E 80, 030903 (2009)]. In particular, we provide an analytical explanation for the form of the exponential exponent observed in the onset rate of uncontrolled cell proliferation.

  17. Energy storage and transport by reversible chemical reactions

    NASA Astrophysics Data System (ADS)

    Beghi, G.

    Reversible thermochemical reactions are one of the possibilities to store and transport high temperature heat (800 K up to 1300 K). There are open cycles and closed cycles. Some reversible systems are described, as the SO2-SO3 system. A typical example of open cycle is the reaction for water decomposition. Results of a pilot plant to verify the decomposition of sulfuric acid are described; the technological feasibility of this method for hydrogen production is shown. The possibility to use other high temperature sources, as solar energy is discussed.

  18. Applications of the ETS-NOCV method in descriptions of chemical reactions.

    PubMed

    Mitoraj, Mariusz Paweł; Parafiniuk, Monika; Srebro, Monika; Handzlik, Michał; Buczek, Agnieszka; Michalak, Artur

    2011-09-01

    The present study characterizes changes in the electronic structure of reactants during chemical reactions based on the combined charge and energy decomposition scheme, ETS-NOCV (extended transition state-natural orbitals for chemical valence). Decomposition of the activation barrier, ΔE (#), into stabilizing (orbital interaction, ΔE (orb), and electrostatic, ΔE (elstat)) and destabilizing (Pauli repulsion, ΔE (Pauli), and geometry distortion energy, ΔE (dist)) factors is discussed in detail for the following reactions: (I) hydrogen cyanide to hydrogen isocyanide, HCN → CNH isomerization; (II) Diels-Alder cycloaddition of ethene to 1,3-butadiene; and two catalytic processes, i.e., (III) insertion of ethylene into the metal-alkyl bond using half-titanocene with phenyl-phenoxy ligand catalyst; and (IV) B-H bond activation catalyzed by an Ir-containing catalyst. Various reference states for fragments were applied in ETS-NOCV analysis. We found that NOCV-based deformation densities (Δρ (i)) and the corresponding energies ΔE (orb)(i) obtained from the ETS-NOCV scheme provide a very useful picture, both qualitatively and quantitatively, of electronic density reorganization along the considered reaction pathways. Decomposition of the barrier ΔE(#) into stabilizing and destabilizing contributions allowed us to conclude that the main factor responsible for the existence of positive values of ΔE (#) for all processes (I, II, III and IV) is Pauli interaction, which is the origin of steric repulsion. In addition, in the case of reactions II, III and IV, a significant degree of structural deformation of the reactants, as measured by the geometry distortion energy, plays an important role. Depending on the reaction type, stabilization of the transition state (relatively to the reactants) originating either from the orbital interaction term or from electrostatic attraction can be of vital importance. Finally, use of the ETS-NOCV method to describe catalytic

  19. Theoretical studies of the dynamics of chemical reactions

    SciTech Connect

    Wagner, A.F.

    1993-12-01

    Recent research effort has focussed on several reactions pertinent to combustion. The formation of the formyl radical from atomic hydrogen and carbon monoxide, recombination of alkyl radicals and halo-alkyl radicals with halogen atoms, and the thermal dissociation of hydrogen cyanide and acetylene have been studied by modeling. In addition, the inelastic collisions of NCO with helium have been investigated.

  20. Chemical Principles Revisited. Redox Reactions and the Electropotential Axis.

    ERIC Educational Resources Information Center

    Vella, Alfred J.

    1990-01-01

    This paper suggests a nontraditional pedagogic approach to the subject of redox reactions and electrode potentials suitable for freshman chemistry. Presented is a method for the representation of galvanic cells without the introduction of the symbology and notation of conventional cell diagrams. (CW)

  1. Exploring Chemical Reaction Mechanisms Through Harmonic Fourier Beads Path Optimization

    DTIC Science & Technology

    2013-01-01

    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...peptide, as shown in Fig. 2. This reaction is biologically important as a model of peptide bond cleavage. When catalyzed by enzymes, the re- action

  2. Theoretical Studies of Chemical Reactions following Electronic Excitation

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.

    2003-01-01

    The use of multi-configurational wave functions is demonstrated for several processes: tautomerization reactions in the ground and excited states of the DNA base adenine, dissociation of glycine molecule after electronic excitation, and decomposition/deformation of novel rare gas molecules HRgF. These processes involve bond brealung/formation and require multi-configurational approaches that include dynamic correlation.

  3. 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.

  4. Hypervelocity accelerators with electro-thermo-chemical reaction

    NASA Astrophysics Data System (ADS)

    Ikuta, Kazunari

    1991-08-01

    A novel kind of electro-thermo-chemical (ETC) launcher for the acceleration of multikilogram-size projectiles to hypervelocity is proposed. The novel launcher concept utilizes the hot hydrogen gas generated by the chemical interaction between water and aluminum in order to accelerate the projectiles to a thermal velocity close to that of the light gas. This interaction is triggered by the Joule heating of the aluminum wire in water. Two possible designs for the accelerator concept are considered in detail. Further acceleration of the projectile near the muzzle is also discussed.

  5. Synthesis and chemical reactions of the steroidal hormone 17α-methyltestosterone.

    PubMed

    El-Desoky, El-Sayed Ibrahim; Reyad, Mahmoud; Afsah, Elsayed Mohammed; Dawidar, Abdel-Aziz Mahmoud

    2016-01-01

    Structural modifications of natural products with complex structures like steroids require great synthetic effort. A review of literature is presented on the chemistry of the steroidal hormone 17α-methyltestosterone that is approved by Food and Drug Administration (FDA) in the United States as an androgen for estrogen-androgen hormone replacement therapy treatment. The analog also offers special possibilities for the prevention/treatment of hormone-sensitive cancers. The testosterone skeleton has important functionalities in the molecule that can act as a carbonyl component, an active methylene compound, α,β-unsaturated enone and tertiary hydroxyl group in various chemical reactions to access stereoisomeric steroidal compounds with potent activity. In addition, microbiological methods of synthesis and transformation of this hormone are presented.

  6. Expanded utility of the native chemical ligation reaction.

    PubMed

    Yeo, Dawn S Y; Srinivasan, Rajavel; Chen, Grace Y J; Yao, Shao Q

    2004-10-04

    The post-genomic era heralds a multitude of challenges for chemists and biologists alike, with the study of protein functions at the heart of much research. The elucidation of protein structure, localization, stability, post-translational modifications, and protein interactions will steadily unveil the role of each protein and its associated biological function in the cell. The push to develop new technologies has necessitated the integration of various disciplines in science. Consequently, the role of chemistry has never been so profound in the study of biological processes. By combining the strengths of recombinant DNA technology, protein splicing, organic chemistry, and the chemoselective chemistry of native chemical ligation, various strategies have been successfully developed and applied to chemoselectively label proteins, both in vitro and in live cells, with biotin, fluorescent, and other small molecule probes. The site-specific incorporation of molecular entities with unique chemical functionalities in proteins has many potential applications in chemical and biological studies of proteins. In this article, we highlight recent progress of these strategies in several areas related to proteomics and chemical biology, namely, in vitro and in vivo protein biotinylation, protein microarray technologies for large-scale protein analysis, and live-cell bioimaging.

  7. EFFICIENT CHEMICAL TRANSFORMATIONS USING ALTERNATIVE REACTION CONDITIONS AND MEDIA

    EPA Science Inventory

    The diverse nature of chemical entities requires various green' strategic pathways in our quest towards attaining sustainability. A solvent-free approach that involves microwave (MW) exposure of neat reactants (undiluted) catalyzed by the surfaces of less-expensive and recyclable...

  8. Effect of Coriolis coupling in chemical reaction dynamics.

    PubMed

    Chu, Tian-Shu; Han, Ke-Li

    2008-05-14

    It is essential to evaluate the role of Coriolis coupling effect in molecular reaction dynamics. Here we consider Coriolis coupling effect in quantum reactive scattering calculations in the context of both adiabaticity and nonadiabaticity, with particular emphasis on examining the role of Coriolis coupling effect in reaction dynamics of triatomic molecular systems. We present the results of our own calculations by the time-dependent quantum wave packet approach for H + D2 and F(2P3/2,2P1/2) + H2 as well as for the ion-molecule collisions of He + H2 +, D(-) + H2, H(-) + D2, and D+ + H2, after reviewing in detail other related research efforts on this issue.

  9. A Study of Organic Chemical Reactions in Microemulsions.

    DTIC Science & Technology

    1984-10-24

    organic synthesis were investigated. The first involved a delineation of the ability of microemulsions to catalyze synthetically useful reactions of water...microemulsions in organic synthesis . We also began the design and synthesis of turnover catalysts for carbon and phosphorus ester hydrolysis. Originator...furnished key words include: microemulsions, organic synthesis , microemulsions, reactive site, microemulsion, destructible (cleavable) surfactant-based, destructible (cleavable) surfactants, turnover catalysts.

  10. Successive splitting of autowaves in a nonlinear chemical reaction medium.

    PubMed

    Okano, Taiji; Matsuda, Yuki; Miyakawa, Kenji

    2006-12-01

    The phenomenon of wave splitting is investigated in a two-dimensional excitable light-sensitive Belousov-Zhabotinsky reaction medium after extremely changing the intensity of illuminated light for a short time. It is found that successive wave splitting and nonannihilation collision between two waves of different amplitudes occur spontaneously under narrow experimental conditions. Experimental observations are approximately reproduced in the specific parameter range by a numerical simulation with a Bär-Eiswirth model.

  11. 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.

  12. Reformulation and solution of the master equation for multiple-well chemical reactions.

    PubMed

    Georgievskii, Yuri; Miller, James A; Burke, Michael P; Klippenstein, Stephen J

    2013-11-21

    We consider an alternative formulation of the master equation for complex-forming chemical reactions with multiple wells and bimolecular products. Within this formulation the dynamical phase space consists of only the microscopic populations of the various isomers making up the reactive complex, while the bimolecular reactants and products are treated equally as sources and sinks. This reformulation yields compact expressions for the phenomenological rate coefficients describing all chemical processes, i.e., internal isomerization reactions, bimolecular-to-bimolecular reactions, isomer-to-bimolecular reactions, and bimolecular-to-isomer reactions. The applicability of the detailed balance condition is discussed and confirmed. We also consider the situation where some of the chemical eigenvalues approach the energy relaxation time scale and show how to modify the phenomenological rate coefficients so that they retain their validity.

  13. Antimicrobial activity of chemically modified dextran derivatives.

    PubMed

    Tuchilus, Cristina G; Nichifor, Marieta; Mocanu, Georgeta; Stanciu, Magdalena C

    2017-04-01

    Cationic amphiphilic dextran derivatives with a long alkyl group attached to the reductive end of the polysaccharide chain and quaternary ammonium groups attached as pendent groups to the main dextran backbone were synthesized and tested for their antimicrobial properties against several bacteria and fungi strains. Dependence of antimicrobial activity on both polymer chemical composition (dextran molar mass, length of end alkyl group and chemical structure of ammonium groups) and type of microbes was highlighted by disc-diffusion method (diameter of inhibition zone) and broth microdilution method (minimum inhibitory concentrations). Polymers had antimicrobial activity for all strains studied, except for Pseudomonas aeruginosa ATCC 27853. The best activity against Staphylococcus aureus (Minimun Inhibitory Concentration 60μg/mL) was provided by polymers obtained from dextran with lower molecular mass (Mn=4500), C12H25 or C18H37 end groups, and N,N-dimethyl-N-benzylammonium pendent groups.

  14. Exact probability distributions of selected species in stochastic chemical reaction networks.

    PubMed

    López-Caamal, Fernando; Marquez-Lago, Tatiana T

    2014-09-01

    Chemical reactions are discrete, stochastic events. As such, the species' molecular numbers can be described by an associated master equation. However, handling such an equation may become difficult due to the large size of reaction networks. A commonly used approach to forecast the behaviour of reaction networks is to perform computational simulations of such systems and analyse their outcome statistically. This approach, however, might require high computational costs to provide accurate results. In this paper we opt for an analytical approach to obtain the time-dependent solution of the Chemical Master Equation for selected species in a general reaction network. When the reaction networks are composed exclusively of zeroth and first-order reactions, this analytical approach significantly alleviates the computational burden required by simulation-based methods. By building upon these analytical solutions, we analyse a general monomolecular reaction network with an arbitrary number of species to obtain the exact marginal probability distribution for selected species. Additionally, we study two particular topologies of monomolecular reaction networks, namely (i) an unbranched chain of monomolecular reactions with and without synthesis and degradation reactions and (ii) a circular chain of monomolecular reactions. We illustrate our methodology and alternative ways to use it for non-linear systems by analysing a protein autoactivation mechanism. Later, we compare the computational load required for the implementation of our results and a pure computational approach to analyse an unbranched chain of monomolecular reactions. Finally, we study calcium ions gates in the sarco/endoplasmic reticulum mediated by ryanodine receptors.

  15. Signatures of chemical reactions in the morphology and fluctuations of giant vesicles

    NASA Astrophysics Data System (ADS)

    Döbereiner, Hans-Günther; Petrov, Peter G.; Riske, Karin A.

    2003-01-01

    The behaviour of an amphiphilic membrane is determined by the physical and chemical properties of the molecules which form the bilayer and their interactions with the surrounding medium. Bulk or interfacial chemical reactions modify interaction parameters and/or affect directly the chemical composition of the membrane. We monitor the morphological response and the thermal fluctuations of giant lipid vesicles to chemical reactions in the external vesicle medium using phase-contrast microscopy. Observation of vesicle conformations as a function of time allows us to characterize the statics and dynamics of membrane response as well as the underlying chemical kinetics. As two examples, we present (a) a photochemical reaction of hexacyanoferrate which induces an increase in pH and (b) the enzymatic cleavage of phosphatidyl choline by the phospholipase C from Bacillus cereus.

  16. Ambient solid-state mechano-chemical reactions between functionalized carbon nanotubes

    PubMed Central

    Kabbani, Mohamad A.; Tiwary, Chandra Sekhar; Autreto, Pedro A.S.; Brunetto, Gustavo; Som, Anirban; Krishnadas, K.R.; Ozden, Sehmus; Hackenberg, Ken P.; Gong, Yongi; Galvao, Douglas S.; Vajtai, Robert; Kabbani, Ahmad T.; Pradeep, Thalappil; Ajayan, Pulickel M.

    2015-01-01

    Carbon nanotubes can be chemically modified by attaching various functionalities to their surfaces, although harsh chemical treatments can lead to their break-up into graphene nanostructures. On the other hand, direct coupling between functionalities bound on individual nanotubes could lead to, as yet unexplored, spontaneous chemical reactions. Here we report an ambient mechano-chemical reaction between two varieties of nanotubes, carrying predominantly carboxyl and hydroxyl functionalities, respectively, facilitated by simple mechanical grinding of the reactants. The purely solid-state reaction between the chemically differentiated nanotube species produces condensation products and unzipping of nanotubes due to local energy release, as confirmed by spectroscopic measurements, thermal analysis and molecular dynamic simulations. PMID:26073564

  17. Mechanical Manipulation of Chemical Reactions: Reactivity Switching of Bergman Cyclizations.

    PubMed

    Krupička, Martin; Sander, Wolfram; Marx, Dominik

    2014-03-06

    Photoswitches incorporated into molecular frameworks have been used since a long time to trigger chemical processes on demand. Here, it is shown how mechanophores can be used as switches in order to drastically change the reactivity of a neighboring functional group as a function of external stress. The reactivities of cyclic enediynes, which are highly toxic agents when undergoing Bergman cyclization, roughly correlate with the distance between the bond-forming carbons in many cases. It is demonstrated how this distance, and thus enediyne reactivity, can be tuned upon applying mechanical stress. Depending on suitable substitution patterns, chemically inert species can be turned into highly reactive ones and vice versa, thus extending the concept of photoswitching to mechanoswitching. Moreover, depending on the derivative, it is found that C1-C5 cyclization becomes energetically preferred over the Bergman (C1-C6) pathway at nano-Newton forces, thus leading to a force-induced switch in selectivity in such cases.

  18. 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.

  19. Sensitive detection of chemical agents and toxic industrial chemicals using active open-path FTIRs

    NASA Astrophysics Data System (ADS)

    Walter, William T.

    2004-03-01

    Active open-path FTIR sensors provide more sensitive detection of chemical agents than passive FTIRs, such as the M21 RSCAAL and JSLSCAD, and at the same time identify and quantify toxic industrial chemicals (TIC). Passive FTIRs are bistatic sensors relying on infrared sources of opportunity. Utilization of earth-based sources of opportunity limits the source temperatures available for passive chemical-agent FTIR sensors to 300° K. Active FTIR chemical-agent sensors utilize silicon carbide sources, which can be operated at 1500° K. The higher source temperature provides more than an 80-times increase in the infrared radiant flux emitted per unit area in the 7 to 14 micron spectral fingerprint region. Minimum detection limits are better than 5 μgm/m3 for GA, GB, GD, GF and VX. Active FTIR sensors can (1) assist first responders and emergency response teams in their assessment of and reaction to a terrorist threat, (2) provide information on the identification of the TIC present and their concentrations and (3) contribute to the understanding and prevention of debilitating disorders analogous to the Gulf War Syndrome for military and civilian personnel.

  20. 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.

  1. Insight into hydroxides-activated coals: chemical or physical activation?

    SciTech Connect

    Alcaniz-Monge, J.; Illan-Gomez, M.J.

    2008-02-15

    The objective of this paper is to get an insight into the chemical activation mechanism using KOH and NaOH as activated agents. Three coals have been selected as carbon precursors. It was found that KOH and NaOH develop a similar narrow microporosity, independently of the coal rank, whereas only KOH generates supermicroporosity. Temperature-programmed desorption experiments, carried out with impregnated anthracite, show differences on the gas evolved during the activated carbon preparation using the two activating agents. Thus, whereas hydrogen profiles are quite similar for both activated agents, the CO and H{sub 2}O profiles are different. It is remarkable the high amount of H{sub 2}O evolved at the maximum treatment temperature for both activating agents. The results obtained to allow conclusion that the chemical activation is due to a combination of different process driving the development of material porosity.

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

    NASA Astrophysics Data System (ADS)

    Bilen, Murat; Gürü, Metin; Çakanyildirim, Çetin

    2017-02-01

    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.

  3. 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-VKQ, prepared by coupling vitamin K3, 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-VKQ is non-emissive, while upon reduction to the hydroquinone form, B-VKQH2, 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-VKQ 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.

  4. Optimal Concentration Configuration of Consecutive Chemical Reaction A ⇔ B ⇔ C for Minimum Entropy Generation

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Chen, Lingen; Xia, Shaojun; Sun, Fengrui

    2016-10-01

    A consecutive chemical reaction A Leftrightarrow B Leftrightarrow C is studied in this paper. The optimal concentration configuration of the reaction for minimum entropy generation with fixed yield of aimed product B is derived. The optimal concentration configuration with different initial conditions and the optimal initial concentration {C_{C0}}_{{{, opt}}} of the by-product C are obtained numerically. Compared with the control method that the concentration of A increases linearly, the entropy production is reduced by more than 90 %. The minimum entropy generation and optimal configuration of elementary reaction A Leftrightarrow B are studied by using variational method and nonlinear programming method. The validity of the nonlinear programming method is verified. The reaction rate of elementary reaction A Leftrightarrow B is in proportion to the square root of the concentration of A when entropy generation of the reaction process is minimum. The results obtained can help one to find the realizable regimes for a chemical reactor.

  5. RPMDRATE: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    NASA Astrophysics Data System (ADS)

    Suleimanov, Yu. V.; Allen, J. W.; Green, W. H.

    2013-03-01

    We present RPMDRATE, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH4, OH+CH4 and H+C2H6 reactions. Catalogue identifier: AENW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 94512 No. of bytes in distributed program, including test data, etc.: 1395674 Distribution format: tar.gz Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). Computer: Not computer specific. Operating system: Any for which Python, Fortran 90/95 compiler and the required external routines are available. Has the code been vectorized or parallelized?: The program can efficiently utilize 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors are reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines.

  6. Reactions of Trimethylaluminium: Modelling the Chemical Degradation of Synthetic Lubricants.

    PubMed

    Slaughter, Jonathan; Peel, Andrew J; Wheatley, Andrew E H

    2017-01-01

    In investigating and seeking to mimic the reactivity of trimethylaluminium (TMA) with synthetic, ester-based lubricating oils, the reaction of methyl propionate 1 was explored with 1, 2 and 3 equivalents of the organoaluminium reagent. Spectroscopic analysis points to the formation of the adduct 1(TMA) accompanied only by the low level 1:1 production of Me2 AlOCEtMe2 2 and Me2 AlOMe 3 when an equimolar amount of TMA is applied. The deployment of excess TMA favours reaction to give 2 and 3 over 1(TMA) adduct formation and spectroscopy reveals that in hydrocarbon solution substitution product 2 traps unreacted TMA to yield 2(TMA). The (1) H NMR spectroscopic observation of two Al-Me signals not attributable to free TMA and in the ratio 1:4 suggests the formation of a previously only postulated, symmetrical metallacycle in Me4 Al2 (μ(2) -Me)(μ(2) -OCEtMe2 ). In the presence of 3, 2(TMA) undergoes thermally induced exchange to yield Me4 Al2 (μ(2) -OMe)(μ(2) -OCEtMe2 ) 4 and TMA. The reaction of methyl phenylacetate 5 with TMA allows isolation of the crystalline product Me2 AlOCBnMe2 (TMA) 6(TMA), which allows the first observation of the Me4 Al2 (μ(2) -Me)(μ(2) -OR) motif in the solid state. Distances of 2.133(3) Å (Al-Mebridging ) and 1.951 Å (mean Al-Meterminal ) are recorded. The abstraction of TMA from 6(TMA) by the introduction of Et2 O has yielded 6, which exists as a dimer.

  7. Effects of reversible chemical reaction on Li diffusion and stresses in spherical composition-gradient electrodes

    SciTech Connect

    Li, Yong; Zhang, Kai; Zheng, Bailin Zhang, Xiaoqian; Wang, Qi

    2015-06-28

    Composition-gradient electrode materials have been proven to be one of the most promising materials in lithium-ion battery. To study the mechanism of mechanical degradation in spherical composition-gradient electrodes, the finite deformation theory and reversible chemical theory are adopted. In homogeneous electrodes, reversible electrochemical reaction may increase the magnitudes of stresses. However, reversible electrochemical reaction has different influences on stresses in composition-gradient electrodes, resulting from three main inhomogeneous factors—forward reaction rate, backward reaction rate, and reaction partial molar volume. The decreasing transition form of forward reaction rate, increasing transition form of backward reaction rate, and increasing transition form of reaction partial molar volume can reduce the magnitudes of stresses. As a result, capacity fading and mechanical degradation are reduced by taking advantage of the effects of inhomogeneous factors.

  8. Quantum chemical study of penicillin: Reactions after acylation

    NASA Astrophysics Data System (ADS)

    Li, Rui; Feng, Dacheng; Zhu, Feng

    The density functional theory methods were used on the model molecules of penicillin to determine the possible reactions after their acylation on ?-lactamase, and the results were compared with sulbactam we have studied. The results show that, the acylated-enzyme tetrahedral intermediate can evolves with opening of ?-lactam ring as well as the thiazole ring; the thiazole ring-open products may be formed via ?-lactam ring-open product or from tetrahedral intermediate directly. Those products, in imine or enamine form, can tautomerize via hydrogen migration. In virtue of the water-assisted, their energy barriers are obviously reduced.

  9. The Modification of Biocellular Chemical Reactions by Environmental Physicochemicals

    NASA Astrophysics Data System (ADS)

    Ishido, M.

    Environmental risk factors affect human biological system to different extent from modification of biochemical reaction to cellular catastrophe. There are considerable public concerns about electromagnetic fields and endocrine disruptors. Their risk assessments have not been fully achieved because of their scientific uncertainty: electromagnetic fields just modify the bioreaction in the restricted cells and endocrine disruptors are quite unique in that their expression is dependent on the exposure periods throughout a life. Thus, we here describe their molecular characterization to establish the new risk assessments for environmental physicochemicals.

  10. Ca + HF - The anatomy of a chemical insertion reaction

    NASA Technical Reports Server (NTRS)

    Jaffe, R. L.; Pattengill, M. D.; Mascarello, F. G.; Zare, R. N.

    1987-01-01

    A comprehensive first-principles theoretical investigation of the gas phase reaction Ca + HF - CaF + H is reported. Ab initio potential energy calculations are first discussed, along with characteristics of the computed potential energy surface. Next, the fitting of the computed potential energy points to a suitable analytical functional form is described, and maps of the fitted potential surface are displayed. The methodology and results of a classical trajectory calculation utilizing the fitted potential surface are presented. Finally, the significance of the trajectory study results is discussed, and generalizations concerning dynamical aspects of Ca + HF scattering are drawn.

  11. Intracellular click reaction with a fluorescent chemical Ca2+ indicator to prolong its cytosolic retention.

    PubMed

    Takei, Yoshiaki; Murata, Atsushi; Yamagishi, Kento; Arai, Satoshi; Nakamura, Hideki; Inoue, Takafumi; Takeoka, Shinji

    2013-08-25

    The powerful strategy of "intracellular click reaction" was used to retain a chemical Ca(2+) indicator in the cytosol. Specifically, a novel clickable Ca(2+) indicator "N3-fura-2 AM" was coupled with dibenzylcyclooctyl-modified biomacromolecules via copper-free click reaction in living cells and Ca(2+) oscillation was observed for an extended period of time.

  12. Consistency and Inconsistency in A Level Students' Understandings of a Number of Chemical Reactions.

    ERIC Educational Resources Information Center

    Kwen, Boo Hong

    1996-01-01

    Explores A level students' conceptions of some common chemical reactions. Findings indicate that students apply frameworks consistently across groups of events that they perceive to be similar. What was found to be lacking was the scientists' view of all the reactions being regarded as realizations of the same underlying conceptual model. Contains…

  13. Chemical kinetics measurements on the reaction between blood and ozone.

    PubMed

    Cataldo, Franco; Gentilini, Luigi

    2005-07-01

    The pseudofirst-order ozonization rate constant of whole bovine blood has been measured in comparison to that of free haemin. The free prosthetic group haemin (which has also the central iron atom in the oxidized form) shows k values in the range of 0.20-0.03 s(-1) while the haeme groups inside haemoglobin protein and contained in the whole blood sample show slightly lower k values, just in the range of 0.10-0.02 s(-1). It has been found that ozone even with whole blood reacts specifically with haemoglobin of the red cells because it is adsorbed selectively on the iron atoms of the haeme prosthetic groups of haemoglobin. The absorption implies the oxidation of the central iron atom of the haeme groups with formation of methaemoglobin followed by an oxidative fission of the haeme rings. The other blood components do not exert any significant protection to the reaction between ozone and haemoglobin, which appear extremely specific and selective like the reaction between CO or HCN and haemoglobin. By analogy with the behaviour of these other gases ozone may be classified as a blood poison. The results of this work are discussed in the frame of the risks connected to the ozonotherapy and autohaemotherapy involving the blood ozonization of human or animal subjects and the re-injection of ozonized blood into the bodies.

  14. Development of a novel fingerprint for chemical reactions and its application to large-scale reaction classification and similarity.

    PubMed

    Schneider, Nadine; Lowe, Daniel M; Sayle, Roger A; Landrum, Gregory A

    2015-01-26

    Fingerprint methods applied to molecules have proven to be useful for similarity determination and as inputs to machine-learning models. Here, we present the development of a new fingerprint for chemical reactions and validate its usefulness in building machine-learning models and in similarity assessment. Our final fingerprint is constructed as the difference of the atom-pair fingerprints of products and reactants and includes agents via calculated physicochemical properties. We validated the fingerprints on a large data set of reactions text-mined from granted United States patents from the last 40 years that have been classified using a substructure-based expert system. We applied machine learning to build a 50-class predictive model for reaction-type classification that correctly predicts 97% of the reactions in an external test set. Impressive accuracies were also observed when applying the classifier to reactions from an in-house electronic laboratory notebook. The performance of the novel fingerprint for assessing reaction similarity was evaluated by a cluster analysis that recovered 48 out of 50 of the reaction classes with a median F-score of 0.63 for the clusters. The data sets used for training and primary validation as well as all python scripts required to reproduce the analysis are provided in the Supporting Information.

  15. Reaction between Chromium(III) and EDTA Ions: an Overlooked Mechanism of Case Study Reaction of Chemical Kinetics.

    PubMed

    Cerar, Janez

    2015-01-01

    Widely cited and accepted explanation of reaction mechanism of the case study reaction of chemical kinetics between Cr(III) ions and ethylenediaminetetraacetic acid (EDTA) contradicts modern chromium(III) coordination chemistry data. Absorption UV and visible light spectra were recorded during the reaction between aqueous solution of Cr(NO(3))(3) and EDTA in order to obtain new information about this reaction. Analysis of the spectra showed that only very small fraction of intermediates may be present in solution during the course of the reaction. The reaction scheme was established and according to it calculations based on a simplified model were carried out. Literature data for constants were used if known, otherwise, adjusted values of their sound estimates were applied. Reasonable agreement of the model calculations with the experimental data was obtained for pH values 3.8 and 4.5 but the model failed to reproduce measured rate of reaction at pH 5.5, probably due to the use of the oversimplified model.

  16. Influence of chemical reaction decreasing interfacial tension on immiscible viscous fingering

    NASA Astrophysics Data System (ADS)

    Tsuzuki, Reiko; Fujimura, Masanari; Yuichiro, Nagatsu

    2016-11-01

    We have experimentally investigated the effects of chemical reaction on immiscible viscous fingering (VF). In the present study, we use a chemical reaction producing a surfactant leading to a decrease in interfacial tension. In our experiment, a more viscous paraffin oil containing linoleic acid is displaced by a less viscous NaOHaq in a radial Hele-Shaw cell. We have found the influence of the reaction on the VF pattern depends on the displacement flow rate. At low flow rate, the reaction makes the fingers narrower. On the other hand, at intermediate flow rate, the reaction makes the fingers wider. At high flow rate, there is little influence of the reaction. These results can be interpreted as follows; when the reaction rate is much faster than the flow rate, interfacial tension is decreased uniformly over the interface. As a result, more finger-splitting occur and the fingers become narrower. When the reaction rate and flow rate are competing, the interfacial tension gradient is formed along the interface. As a result, Marangoni convection is produced, which leads to wider fingers. When the flow rate is much faster than the reaction rate, little reaction occurs during the formation of VF. As a result, the reaction does not influence on VF pattern.

  17. 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…

  18. Depurinating acylfulvene-DNA adducts: characterizing cellular chemical reactions of a selective antitumor agent.

    PubMed

    Gong, Jiachang; Vaidyanathan, V G; Yu, Xiang; Kensler, Thomas W; Peterson, Lisa A; Sturla, Shana J

    2007-02-21

    Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.

  19. Collective surfing of chemically active particles.

    PubMed

    Masoud, Hassan; Shelley, Michael J

    2014-03-28

    We study theoretically the collective dynamics of immotile particles bound to a 2D surface atop a 3D fluid layer. These particles are chemically active and produce a chemical concentration field that creates surface-tension gradients along the surface. The resultant Marangoni stresses create flows that carry the particles, possibly concentrating them. For a 3D diffusion-dominated concentration field and Stokesian fluid we show that the surface dynamics of active particle density can be determined using nonlocal 2D surface operators. Remarkably, we also show that for both deep or shallow fluid layers this surface dynamics reduces to the 2D Keller-Segel model for the collective chemotactic aggregation of slime mold colonies. Mathematical analysis has established that the Keller-Segel model can yield finite-time, finite-mass concentration singularities. We show that such singular behavior occurs in our finite-depth system, and study the associated 3D flow structures.

  20. "JCE" Classroom Activity #111: Redox Reactions in Three Representations

    ERIC Educational Resources Information Center

    Nieves, Edgardo L. Ortiz; Barreto, Reizelie; Medina, Zuleika

    2012-01-01

    This activity introduces students to the concept of reduction-oxidation (redox) reactions. To help students obtain a thorough understanding of redox reactions, the concept is explored at three levels: macroscopic, submicroscopic, and symbolic. In this activity, students perform hands-on investigations of the three levels as they work at different…

  1. A Photoacoustic Study of Chemically Active Systems.

    DTIC Science & Technology

    1983-09-01

    unless so designated by other documentation IS. KEY WORDS (Continue w reverse aide If neceeairy wd Identify by block nmber) Photoacoustic, Spectroscopy ...CwcAhnm i, pwo If w M Idntitty by block nin1b9) -,xThe method of gas-microphone photoacoustic spectroscopy and the related photothermal deflection... spectroscopy have been developed for application to chemically active systems. Fourier Transform Infrared Photoacoustic Spectros- copy has been used to study

  2. 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.

  3. 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.

  4. Aligned carbon nanotube with electro-catalytic activity for oxygen reduction reaction

    DOEpatents

    Liu, Di-Jia; Yang, Junbing; Wang, Xiaoping

    2010-08-03

    A catalyst for an electro-chemical oxygen reduction reaction (ORR) of a bundle of longitudinally aligned carbon nanotubes having a catalytically active transition metal incorporated longitudinally in said nanotubes. A method of making an electro-chemical catalyst for an oxygen reduction reaction (ORR) having a bundle of longitudinally aligned carbon nanotubes with a catalytically active transition metal incorporated throughout the nanotubes, where a substrate is in a first reaction zone, and a combination selected from one or more of a hydrocarbon and an organometallic compound containing an catalytically active transition metal and a nitrogen containing compound and an inert gas and a reducing gas is introduced into the first reaction zone which is maintained at a first reaction temperature for a time sufficient to vaporize material therein. The vaporized material is then introduced to a second reaction zone maintained at a second reaction temperature for a time sufficient to grow longitudinally aligned carbon nanotubes over the substrate with a catalytically active transition metal incorporated throughout the nanotubes.

  5. Regular Wave Propagation Out of Noise in Chemical Active Media

    SciTech Connect

    Alonso, S.; Sendina-Nadal, I.; Perez-Munuzuri, V.; Sancho, J. M.; Sagues, F.

    2001-08-13

    A pacemaker, regularly emitting chemical waves, is created out of noise when an excitable photosensitive Belousov-Zhabotinsky medium, strictly unable to autonomously initiate autowaves, is forced with a spatiotemporal patterned random illumination. These experimental observations are also reproduced numerically by using a set of reaction-diffusion equations for an activator-inhibitor model, and further analytically interpreted in terms of genuine coupling effects arising from parametric fluctuations. Within the same framework we also address situations of noise-sustained propagation in subexcitable media.

  6. Regular wave propagation out of noise in chemical active media.

    PubMed

    Alonso, S; Sendiña-Nadal, I; Pérez-Muñuzuri, V; Sancho, J M; Sagués, F

    2001-08-13

    A pacemaker, regularly emitting chemical waves, is created out of noise when an excitable photosensitive Belousov-Zhabotinsky medium, strictly unable to autonomously initiate autowaves, is forced with a spatiotemporal patterned random illumination. These experimental observations are also reproduced numerically by using a set of reaction-diffusion equations for an activator-inhibitor model, and further analytically interpreted in terms of genuine coupling effects arising from parametric fluctuations. Within the same framework we also address situations of noise-sustained propagation in subexcitable media.

  7. 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.

  8. Chemical inhibition of nitrification in activated sludge.

    PubMed

    Kelly, R T; Henriques, I D S; Love, N G

    2004-03-20

    Conventional aerobic nitrification was adversely affected by single pulse inputs of six different classes of industrially relevant chemical toxins: an electrophilic solvent (1-chloro-2,4-dinitrobenzene, CDNB), a heavy metal (cadmium), a hydrophobic chemical (1-octanol), an uncoupling agent (2,4-dinitrophenol, DNP), alkaline pH, and cyanide in its weak metal complexed form. The concentrations of each chemical source that caused 1 5, 25, and 50% respiratory inhibition of a nitrifying mixed liquor during a short-term assay were used to shock sequencing batch reactors containing nitrifying conventional activated sludge. The reactors were monitored for recovery over a period of 30 days or less. All shock conditions inhibited nitrification, but to different degrees. The nitrate generation rate (NGR) of the shocked reactors recovered overtime to control reactor levels and showed that it was a more sensitive indicator of nitrification inhibition than both initial respirometric tests conducted on unexposed biomass and effluent nitrogen species analyses. CDNB had the most severe impact on nitrification, followed by alkaline pH 11, cadmium, cyanide, octanol, and DNP. Based on effluent data, cadmium and octanol primarily inhibited ammonia-oxidizing bacteria (AOB) while CDNB, pH 11,and cyanide inhibited both AOB and nitrite-oxidizing bacteria (NOB). DNP initially inhibited nitrification but quickly increased the NGR relative to the control and stimulated nitrification after several days in a manner reflective of oxidative uncoupling. The shocked mixed liquor showed trends toward recovery from inhibition for all chemicals tested, but in some cases this reversion was slow. These results contribute to our broader effort to identify relationships between chemical sources and the process effects they induce in activated sludge treatment systems.

  9. Systematic trends in photonic reagent induced reactions in a homologous chemical family.

    PubMed

    Tibbetts, Katharine Moore; Xing, Xi; Rabitz, Herschel

    2013-08-29

    The growing use of ultrafast laser pulses to induce chemical reactions prompts consideration of these pulses as "photonic reagents" in analogy to chemical reagents. This work explores the prospect that photonic reagents may affect systematic trends in dissociative ionization reactions of a homologous family of halomethanes, much as systematic outcomes are often observed for reactions between homologous families of chemical reagents and chemical substrates. The experiments in this work with photonic reagents of varying pulse energy and linear spectral chirp reveal systematic correlations between observable ion yields and the following set of natural variables describing the substrate molecules: the ionization energy of the parent molecule, the appearance energy of each fragment ion, and the relative strength of carbon-halogen bonds in molecules containing two different halogens. The results suggest that reactions induced by photonic reagents exhibit systematic behavior analogous to that observed in reactions driven by chemical reagents, which provides a basis to consider empirical "rules" for predicting the outcomes of photonic reagent induced reactions.

  10. Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere

    NASA Astrophysics Data System (ADS)

    Hynes, James T.

    2015-04-01

    After my acceptance of the kind invitation from Todd Martínez and Mark Johnson, Co-Editors of this journal, to write this article, I had to decide just how to actually do this, given the existence of a fairly personal and extended autobiographical account of recent vintage detailing my youth, education, and assorted experiences and activities at the University of Colorado, Boulder, and later also at Ecole Normale Supérieure in Paris ( 1 ). In the end, I settled on a differently styled recounting of the adventures with my students, postdocs, collaborators, and colleagues in trying to unravel, comprehend, describe, and occasionally even predict the manifestations and consequences of the myriad assortment of molecular dances that contribute to and govern the rates and mechanisms of chemical reactions in solution (and elsewhere). The result follows.

  11. Detailed Chemical Kinetic Reaction Mechanisms for Incineration of Organophosphorus and Fluoro-Organophosphorus Compounds

    SciTech Connect

    Glaude, P A; Melius, C; Pitz, W J; Westbrook, C K

    2001-12-13

    A detailed chemical kinetic reaction mechanism is developed to describe incineration of the chemical warfare nerve agent sarin (GB), based on commonly used principles of bond additivity and hierarchical reaction mechanisms. The mechanism is based on previous kinetic models of organophosphorus compounds such as TMP, DMMP and DIMP that are often used as surrogates to predict incineration of GB. Kinetic models of the three surrogates and GB are then used to predict their consumption in a perfectly stirred reactor fueled by natural gas to simulate incineration of these chemicals. Computed results indicate that DIMP is the only one of these surrogates that adequately describes combustion of GB under comparable conditions. The kinetic pathways responsible for these differences in reactivity are identified and discussed. The most important reaction in GB and DIMP that makes them more reactive than TMP or DMMP is found to be a six-center molecular elimination reaction producing propene.

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

    PubMed

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

    2016-11-03

    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 for calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.

  13. Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law

    NASA Astrophysics Data System (ADS)

    Ge, Hao; Qian, Hong

    2017-01-01

    This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with N species, M reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical thermodynamics under G. N. Lewis' kinetic law of entire equilibrium (detailed balance in nonlinear chemical kinetics). In doing so, the equilibrium thermodynamics is then naturally generalized to nonequilibrium settings without detailed balance. The kinetic models are represented by a Markovian jumping process. A generalized macroscopic chemical free energy function and its associated balance equation with nonnegative source and sink are the major discoveries. The proof is based on the large deviation principle of this type of Markov processes. A general fluctuation dissipation theorem for stochastic reaction kinetics is also proved. The mathematical theory illustrates how a novel macroscopic dynamic law can emerges from the mesoscopic kinetics in a multi-scale system.

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

    DOE PAGES

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

    2016-11-03

    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

  15. Fluctuation Spectroscopy: Determination of Chemical Reaction Kinetics from the Frequency Spectrum of Fluctuations

    PubMed Central

    Feher, George; Weissman, Mike

    1973-01-01

    The kinetic parameters of a chemical reaction were obtained from analysis of the frequency spectrum of the fluctuations (i.e., “noise”) in the concentrations of the reactants. In “fluctuation spectroscopy,” no external perturbation is applied and the system remains in macroscopic chemical equilibrium during the experiment. Results obtained by this method for the dissociation reaction of beryllium sulfate agree well with those obtained by relaxation methods in which the approach to equilibrium is analyzed. Other noise sources not originating from a chemical reaction were observed and analyzed. The most prominent of these arose from the flow of an electrolyte through a capillary. The method of fluctuation spectroscopy should be applicable to problems of physical, chemical, and biological interest. PMID:16592071

  16. 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.

  17. Students' Dilemmas in Reaction Stoichiometry Problem Solving: Deducing the Limiting Reagent in Chemical Reactions

    ERIC Educational Resources Information Center

    Chandrasegaran, A. L.; Treagust, David F.; Waldrip, Bruce G.; Chandrasegaran, Antonia

    2009-01-01

    A qualitative case study was conducted to investigate the understanding of the limiting reagent concept and the strategies used by five Year 11 students when solving four reaction stoichiometry problems. Students' written problem-solving strategies were studied using the think-aloud protocol during problem-solving, and retrospective verbalisations…

  18. Proposed experimental probes of chemical reaction molecular dynamics in solution: ICN photodissociation

    NASA Astrophysics Data System (ADS)

    Benjamin, I.; Wilson, Kent R.

    1989-04-01

    Knowledge of how translational and rotational motions are influenced by the solvent during the course of a photodissociation ``half-collision'' reaction in solution is of interest in itself and can also help our understanding of how thermally activated reactions take place in solution by means of fluctuations in translational and rotational motion. With this goal, the molecular dynamics of the photodissociation of the triatomic molecule ICN are compared in the gas phase and in Xe solution. The time evolution of the trajectories (particularly with respect to interfragment distance and CN orientation) and of the energy partitioning (particularly into fragment translational recoil and into rotation of the CN) are displayed. Two types of solution experiments are proposed and simulated, both closely related to recent gas phase studies by Dantus, Rosker, and Zewail. These experiments are designed to probe the detailed dynamics of chemical reactions in solution during the time period the reaction is in progress, in particular to reveal the dramatic effects of the solvent on translational motions and energies. Both are pump-probe experiments in which the first photon dissociates the ICN and the second induces fluorescence in the CN fragment. In the first type of experiment, which is particularly sensitive to fragment translational motion, the fluorescence intensity is measured as a function of photon energy and of time delay. In the second type of experiment, which is particularly sensitive to fragment rotation, in addition the angle between the polarizations of the pump and probe photons is varied. In the calculations presented here, the effect of the absorption of the photodissociation photon is treated using the classical Frank-Condon principle. The coupling between the assumed two upper electronic surfaces is taken into account semiclassically using a generalization to the condensed phase of the classical electron model of Miller and Meyer, which was applied to ICN

  19. A New Method for Describing the Mechanism of a Chemical Reaction Based on the Unified Reaction Valley Approach.

    PubMed

    Zou, Wenli; Sexton, Thomas; Kraka, Elfi; Freindorf, Marek; Cremer, Dieter

    2016-02-09

    The unified reaction valley approach (URVA) used for a detailed mechanistic analysis of chemical reactions is improved in three different ways: (i) Direction and curvature of path are analyzed in terms of internal coordinate components that no longer depend on local vibrational modes. In this way, the path analysis is no longer sensitive to path instabilities associated with the occurrences of imaginary frequencies. (ii) The use of third order terms of the energy for a local description of the reaction valley allows an extension of the URVA analysis into the pre- and postchemical regions of the reaction path, which are typically characterized by flat energy regions. (iii) Configurational and conformational processes of the reaction complex are made transparent even in cases where these imply energy changes far less than a kcal/mol by exploiting the topology of the potential energy surface. As examples, the rhodium-catalyzed methanol carbonization, the Diels-Alder reaction between 1,3-butadiene and ethene, and the rearrangement of HCN to CNH are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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.

  1. 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.

  2. From graphite to porous carbon containing nanoparticles through chemical reactions

    SciTech Connect

    Hung, C.C.; Corbin, J.

    1996-12-31

    Porous carbon containing large quantities of separated individual nanoparticles (2--100 nm) was produced. The chemical process includes fluorination or oxygenation of graphite, and then exposing the product (graphite fluoride or graphite oxide) to metal chlorides. The nanoparticles were metal halides or metal oxides, which could contain dopants if they were added during the synthesis process. The chlorides used in this research include those of Pd, Zn, Al and Li. Depending on the synthesis process, the carbon pores could be either filled with the nanoparticles, resulting in near-zero surface area and high metal concentration, or partially filled with nanoparticles, resulting in large surface areas. In this report, near zero surface areas were observed for a product of LiCl in carbon, and a surface area of 75 m{sup 2}/g was observed for the product of {gamma}-Al{sub 2}O{sub 3} in carbon. Heating these products in 1 atm air allowed the nanoparticles to become fused together in the form of metal oxide while the carbon was oxidized, producing metal oxides which have the same shape as the carbon precursors (fibers, fabrics, or powder) and large surface areas. These products are potentially useful in the area of batteries, high temperature gas sensors, and catalysts.

  3. Supercritical fluid phase separations induced by chemical reactions

    SciTech Connect

    Ree, F.H.; Viecelli, J.A.; van Thiel, M.

    1997-11-01

    Our statistical mechanical studies predict that a chemically reactive system containing species composed of C, H, N, O atoms can exhibit a phase separation into a N{sub 2}-rich and a N{sub 2}-poor phase. The preset work is concerned with the effect of the fluid phase separation upon addition of F atoms in the system. Our study shows that F atoms mainly appear as a constituent of HF in a N{sub 2}-poor fluid phase up to a certain pressure beyond which they occur as CF{sub 4} in a N{sub 2}-rich phase and that the phase separation may be abrupt in thermodynamic sense. The pressure at the phase boundary can occur at about 30 GPa at 3000 K and about 10 GPa to 20 GPa at 1000 K.Some of these ranges maybe accessible by present-day experimental high-pressure techniques. We discuss implications of this study to detonation physics.

  4. New chemical reactions in methane at high temperatures and pressures

    SciTech Connect

    Culler, T.S.; Schiferl, D. )

    1993-01-21

    The authors have used a Merrill-Bassett diamond anvil cell and Raman spectroscopy to study methane at high pressures (up to 13 GPa) and high temperatures (up to 912 K). At 2.5-5.0 GPa and 912 K, methane photoreacts with the laser light used for Raman spectroscopy and forms a graphitelike soot compound. At room temperature and pressure the Raman spectrum of the new material has an intense peak with a frequency of 1597 cm[sup [minus]1]. At higher pressures and temperatures (10-13 GPa and 948 K) a sample of [sup 13]CD[sub 4] methane photoreacted with the laser light and formed a hard, clear, solid film. At 0.34 GPa and 300 K, this film had Raman peaks at 541 and 1605 cm[sup [minus]1]. The 541-cm[sup [minus]1] peak may correspond to the 550-cm[sup [minus]1] peak found in some diamondlike carbon (DLC) films formed by chemical vapor deposition (CVD), but the 1605-cm[sup [minus]1] peak does not appear to have any such counterpart. Other possible Raman peaks were masked by interference from the diamond anvils. Thus, while the hard, clear film has some similarities to CVD DLC films, some important differences and questions remain. 35 refs., 5 figs.

  5. Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms

    DOE R&D Accomplishments Database

    Continetti, R. E.; Balko, B. A.; Lee, Y. T.

    1989-02-01

    A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H{sub 2} -> DH + H and the substitution reaction D + C{sub 2}H{sub 2} -> C{sub 2}HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible.

  6. Chemical Model Systems for Cellular Nitros(yl)ation Reactions

    PubMed Central

    Daiber, Andreas; Schildknecht, Stefan; Müller, Johanna; Bachschmid, Markus M.; Ullrich, Volker

    2014-01-01

    S-nitros(yl)ation belongs to the redox-based posttranslational modifications of proteins but the underlying chemistry is controversial. In contrast to current concepts involving the autoxidation of nitric oxide (•NO, nitrogen monoxide), we and others have proposed the formation of peroxynitrite (oxoperoxonitrate(1-)) as an essential intermediate. This requires low cellular fluxes of •NO and superoxide (•O2−), for which model systems have been introduced. We here propose two new systems for nitros(yl)ation that avoid the shortcomings of previous models. Based on the thermal decomposition of 3-morpholinosydnonimine, equal fluxes of •NO and •O2− were generated and modulated by the addition of •NO donors or Cu,Zn-superoxide dismutase. As reactants for S-nitros(yl)ation, NADP+-dependent isocitrate dehydrogenase and glutathione were employed, for which optimal S-nitros(yl)ation was observed at nanomolar fluxes of •NO and •O2− at a ratio of about 3:1. The previously used reactants phenol and diaminonaphthalene, (C- and N-nitrosation) demonstrated potential participation of multiple pathways for nitros(yl)ation. According to our data, neither peroxynitrite nor autoxidation of •NO was as efficient as the 3•NO/1•O2− system in mediating S-nitros(yl)ation. In theory this could lead to an elusive nitrosonium (nitrosyl cation)-like species in the first step and to N2O3 in the subsequent reaction. Which of these two species or whether both together will participate in biological S-nitros(yl)ation remains to be elucidated. Finally, we developed several hypothetical scenarios to which the described U flux model could apply, providing conditions that allow either direct electrophilic substitution at a thiolate or S-nitros(yl)ation via transnitrosation from S-nitrosoglutathione. PMID:19477267

  7. 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.

  8. Quantum chemical study of the acrolein (CH2CHCHO) + OH + O2 reactions.

    PubMed

    Asatryan, Rubik; da Silva, Gabriel; Bozzelli, Joseph W

    2010-08-19

    Acrolein, a beta-unsaturated (acrylic) aldehyde, is one of the simplest multifunctional molecules, containing both alkene and aldehyde groups. Acrolein is an atmospheric pollutant formed in the photochemical oxidation of the anthropogenic VOC 1,3-butadiene, and serves as a model compound for methacrolein (MACR) and methyl vinyl ketone (MVK), the major oxidation products of the biogenic VOC isoprene. In addition, acrolein is involved in combustion and biological oxidation processes. This study presents a comprehensive theoretical analysis of the acrolein + OH + O(2) addition reactions, which is a key photochemical oxidation sequence, using the G3SX and CBS-QB3 theoretical methods. Both ab initio protocols provide relatively similar results, although the CBS-QB3 method systematically under-predicts literature heats of formation using atomization enthalpies, and also provides lower transition state barrier heights. Several new low-energy pathways for unimolecular reaction of the acrolein-OH-O(2) radicals are identified, with energy at around or below that of the acrolein-OH isomers + O(2). In each case these novel reactions have the potential to reform the hydroxyl radical (OH) and form coproducts that include glyoxal, glycolaldehyde (HOCH(2)CHO), formaldehyde (HCHO), CO, and substituted epoxides. Analogous reaction schemes are developed for the photochemical oxidation of MACR and MVK, producing a number of observed oxidation products. The reaction MACR + OH + O(2) --> hydroxyacetone + OH + CO is expected to be of particular importance. This study also proposes that O(2) addition to chemically activated acrolein-OH adducts can provide prompt regeneration of OH in the atmospheric oxidation of acrolein, via a double activation mechanism. This mechanism can also be extended to isoprene, MVK, and MACR. The importance of the novel chemistry revealed here in the atmospheric oxidation of acrolein and other structurally related OVOCs and VOCs requires further investigation

  9. 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.

  10. 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.

  11. State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

    NASA Astrophysics Data System (ADS)

    Yang, Xueming

    In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The studies of the O(1D) + H2 → OH + H reaction has also been reviewed here. A prototype example of state-to-state dynamics of pure insertion chemical reaction is provided. Effect of the reagent rotational excitation and the isotope effect on the dynamics of this reaction have also been investigated. The detailed mechanism for abstraction channel in this reaction has also been closely studied. The experimental investigations of the simplest chemical reaction, the H3 system, have also been described here. Through extensive collaborations between theory and experiment, the mechanism for forward scattering product at high collision energies for the H + HD reaction was clarified, which is attributed to a slow down mechanism on the top of a quantized barrier transition state. Oscillations in the product quantum state resolved different cross sections have also been observed in the H + D2 reaction, and were attributed to the interference of adiabatic transition state pathways from detailed theoretical analysis. The results reviewed here clearly show the significant advances we have made in the studies of the state-to-state molecular reaction dynamics.

  12. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    PubMed

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle.

  13. Entropy-enthalpy compensation in chemical reactions and adsorption: an exactly solvable model.

    PubMed

    Freed, Karl F

    2011-02-24

    The free energies of reaction or activation for many systems respond in a common fashion to a perturbing parameter, such as the concentration of an "inert" additive. Arrhenius plots as a function of the perturbing parameter display a "'compensation temperature" at which the free energy appears to be independent of the perturber, an entropy-enthalpy compensation process. Thus, as the perturber's concentration varies, Arrhenius plots of the rate constant or equilibrium constant exhibit a rotation about the fixed compensation temperature. While this (isokinetic/isoequilibrium) component of the phenomenon of entropy-enthalpy compensation appears in a huge number of situations of relevance to chemistry, biology, and materials science, statistical mechanical descriptions have been almost completely lacking. We provide the general statistical mechanical basis for solvent induced isokinetic/isoequilibrium entropy-enthalpy compensation in chemical reactions and adsorption, understanding that can be used to control of rate processes and binding constants in diverse applications. The general behavior is illustrated with an analytical solution for the dilute gas limit.

  14. ThermoData engine (TDE): software implementation of the dynamic data evaluation concept. 4. Chemical reactions.

    PubMed

    Diky, Vladimir; Chirico, Robert D; Kazakov, Andrei F; Muzny, Chris D; Frenkel, Michael

    2009-12-01

    ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. This paper describes the first application of this concept to the evaluation of thermodynamic properties for chemical reactions. Reaction properties evaluated are the enthalpies, entropies, Gibbs energies, and thermodynamic equilibrium constants. Details of key considerations in the critical evaluation of enthalpies of formation and of standard entropies for organic compounds are discussed in relation to their application in the calculation of reaction properties. Extensions to the class structure of the program are described that allow close linkage between the derived reaction properties and the underlying pure-component properties. Derivation of pure-component enthalpies of formation and of standard entropies through the use of directly measured reaction properties (enthalpies of reaction and equilibrium constants) is described. Directions for future enhancements are outlined.

  15. Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces.

    PubMed

    Maeda, Satoshi; Harabuchi, Yu; Takagi, Makito; Taketsugu, Tetsuya; Morokuma, Keiji

    2016-10-01

    In this account, a technical overview of the artificial force induced reaction (AFIR) method is presented. The AFIR method is one of the automated reaction-path search methods developed by the authors, and has been applied extensively to a variety of chemical reactions, such as organocatalysis, organometallic catalysis, and photoreactions. There are two modes in the AFIR method, i.e., a multicomponent mode and a single-component mode. The former has been applied to bimolecular and multicomponent reactions and the latter to unimolecular isomerization and dissociation reactions. Five numerical examples are presented for an Aldol reaction, a Claisen rearrangement, a Co-catalyzed hydroformylation, a fullerene structure search, and a nonradiative decay path search in an electronically excited naphthalene molecule. Finally, possible applications of the AFIR method are discussed.

  16. Coherent chemical kinetics as quantum walks. I. Reaction operators for radical pairs.

    PubMed

    Chia, A; Tan, K C; Pawela, Ł; Kurzyński, P; Paterek, T; Kaszlikowski, D

    2016-03-01

    Classical chemical kinetics uses rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, in other words, a reaction that contains only incoherent transitions. A prominent example of a reaction containing coherent transitions is the radical-pair model. The kinetics of such reactions is defined by the so-called reaction operator that determines the radical-pair state as a function of intermediate transition rates. We argue that the well-known concept of quantum walks from quantum information theory is a natural and apt framework for describing multisite chemical reactions. By composing Kraus maps that act only on two sites at a time, we show how the quantum-walk formalism can be applied to derive a reaction operator for the standard avian radical-pair reaction. Our reaction operator predicts the same recombination dephasing rate as the conventional Haberkorn model, which is consistent with recent experiments [K. Maeda et al., J. Chem. Phys. 139, 234309 (2013)], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010)]. The standard radical-pair reaction has conventionally been described by either a normalized density operator incorporating both the radical pair and reaction products or a trace-decreasing density operator that considers only the radical pair. We demonstrate a density operator that is both normalized and refers only to radical-pair states. Generalizations to include additional dephasing processes and an arbitrary number of sites are also discussed.

  17. Coherent chemical kinetics as quantum walks. I. Reaction operators for radical pairs

    NASA Astrophysics Data System (ADS)

    Chia, A.; Tan, K. C.; Pawela, Ł.; Kurzyński, P.; Paterek, T.; Kaszlikowski, D.

    2016-03-01

    Classical chemical kinetics uses rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, in other words, a reaction that contains only incoherent transitions. A prominent example of a reaction containing coherent transitions is the radical-pair model. The kinetics of such reactions is defined by the so-called reaction operator that determines the radical-pair state as a function of intermediate transition rates. We argue that the well-known concept of quantum walks from quantum information theory is a natural and apt framework for describing multisite chemical reactions. By composing Kraus maps that act only on two sites at a time, we show how the quantum-walk formalism can be applied to derive a reaction operator for the standard avian radical-pair reaction. Our reaction operator predicts the same recombination dephasing rate as the conventional Haberkorn model, which is consistent with recent experiments [K. Maeda et al., J. Chem. Phys. 139, 234309 (2013), 10.1063/1.4844355], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010), 10.1016/j.cplett.2010.01.063]. The standard radical-pair reaction has conventionally been described by either a normalized density operator incorporating both the radical pair and reaction products or a trace-decreasing density operator that considers only the radical pair. We demonstrate a density operator that is both normalized and refers only to radical-pair states. Generalizations to include additional dephasing processes and an arbitrary number of sites are also discussed.

  18. Competition between charge exchange and chemical reaction - The D2/+/ + H system

    NASA Technical Reports Server (NTRS)

    Preston, R. K.; Cross, R. J., Jr.

    1973-01-01

    Study of the special features of molecular charge exchange and its competition with chemical reaction in the case of the D2(+) + H system. The trajectory surface hopping (TSH) model proposed by Tully and Preston (1971) is used to study this competition for a number of reactions involving the above system. The diatomics-in-molecules zero-overlap approximation is used to calculate the three adiabatic surfaces - one triplet and two singlet - which are needed to describe this system. One of the significant results of this study is that the chemical reaction and charge exchange are strongly coupled. It is also found that the number of trajectories passing into the chemical regions of the three surfaces depends very strongly on the surface crossings.-

  19. Chemical Characterization and Reactivity Testing of Fuel-Oxidizer Reaction Product (Test Report)

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The product of incomplete reaction of monomethylhydrazine (MMH) and nitrogen tetroxide (NTO) propellants, or fuel-oxidizer reaction product (FORP), has been hypothesized as a contributory cause of an anomaly which occurred in the chamber pressure (PC) transducer tube on the Reaction Control Subsystem (RCS) aft thruster 467 on flight STS-51. A small hole was found in the titanium-alloy PC tube at the first bend below the pressure transducer. It was surmised that the hole may have been caused by heat and pressure resulting from ignition of FORP. The NASA Johnson Space Center (JSC) White Sands Test Facility (WSTF) was requested to define the chemical characteristics of FORP, characterize its reactivity, and simulate the events in a controlled environment which may have lead to the Pc-tube failure. Samples of FORP were obtained from the gas-phase reaction of MMH with NTO under laboratory conditions, the pulsed firings of RCS thrusters with modified PC tubes using varied oxidizer or fuel lead times, and the nominal RCS thruster firings at WSTF and Kaiser-Marquardt. Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), accelerating rate calorimetry (ARC), ion chromatography (IC), inductively coupled plasma (ICP) spectrometry, thermogravimetric analysis (TGA) coupled to FTIR (TGA/FTIR), and mechanical impact testing were used to qualitatively and quantitatively characterize the chemical, thermal, and ignition properties of FORP. These studies showed that the composition of FORP is variable but falls within a limited range of compositions that depends on the fuel loxidizer ratio at the time of formation, composition of the post-formation atmosphere (reducing or oxidizing), and reaction or postreaction temperature. A typical composition contains methylhydrazinium nitrate (MMHN), ammonium nitrate (AN), methylammonium nitrate (MAN), and trace amounts of hydrazinium nitrate and 1,1-dimethylhydrazinium nitrate. The thermal decomposition

  20. 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.

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

    SciTech Connect

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

    2015-07-15

    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.

  2. A review of dynamical resonances in A  +  BC chemical reactions

    NASA Astrophysics Data System (ADS)

    Ren, Zefeng; Sun, Zhigang; Zhang, Donghui; Yang, Xueming

    2017-02-01

    The concept of the transition state has played an important role in the field of chemical kinetics and reaction dynamics. Reactive resonances in the transition-state region can dramatically enhance the reaction probability; thus investigation of the reactive resonances has attracted great attention from chemical physicists for many decades. In this review, we mainly focus on the recent progress made in probing the elusive resonance phenomenon in the simple A  +  BC reaction and understanding its nature, especially in the benchmark F/Cl  +  H2 and their isotopic variants. The signatures of reactive resonances in the integral cross section, differential cross section (DCS), forward- and backward-scattered DCS, and anion photodetachment spectroscopy are comprehensively presented in individual prototype reactions. The dynamical origins of reactive resonances are also discussed in this review, based on information on the wave function in the transition-state region obtained by time-dependent quantum wave-packet calculations.

  3. A review of dynamical resonances in A  +  BC chemical reactions.

    PubMed

    Ren, Zefeng; Sun, Zhigang; Zhang, Donghui; Yang, Xueming

    2017-02-01

    The concept of the transition state has played an important role in the field of chemical kinetics and reaction dynamics. Reactive resonances in the transition-state region can dramatically enhance the reaction probability; thus investigation of the reactive resonances has attracted great attention from chemical physicists for many decades. In this review, we mainly focus on the recent progress made in probing the elusive resonance phenomenon in the simple A  +  BC reaction and understanding its nature, especially in the benchmark F/Cl  +  H2 and their isotopic variants. The signatures of reactive resonances in the integral cross section, differential cross section (DCS), forward- and backward-scattered DCS, and anion photodetachment spectroscopy are comprehensively presented in individual prototype reactions. The dynamical origins of reactive resonances are also discussed in this review, based on information on the wave function in the transition-state region obtained by time-dependent quantum wave-packet calculations.

  4. Molecular dynamics study of phase separation in fluids with chemical reactions.

    PubMed

    Krishnan, Raishma; Puri, Sanjay

    2015-11-01

    We present results from the first d=3 molecular dynamics (MD) study of phase-separating fluid mixtures (AB) with simple chemical reactions (A⇌B). We focus on the case where the rates of forward and backward reactions are equal. The chemical reactions compete with segregation, and the coarsening system settles into a steady-state mesoscale morphology. However, hydrodynamic effects destroy the lamellar morphology which characterizes the diffusive case. This has important consequences for the phase-separating structure, which we study in detail. In particular, the equilibrium length scale (ℓ(eq)) in the steady state suggests a power-law dependence on the reaction rate ε:ℓ(eq)∼ε(-θ) with θ≃1.0.

  5. Significance of vapor phase chemical reactions on CVD rates predicted by chemically frozen and local thermochemical equilibrium boundary layer theories

    NASA Technical Reports Server (NTRS)

    Gokoglu, Suleyman A.

    1988-01-01

    This paper investigates the role played by vapor-phase chemical reactions on CVD rates by comparing the results of two extreme theories developed to predict CVD mass transport rates in the absence of interfacial kinetic barrier: one based on chemically frozen boundary layer and the other based on local thermochemical equilibrium. Both theories consider laminar convective-diffusion boundary layers at high Reynolds numbers and include thermal (Soret) diffusion and variable property effects. As an example, Na2SO4 deposition was studied. It was found that gas phase reactions have no important role on Na2SO4 deposition rates and on the predictions of the theories. The implications of the predictions of the two theories to other CVD systems are discussed.

  6. Incorporation of large guest molecules into liposomes via chemical reactions in lipid membranes.

    PubMed

    Tsuchiya, Yuki; Sugikawa, Kouta; Ueda, Masafumi; Ikeda, Atsushi

    2017-02-22

    The incorporation of hydrophobic guest molecules into lipid membranes by the exchange of the guest molecule from a cyclodextrin (CDx) complex to a liposome is limited to guest molecules that can be included in CDxs. To solve this problem, large guest molecules were incorporated into liposomes by chemical reactions of guest molecules in lipid membranes. Stable lipid-membrane-incorporated fullerene derivatives with large substituent(s) were prepared by Diels-Alder reactions in lipid membranes.

  7. Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.

    PubMed

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-07-08

    Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.

  8. 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.

  9. Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

    DTIC Science & Technology

    1989-09-01

    following six elemen- taxy reactions: (2.1) CH3CHO --> CH3 + CHO Acceso , " (2.2) CHO --> CO + H NTIS Cq-.’ d- (2.3) CH3 + CH3CHO --> CH4 + CH3CO (2.4) CH3CO...1981 [2] Feinberg, M. Chemical Oscillations, Multiple Equilibria, and Reaction Network Structure. In Dynamics and Modelling of Reactive Systems, W. E

  10. Insights into the mechanism and catalysis of the native chemical ligation reaction.

    PubMed

    Johnson, Erik C B; Kent, Stephen B H

    2006-05-24

    Native chemical ligation of unprotected peptide segments involves reaction between a peptide-alpha-thioester and a cysteine-peptide, to yield a product with a native amide bond at the ligation site. Peptide-alpha-thioalkyl esters are commonly used because of their ease of preparation. These thioalkyl esters are rather unreactive so the ligation reaction is catalyzed by in situ transthioesterification with thiol additives. The most common thiol catalysts used to date have been either a mixture of thiophenol/benzyl mercaptan, or the alkanethiol MESNA. Despite the use of these thiol catalysts, ligation reactions typically take 24-48 h. To gain insight into the mechanism of native chemical ligaton and in order to find a better catalyst, we investigated the use of a number of thiol compounds. Substituted thiophenols with pK(a) > 6 were found to best combine the ability to exchange rapidly and completely with thioalkyl esters, and to then act as effective leaving groups in reaction of the peptide-thioester with the thiol side chain of a cysteine-peptide. A highly effective and practical catalyst was (4-carboxylmethyl)thiophenol ('MPAA'), a nonmalodorous, water-soluble thiol. Use of MPAA gave an order of magnitude faster reaction in model studies of native chemical ligation and in the synthesis of a small protein, turkey ovomucoid third domain (OMTKY3). MPAA should find broad use in native chemical ligation and in the total synthesis of proteins.

  11. Optimal path of the consecutive chemical reactions xA⇔yB⇔zC

    NASA Astrophysics Data System (ADS)

    Chen, Lingen; Song, Hanjiang; Sun, Fengrui

    2009-05-01

    The optimal path of the consecutive chemical reactions xA⇔yB⇔zC (x, y and z are the orders of chemical reactions) is analyzed numerically by taking temperature as a control variable, using the optimal-control theory based on Bak et al's work (2002 J. Phys. Chem. A 106 10961-4). Starting with pure A and maximizing the yield of B at the end of the given process duration, the optimal path starts with a branch at infinite temperature. A curve in which switching from this temperature to a lower temperature is possible is derived. For given parameters, there is a unique 'maximal useful time' that results in the highest possible yield of B. If a duration longer than this is specified, all reactions should be shut off during that excess amount of time in the optimal path. A numerical example for the optimal path is provided by the Taylor method. Finally, the results obtained are compared with the results of A⇔B⇔C (the orders of chemical reactions are all equal to 1) (Bak et al 2002 J. Phys. Chem. A 106 10961-4). When the orders of chemical reactions are taken into account, the optimal time sequences of the concentrations change markedly, the maximum obtainable yield is smaller, the initial values of co-state variables are bigger and the optimal phase trajectory changes.

  12. The lifetime of aerosols in ambient air: Consideration of the effects of surfactants and chemical reactions

    SciTech Connect

    Toossi, R.; Novakov, T.

    1985-01-01

    In this paper, the relatively long lifetime of droplets in atmospheric haze and fog in comparison with similar droplets of pure water is attributed to the presence of a monolayer of surfactant film and to the accumulation of soluble salts from chemical reactions. The lifetime of these droplets is a significant factor in the evaluation of the role of heterogeneous aqueous chemical reactions occurring in the troposphere. Several mechanisms of SO2 oxidation in the presence of liquid water are investigated. Finally, it is shown that soot-catalyzed oxidation of sulfur dioxide could be responsible for the high level of sulfate concentration observed in the coastal industrial areas.

  13. 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.

  14. Thermodynamical vibronic coupling constant and density: Chemical potential and vibronic coupling in reactions

    NASA Astrophysics Data System (ADS)

    Sato, Tohru; Haruta, Naoki; Tanaka, Kazuyoshi

    2016-05-01

    Vibronic coupling constant (VCC) and density (VCD) defined for a pure state, which have been successfully applied for reactions of fullerenes and nanographenes as reactivity indices, are extended for a mixed state. The extended VCC and VCD, thermodynamical vibronic coupling constant (ThVCC) and density (ThVCD), are formulated in the finite-temperature grand-canonical ensemble. ThVCD can be applied for charge transfer of a fractional number of electron. Based on the total differential of chemical potential, the relationship between chemical potential, absolute hardness, and vibronic coupling in a bimolecular reaction is discussed.

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

    SciTech Connect

    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 the contribution to the chemical reaction rate related to the affinity is much larger than that of the velocity divergence.

  16. Network structural analysis using directed graph for chemical reaction analysis in weakly-ionized plasmas

    NASA Astrophysics Data System (ADS)

    Nobuto, Kyosuke; Mizui, Yasutaka; Miyagi, Shigeyuki; Sakai, Osamu; Murakami, Tomoyuki

    2016-09-01

    We visualize complicated chemical reaction systems in weakly-ionized plasmas by analysing network structure for chemical processes, and calculate some indexes by assuming interspecies relationships to be a network to clarify them. With the current social evolution, the mean size of general data which we can use in computers grows huge, and significance of the data analysis increases. The methods of the network analysis which we focus on in this study do not depend on a specific analysis target, but the field where it has been already applied is still limited. In this study, we analyse chemical reaction systems in plasmas for configuring the network structure. We visualize them by expressing a reaction system in a specific plasma by a directed graph and examine the indexes and the relations with the characteristic of the species in the reaction system. For example, in the methane plasma network, the centrality index reveals importance of CH3 in an influential position of species in the reaction. In addition, silane and atmospheric pressure plasmas can be also visualized in reaction networks, suggesting other characteristics in the centrality indexes.

  17. Adsorption, partition, ion exchange and chemical reaction in batch reactors or in columns — A review

    NASA Astrophysics Data System (ADS)

    Schweich, D.; Sardin, M.

    The role of linear or non-linear adsorption, mass transfer kinetics, chemical reactions and ion exchange in column tracer experiments is qualitatively dealt with. The similarity of elution curves is emphasized even for very different phenomena. Some experimental procedures are proposed to point out the principal physico-chemical phenomenon which is responsible for the shape of the adsorption isotherm deduced from batch or column experiments.

  18. A Review of the Thermodynamic, Transport, and Chemical Reaction Rate Properties of High-temperature Air

    NASA Technical Reports Server (NTRS)

    Hansen, C Frederick; Heims, Steve P

    1958-01-01

    Thermodynamic and transport properties of high temperature air, and the reaction rates for the important chemical processes which occur in air, are reviewed. Semiempirical, analytic expressions are presented for thermodynamic and transport properties of air. Examples are given illustrating the use of these properties to evaluate (1) equilibrium conditions following shock waves, (2) stagnation region heat flux to a blunt high-speed body, and (3) some chemical relaxation lengths in stagnation region flow.

  19. On the possibility of negative activation energies in bimolecular reactions

    NASA Technical Reports Server (NTRS)

    Jaffe, R. L.

    1978-01-01

    The temperature dependence of the rate constants for model reacting systems was studied to understand some recent experimental measurements which imply the existence of negative activation energies. A collision theory model and classical trajectory calculations are used to demonstrate that the reaction probability can vary inversely with collision energy for bimolecular reactions occurring on attractive potential energy surfaces. However, this is not a sufficient condition to ensure that the rate constant has a negative temperature dependence. On the basis of these calculations, it seems unlikely that a true bimolecular reaction between neutral molecules will have a negative activation energy.

  20. Strong counteranion effects on the catalytic activity of cationic silicon Lewis acids in Mukaiyama aldol and Diels-Alder reactions.

    PubMed

    Hara, Kenji; Akiyama, Ryuto; Sawamura, Masaya

    2005-12-08

    [chemical reaction: see text]. A toluene-coordinated silyl borate, [Et3Si(toluene)]B(C6F5)4, demonstrated catalytic activities significantly higher than those of Me3SiOTf and Me3SiNTf2 in Mukaiyama aldol and Diels-Alder reactions.