Sample records for chemical reaction mechanical

  1. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms (United States)

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


    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.

  2. Physical Chemistry Chemical Kinetics and Reaction Mechanism

    CERN Document Server

    Trimm, Harold H


    Physical chemistry covers diverse topics, from biochemistry to materials properties to the development of quantum computers. Physical chemistry applies physics and math to problems that interest chemists, biologists, and engineers. Physical chemists use theoretical constructs and mathematical computations to understand chemical properties and describe the behavior of molecular and condensed matter. Their work involves manipulations of data as well as materials. Physical chemistry entails extensive work with sophisticated instrumentation and equipment as well as state-of-the-art computers. This

  3. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization. (United States)

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


    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.

  4. Chemical reactions modulated by mechanical stress: extended Bell theory. (United States)

    Konda, Sai Sriharsha M; Brantley, Johnathan N; Bielawski, Christopher W; Makarov, Dmitrii E


    A number of recent studies have shown that mechanical stress can significantly lower or raise the activation barrier of a chemical reaction. Within a common approximation due to Bell [Science 200, 618 (1978)], this barrier is linearly dependent on the applied force. A simple extension of Bell's theory that includes higher order corrections in the force predicts that the force-induced change in the activation energy will be given by -FΔR - ΔχF(2)∕2. Here, ΔR is the change of the distance between the atoms, at which the force F is applied, from the reactant to the transition state, and Δχ is the corresponding change in the mechanical compliance of the molecule. Application of this formula to the electrocyclic ring-opening of cis and trans 1,2-dimethylbenzocyclobutene shows that this extension of Bell's theory essentially recovers the force dependence of the barrier, while the original Bell formula exhibits significant errors. Because the extended Bell theory avoids explicit inclusion of the mechanical stress or strain in electronic structure calculations, it allows a computationally efficient characterization of the effect of mechanical forces on chemical processes. That is, the mechanical susceptibility of any reaction pathway is described in terms of two parameters, ΔR and Δχ, both readily computable at zero force.

  5. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    Energy Technology Data Exchange (ETDEWEB)

    Ziaul Huque


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gray, S.K. [Argonne National Laboratory, IL (United States)


    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.

  7. Program Helps To Determine Chemical-Reaction Mechanisms (United States)

    Bittker, D. A.; Radhakrishnan, K.


    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.

  8. Peptide Bond Synthesis by a Mechanism Involving an Enzymatic Reaction and a Subsequent Chemical Reaction. (United States)

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


    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.

  9. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: hidden intermediates and hidden transition States. (United States)

    Kraka, Elfi; Cremer, Dieter


    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

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

    Vorotilin, V. P.


    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. Chemical kinetics of gas reactions

    CERN Document Server

    Kondrat'Ev, V N


    Chemical Kinetics of Gas Reactions explores the advances in gas kinetics and thermal, photochemical, electrical discharge, and radiation chemical reactions. This book is composed of 10 chapters, and begins with the presentation of general kinetic rules for simple and complex chemical reactions. The next chapters deal with the experimental methods for evaluating chemical reaction mechanisms and some theories of elementary chemical processes. These topics are followed by discussions on certain class of chemical reactions, including unimolecular, bimolecular, and termolecular reactions. The rema

  12. Assessment of existing H2/O2 chemical reaction mechanisms at reheat gas turbine conditions

    CERN Document Server

    Weydahl, Torleif; Seljeskog, Morten; Haugen, Nils Erland L


    This paper provides detailed comparisons of chemical reaction mechanisms of H2 applicable at high preheat temperatures and pressures relevant to gas turbine and particularly Alstom's reheat gas turbine conditions. It is shown that the available reaction mechanisms exhibit large differences in several important elementary reaction coefficients. The reaction mechanisms are assessed by comparing ignition delay and laminar flame speed results obtained from CHEMKIN with available data, however, the amount of data at these conditions is scarce and a recommended candidate among the mechanisms can presently not be selected. Generally, the results with the GRI-Mech and Leeds mechanisms deviate from the Davis, Li, O'Conaire, Konnov and San Diego mechanisms, but there are also significant deviations between the latter five mechanisms that altogether are better adapted to hydrogen. The differences in ignition delay times between the dedicated hydrogen mechanisms (O'Conaire, Li and Konnov) range from approximately a maxim...

  13. Chemical reaction of hexagonal boron nitride and graphite nanoclusters in mechanical milling systems

    Energy Technology Data Exchange (ETDEWEB)

    Muramatsu, Y.; Grush, M.; Callcott, T.A. [Univ. of Tennessee, Knoxville, TN (United States)] [and others


    Synthesis of boron-carbon-nitride (BCN) hybrid alloys has been attempted extensively by many researchers because the BCN alloys are considered an extremely hard material called {open_quotes}super diamond,{close_quotes} and the industrial application for wear-resistant materials is promising. A mechanical alloying (MA) method of hexagonal boron nitride (h-BN) with graphite has recently been studied to explore the industrial synthesis of the BCN alloys. To develop the MA method for the BCN alloy synthesis, it is necessary to confirm the chemical reaction processes in the mechanical milling systems and to identify the reaction products. Therefore, the authors have attempted to confirm the chemical reaction process of the h-BN and graphite in mechanical milling systems using x-ray absorption near edge structure (XANES) methods.

  14. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions. (United States)

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


    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.

  15. Insights into the mechanism and catalysis of the native chemical ligation reaction. (United States)

    Johnson, Erik C B; Kent, Stephen B H


    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.

  16. Reduced chemical reaction mechanisms: experimental and HCCI modelling investigations of autoignition processes of iso-octane in internal combustion engines


    Machrafi, Hatim; Lombaert, K.; Cavadias, S; Guibert, P.; Amouroux, J


    A semi-reduced (70 species, 210 reactions) and a skeletal (27 species, 29 reactions) chemical reaction mechanism for iso-octane are constructed from a semi-detailed iso-octane mechanism (84 species, 412 reactions) of the Chalmers University of Technology in Sweden. The construction of the reduced mechanisms is performed by using reduction methods such as the quasi-steady-state assumption and the partial equilibrium assumption. The obtained reduced iso-octane mechanisms show, at the mentioned ...

  17. Chemical reaction mechanisms in solution from brute force computational Arrhenius plots. (United States)

    Kazemi, Masoud; Åqvist, Johan


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

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

    Cerar, Janez


    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.

  19. A coupled mechanical and chemical damage model for concrete affected by alkali–silica reaction

    Energy Technology Data Exchange (ETDEWEB)

    Pignatelli, Rossella, E-mail: [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Lombardi Ingegneria S.r.l., Via Giotto 36, 20145 Milano (Italy); Comi, Claudia, E-mail: [Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano (Italy); Monteiro, Paulo J.M., E-mail: [Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720 (United States)


    To model the complex degradation phenomena occurring in concrete affected by alkali–silica reaction (ASR), we formulate a poro-mechanical model with two isotropic internal variables: the chemical and the mechanical damage. The chemical damage, related to the evolution of the reaction, is caused by the pressure generated by the expanding ASR gel on the solid concrete skeleton. The mechanical damage describes the strength and stiffness degradation induced by the external loads. As suggested by experimental results, degradation due to ASR is considered to be localized around reactive sites. The effect of the degree of saturation and of the temperature on the reaction development is also modeled. The chemical damage evolution is calibrated using the value of the gel pressure estimated by applying the electrical diffuse double-layer theory to experimental values of the surface charge density in ASR gel specimens reported in the literature. The chemo-damage model is first validated by simulating expansion tests on reactive specimens and beams; the coupled chemo-mechanical damage model is then employed to simulate compression and flexure tests results also taken from the literature. -- Highlights: •Concrete degradation due to ASR in variable environmental conditions is modeled. •Two isotropic internal variables – chemical and mechanical damage – are introduced. •The value of the swelling pressure is estimated by the diffuse double layer theory. •A simplified scheme is proposed to relate macro- and microscopic properties. •The chemo-mechanical damage model is validated by simulating tests in literature.

  20. Microfluidic chemical reaction circuits (United States)

    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


    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.

  1. Reaction mechanisms of aqueous monoethanolamine with carbon dioxide: a combined quantum chemical and molecular dynamics study. (United States)

    Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya


    Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.

  2. Chemical nature and reaction mechanisms of the molybdenum cofactor of xanthine oxidoreductase. (United States)

    Okamoto, Ken; Kusano, Teruo; Nishino, Takeshi


    Xanthine oxidoreductase (XOR), a complex flavoprotein, catalyzes the metabolic reactions leading from hypoxanthine to xanthine and from xanthine to urate, and both reactions take place at the molybdenum cofactor. The enzyme is a target of drugs for therapy of gout or hyperuricemia. We review the chemical nature and reaction mechanisms of the molybdenum cofactor of XOR, focusing on molybdenum-dependent reactions of actual or potential medical importance, including nitric oxide (NO) synthesis. It is now generally accepted that XOR transfers the water-exchangeable -OH ligand of the molybdenum atom to the substrate. The hydroxyl group at OH-Mo(IV) can be replaced by urate, oxipurinol and FYX-051 derivatives and the structures of these complexes have been determined by xray crystallography under anaerobic conditions. Although formation of NO from nitrite or formation of xanthine from urate by XOR ischemically feasible, it is not yet clear whether these reactions have any physiological significance since the reactions are catalyzed at a slow rate even under anaerobic conditions.

  3. Phenomenological description of selected elementary chemical reaction mechanisms: An information-theoretic study

    Energy Technology Data Exchange (ETDEWEB)

    Esquivel, R.O., E-mail: esquivel@xanum.uam.m [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340 Mexico D.F. (Mexico); Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain); Flores-Gallegos, N.; Iuga, C.; Carrera, E.M. [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340 Mexico D.F. (Mexico); Angulo, J.C. [Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain); Antolin, J. [Departamento de Fisica Aplicada, EUITIZ, Universidad de Zaragoza, 50018-Zaragoza (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain)


    The information-theoretic description of the course of two elementary chemical reactions allows a phenomenological description of the chemical course of the hydrogenic abstraction and the S{sub N}2 identity reactions by use of Shannon entropic measures in position and momentum spaces. The analyses reveal their synchronous/asynchronous mechanistic behavior.

  4. Product lambda-doublet ratios as an imprint of chemical reaction mechanism (United States)

    Jambrina, P. G.; Zanchet, A.; Aldegunde, J.; Brouard, M.; Aoiz, F. J.


    In the last decade, the development of theoretical methods has allowed chemists to reproduce and explain almost all of the experimental data associated with elementary atom plus diatom collisions. However, there are still a few examples where theory cannot account yet for experimental results. This is the case for the preferential population of one of the Λ-doublet states produced by chemical reactions. In particular, recent measurements of the OD(2Π) product of the O(3P)+D2 reaction have shown a clear preference for the Π(A') Λ-doublet states, in apparent contradiction with ab initio calculations, which predict a larger reactivity on the A'' potential energy surface. Here we present a method to calculate the Λ-doublet ratio when concurrent potential energy surfaces participate in the reaction. It accounts for the experimental Λ-doublet populations via explicit consideration of the stereodynamics of the process. Furthermore, our results demonstrate that the propensity of the Π(A') state is a consequence of the different mechanisms of the reaction on the two concurrent potential energy surfaces

  5. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology. (United States)

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi


    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

  6. Chemical burn or reaction (United States)

    ... this page: // Chemical burn or reaction To use the sharing features on this page, please enable JavaScript. Chemicals that touch skin can lead to a reaction on the skin, throughout the body, or both. ...

  7. A Detailed Chemical Kinetic Reaction Mechanism for Oxidation of Four Small Alkyl Esters in Laminar Premixed Flames

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C K; Pitz, W J; Westmoreland, P R; Dryer, F L; Chaos, M; Osswald, P; Kohse-Hoinghaus, K; Cool, T A; Wang, J; Yang, B; Hansen, N; Kasper, T


    A detailed chemical kinetic reaction mechanism has been developed for a group of four small alkyl ester fuels, consisting of methyl formate, methyl acetate, ethyl formate and ethyl acetate. This mechanism is validated by comparisons between computed results and recently measured intermediate species mole fractions in fuel-rich, low pressure, premixed laminar flames. The model development employs a principle of similarity of functional groups in constraining the H atom abstraction and unimolecular decomposition reactions in each of these fuels. As a result, the reaction mechanism and formalism for mechanism development are suitable for extension to larger oxygenated hydrocarbon fuels, together with an improved kinetic understanding of the structure and chemical kinetics of alkyl ester fuels that can be extended to biodiesel fuels. Variations in concentrations of intermediate species levels in these flames are traced to differences in the molecular structure of the fuel molecules.

  8. Magnetic isotope effect and theory of atomic orbital hybridization to predict a mechanism of chemical exchange reactions. (United States)

    Epov, Vladimir N


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

  9. Chemical transport reactions

    CERN Document Server

    Schäfer, Harald


    Chemical Transport Reactions focuses on the processes and reactions involved in the transport of solid or liquid substances to form vapor phase reaction products. The publication first offers information on experimental and theoretical principles and the transport of solid substances and its special applications. Discussions focus on calculation of the transport effect of heterogeneous equilibria for a gas motion between equilibrium spaces; transport effect and the thermodynamic quantities of the transport reaction; separation and purification of substances by means of material transport; and

  10. Impact of supersonic and subsonic aircraft on ozone: Including heterogeneous chemical reaction mechanisms (United States)

    Kinnison, Douglas E.; Wuebbles, Donald J.


    Preliminary calculations suggest that heterogeneous reactions are important in calculating the impact on ozone from emissions of trace gases from aircraft fleets. In this study, three heterogeneous chemical processes that occur on background sulfuric acid aerosols are included and their effects on O3, NO(x), Cl(x), HCl, N2O5, ClONO2 are calculated.

  11. A New Method for Describing the Mechanism of a Chemical Reaction Based on the Unified Reaction Valley Approach. (United States)

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


    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.

  12. Evaluation of Aromatic Oxidation Reactions in Seven Chemical Mechanisms with an Outdoor Chamber (United States)

    Simulations using seven chemical mechanisms are intercompared against O3, NOx and hydrocarbon data from photooxidation experiments conducted at the University of North Carolina outdoor smog chamber. The mechanisms include CB4–2002, CB05, CB05-TU, a CB05 vari...

  13. Detailed Chemical Kinetic Reaction Mechanisms for Primary Reference Fuels for Diesel Cetane Number and Spark-Ignition Octane Number

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C K; Pitz, W J; Mehl, M; Curran, H J


    For the first time, a detailed chemical kinetic reaction mechanism is developed for primary reference fuel mixtures of n-hexadecane and 2,2,4,4,6,8,8-heptamethyl nonane for diesel cetane ratings. The mechanisms are constructed using existing rules for reaction pathways and rate expressions developed previously for the primary reference fuels for gasoline octane ratings, n-heptane and iso-octane. These reaction mechanisms are validated by comparisons between computed and experimental results for shock tube ignition and for oxidation under jet-stirred reactor conditions. The combined kinetic reaction mechanism contains the submechanisms for the primary reference fuels for diesel cetane ratings and submechanisms for the primary reference fuels for gasoline octane ratings, all in one integrated large kinetic reaction mechanism. Representative applications of this mechanism to two test problems are presented, one describing fuel/air autoignition variations with changes in fuel cetane numbers, and the other describing fuel combustion in a jet-stirred reactor environment with the fuel varying from pure 2,2,4,4,6,8,8-heptamethyl nonane (Cetane number of 15) to pure n-hexadecane (Cetane number of 100). The final reaction mechanism for the primary reference fuels for diesel fuel and gasoline is available on the web.

  14. An automatic modeling system of the reaction mechanisms for chemical vapor deposition processes using real-coded genetic algorithms. (United States)

    Takahashi, Takahiro; Nakai, Hiroyuki; Kinpara, Hiroki; Ema, Yoshinori


    The identification of appropriate reaction models is very helpful for developing chemical vapor deposition (CVD) processes. In this study, we have developed an automatic system to model reaction mechanisms in the CVD processes by analyzing the experimental results, which are cross-sectional shapes of the deposited films on substrates with micrometer- or nanometer-sized trenches. We designed the inference engine to model the reaction mechanism in the system by the use of real-coded genetic algorithms (RCGAs). We studied the dependence of the system performance on two methods using simple genetic algorithms (SGAs) and the RCGAs; the one involves the conventional GA operators and the other involves the blend crossover operator (BLX-alpha). Although we demonstrated that the systems using both the methods could successfully model the reaction mechanisms, the RCGAs showed the better performance with respect to the accuracy and the calculation cost for identifying the models.

  15. FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms

    Institute of Scientific and Technical Information of China (English)

    NAIDOO Kevin J.


    The development and implementation of a computational method able to produce free energies in multiple dimensions,descriptively named the free energies from adaptive reaction coordinate forces (FEARCF) method is described in this paper.While the method can be used to calculate free energies of association,conformation and reactivity here it is shown in the context of chemical reaction landscapes.A reaction free energy surface for the Claisen rearrangement of chorismate to prephenate is used as an illustration of the method's efficient convergence.FEARCF simulations are shown to achieve fiat histograms for complex multidimensional free energy volumes.The sampling efficiency by which it produces multidimensional free energies is demonstrated on the complex puckering of a pyranose ring,that is described by a three dimensional W(θ1,θ2,θ3) potential of mean force.

  16. Translated chemical reaction networks. (United States)

    Johnston, Matthew D


    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.

  17. Inorganic Reaction Mechanisms. Part I (United States)

    Cooke, D. O.


    Provides a collection of data on the mechanistic aspects of inorganic chemical reactions. Wherever possible includes procedures for classroom demonstration or student project work. The material covered includes gas phase reactions, reactions in solution, mechanisms of electron transfer, the reaction between iron III and iodine, and hydrolysis. (GS)

  18. The influence of the "cage effect" on the mechanism of reversible bimolecular multistage chemical reactions in solutions. (United States)

    Doktorov, Alexander B


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

  19. Quantum Chemical Study on a New Mechanism of One-carbon Unit Transfer Reaction:The Water-assisted Mechanism

    Institute of Scientific and Technical Information of China (English)

    QIAO,Qing-An(乔青安); CAI,Zheng-Ting(蔡政亭); FENG,Da-Cheng(冯大诚)


    It is a theoretical study on the water-assisted mechanism of one-carbon unit transfer reaction, in which the energy barrier for each transition state lowered by about 80-100 kJ/mol when compared with the one in no-water-involved mechanism. The water-assisted path 4 is the favorite reaction way. Our results well explained the presumption from experiments.

  20. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. (United States)

    Sunoj, Raghavan B; Anand, Megha


    Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.

  1. Quantum Chemical Study on the Reaction Mechanism of OBrO Radical with OH Radical

    Institute of Scientific and Technical Information of China (English)

    ZhAO,Min(赵岷); ZHAO,Yan-Ling(赵艳玲); LIU,Peng-Jun(刘朋军); CHANG,Ying-Fei(常鹰飞); PAN,Xiu-Mei(潘秀梅); SU,Zhong-Min(苏忠民); WANG,Rong-Shun(王荣顺)


    The reaction mechanism of OBrO with OH has been studied using the B3LYP/6-31 l+G(d,p) and the high-level electron-correlation CCSD(T)/6-311 +G(d,p) at single-point. The results show that the title reaction could probably proceed by four possible schemes, generating HOBr+O2, HBr+O3, BrO+HO2 and HOBrO2 products, respectively. The main channel is the one to yield HOBr+ O2. The whole reaction involves the formation of three-membered, four-membered and five-membered rings, followed by the complicated processes of association,H-shift, Br-shift and dissociation. All routes are exothermic.

  2. Kinematically complete chemical reaction dynamics (United States)

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


    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.

  3. Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. (United States)

    Maeda, Satoshi; Ohno, Koichi; Morokuma, Keiji


    Global reaction route mapping (GRRM), a fully-automated search for all important reaction pathways relevant to a given purpose, on the basis of quantum chemical calculations enables systematic elucidation of complex chemical reaction mechanisms. However, GRRM had previously been limited to very simple systems. This is mainly because such calculations are highly demanding even in small systems when a brute-force sampling is considered. Hence, we have developed two independent but complementary methods: anharmonic downward distortion following (ADDF) and artificial force induced reaction (AFIR) methods. ADDF can follow reaction pathways starting from local minima on the potential energy surface (PES) toward transition structures (TSs) and dissociation channels. AFIR can find pathways starting from two or more reactants toward TSs for their associative reactions. In other words, ADDF searches for A → X type isomerization and A → X + Y type dissociation pathways, whereas AFIR finds A + B → X (+ Y) type associative pathways. Both follow special paths called the ADDF path and the AFIR path, and these tend to pass through near TSs of corresponding reaction pathways, giving approximate TSs. Such approximate TSs can easily be re-optimized to corresponding true TSs by standard geometry optimizations. On the basis of these two methods, we have proposed practical strategies of GRRM. The GRRM strategies have been applied to a variety of chemical systems ranging from thermal- and photochemical-reactions in small systems to organometallic- and enzyme-catalysis, on the basis of quantum chemical calculations. In this perspective, we present an overview of the GRRM strategies and some results of applications. Their practical usage for systematic prediction is also discussed.

  4. Chlorination of N-methylacetamide and amide-containing pharmaceuticals. Quantum-chemical study of the reaction mechanism. (United States)

    Šakić, Davor; Šonjić, Pavica; Tandarić, Tana; Vrček, Valerije


    Chlorination of amides is of utmost importance in biochemistry and environmental chemistry. Despite the huge body of data, the mechanism of reaction between amides and hypochlorous acid in aqueous environment remains unclear. In this work, the three different reaction pathways for chlorination of N-methylacetamide by HOCl have been considered: the one-step N-chlorination of the amide, the chlorination via O-chlorinated intermediate, and the N-chlorination of the iminol intermediate. The high-level quantum chemical G3B3 composite procedure, double-hybrid B2-PLYPD, B2K-PLYP methods, and global hybrid M06-2X and BMK methods have been employed. The calculated energy barriers have been compared to the experimental value of ΔG(#)298 ≈ 87 kJ/mol, which corresponds to reaction rate constant k(r) ≈ 0.0036 M(-1) s(-1). Only the mechanism in which the iminol form of N-methylacetamide reacts with HOCl is consistent (ΔG(#)298 = 87.3 kJ/mol at G3B3 level) with experimental results. The analogous reaction mechanism has been calculated as the most favorable pathway in the chlorination of small-sized amides and amide-containing pharmaceuticals: carbamazepine, acetaminophen, and phenytoin. We conclude that the formation of the iminol intermediate followed by its reaction with HOCl is the general mechanism of N-chlorination for a vast array of amides.

  5. Kinetic mechanism of molecular energy transfer and chemical reactions in low-temperature air-fuel plasmas. (United States)

    Adamovich, Igor V; Li, Ting; Lempert, Walter R


    This work describes the kinetic mechanism of coupled molecular energy transfer and chemical reactions in low-temperature air, H2-air and hydrocarbon-air plasmas sustained by nanosecond pulse discharges (single-pulse or repetitive pulse burst). The model incorporates electron impact processes, state-specific N(2) vibrational energy transfer, reactions of excited electronic species of N(2), O(2), N and O, and 'conventional' chemical reactions (Konnov mechanism). Effects of diffusion and conduction heat transfer, energy coupled to the cathode layer and gasdynamic compression/expansion are incorporated as quasi-zero-dimensional corrections. The model is exercised using a combination of freeware (Bolsig+) and commercial software (ChemKin-Pro). The model predictions are validated using time-resolved measurements of temperature and N(2) vibrational level populations in nanosecond pulse discharges in air in plane-to-plane and sphere-to-sphere geometry; temperature and OH number density after nanosecond pulse burst discharges in lean H(2)-air, CH(4)-air and C(2)H(4)-air mixtures; and temperature after the nanosecond pulse discharge burst during plasma-assisted ignition of lean H2-mixtures, showing good agreement with the data. The model predictions for OH number density in lean C(3)H(8)-air mixtures differ from the experimental results, over-predicting its absolute value and failing to predict transient OH rise and decay after the discharge burst. The agreement with the data for C(3)H(8)-air is improved considerably if a different conventional hydrocarbon chemistry reaction set (LLNL methane-n-butane flame mechanism) is used. The results of mechanism validation demonstrate its applicability for analysis of plasma chemical oxidation and ignition of low-temperature H(2)-air, CH(4)-air and C(2)H(4)-air mixtures using nanosecond pulse discharges. Kinetic modelling of low-temperature plasma excited propane-air mixtures demonstrates the need for development of a more accurate

  6. Chemical Reactions at Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Michael Henderson and Nancy Ryan Gray


    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.

  7. Mechanisms of chemical vapor generation by aqueous tetrahydridoborate. Recent developments toward the definition of a more general reaction model (United States)

    D'Ulivo, Alessandro


    A reaction model describing the reactivity of metal and semimetal species with aqueous tetrahydridoborate (THB) has been drawn taking into account the mechanism of chemical vapor generation (CVG) of hydrides, recent evidences on the mechanism of interference and formation of byproducts in arsane generation, and other evidences in the field of the synthesis of nanoparticles and catalytic hydrolysis of THB by metal nanoparticles. The new "non-analytical" reaction model is of more general validity than the previously described "analytical" reaction model for CVG. The non-analytical model is valid for reaction of a single analyte with THB and for conditions approaching those typically encountered in the synthesis of nanoparticles and macroprecipitates. It reduces to the previously proposed analytical model under conditions typically employed in CVG for trace analysis (analyte below the μM level, borane/analyte ≫ 103 mol/mol, no interference). The non-analytical reaction model is not able to explain all the interference effects observed in CVG, which can be achieved only by assuming the interaction among the species of reaction pathways of different analytical substrates. The reunification of CVG, the synthesis of nanoparticles by aqueous THB and the catalytic hydrolysis of THB inside a common frame contribute to rationalization of the complex reactivity of aqueous THB with metal and semimetal species.

  8. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    CERN Document Server

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V


    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

  9. The mechanism of bursting phenomena in Belousov-Zhabotinsky(BZ) chemical reaction with multiple time scales

    Institute of Scientific and Technical Information of China (English)


    The dynamics of a typical Belousov-Zhabotinsky(BZ)reaction with multiple time scales is investigated in this paper.Different forms of periodic bursting phenomena,and specially,three types of chaotic bursters with different structures can be obtained,which are in common with the behaviors observed in experiments.The bifurcations connecting the quiescent state and the repetitive spikes are presented to account for the occurrence of the NKoscillations as well as the different forms of chaotic bursters.The mechanism of the period-adding bifurcation sequences is explored to reveal why the length of the periods in the sequences does not change continuously with the continuous variation of the parameters.

  10. Surface damage of metallic implants due to mechanical loading and chemical reactions (United States)

    Ryu, Jaejoong

    indicate that surface roughness undergoes continuous evolution during alternating contact loading and exposure to etchant. Surface roughness evolution is governed by the residual stress induced due to contact loading. Two different stress-assisted dissolution driven instabilities in roughness evolution have been identified. In order to investigate stressed surface damage by electrochemical reaction during active contact loading, in the first stage, surface failure due to sliding contact was investigated as a function of different residual stress states from compressive to tensile. Residual stress is usually developed during manufacturing process or former mechanical interactions playing an important role on service life of the surface. The wear mechanism of fatigue contact in the presence of residual stresses was explored by analytical model of fatigue crack growth by utilizing modified delamination wear theory with surface layer spalling model. Fatigue stress intensity factors (DeltaKI) loaded by contact stress and combined residual stress implied that buckling of subsurface crack with compressive residual stress opens crack-tip and consequently increase wear rate during sliding contact. As for the experimental verification of the modified delamination model, cyclic sliding contact experiment on metallic implant materials in ambient was conducted by utilizing atomic force microscope (AFM) and four-point-bending set up by which well characterized pre-stress was established on rectangular specimen. In addition, complex mechanism of corrosion on the damaged surface illustrated strong stress-dependent effects on wear rate in repassivating environment and dissolution rates in reactive environment.

  11. Generalization of classical mechanics for nuclear motions on nonadiabatically coupled potential energy surfaces in chemical reactions. (United States)

    Takatsuka, Kazuo


    Classical trajectory study of nuclear motion on the Born-Oppenheimer potential energy surfaces is now one of the standard methods of chemical dynamics. In particular, this approach is inevitable in the studies of large molecular systems. However, as soon as more than a single potential energy surface is involved due to nonadiabatic coupling, such a naive application of classical mechanics loses its theoretical foundation. This is a classic and fundamental issue in the foundation of chemistry. To cope with this problem, we propose a generalization of classical mechanics that provides a path even in cases where multiple potential energy surfaces are involved in a single event and the Born-Oppenheimer approximation breaks down. This generalization is made by diagonalization of the matrix representation of nuclear forces in nonadiabatic dynamics, which is derived from a mixed quantum-classical representation of the electron-nucleus entangled Hamiltonian [Takatsuka, K. J. Chem. Phys. 2006, 124, 064111]. A manifestation of quantum fluctuation on a classical subsystem that directly contacts with a quantum subsystem is discussed. We also show that the Hamiltonian thus represented gives a theoretical foundation to examine the validity of the so-called semiclassical Ehrenfest theory (or mean-field theory) for electron quantum wavepacket dynamics, and indeed, it is pointed out that the electronic Hamiltonian to be used in this theory should be slightly modified.

  12. Chemical reaction and separation method

    NARCIS (Netherlands)

    Jansen, J.C.; Kapteijn, F.; Strous, S.A.


    The invention is directed to process for performing a chemical reaction in a reaction mixture, which reaction produces water as by-product, wherein the reaction mixture is in contact with a hydroxy sodalite membrane, through which water produced during the reaction is removed from the reaction mixtu

  13. Mass Transfer with Chemical Reaction. (United States)

    DeCoursey, W. J.


    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)

  14. Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions (United States)

    Schultz, Emeric


    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…

  15. Singular characteristics and unique chemical bond activation mechanisms of photocatalytic reactions on plasmonic nanostructures (United States)

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


    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 ∝intensityn, 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.

  16. Reduction of Large Detailed Chemical Kinetic Mechanisms for Autoignition Using Joint Analyses of Reaction Rates and Sensitivities

    Energy Technology Data Exchange (ETDEWEB)

    Saylam, A; Ribaucour, M; Pitz, W J; Minetti, R


    A new technique of reduction of detailed mechanisms for autoignition, which is based on two analysis methods is described. An analysis of reaction rates is coupled to an analysis of reaction sensitivity for the detection of redundant reactions. Thresholds associated with the two analyses have a great influence on the size and efficiency of the reduced mechanism. Rules of selection of the thresholds are defined. The reduction technique has been successfully applied to detailed autoignition mechanisms of two reference hydrocarbons: n-heptane and iso-octane. The efficiency of the technique and the ability of the reduced mechanisms to reproduce well the results generated by the full mechanism are discussed. A speedup of calculations by a factor of 5.9 for n-heptane mechanism and by a factor of 16.7 for iso-octane mechanism is obtained without losing accuracy of the prediction of autoignition delay times and concentrations of intermediate species.

  17. The influence of the "cage" effect on the mechanism of reversible bimolecular multistage chemical reactions proceeding from different sites in solutions. (United States)

    Doktorov, Alexander B


    Manifestations of the "cage" effect at the encounters of reactants have been theoretically treated on the example of multistage reactions (including bimolecular exchange reactions as elementary stages) proceeding from different active sites in liquid solutions. It is shown that for reactions occurring near the contact of reactants, consistent consideration of quasi-stationary kinetics of such multistage reactions (possible in the framework of the encounter theory only) can be made on the basis of chemical concepts of the "cage complex," just as in the case of one-site model described in the literature. Exactly as in the one-site model, the presence of the "cage" effect gives rise to new channels of reactant transformation that cannot result from elementary event of chemical conversion for the given reaction mechanism. Besides, the multisite model demonstrates new (as compared to one-site model) features of multistage reaction course.

  18. Chemical reactions at aqueous interfaces (United States)

    Vecitis, Chad David


    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

  19. Speeding chemical reactions by focusing

    CERN Document Server

    Lacasta, A M; Sancho, J M; Lindenberg, K


    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, obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate (t to the power -1/2) to very close to the perfect mixing rate, (t to the power -1).

  20. Learning to predict chemical reactions. (United States)

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


    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

  1. Fundamentals of chemical reaction engineering

    CERN Document Server

    Davis, Mark E


    Appropriate for a one-semester undergraduate or first-year graduate course, this text introduces the quantitative treatment of chemical reaction engineering. It covers both homogeneous and heterogeneous reacting systems and examines chemical reaction engineering as well as chemical reactor engineering. The authors take a chemical approach, helping students develop an intuitive feeling for concepts, rather than an engineering approach, which tends to overlook the inner workings of systems and objects.Each chapter contains numerous worked-out problems and real-world vignettes involving commercia

  2. Computed potential energy surfaces for chemical reactions (United States)

    Walch, Stephen P.


    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).

  3. A new look at the chemical reaction

    Directory of Open Access Journals (Sweden)

    Johannes A.A.W. Elemans


    Full Text Available At the heart of chemistry has always been the chemical reaction, and numerous analytical tools, such as NMR, UV-vis spectroscopy and mass spectrometry, are commonly used to elucidate reaction mechanisms. These conventional techniques have, however, an important limitation: they measure ensembles of millions of molecules at the same time and give only an average picture of a reaction mechanism, which might be incomplete and misleading because certain molecules might react whilst others are inactive. It is for this reason that during the past decade the interest is increasingly focusing on studying chemical reactions at the level of single molecules, and the stormy development of methods that allow such single molecule investigations, in particular Scanning Probe Microscopy, makes totally new insights in reaction mechanisms possible.

  4. Reduction of chemical reaction models (United States)

    Frenklach, Michael


    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.

  5. Curly arrows meet electron density transfers in chemical reaction mechanisms: from electron localization function (ELF) analysis to valence-shell electron-pair repulsion (VSEPR) inspired interpretation. (United States)

    Andrés, Juan; Berski, Sławomir; Silvi, Bernard


    Probing the electron density transfers during a chemical reaction can provide important insights, making possible to understand and control chemical reactions. This aim has required extensions of the relationships between the traditional chemical concepts and the quantum mechanical ones. The present work examines the detailed chemical insights that have been generated through 100 years of work worldwide on G. N. Lewis's ground breaking paper on The Atom and the Molecule (Lewis, G. N. The Atom and the Molecule, J. Am. Chem. Soc. 1916, 38, 762-785), with a focus on how the determination of reaction mechanisms can be reached applying the bonding evolution theory (BET), emphasizing how curly arrows meet electron density transfers in chemical reaction mechanisms and how the Lewis structure can be recovered. BET that combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT) provides a powerful tool providing insight into molecular mechanisms of chemical rearrangements. In agreement with physical laws and quantum theoretical insights, BET can be considered as an appropriate tool to tackle chemical reactivity with a wide range of possible applications. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds for a given reaction mechanism, providing detailed physical grounds for this type of representation. The ideas underlying the valence-shell-electron pair-repulsion (VSEPR) model applied to non-equilibrium geometries provide simple chemical explanations of density transfers. For a given geometry around a central atom, the arrangement of the electronic domain may comply or not with the VSEPR rules according with the valence shell population of the considered atom. A deformation yields arrangements which are either VSEPR defective (at least a domain is missing to match the VSEPR arrangement corresponding to the geometry of the ligands), VSEPR compliant

  6. Mechanisms of stochastic focusing and defocusing in biological reaction networks: insight from accurate chemical master equation (ACME) solutions. (United States)

    Giirsoy, Gamze; Terebus, Anna; Cao, Youfang; Liang, Jie; Gursoy, Gamze; Terebus, Anna; Youfang Cao; Jie Liang; Gursoy, Gamze; Cao, Youfang; Terebus, Anna; Liang, Jie


    Stochasticity plays important roles in regulation of biochemical reaction networks when the copy numbers of molecular species are small. Studies based on Stochastic Simulation Algorithm (SSA) has shown that a basic reaction system can display stochastic focusing (SF) by increasing the sensitivity of the network as a result of the signal noise. Although SSA has been widely used to study stochastic networks, it is ineffective in examining rare events and this becomes a significant issue when the tails of probability distributions are relevant as is the case of SF. Here we use the ACME method to solve the exact solution of the discrete Chemical Master Equations and to study a network where SF was reported. We showed that the level of SF depends on the degree of the fluctuations of signal molecule. We discovered that signaling noise under certain conditions in the same reaction network can lead to a decrease in the system sensitivities, thus the network can experience stochastic defocusing. These results highlight the fundamental role of stochasticity in biological reaction networks and the need for exact computation of probability landscape of the molecules in the system.

  7. Apparent tunneling in chemical reactions

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm; Hansen, Flemming Yssing; Billing, G. D.


    A necessary condition for tunneling in a chemical reaction is that the probability of crossing a barrier is non-zero, when the energy of the reactants is below the potential energy of the barrier. Due to the non-classical nature (i.e, momentum uncertainty) of vibrational states this is, however...

  8. Quantum chemical study on the catalytic mechanism of Na/K on NO-char heterogeneous reactions during the coal reburning process

    Institute of Scientific and Technical Information of China (English)

    Zheng-cheng WEN; Zhi-hua WANG; Jun-hu ZHOU; Ke-fa CEN


    Quantum chemical simulation was used to investigate the catalytic mechanism of Na/K on NO-char heterogeneous reactions during the coal reburning process. Both NO-char and NO-NaYK reactions were considered as three-step processes in this calculation. Based on geometry optimizations made using the UB3LYP/6-31 G(d) method, the activation energies of NO-char and NO-Na/K reactions were calculated using the QC1SD(T)/6-3 i 1G(d, p) method; Results showed that the activation energy of the NO-Na/K reaction (107.9/82.0 kJ/mol) was much lower than that of the NO-char reaction (245.1 kJ/mol). The reactions of NaO/KO and Na2P/K2O reduced by char were also studied, and their thermodynamics were calculated using the UB3LYP/6-31G(d) method; Results showed that both Na and K can be refreshed easily and rapidly by char at high temperature during the coal rebuming process. Based on the calculations and analyses, the catalytic mechanism of Na/K on NO-char het-erogeneous reactions during the coal reburning process was clarified.

  9. Mechanism for the stabilization of protein clusters above the solubility curve: the role of non-ideal chemical reactions

    CERN Document Server

    Lutsko, James F


    Dense protein clusters are known to play an important role in nucleation of protein crystals from dilute solutions. While these have generally been thought to be formed from a metastable phase, the observation of similar, if not identical, clusters above the critical point for the dilute-solution/strong-solution phase transition has thrown this into doubt. Furthermore, the observed clusters are stable for relatively long times. Because protein aggregation plays an important role in some pathologies, understanding the nature of such clusters is an important problem. One mechanism for the stabilization of such structures was proposed by Pan, Vekilov and Lubchenko and was investigated using a DDFT model which confirmed the viability of the model. Here, we revisit that model and incorporate additional physics in the form of state-dependent reaction rates. We show by a combination of numerical results and general arguments that the state-dependent rates disrupt the stability mechanism. Finally, we argue that the s...

  10. Experimental Demonstrations in Teaching Chemical Reactions. (United States)

    Hugerat, Muhamad; Basheer, Sobhi


    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. Complementarity between Quantum and Classical Mechanics in Chemical Modeling. The H + HeH+ → H2 + + He Reaction: A Rigourous Test for Reaction Dynamics Methods. (United States)

    Esposito, Fabrizio; Coppola, Carla Maria; De Fazio, Dario


    In this work we present a dynamical study of the H + HeH+ → H2+ + He reaction in a collision energy range from 0.1 meV to 10 eV, suitable to be used in applicative models. The paper extends and complements a recent work [ Phys. Chem. Chem. Phys. 2014, 16, 11662] devoted to the characterization of the reactivity from the ultracold regime up to the three-body dissociation breakup. In particular, the accuracy of the quasi-classical trajectory method below the three-body dissociation threshold has been assessed by a detailed comparison with previous calculations performed with different reaction dynamics methods, whereas the reliability of the results in the high energy range has been checked by a direct comparison with the available experimental data. Integral cross sections for several HeH+ roto-vibrational states have been analyzed and used to understand the extent of quantum effects in the reaction dynamics. By using the quasi-classical trajectory method and quantum mechanical close coupling data, respectively, in the high and low collision energy ranges, we obtain highly accurate thermal rate costants until 15 000 K including all (178) the roto-vibrational bound and quasi-bound states of HeH+. The role of the collision-induced dissociation is also discussed and explicitly calculated for the ground roto-vibrational state of HeH+.

  12. Heuristics-Guided Exploration of Reaction Mechanisms

    CERN Document Server

    Bergeler, Maike; Proppe, Jonny; Reiher, Markus


    For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is inevitable. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules and subsequently optimized by electronic-structure methods. Pairs of reactive complexes related by an elementary reaction are then automatically detected and subjected to an automated search for the connecting transition state. The results are...

  13. Heuristics-Guided Exploration of Reaction Mechanisms. (United States)

    Bergeler, Maike; Simm, Gregor N; Proppe, Jonny; Reiher, Markus


    For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules derived from conceptual electronic-structure theory and subsequently optimized by quantum-chemical methods to produce stable intermediates of an emerging reaction network. Pairs of intermediates in this network that might be related by an elementary reaction according to some structural similarity measure are then automatically detected and subjected to an automated search for the connecting transition state. The results are visualized as an automatically generated network graph, from which a comprehensive picture of the mechanism of a complex chemical process can be obtained that greatly facilitates the analysis of the whole network. We apply our protocol to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production.

  14. 2005 Chemical Reactions at Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Cynthia M. Friend


    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.

  15. Chemical reaction due to stronger Ramachandran interaction

    Indian Academy of Sciences (India)

    Andrew Das Arulsamy


    The origin of a chemical reaction between two reactant atoms is associated with the activation energy, on the assumption that, high-energy collisions between these atoms, are the ones that overcome the activation energy. Here, we show that a stronger attractive van der Waals (vdW) and electron-ion Coulomb interactions between two polarized atoms are responsible for initiating a chemical reaction, either before or after the collision. We derive this stronger vdW attraction formula exactly using the quasi one-dimensional Drude model within the ionization energy theory and the energy-level spacing renormalization group method. Along the way, we expose the precise physical mechanism responsible for the existence of a stronger vdW interaction for both long and short distances, and also show how to technically avoid the electron-electron Coulomb repulsion between polarized electrons from these two reactant atoms. Finally, we properly and correctly associate the existence of this stronger attraction with Ramachandran’s `normal limits’ (distance shorter than what is allowed by the standard vdW bond) between chemically nonbonded atoms.

  16. Chemical reactions in low-g (United States)

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


    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.

  17. Modelling Chemical Reasoning to Predict Reactions

    CERN Document Server

    Segler, Marwin H S


    The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which 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. We show that our 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 ac...

  18. Chemical and genomic evolution of enzyme-catalyzed reaction networks. (United States)

    Kanehisa, Minoru


    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.

  19. Modelling Chemical Reasoning to Predict Reactions


    Segler, Marwin H. S.; Waller, Mark P.


    The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which 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 outpe...

  20. A Unified Theory of Chemical Reactions

    CERN Document Server

    Aubry, S


    We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent. Our theory reveals the existence of an intermediate situation between ionic and covalent which may be almost barrierless and isoenegetic and which should be of high interest for understanding biochemistry.

  1. [Mechanisms of cutaneous drug reactions]. (United States)

    Vaillant, L


    Two main mechanisms, pharmacologic and immunoallergic, are responsible for cutaneous reactions to drugs. Pharmacologic mechanisms can be predictable (overdosage, cumulative or delayed toxicity, adverse effects) or unpredictable (idiosyncratic, intolerance, or anaphylactic reaction). Immunoallergic mechanisms can be mediated by IgE (some types of urticaria and anaphylactic shock), due to circulating immune complexes (leukocytoclastic vasculitis, serum sickness-type reactions) or mediated by lymphocytes (exanthema, Lyell's syndrome, fixed pigmented erythema, photosensitization). The diagnostic work-up varies according to the causative mechanism. When the reaction is predictable, the responsible drug can be identified according to the data in the present bibliography. When the reaction is immunologic, only the chronologic sequence of events can identify the responsible drug. The risk of recurrence with an identical or related molecule also varies according to the causative mechanism. For urticaria, diagnosis and the risk of recurrence differ according to whether the cause is allergic (mediated by IgE or urticarial vasculitis) or is pharmacologic (urticaria due to aspirin or to conversion enzyme inhibitors).

  2. Chemical potential and reaction electronic flux in symmetry controlled reactions. (United States)

    Vogt-Geisse, Stefan; Toro-Labbé, Alejandro


    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.

  3. Writing mistakes and skill in organic chemical reaction mechanism%有机化学反应机理常见的书写错误及书写技巧

    Institute of Scientific and Technical Information of China (English)



    In connection with mistakes when students write organic chemical reaction mechanism,pointed out problems which should be paid attention in writing organic chemical reaction mechanism,summarize writing skills, and hoped to provide certain instructive significance for students in writing organic chemical reaction mechanism.%针对学生在书写有机化学反应机理时易出现的错误,指出在书写反应机理时应注意的问题,并总结出书写技巧,对学生能够准确写出有机化学反应机理具有重要的指导意义。

  4. Theoretical study of stability and reaction mechanism of CuO supported on ZrO{sub 2} during chemical looping combustion

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Minjun; Liu, Jing, E-mail:; Shen, Fenghua; Cheng, Hao; Dai, Jinxin; Long, Yan


    Graphical abstract: - Highlights: • The stability and reaction mechanism of CuO supported on ZrO{sub 2} were studied by DFT. • ZrO{sub 2} provides a high resistance to CuO sintering. • ZrO{sub 2} promotes the activity of CuO for CO oxidation in fuel reactor. • The energy barriers are low enough for CuO/ZrO{sub 2} oxidation reaction in air reactor. - Abstract: The addition of inert support is important for the Cu-based oxygen carrier used in chemical looping combustion (CLC). The effects of the ZrO{sub 2} support on the stability and reactivity of Cu-based oxygen carrier were investigated using the density functional theory (DFT). First, the sintering inhibition mechanism of ZrO{sub 2} that support active CuO was investigated. The optimized Cu{sub 4}O{sub 4}/ZrO{sub 2} structure showed a strong interaction occurred between the Cu{sub 4}O{sub 4} cluster and ZrO{sub 2}(1 0 1) surface. The interaction prevented the migration and agglomeration of CuO. Next, the adsorption of CO on Cu{sub 4}O{sub 4}/ZrO{sub 2} and the mechanism of the CuO/ZrO{sub 2} reduction by CO were studied. CO mainly chemisorbed on the Cu site and ZrO{sub 2} acted as an electron donor in the adsorption system. The energy barrier of CuO/ZrO{sub 2} reduction by CO (0.79 eV) was much lower than that of the pure CuO cluster (1.44 eV), indicating that ZrO{sub 2} had a positive effect on CuO/ZrO{sub 2} reduction by CO. After CO was oxidized in the fuel reactor, the CuO was reduced into Cu. The adsorption of O{sub 2} on Cu{sub 2}/ZrO{sub 2} and the most likely pathway of Cu{sub 2}/ZrO{sub 2} oxidation by O{sub 2} were investigated. The adsorption of O{sub 2} was found a strong chemisorption behavior. The energy barriers were low enough for the Cu-based oxygen carrier oxidation reaction.

  5. Controlling chemical reactions of a single particle

    CERN Document Server

    Ratschbacher, Lothar; Sias, Carlo; Köhl, Michael


    The control of chemical reactions is a recurring theme in physics and chemistry. Traditionally, chemical reactions have been investigated by tuning thermodynamic parameters, such as temperature or pressure. More recently, physical methods such as laser or magnetic field control have emerged to provide completely new experimental possibilities, in particular in the realm of cold collisions. The control of reaction pathways is also a critical component to implement molecular quantum information processing. For these undertakings, single particles provide a clean and well-controlled experimental system. Here, we report on the experimental tuning of the exchange reaction rates of a single trapped ion with ultracold neutral atoms by exerting control over both their quantum states. We observe the influence of the hyperfine interaction on chemical reaction rates and branching ratios, and monitor the kinematics of the reaction products. These investigations advance chemistry with single trapped particles towards achi...

  6. Chemical reactions in solvents and melts

    CERN Document Server

    Charlot, G


    Chemical Reactions in Solvents and Melts discusses the use of organic and inorganic compounds as well as of melts as solvents. This book examines the applications in organic and inorganic chemistry as well as in electrochemistry. Organized into two parts encompassing 15 chapters, this book begins with an overview of the general properties and the different types of reactions, including acid-base reactions, complex formation reactions, and oxidation-reduction reactions. This text then describes the properties of inert and active solvents. Other chapters consider the proton transfer reactions in

  7. Flows and chemical reactions in heterogeneous mixtures

    CERN Document Server

    Prud'homme, Roger


    This book - a sequel of previous publications 'Flows and Chemical Reactions' and 'Chemical Reactions in Flows and Homogeneous Mixtures' - is devoted to flows with chemical reactions in heterogeneous environments.  Heterogeneous media in this volume include interfaces and lines. They may be the site of radiation. Each type of flow is the subject of a chapter in this volume. We consider first, in Chapter 1, the question of the generation of environments biphasic individuals: dusty gas, mist, bubble flow.  Chapter 2 is devoted to the study at the mesoscopic scale: particle-fluid exchange of mom

  8. Detailed reduction of reaction mechanisms for flame modeling (United States)

    Wang, Hai; Frenklach, Michael


    A method for reduction of detailed chemical reaction mechanisms, introduced earlier for ignition system, was extended to laminar premixed flames. The reduction is based on testing the reaction and reaction-enthalpy rates of the 'full' reaction mechanism using a zero-dimensional model with the flame temperature profile as a constraint. The technique is demonstrated with numerical tests performed on the mechanism of methane combustion.

  9. Chemical-reaction model for Mexican wave (United States)

    Nagatani, Takashi


    We present a chemical-reaction model to describe the Mexican wave ( La Ola) in football stadia. The spectator's action is described in terms of chemical reactions. The model is governed by three reaction rates k 1, k 2, and k3. We study the nonlinear waves on one- and two-dimensional lattices. The Mexican wave is formulated as a clockwise forwardly propagating wave. Waves are growing or disappear, depending on the values of reaction rates. In the specific case of k1= k2= k3=1, the nonlinear-wave equation produces a propagating pulse like soliton.

  10. Modeling of turbulent chemical reaction (United States)

    Chen, J.-Y.


    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.

  11. Chemical kinetics and reaction dynamics

    CERN Document Server

    Houston, Paul L


    This text teaches the principles underlying modern chemical kinetics in a clear, direct fashion, using several examples to enhance basic understanding. It features solutions to selected problems, with separate sections and appendices that cover more technical applications.Each chapter is self-contained and features an introduction that identifies its basic goals, their significance, and a general plan for their achievement. This text's important aims are to demonstrate that the basic kinetic principles are essential to the solution of modern chemical problems, and to show how the underlying qu

  12. Chemical dynamics simulations of the monohydrated OH(-)(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment. (United States)

    Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L


    Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH(-)(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I(-), and to a lesser extent CH2I(-) (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH](-). In contrast, for the unsolvated OH(-) + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH(-)(H2O) + CH3I SN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I(-) post-reaction complex for the SN2 reaction is negligible.

  13. Chemical Reactions at Surfaces. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)



    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.

  14. Explorations into Chemical Reactions and Biochemical Pathways. (United States)

    Gasteiger, Johann


    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.

  15. Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments. (United States)

    Molina, Estefanía Rossich; Ortiz, Daniel; Salpin, Jean-Yves; Spezia, Riccardo


    In this study we have coupled mixed quantum-classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling.

  16. Kinetic studies of elementary chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Durant, J.L. Jr. [Sandia National Laboratories, Livermore, CA (United States)


    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.

  17. Entropy Generation in a Chemical Reaction (United States)

    Miranda, E. N.


    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…

  18. Chemical Reactions in Turbulent Mixing Flows (United States)


    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 ...0. [19621 Chemical Reaction Engineering. An Introduc- ALAA J. 23(12), 1937-1945. tion to the Design of Chemical Reactors . (John Wiley). KERSTEIN. A


    Grove, David B.; Stollenwerk, Kenneth G.


    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 on solid surfaces using molecular beam techniques (United States)

    Palmer, R. L.


    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 reactions confined within carbon nanotubes. (United States)

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


    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.

  2. Inorganic Reaction Mechanisms Part II: Homogeneous Catalysis (United States)

    Cooke, D. O.


    Suggests several mechanisms for catalysis by metal ion complexes. Discusses the principal factors of importance in these catalysis reactions and suggests reactions suitable for laboratory study. (MLH)

  3. Negative Temperature Coefficient in Chemical Reactions (United States)

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


    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.

  4. The effect of carbon nanotubes on chiral chemical reactions (United States)

    Rance, Graham A.; Miners, Scott A.; Chamberlain, Thomas W.; Khlobystov, Andrei N.


    The intrinsic helicity of carbon nanotubes influences the formation of chiral molecules in chemical reactions. A racemic mixture of P and M enantiomers of nanotubes affects the enantiomeric excess of the products of the autocatalytic Soai reaction proportional to the amount of nanotubes added in the reaction mixture. An intermediate complex formed between the nanotube and the organometallic reagent is essential and explains the observed correlation between the enantiomeric distribution of products and the curvature of the carbon nanostructure. This Letter establishes a key mechanism for harnessing the helicity of nanoscale carbon surfaces for preparative organic reactions.

  5. Synthesis of 7-Ethyl-10-hydroxycamptothecin and Proposed Reaction Mechanism

    Institute of Scientific and Technical Information of China (English)


    The improved 3-step preparation of a key antitumor agent, 7-ethyl-10-hydroxycamptothecin(SN-38), which consists of ethylation, oxidation and photo-chemical rearrangement, is described. The proposed reaction mechanism is also discussed.

  6. Quantum-State Controlled Chemical Reactions of Ultracold KRb Molecules

    CERN Document Server

    Ospelkaus, S; Wang, D; de Miranda, M H G; Neyenhuis, B; Quéméner, G; Julienne, P S; Bohn, J L; Jin, D S; Ye, J


    How does a chemical reaction proceed at ultralow temperatures? Can simple quantum mechanical rules such as quantum statistics, single scattering partial waves, and quantum threshold laws provide a clear understanding for the molecular reactivity under a vanishing collision energy? Starting with an optically trapped near quantum degenerate gas of polar $^{40}$K$^{87}$Rb molecules prepared in their absolute ground state, we report experimental evidence for exothermic atom-exchange chemical reactions. When these fermionic molecules are prepared in a single quantum state at a temperature of a few hundreds of nanoKelvins, we observe p-wave-dominated quantum threshold collisions arising from tunneling through an angular momentum barrier followed by a near-unity probability short-range chemical reaction. When these molecules are prepared in two different internal states or when molecules and atoms are brought together, the reaction rates are enhanced by a factor of 10 to 100 due to s-wave scattering, which does not ...

  7. Matrix isolation as a tool for studying interstellar chemical reactions (United States)

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


    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.

  8. Classification of Chemical Reactions: Stages of Expertise (United States)

    Stains, Marilyne; Talanquer, Vicente


    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…

  9. Chemical memory reactions induced bursting dynamics in gene expression. (United States)

    Tian, Tianhai


    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.

  10. Atoms of multistationarity in chemical reaction networks

    CERN Document Server

    Joshi, Badal


    Chemical reaction networks taken with mass-action kinetics are dynamical systems that arise in chemical engineering and systems biology. Deciding whether a chemical reaction network admits multiple positive steady states is to determine existence of multiple positive solutions to a system of polynomials with unknown coefficients. In this work, we consider the question of whether the minimal (in a precise sense) networks, which we propose to call `atoms of multistationarity,' characterize the entire set of multistationary networks. We show that if a subnetwork admits multiple nondegenerate positive steady states, then these steady states can be extended to establish multistationarity of a larger network, provided that the two networks share the same stoichiometric subspace. Our result provides the mathematical foundation for a technique used by Siegal-Gaskins et al. of establishing bistability by way of `network ancestry.' Here, our main application is for enumerating small multistationary continuous-flow stir...

  11. Calculation of the energetics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Dunning, T.H. Jr.; Harding, L.B.; Shepard, R.L.; Harrison, R.J.


    To calculate the energetics of chemical reactions we must solve the electronic Schroedinger equation for the molecular conformations of importance for the reactive encounter. Substantial changes occur in the electronic structure of a molecular system as the reaction progresses from reactants through the transition state to products. To describe these changes, our approach includes the following three elements: the use of multiconfiguration self-consistent field wave functions to provide a consistent zero-order description of the electronic structure of the reactants, transition state, and products; the use of configuration interaction techniques to describe electron correlation effects needed to provide quantitative predictions of the reaction energetics; and the use of large, optimized basis sets to provide the flexibility needed to describe the variations in the electronic distributions. With this approach we are able to study reactions involving as many as 5--6 atoms with errors of just a few kcal/mol in the predicted reaction energetics. Predictions to chemical accuracy, i.e., to 1 kcal/mol or less, are not yet feasible, although continuing improvements in both the theoretical methodology and computer technology suggest that this will soon be possible, at least for reactions involving small polyatomic species. 4 figs.

  12. New Method to Acquire Chemomechanical Parameters of Diverse Chemical Reactions (United States)


    a model for reversible and pseudoreversible isothermal photoactuation based on the Carnot -type formalism and used it to estimate the maximum single...reactions offers unique attributes, e.g., potentially fast actuation cycles , high chemical and mechanical stability, flexible device design and

  13. Chemical computing with reaction-diffusion processes. (United States)

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


    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.

  14. Chemical reactions in reverse micelle systems (United States)

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


    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.

  15. The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ(3)-iodanes): facing the limit of the stationary quantum chemical approach. (United States)

    Sala, Oliver; Lüthi, Hans Peter; Togni, Antonio


    Trifluoromethylation of acetonitrile with 3,3-dimethyl-1-(trifluoromethyl)-1λ(3),2- benziodoxol is assumed to occur via reductive elimination (RE) of the electrophilic CF3-ligand and MeCN bound to the hypervalent iodine. Computations in gas phase showed that the reaction might also occur via an SN2 mechanism. There is a substantial solvent effect present for both reaction mechanisms, and their energies of activation are very sensitive toward the solvent model used (implicit, microsolvation, and cluster-continuum). With polarizable continuum model-based methods, the SN2 mechanism becomes less favorable. Applying the cluster-continuum model, using a shell of solvent molecules derived from ab initio molecular dynamics (AIMD) simulations, the gap between the two activation barriers ( ΔΔG‡) is lowered to a few kcal mol(-1) and also shows that the activation entropies (ΔS‡) and volumes (ΔV‡) for the two mechanisms differ substantially. A quantitative assessment of ΔΔG‡ will therefore only be possible using AIMD. A natural bond orbital-analysis gives further insight into the activation of the CF3-reagent by protonation.

  16. Concordant chemical reaction networks and the Species-Reaction Graph. (United States)

    Shinar, Guy; Feinberg, Martin


    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.

  17. Minimum Energy Pathways for Chemical Reactions (United States)

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


    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.

  18. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schatz, G.C. [Argonne National Laboratory, IL (United States)


    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.

  19. Flows and chemical reactions in homogeneous mixtures

    CERN Document Server

    Prud'homme, Roger


    Flows with chemical reactions can occur in various fields such as combustion, process engineering, aeronautics, the atmospheric environment and aquatics. The examples of application chosen in this book mainly concern homogeneous reactive mixtures that can occur in propellers within the fields of process engineering and combustion: - propagation of sound and monodimensional flows in nozzles, which may include disequilibria of the internal modes of the energy of molecules; - ideal chemical reactors, stabilization of their steady operation points in the homogeneous case of a perfect mixture and c

  20. Quantum Theory of Fast Chemical Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Light, John C


    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.

  1. Chemical reactions directed Peptide self-assembly. (United States)

    Rasale, Dnyaneshwar B; Das, Apurba K


    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.

  2. Optimization of a Chemical Reaction Train

    Directory of Open Access Journals (Sweden)

    Bahar Sansar


    Full Text Available This project consists of the optimization of a chemical reactor train. The reactor considered here is the continuous stirred tank reactor (CSTR, one of the reactor models used in engineering. Given the design equation for the CSTR and the cost function for a reactor, the following values are determined; the optimum number of reactors in the reaction train, the volume of each reactor and the total cost.

  3. Neural Networks in Chemical Reaction Dynamics

    CERN Document Server

    Raff, Lionel; Hagan, Martin


    This monograph presents recent advances in neural network (NN) approaches and applications to chemical reaction dynamics. Topics covered include: (i) the development of ab initio potential-energy surfaces (PES) for complex multichannel systems using modified novelty sampling and feedforward NNs; (ii) methods for sampling the configuration space of critical importance, such as trajectory and novelty sampling methods and gradient fitting methods; (iii) parametrization of interatomic potential functions using a genetic algorithm accelerated with a NN; (iv) parametrization of analytic interatomic

  4. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning. (United States)

    Kayala, Matthew A; Baldi, Pierre


    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

  5. Theoretical study on aquation reaction of cis-platin complex: RISM-SCF-SEDD, a hybrid approach of accurate quantum chemical method and statistical mechanics. (United States)

    Yokogawa, Daisuke; Ono, Kohei; Sato, Hirofumi; Sakaki, Shigeyoshi


    The ligand exchange process of cis-platin in aqueous solution was studied using RISM-SCF-SEDD (reference interaction site model-self-consistent field with spatial electron density distribution) method, a hybrid approach of quantum chemistry and statistical mechanics. The analytical nature of RISM theory enables us to compute accurate reaction free energy in aqueous solution based on CCSD(T), together with the microscopic solvation structure around the complex. We found that the solvation effect is indispensable to promote the dissociation of the chloride anion from the complex.

  6. Suppression of Ostwald Ripening by Chemical Reactions (United States)

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


    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. Chemical Reaction Networks for Computing Polynomials. (United States)

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


    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.

  8. CH 1 Introduction to Chemistry. Study Guide to Minicourse I - 13 Chemical Reaction Principles. (United States)

    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)

  9. New methods for quantum mechanical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, W.H. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States)


    Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L{sup 2}) representation of the outgoing wave scattering Green`s function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green`s function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC{sup -} can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC{sup -} geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H{sub 3}O{sup -} system, providing information about the potential energy surface for the OH + H{sub 2} reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the Boltzmannized flux operator.

  10. Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms. (United States)

    Maeda, Satoshi; Morokuma, Keiji


    In these five decades, many useful tools have been developed for exploring quantum chemical potential energy surfaces. The success in theoretical studies of chemical reaction mechanisms has been greatly supported by these tools. However, systematic prediction of reaction mechanisms starting only from given reactants and catalysts is still very difficult. Toward this goal, we describe the artificial force induced reaction (AFIR) method for automatically finding reaction paths of type A + B → X (+ Y). By imposing an artificial force to given reactants and catalysts, the method can find the reactive sites very efficiently. Further pressing by the artificial force provides approximate transition states and product structures, which can be easily reoptimized to the corresponding true ones. This procedure can be executed very efficiently just by minimizing a single function called the AFIR function. All important reaction paths can be found by repeating this cycle starting from many initial orientations. We also discuss perspectives of automated reaction path search methods toward the above goal.

  11. Uncertainty quantification for quantum chemical models of complex reaction networks. (United States)

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


    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.

  12. Quantum dynamics of fast chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Light, J.C. [Univ. of Chicago, IL (United States)


    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.

  13. Chemical Reaction Dynamics in Nanoscle Environments

    Energy Technology Data Exchange (ETDEWEB)

    Evelyn M. Goldfield


    The major focus of the research in this program is the study of the behavior of molecular systems confined in nanoscale environments. The goal is to develop a theoretical framework for predicting how chemical reactions occur in nanoscale environments. To achieve this goal we have employed ab initio quantum chemistry, classical dynamics and quantum dynamics methods. Much of the research has focused on the behavior of molecules confined within single-walled carbon nanotubes (SWCNTs). We have also studied interactions of small molecules with the exterior surface of SWCNTs. Nonequilibrium molecular dynamics of interfaces of sliding surface interfaces have also been performed.

  14. Law of localization in chemical reaction networks

    CERN Document Server

    Okada, Takashi


    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. Responses turn out to exhibit two characteristic patterns, $localization$ 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.

  15. Development of Green and Sustainable Chemical Reactions

    DEFF Research Database (Denmark)

    Taarning, Esben

    in chapter one and two which can be helpful to know when reading the subsequent chapters. The first chapter is an introduction into the fundamentals of green and sustainable chemistry. The second chapter gives an overview of some of the most promising methods to produce value added chemicals from biomass...... and only leads to small amounts of waste formation due to the all-catalytic nature of the procedure. This chapter involves the use of transition metal catalysis as well as classic organic chemistry. In chapter four, supported gold nanoparticles are used as catalysts for the aerobic oxidation of primary......Abstract This thesis entitled Development of Green and Sustainable Chemical Reactions is divided into six chapters involving topics and projects related to green and sustainable chemistry. The chapters can be read independently, however a few concepts and some background information is introduced...

  16. Colloidal Assemblies Effect on Chemical Reactions. (United States)


    MICROEMULSIONS - SURFACTANTS - OXIDATION - PHOTOCATALYSIS - DEGRADATION - HALOAROMATIC COMPOUNDS - REACTION MECHANISM - KINETICS 20. ABmT’AcT (cthwe - 0...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

  17. Quantum chemical study of mechanisms of dissociation and isomerization reactions in some molecules and radicals of astrophysical significance: Cyanides and related molecules

    Indian Academy of Sciences (India)

    V P Gupta; Archina Sharma


    A theoretical study of the mechanism of photodecomposition in carbonyl cyanide, diethynyl ketone, acetyl cyanide and formyl cyanide has been conducted using density functional and MP2 theories. A complete analysis of the electronic spectra of these molecules in terms of nature, energy and intensity of electronic transitions has been provided by time-dependent density functional theory. Mixing coefficients and main configurations of the electronic states have been used to identify the states leading to the photodecomposition process. While the Rydberg state 1(n,3s) is involved in the dissociation of formyl cyanide and acetyl cyanide, the $^{*}_{CC} / ^{*}_{CN}$ states are involved in the case of carbonyl cyanide and diethynyl ketone. In all cases, however, stepwise decomposition process is preferred over the concerted reaction process. Based on potential energy curves for bond dissociation and the transition state and IRC studies, it is found that besides the direct dissociation of carbonyl cyanide, a photoisomerization process through a non-planar transition state may also occur resulting in the formation of a stable and planar isomer CNC(O)CN. A complete vibrational analysis of the higher energy isomer has been conducted and several new fundamental bands are predicted. Some of the earlier experimental results on the photodecomposition mechanism and energies of photofragments in carbonyl cyanide and acetyl cyanide have also been rationalized.

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

    Energy Technology Data Exchange (ETDEWEB)



    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.

  19. Computerized approaches to enhance understanding of organic reaction mechanisms: CAN reaction mechanisms and CPLEX prelaboratory methodology (United States)

    Al-Shammari, Abdulrahman G. Alhamzani


    Two approaches to enhance the understanding of organic reaction mechanisms are described. First, a new method for teaching organic reaction mechanisms that can be used in a Computer-Assisted Instruction (CAI) environment is proposed and tested (Chapter 1). The method concentrates upon the important intermediate structures, which are assumed to be on the reaction coordinate, and which can be evaluated and graded by currently available computer techniques. At the same time, the "curved arrows" that show the electron flow in a reaction mechanism are neglected, since they cannot be evaluated and graded with currently available computer techniques. By allowing student practice for learning organic reaction mechanisms using the Curved Arrow Neglect (CAN) method within a "Practice Makes Perfect" CAI method, student performance in the drawing of traditional reaction mechanisms, in which students had to include the "curved arrows" on their written classroom exams, was significantly enhanced. Second, computerized prelaboratory experiments (CPLEX) for organic chemistry laboratory 1 & 2 courses have been created, used, and evaluated (Chapters 2 and 3). These computerized prelabs are unique because they combine both "dry lab" actions with detailed animations of the actual chemistry occurring at the molecular level. The "dry lab" serves to simulate the actual physical manipulations of equipment and chemicals that occur in the laboratory experiment through the use of drag-and-drop computer technology. At the same time, these physical actions are accompanied on a separate part of the computer screen by animations showing the chemistry at the molecular level that is occurring in the experiment. These CPLEX modules were made into Internet accessible modules. The students were allowed to access the CPLEX modules prior to performing the actual laboratory experiment. A detailed evaluation of students' perception of the modules was accomplished via survey methodology during the entire

  20. Quantum Chemical Study on Reaction of Acetaldehyde with Hydroxyl Radical

    Institute of Scientific and Technical Information of China (English)

    LI,Ming(李明); ZHANG,Jin-Sheng(张金生); SHEN,Wei(申伟); MENG,Qing-Xi(孟庆喜)


    The reaction of acetaldehyde with hydroxyl radical was studied by means of quantum chemical methods. The geometries for all the stationary points on the potential energy surfaces were optimized fully, respectively, at the G3MP2, G3, and MP2/6-311++G(d,p) levels. Single-point energies of all the species were calculated at the QCISD/6-311 + +G(d,p) level. The mechanism of the reaction studied was confirmed. The predicted product is acetyl radical that is in agreement with the experiment.

  1. Mechanisms of severe transfusion reactions. (United States)

    Kopko, P M; Holland, P V


    Serious adverse effects of transfusion may be immunologically or non-immunologically mediated. Currently, bacterial contamination of blood products, particularly platelets, is one of the most significant causes of transfusion-related morbidity and mortality. Septic transfusion reactions can present with clinical symptoms similar to immune-mediated hemolytic transfusion reactions and transfusion-related acute lung injury. Extremely high fever and/or gastrointestinal symptoms, in a transfusion recipient, may be indicative of sepsis. The diagnosis is based upon culturing the same organism from both the patient and the transfused blood component. Numerous organisms have been implicated as the cause of septic transfusion reactions. Due to different storage conditions, gram negative organisms are more often isolated from red blood cell components; gram positive organisms are more often isolated from platelets. Prevention of septic transfusion reactions is primarily dependent on an adequate donor history and meticulous preparation of the donor phlebotomy site. Visual inspection of blood components prior to transfusion is also vital to preventing these reactions. Several methods of detection of bacterial contamination and inactivation of pathogens are currently under active investigation.

  2. Molecular Dynamics Simulations of Chemical Reactions for Use in Education (United States)

    Qian Xie; Tinker, Robert


    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. Chemical Reaction Optimization for Max Flow Problem

    Directory of Open Access Journals (Sweden)

    Reham Barham


    Full Text Available This study presents an algorithm for MaxFlow problem using "Chemical Reaction Optimization algorithm (CRO". CRO is a recently established meta-heuristics algorithm for optimization, inspired by the nature of chemical reactions. The main concern is to find the best maximum flow value at which the flow can be shipped from the source node to the sink node in a flow network without violating any capacity constraints in which the flow of each edge remains within the upper bound value of the capacity. The proposed MaxFlow-CRO algorithm is presented, analyzed asymptotically and experimental test is conducted. Asymptotic runtime is derived theoretically. The algorithm is implemented using JAVA programming language. Results show a good performance with a complexity of O(I E2, for I iterations and E edges. The number of iterations I in the algorithm, is an important factor that will affect the results obtained. As number of iterations is increased, best possible max-Flow value is obtained.

  4. Organic Reaction Mechanisms at A-Level. (United States)

    Norman, R. O. C.; Waddington, D. J.


    Advocates teaching of organic reaction mechanisms through the methods which are used in elucidating them. This also provides a useful way of illustrating the theories and methods of physical chemistry. Describes an approach to teaching three reaction mechanisms: substitution in alkanes; addition to alkenes; and ester hydrolysis. (Author/GA)

  5. Quantum theory of chemical reaction rates

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States). Chemical Sciences Div.


    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.

  6. Systematic development of reduced reaction mechanisms for dynamic modeling (United States)

    Frenklach, M.; Kailasanath, K.; Oran, E. S.


    A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.

  7. Study on the key problems of interaction between microwave and chemical reaction

    Institute of Scientific and Technical Information of China (English)

    YANG Xiaoqing; HUANG Kama


    Microwave has been found as an efficient heating method in chemical industry.However,in present days the interaction between microwave and chemical reactions has not been deeply understood,which restricts a wider application of high power microwave in chemical industry.In this Paper,the key problems of interaction between microwave and chemical reaction are investigated,such as complex effective permittivity of chemical reaction,simulation of microwave heating on chemical reaction and non-thermal effect of microwave,which will enhance further knowledge of the mechanism of interaction between microwave and chemical reaction.Moreover,such an analysis is beneficial for handling with difficulties in application of microwave chemical industry.

  8. Reaction mechanisms of DNA photolyase. (United States)

    Brettel, Klaus; Byrdin, Martin


    DNA photolyase uses visible light and a fully reduced flavin cofactor FADH(-) to repair major UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). Electron transfer from photoexcited FADH(-) to CPD, splitting of the two intradimer bonds, and back electron transfer to the transiently formed flavin radical FADH° occur in overall 1ns. Whereas the kinetics of FADH° was resolved, the DNA-based intermediates escaped unambiguous detection yet. Another light reaction, named photoactivation, reduces catalytically inactive FADH° to FADH(-) without implication of DNA. It involves electron hopping along a chain of three tryptophan residues in 30ps, as elucidated in detail by transient absorption spectroscopy. The same triple tryptophan chain is found in cryptochrome blue-light photoreceptors and may be involved in their primary photoreaction.

  9. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models. (United States)

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


    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.

  10. Quantum mechanical calculations of vibrational population inversion in chemical reactions - Numerically exact L-squared-amplitude-density study of the H2Br reactive system (United States)

    Zhang, Y. C.; Zhang, J. Z. H.; Kouri, D. J.; Haug, K.; Schwenke, D. W.


    Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.

  11. The mechanism of the modified Ullmann reaction


    Sperotto, Elena; Klink, Gerard P.M. van; van Koten, Gerard; Vries, Johannes G. de


    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) made these reactions truly catalytic, with catalyst amounts as low as 1 mol% or even lower. Since these catalysts are homogeneous, it has opened up the possibility to investigate the mechanism of the...

  12. Reaction mechanisms: Stripping down SN2 (United States)

    Orr-Ewing, Andrew J.


    The mechanism of the SN2 reaction is fundamental to understanding and controlling the stereochemistry of organic reactions, but surrounding solvent molecules may complicate the textbook picture. Micro-solvation studies have now explored the stereochemical consequences of the presence of one or two solvent molecules.

  13. Plasmon-driven sequential chemical reactions in an aqueous environment. (United States)

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


    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. Reaction mechanism of -acylhydroxamate with cysteine proteases

    Indian Academy of Sciences (India)

    R Shankar; P Kolandaivel


    The gas-phase reaction mechanism of -acylhydroxamate with cysteine proteases has been investigated using ab initio and density functional theory. On the irreversible process, after breakdown of tetrahedral intermediate (INT1), small 1-2 anionotropic has been formed and rearranged to give stable by-products sulfenamide (P1) and thiocarbamate (P2) with considerable energy loss. While, on the reversible part of this reaction mechanism, intermediate (INT2) breaks down on oxidation, to form a stable product (P3). Topological and AIM analyses have been performed for hydrogen bonded complex in this reaction profile. Intrinsic reaction coordinates [IRC, minimum-energy path (MEP)] calculation connects the transition state between R-INT1, INT1-P1 and INT1-P2. The products P1, P2 and P3 are energetically more stable than the reactant and hence the reaction enthalpy is found to be exothermic.

  15. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry. (United States)

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


    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.

  16. [Recent results in research on oscillatory chemical reactions]. (United States)

    Poros, Eszter; Kurin-Csörgei, Krisztina


    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.

  17. A Reduced Reaction Mechanism For Isooctane Combustion

    Directory of Open Access Journals (Sweden)

    C.R.Berlin Selva Rex,


    Full Text Available A reduced chemical kinetic mechanism for the oxidation of iso-octane has been developed and a detailed study on the ignition of iso-octane has been conducted analytically using a kinetic scheme with 994 elementary reactions and 201 species. The activation energies of isooctane are higher than n-octane. Hence iso-octane is widelyused for combustion simulations. A program has been developed in MATLAB for the calculation and prediction of the concentration of 201 intermediate species and the ignition delay in the combustion of Iso-octane. The various initial conditions considered was in between the temperatures of 600K to 1250K with pressure ranging from 10atm to40atm at various equivalence ratios of 0.3 and 0.6. Nitrogen is considered as the diluent. The diluent percentage is assumed as 79% to make a comparison with atmospheric condition. The criteria for determination of ignition delay times are based on the OH concentrations to reach to a value of 1x10-9 moles/cc. The ignition delay times are obtained by varying initial conditions of the mixture in the combustion of Iso-octane. The results on ignition delays have been found to be agreeable with those available in the literature. Cantera (an object oriented software for reacting flows software is used in this study.

  18. Flows and chemical reactions in an electromagnetic field

    CERN Document Server

    Prud'homme, Roger


    This book - a sequel of previous publications 'Flows and Chemical Reactions', 'Chemical Reactions Flows in Homogeneous Mixtures' and 'Chemical Reactions and Flows in Heterogeneous Mixtures' - is devoted to flows with chemical reactions in the electromagnetic field. The first part, entitled basic equations, consists of four chapters. The first chapter provides an overview of the equations of electromagnetism in Minkowski spacetime. This presentation is extended to balance equations, first in homogeneous media unpolarized in the second chapter and homogeneous fluid medium polarized in the thir

  19. Detailed surface reaction mechanism in a three-way catalyst. (United States)

    Chatterjee, D; Deutschmann, O; Warnatz, J


    Monolithic three-way catalysts are applied to reduce the emission of combustion engines. The design of such a catalytic converter is a complex process involving the optimization of different physical and chemical parameters (in the simplest case, e.g., length, cell densities or metal coverage of the catalyst). Numerical simulation can be used as an effective tool for the investigation of the catalytic properties of a catalytic converter and for the prediction of the performance of the catalyst. To attain this goal, a two-dimensional flow-field description is coupled with a detailed surface reaction model (gas-phase reactions can be neglected in three-way catalysts). This surface reaction mechanism (with C3H6 taken as representative of unburnt hydrocarbons) was developed using sub-mechanisms recently developed for hydrogen, carbon monoxide and methane oxidation, literature values for C3H6 oxidation, and estimates for the remaining unknown reactions. Results of the simulation of a monolithic single channel are used to validate the surface reaction mechanism. The performance of the catalyst was simulated under lean, nearly stoichiometric and rich conditions. For these characteristic conditions, the oxidation of propene and carbon monoxide and the reduction of NO on a typical Pt/Rh coated three-way catalyst were simulated as a function of temperature. The numerically predicted conversion data are compared with experimentally measured data. The simulation further reveals the coupling between chemical reactions and transport processes within the monolithic channel.

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

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)


    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.

  1. Incidents of chemical reactions in cell equipment

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, N.M.; Barlow, C.R. [Uranium Enrichment Organization, Oak Ridge, TN (United States)


    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.

  2. Characterizing the mechanism(s) of heavy element synthesis reactions (United States)

    Loveland, Walter


    A review of the current state of our understanding of complete fusion reaction mechanisms is presented, from the perspective of an experimentalist. For complete fusion reactions, the overall uncertainties in predicting heavy element synthesis cross sections are examined in terms of the uncertainties associated with the calculations of capture cross sections, fusion probabilities and survival probabilities.

  3. A new comprehensive reaction mechanism for combustion of hydrocarbon fuels

    Energy Technology Data Exchange (ETDEWEB)

    Ranzi, E.; Sogaro, A.; Gaffuri, P.; Pennati, G. [Politecnico di Milano (Italy). Dipt. di Chimica Industriale e Ingegneria Chimica; Westbrook, C.K.; Pitz, W.J. [Lawrence Livermore National Lab., CA (United States)


    A chemical kinetic model has been developed which describes pyrolysis, ignition and oxidation of many small hydrocarbon fuels over a wide range of experimental conditions. Fuels include carbon monoxide and hydrogen, methane and other alkane species up to n-butane, ethylene, propene, acetylene, and oxygenated species such as methanol, acetaldehyde and ethanol. Formation of some larger intermediate and product species including benzene, butadiene, large olefins, and cyclopentadiene has been treated in a semi-empirical manner. The reaction mechanism has been tested for conditions that do not involve transport and diffusional processes, including plug flow and stirred reactors, batch reactors and shock tubes. The present kinetic model and its validation differ from previous reaction mechanisms in two ways. First, in addition to conventional combustion data, experiments more commonly associated with chemical engineering problems such as oxidative coupling, oxidative pyrolysis and steam cracking are used to test the reaction mechanism, making it even more general than previous models. In addition, H atom abstraction and some other reaction rates, even for the smaller C{sub 2}, C{sub 3} and C{sub 4} species, are treated using approximations that facilitate future extensions to larger fuels in a convenient manner. Construction of the reaction mechanism and comparisons with experimental data illustrate the generality of the model.

  4. Chemical Looping Combustion Reactions and Systems

    Energy Technology Data Exchange (ETDEWEB)

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


    , 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.

  5. Development and validation of a reduced combined biodiesel–diesel reaction mechanism

    DEFF Research Database (Denmark)

    Ng, Hoon Kiat; Gan, Suyin; Ng, Jo-Han;


    In this study, a compact combined biodiesel–diesel (CBD) reaction mechanism for diesel engine simulations is proposed through the combination of three component mechanisms using a chemical class-based approach. The proposed mechanism comprises the reaction mechanisms of methyl crotonate (MC...

  6. Nanoscale wear as a stress-assisted chemical reaction. (United States)

    Jacobs, Tevis D B; Carpick, Robert W


    Wear of sliding contacts leads to energy dissipation and device failure, resulting in massive economic and environmental costs. Typically, wear phenomena are described empirically, because physical and chemical interactions at sliding interfaces are not fully understood at any length scale. Fundamental insights from individual nanoscale contacts are crucial for understanding wear at larger length scales, and to enable reliable nanoscale devices, manufacturing and microscopy. Observable nanoscale wear mechanisms include fracture and plastic deformation, but recent experiments and models propose another mechanism: wear via atom-by-atom removal ('atomic attrition'), which can be modelled using stress-assisted chemical reaction kinetics. Experimental evidence for this has so far been inferential. Here, we quantitatively measure the wear of silicon--a material relevant to small-scale devices--using in situ transmission electron microscopy. We resolve worn volumes as small as 25 ± 5 nm(3), a factor of 10(3) lower than is achievable using alternative techniques. Wear of silicon against diamond is consistent with atomic attrition, and inconsistent with fracture or plastic deformation, as shown using direct imaging. The rate of atom removal depends exponentially on stress in the contact, as predicted by chemical rate kinetics. Measured activation parameters are consistent with an atom-by-atom process. These results, by direct observation, establish atomic attrition as the primary wear mechanism of silicon in vacuum at low loads.

  7. The mechanism of the modified Ullmann reaction. (United States)

    Sperotto, Elena; van Klink, Gerard P M; van Koten, Gerard; de Vries, Johannes G


    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) made these reactions truly catalytic, with catalyst amounts as low as 1 mol% or even lower. Since these catalysts are homogeneous, it has opened up the possibility to investigate the mechanism of these modified Ullmann reactions. Most authors agree that Cu(I) is the true catalyst even though Cu(0) and Cu(II) catalysts have also shown to be active. It should be noted however that Cu(I) is capable of reversible disproportionation into Cu(0) and Cu(II). In the first step, the nucleophile displaces the halide in the LnCu(I)X complex forming LnCu(I)ZR (Z = O, NR′, S). Quite a number of mechanisms have been proposed for the actual reaction of this complex with the aryl halide: 1. Oxidative addition of ArX forming a Cu(III) intermediate followed by reductive elimination; 2. Sigma bond metathesis; in this mechanism copper remains in the Cu(II) oxidation state; 3. Single electron transfer (SET) in which a radical anion of the aryl halide is formed (Cu(I)/Cu(II)); 4. Iodine atom transfer (IAT) to give the aryl radical (Cu(I)/Cu(II)); 5. π-complexation of the aryl halide with the Cu(I) complex, which is thought to enable the nucleophilic substitution reaction. Initially, the radical type mechanisms 3 and 4 where discounted based on the fact that radical clock-type experiments with ortho-allyl aryl halides failed to give the cyclised products. However, a recent DFT study by Houk, Buchwald and co-workers shows that the modified Ullmann reaction between aryl iodide and amines or primary alcohols proceeds either via an SET or an IAT mechanism. Van Koten has shown that stalled aminations can be rejuvenated by the addition of Cu(0), which serves to reduce the formed Cu(II) to Cu

  8. Mechanisms of inorganic and organometallic reactions

    CERN Document Server

    The purpose of this series is to provide a continuing critical review of the literature concerned with mechanistic aspects of inorganic and organo­ metallic reactions in solution, with coverage being complete in each volume. The papers discussed are selected on the basis of relevance to the elucidation of reaction mechanisms and many include results of a nonkinetic nature when useful mechanistic information can be deduced. The period of literature covered by this volume is July 1982 through December 1983, and in some instances papers not available for inclusion in the previous volume are also included. Numerical results are usually reported in the units used by the original authors, except where data from different papers are com­ pared and conversion to common units is necessary. As in previous volumes material included covers the major areas of redox processes, reactions of the nonmetallic elements, reaction of inert and labile metal complexes and the reactions of organometallic compounds. While m...

  9. 45钢表面原位摩擦化学反应膜形成过程及力学性能%Formation and mechanical properties of in situ tribo-chemical reaction film on surface of 45 steel

    Institute of Scientific and Technical Information of China (English)

    张保森; 许一; 徐滨士; 高飞; 史佩京; 吴毅雄


    A kind of tribo-treatment agent, which can be applied to in situ tribo-chemical treatment, was prepared using natural mineral powders. Addition of the as-prepared agent to diesel engine oil was optimized by means of wearing test on a ring-block friction and wear tester. Forming process and mechanical properties of in situ tribo-chernical reaction film on surface of 45 steel were investigated and forming mechanism of the film was discussed. Results show that the addition of 0. 5 wt% agent is most efficient for formation of in situ tribo-chemical reaction film to improve wearing performance of the surface of 45 steel. The friction coefficient and mass wear rate decreases by 19. 7% and 71.8% compared to those of the base oil, respectively. The tribo-treated surface is rather smooth and a tribo-chemical reaction film mainly consisting of iron oxides, iron and/or magnesium silicates and carbon-containing compounds is formed on the steel substrate. Moreover, the porous film tended to become compact and continuous as the wearing time increased, contributing to the improvement in surface strength and wear resistance of 45 steel.%制备了一种用于原位摩擦化学处理技术的天然矿物微粉摩擦处理剂.采用环-块摩擦磨损试验机对其在柴油机油中的添加量进行了优化,研究了其在45钢表面的原位摩擦化学反应膜的形成过程及力学性能,探讨了形成机理.结果表明:处理剂含量为0.5 wt%时对45钢表面具有较好的优化效果,其摩擦因数和质量磨损率分别较基础油降低约19.7%和71.8%.摩擦处理表面较为光滑平整,形成了由铁的氧化物、铁镁硅酸盐及含碳化合物构成的摩擦化学反应膜,且随着时间的增加逐步由疏松多孔趋于致密连续,具有较高的力学性能,显著提高了45钢的表面强度及磨损抗力.

  10. Thermal, chemical, and mechanical cookoff modeling

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, M.L.; Baer, M.R.; Gross, R.J.


    A Thermally Reactive, Elastic-plastic eXplosive code, TREX, has been developed to analyze coupled thermal, chemical and mechanical effects associated with cookoff simulation of confined or unconfined energetic materials. In confined systems, pressure buildup precedes thermal runaway, and unconfined energetic material expands to relieve high stress. The model was developed based on nucleation, decomposition chemistry, and elastic/plastic mechanical behavior of a material with a distribution of internal defects represented as clusters of spherical inclusions. A local force balance, with mass continuity constraints, forms the basis of the model requiring input of temperature and reacted gas fraction. This constitutive material model has been incorporated into a quasistatic mechanics code SANTOS as a material module which predicts stress history associated with a given strain history. The thermal-chemical solver XCHEM has been coupled to SANTOS to provide temperature and reacted gas fraction. Predicted spatial history variables include temperature, chemical species, solid/gas pressure, solid/gas density, local yield stress, and gas volume fraction. One-Dimensional Time to explosion (ODTX) experiments for TATB and PBX 9404 (HMX and NC) are simulated using global multistep kinetic mechanisms and the reactive elastic-plastic constitutive model. Pressure explosions, rather than thermal runaway, result in modeling slow cookoff experiments of confined conventional energetic materials such as TATB. For PBX 9404, pressure explosions also occur at fast cookoff conditions because of low temperature reactions of nitrocellulose resulting in substantial pressurization. A demonstrative calculation is also presented for reactive heat flow in a hollow, propellant-filled, stainless steel cylinder, representing a rocket motor. This example simulation show

  11. Chemical Looping Combustion Reactions and Systems

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  12. Determination of caffeine using oscillating chemical reaction in a CSTR. (United States)

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


    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.

  13. Stereodynamics: From elementary processes to macroscopic chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Kasai, Toshio [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Graduate School of Science, Department of Chemistry, Osaka University, Toyonaka, 560-0043 Osaka (Japan); Che, Dock-Chil [Graduate School of Science, Department of Chemistry, Osaka University, Toyonaka, 560-0043 Osaka (Japan); Tsai, Po-Yu [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Lin, King-Chuen [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Palazzetti, Federico [Scuola Normale Superiore, Pisa (Italy); Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Aquilanti, Vincenzo [Dipartimento di Chimica Biologia e Biotecnologie, Università di Perugia, 06123 Perugia (Italy); Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Roma (Italy); Instituto de Fisica, Universidade Federal da Bahia, Salvador (Brazil)


    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. Mesoscale simulations of shockwave energy dissipation via chemical reactions. (United States)

    Antillon, Edwin; Strachan, Alejandro


    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.

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


    Rappoport, Dmitrij; Galvin, Cooper J.; Zubarev, Dmitry; Aspuru-Guzik, Alan


    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 reacti...

  16. Formal modeling of a system of chemical reactions under uncertainty. (United States)

    Ghosh, Krishnendu; Schlipf, John


    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.

  17. Modular verification of chemical reaction network encodings via serializability analysis. (United States)

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


    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.

  18. Localized basis functions and other computational improvements in variational nonorthogonal basis function methods for quantum mechanical scattering problems involving chemical reactions (United States)

    Schwenke, David W.; Truhlar, Donald G.


    The Generalized Newton Variational Principle for 3D quantum mechanical reactive scattering is briefly reviewed. Then three techniques are described which improve the efficiency of the computations. First, the fact that the Hamiltonian is Hermitian is used to reduce the number of integrals computed, and then the properties of localized basis functions are exploited in order to eliminate redundant work in the integral evaluation. A new type of localized basis function with desirable properties is suggested. It is shown how partitioned matrices can be used with localized basis functions to reduce the amount of work required to handle the complex boundary conditions. The new techniques do not introduce any approximations into the calculations, so they may be used to obtain converged solutions of the Schroedinger equation.

  19. Dynamical resonance in F+H2 chemical reaction and rotational excitation effect

    Institute of Scientific and Technical Information of China (English)

    YANG XueMing; XIE DaiQian; ZHANG DongHui


    Reaction resonance is a frontier topic in chemical dynamics research, and it is also essential to the understanding of mechanisms of elementary chemical reactions. This short article describes an important development in the frontier of research. Experimental evidence of reaction resonance has been detected in a full quantum state resolved reactive scattering study of the F+H2 reaction. Highly accurate full quantum scattering theoretical modeling shows that the reaction resonance is caused by two Feshbach resonance states. Further studies show that quantum interference is present between the two resonance states for the forward scattering product. This study is a significant step forward in our understanding of chemical reaction resonance in the benchmark F+H2 system. Further experimental studies on the effect of H2 rotational excitation on dynamical resonance have been carried out. Dynamical resonance in the F+H2 (j = 1) reaction has also been observed.

  20. Localized nonequilibrium nanostructures in surface chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrand, M; Ipsen, M; Mikhailov, A S; Ertl, G [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin (Germany)


    Nonequilibrium localized stationary structures of submicrometre and nanometre sizes can spontaneously develop under reaction conditions on a catalytic surface. These self-organized structures emerge because of the coupling between the reaction and a structural phase transition in the substrate. Depending on the reaction conditions they can either correspond to densely covered spots (islands), inside which the reaction predominantly proceeds, or local depletions (holes) in a dense adsorbate layer with a very small reactive output in comparison to the surroundings. The stationary localized solutions are constructed using the singular perturbation approximation. These results are compared with numerical simulations, where special adaptive grid algorithms and numerical continuation of stationary profiles are used. Numerical investigations beyond the singular perturbation limit are also presented.

  1. Possible atmospheric lifetimes and chemical reaction mechanisms for selected HCFCs, HFCs, CH3CCl3, and their degradation products against dissolution and/or degradation in seawater and cloudwater (United States)

    Wine, P. H.; Chameides, W. L.


    For a wide variety of atmospheric species including CO2, HNO3, and SO2, dissolution in seawater or cloudwater followed by hydrolysis or chemical reaction represents a primary pathway for removal from the atmosphere. In order to determine if this mechanism can also remove significant amounts of atmospheric chlorofluorocarbons (HCFC's), fluorocarbons (HFC's), and their degradation products, an investigation was undertaken as part of the Alternative Fluorocarbons Environmental Acceptability Study (AFEAS). In this investigation, the rates at which CHCl2CF3 (HCFC-123), CCl2FCH3 (HCFC-141b), CClF2CH3 (HCFC-142b), CHClF2 (HCFC-22), CHClFCF3 (HCFC-124) CH2FCF3 (HFC-134a) CHF2CH3 (HFC-152a), CHF2CF3 (HFC-125), and CH3CCl3 can be dissolved in the oceans and in cloudwater were estimated from the species' thermodynamic and chemical properties using simple mathematical formulations to simulate the transfer of gases from the atmosphere to the ocean or cloudwater. The ability of cloudwater and rainwater to remove gas phase degradation products of these compounds was also considered as was the aqueous phase chemistry of the degradation products. The results of this investigation are described.

  2. Chemical tailoring of teicoplanin with site-selective reactions. (United States)

    Pathak, Tejas P; Miller, Scott J


    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.

  3. Theoretical study of reaction mechanism for NCO + HCNO (United States)

    Zhang, Weichao; Du, Benni; Feng, Changjun


    A detailed quantum chemical study is performed on the mechanism of the NCO + HCNO reaction, which has never been studied by theory. The potential energy surface for this reaction is characterized at the B3LYP/6-311++G(d,p) level of theory, combined with high-level CBS-QB3 single point energy calculation. Four possible product channels have been investigated. From the calculations it can be seen that the formation of HCN + NO + CO is the dominant product channel, while the pathway to products of HCNN + CO 2 is expected to be minor one, and these conclusions are in good agreement with the experimental results.

  4. Non-equilibrium effects in high temperature chemical reactions (United States)

    Johnson, Richard E.


    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.

  5. Molecular-dynamics study of detonation. II. The reaction mechanism (United States)

    Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.


    In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.

  6. Communication: Control of chemical reactions using electric field gradients. (United States)

    Deshmukh, Shivaraj D; Tsori, Yoav


    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.

  7. Communication: Control of chemical reactions using electric field gradients (United States)

    Deshmukh, Shivaraj D.; Tsori, Yoav


    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.

  8. Extracting Chemical Reactions from Biological Literature (United States)


    positive example is due to incorrect chemical  recognition. In the sentence, “ lactic   acid ” is a chemical used as an adjective describing the  bacteria  and...d-gluconate False Positive A study of the effects of histamine histidine and growth phase on histamine production by lactic acid bacteria isolated...from wine is reported here. lactic acid => histamine n/a False Negative Human 17 beta-hydroxysteroid dehydrogenase 17-HSD type 1 catalyzes

  9. Why Do Lithium-Oxygen Batteries Fail: Parasitic Chemical Reactions and Their Synergistic Effect. (United States)

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


    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.

  10. Mechanical gating of a mechanochemical reaction cascade (United States)

    Wang, Junpeng; Kouznetsova, Tatiana B.; Boulatov, Roman; Craig, Stephen L.


    Covalent polymer mechanochemistry offers promising opportunities for the control and engineering of reactivity. To date, covalent mechanochemistry has largely been limited to individual reactions, but it also presents potential for intricate reaction systems and feedback loops. Here we report a molecular architecture, in which a cyclobutane mechanophore functions as a gate to regulate the activation of a second mechanophore, dichlorocyclopropane, resulting in a mechanochemical cascade reaction. Single-molecule force spectroscopy, pulsed ultrasonication experiments and DFT-level calculations support gating and indicate that extra force of >0.5 nN needs to be applied to a polymer of gated gDCC than of free gDCC for the mechanochemical isomerization gDCC to proceed at equal rate. The gating concept provides a mechanism by which to regulate stress-responsive behaviours, such as load-strengthening and mechanochromism, in future materials designs.

  11. Charge Exchange and Chemical Reactions with Trapped Th$^{3+}$

    CERN Document Server

    Churchill, L R; Chapman, M S


    We have measured the reaction rates of trapped, buffer gas cooled Th$^{3+}$ and various gases and have analyzed the reaction products using trapped ion mass spectrometry techniques. Ion trap lifetimes are usually limited by reactions with background molecules, and the high electron affinity of multiply charged ions such as Th$^{3+}$ make them more prone to loss. Our results show that reactions of Th$^{3+}$ with carbon dioxide, methane, and oxygen all occur near the classical Langevin rate, while reaction rates with argon, hydrogen, and nitrogen are orders of magnitude lower. Reactions of Th$^{3+}$ with oxygen and methane proceed primarily via charge exchange, while simultaneous charge exchange and chemical reaction occurs between Th$^{3+}$ and carbon dioxide. Loss rates of Th$^{3+}$ in helium are consistent with reaction with impurities in the gas. Reaction rates of Th$^{3+}$ with nitrogen and argon depend on the internal electronic configuration of the Th$^{3+}$.

  12. New Possibilities for Magnetic Control of Chemical and Biochemical Reactions. (United States)

    Buchachenko, Anatoly; Lawler, Ronald G


    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

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

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


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

  14. Systematic Error Estimation for Chemical Reaction Energies

    CERN Document Server

    Simm, Gregor N


    For the theoretical understanding of the reactivity of complex chemical systems accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to provide sufficiently accurate data, especially for molecules containing transition metals. Due to the huge number of intermediates that need to be studied for all but the simplest chemical processes, DFT is to date the only method that is computationally feasible. Here, we present a Bayesian framework for DFT that allows for error estimation of calculated properties. Since the optimal choice of parameters in present-day density functionals is strongly system dependent, we advocate for a system-focused re-parameterization. While, at first sight, this approach conflicts with the first-principles character of DFT that should make it in principle system independent, we deliberately introduce system dependence because we can then assign a stochastically meaningful error to the syste...

  15. Quantum chemical investigation of mechanisms of silane oxidation

    DEFF Research Database (Denmark)

    Mader, Mary M.; Norrby, Per-Ola


    Several mechanisms for the peroxide oxidation of organosilanes to alcohols are compared by quantum chemical calculations, including solvation with the PCM method. Without doubt, the reaction proceeds via anionic, pentacoordinate silicate species, but a profound difference is found between in vacuo...

  16. Electronic dissipation processes during chemical reactions on surfaces

    CERN Document Server

    Stella, Kevin


    Hauptbeschreibung Every day in our life is larded with a huge number of chemical reactions on surfaces. Some reactions occur immediately, for others an activation energy has to be supplied. Thus it happens that though a reaction should thermodynamically run off, it is kinetically hindered. Meaning the partners react only to the thermodynamically more stable product state within a mentionable time if the activation energy of the reaction is supplied. With the help of catalysts the activation energy of a reaction can be lowered. Such catalytic processes on surfaces are widely used in industry. A

  17. Quantifying chemical reactions by using mixing analysis. (United States)

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


    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.

  18. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions (United States)

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


    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

  19. Quantum chemical approach to estimating the thermodynamics of metabolic reactions. (United States)

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


    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.

  20. Accelerated Chemical Reactions and Organic Synthesis in Leidenfrost Droplets. (United States)

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


    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.

  1. Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks (United States)

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


    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…

  2. Plasmonic smart dust for probing local chemical reactions. (United States)

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


    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.

  3. The Heck reaction in the production of fine chemicals

    NARCIS (Netherlands)

    Vries, Johannes G. de


    An overview is given of the use of the Heck reaction for the production of fine chemicals. Five commercial products have been identified that are produced on a scale in excess of 1 ton/year. The herbicide Prosulfuron™ is produced via a Matsuda reaction of 2-sulfonatobenzenediazonium on 3,3,3-trifluo

  4. The quantum dynamics of electronically nonadiabatic chemical reactions (United States)

    Truhlar, Donald G.


    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

  5. Modelling Chemical Reasoning to Predict and Invent Reactions. (United States)

    Segler, Marwin H S; Waller, Mark P


    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.

  6. Modeling Electric Double-Layers Including Chemical Reaction Effects

    DEFF Research Database (Denmark)

    Paz-Garcia, Juan Manuel; Johannesson, Björn; Ottosen, Lisbeth M.


    A physicochemical and numerical model for the transient formation of an electric double-layer between an electrolyte and a chemically-active flat surface is presented, based on a finite elements integration of the nonlinear Nernst-Planck-Poisson model including chemical reactions. The model works...

  7. Results of the 2010 Survey on Teaching Chemical Reaction Engineering (United States)

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


    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…

  8. Real time monitoring of accelerated chemical reactions by ultrasonication-assisted spray ionization mass spectrometry. (United States)

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


    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.

  9. Reaction mechanisms in heavy ion fusion

    Directory of Open Access Journals (Sweden)

    Lubian J.


    Full Text Available We discuss the reaction mechanisms involved in heavy ion fusion. We begin with collisions of tightly bound systems, considering three energy regimes: energies above the Coulomb barrier, energies just below the barrier and deep sub-barrier energies. We show that channel coupling effects may influence the fusion process at above-barrier energies, increasing or reducing the cross section predicted by single barrier penetration model. Below the Coulomb barrier, it enhances the cross section, and this effect increases with the system’s size. It is argued that this behavior can be traced back to the increasing importance of Coulomb coupling with the charge of the collision partners. The sharp drop of the fusion cross section observed at deep sub-barrier energies is addressed and the theoretical approaches to this phenomenon are discussed. We then consider the reaction mechanisms involved in fusion reactions of weakly bound systems, paying particular attention to the calculations of complete and incomplete fusion available in the literature.

  10. On the Complexity of Reconstructing Chemical Reaction Networks

    DEFF Research Database (Denmark)

    Fagerberg, Rolf; Flamm, Christoph; Merkle, Daniel


    The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network properties are typically made on standard graphs derived from...... the full hypergraph description, e.g. on the so-called species and reaction graphs. However, a reconstruction of the underlying hypergraph from these graphs is not necessarily unique. In this paper, we address the problem of reconstructing a hypergraph from its species and reaction graph and show NP...

  11. Chemical kinetic mechanism for the oxidation of paraffinic hydrocarbons needed for primary reference fuels

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C.K.; Pitz, W.J.


    A detailed chemical kinetic reaction mechanism is described which simulates the oxidation of the primary reference fuels n-heptane and iso-octane. The high temperature subset of these mechanisms is identified, and the extensions to deal with low temperature conditions are also explained. The algorithms used to assign reaction rates to elementary steps in the reaction mechanism are described, and the means of identifying the different chemical species and the relevant reactions are outlined. Finally, we show how interested kinetic modeling researchers can obtain copies of this reaction mechanism.

  12. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. (United States)

    Liu, Haiyan; Lu, Zhenyu; Cisneros, G Andres; Yang, Weitao


    The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

  13. ReactionMap: an efficient atom-mapping algorithm for chemical reactions. (United States)

    Fooshee, David; Andronico, Alessio; Baldi, Pierre


    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 .

  14. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics. (United States)

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


    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.

  15. NATO Advanced Research Workshop on The Theory of Chemical Reaction Dynamics

    CERN Document Server


    The calculation of cross sections and rate constants for chemical reactions in the gas phase has long been a major problem in theoretical chemistry. The need for reliable and applicable theories in this field is evident when one considers the significant recent advances that have been made in developing experimental techniques, such as lasers and molecular beams, to probe the microscopic details of chemical reactions. For example, it is now becoming possible to measure cross sections for chemical reactions state selected in the vibrational­ rotational states of both reactants and products. Furthermore, in areas such as atmospheric, combustion and interstellar chemistry, there is an urgent need for reliable reaction rate constant data over a range of temperatures, and this information is often difficult to obtain in experiments. The classical trajectory method can be applied routinely to simple reactions, but this approach neglects important quantum mechanical effects such as tunnelling and resonances. For al...

  16. Sequential Voronoi diagram calculations using simple chemical reactions

    CERN Document Server

    Costello, Ben de Lacy; Adamatzky, Andy


    In our recent paper [de Lacy Costello et al. 2010] we described the formation of complex tessellations of the plane arising from the various reactions of metal salts with potassium ferricyanide and ferrocyanide loaded gels. In addition to producing colourful tessellations these reactions are naturally computing generalised Voronoi diagrams of the plane. The reactions reported previously were capable of the calculation of three distinct Voronoi diagrams of the plane. As diffusion coupled with a chemical reaction is responsible for the calculation then this is achieved in parallel. Thus an increase in the complexity of the data input does not utilise additional computational resource. Additional benefits of these chemical reactions is that a permanent record of the Voronoi diagram calculation (in the form of precipitate free bisectors) is achieved, so there is no requirement for further processing to extract the calculation results. Previously it was assumed that the permanence of the results was also a potenti...

  17. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions. (United States)

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


    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

  18. Photochromic properties and reaction mechanism of naphthopyran

    Institute of Scientific and Technical Information of China (English)


    The photochromic properties and reaction mechanism of title compounds have been examined with steady method on compounds 3-phenyl-3-[3-methylbenzothiophene-2-yl]-3H- naphtho[2,1-b]pyran (1) and 3-phenyl-3-[benzofuran-2-yl]-3H-naphtho[2,1-b]pyran (2) and nanosecond laser flash photolysis techniques on compound 3-phenyl-3-[1,2-dimethylindol-3-yl]- 3H-naphtho[2,1-b]pyran (3). The influence of oxygen on transient spectra and decay kinetics of compound 3 has been investigated. Both excited singlet state and triplet state are involved in the photochromic mechanism of compound 3. The influence of molecular structure on photochromic behavior has been studied also. Decay kinetics indicated that the lifetime of colored forms of 1 and 2 were several orders of magnitude longer than that of 3.

  19. Photochromic properties and reaction mechanism of naphthopyran

    Institute of Scientific and Technical Information of China (English)

    潘桂兰; 魏景强; 朱爱平; 明阳福; 樊美公; 姚思德


    The photochromic properties and reaction mechanism of title compounds have been examined with steady method on compounds 3-phenyl-3-[3-methylbenzothiophene-2-yl]-3H-naphtho[2,1-b]pyran (1) and 3-phenyl-3-[benzofuran-2-yl]-3H-naphtho[2,1-b]pyran (2) and nanosecond laser flash photolysis techniques on compound 3-phenyl-3-[1,2-dimethylindol-3-yl]-3H-naphtho[2,1-b]pyran (3). The influence of oxygen on transient spectra and decay kinetics of compound 3 has been investigated. Both excited singlet state and triplet state are involved in the photochromic mechanism of compound 3. The influence of molecular structure on photochromic behavior has been studied also. Decay kinetics indicated that the lifetime of colored forms of 1 and 2 were several orders of magnitude longer than that of 3.

  20. Asymmetric chemical reactions by polarized quantum beams (United States)

    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

  1. An Efficient Chemical Reaction Optimization Algorithm for Multiobjective Optimization. (United States)

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


    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.

  2. Investigation of Electric Arc Furnace Chemical Reactions and stirring effect


    Deng, Lei


    Chemical energy plays a big role in the process of modern Electric Arc Furnace (EAF). The objective of this study is to compare the results of chemical reaction enthalpies calculated by four different methods. In general, the “PERRY-NIST-JANAF method” is used to calculate the chemical energies. However, this method heavily depend on heat capacities of the substances which have to be deduced from  “Perry’s Chemical Engineers’ Handbook” and “NIST-JANAF Thermochemical Tables”, even the calculati...

  3. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule (United States)

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


    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.

  4. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule. (United States)

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


    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.

  5. Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches. (United States)

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


    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.

  6. Structural simplification of chemical reaction networks in partial steady states. (United States)

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


    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.

  7. Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism. (United States)

    Demissie, Taye B; Garabato, Brady D; Ruud, Kenneth; Kozlowski, Pawel M


    The methylation of Hg(II) (SCH3 )2 by corrinoid-based methyl donors proceeds in a concerted manner through a single transition state by transfer of a methyl radical, in contrast to previously proposed reaction mechanisms. This reaction mechanism is a consequence of relativistic effects that lower the energies of the mercury 6p1/2 and 6p3/2 orbitals, making them energetically accessible for chemical bonding. In the absence of spin-orbit coupling, the predicted reaction mechanism is qualitatively different. This is the first example of relativity being decisive for the nature of an observed enzymatic reaction mechanism.

  8. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis (United States)

    Hla, Saw-Wai; Rieder, Karl-Heinz


    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.

  9. Exact probability distributions of selected species in stochastic chemical reaction networks. (United States)

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


    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.

  10. State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy (United States)

    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.

  11. The thermodynamic natural path in chemical reaction kinetics

    Directory of Open Access Journals (Sweden)

    Moishe garfinkle


    Full Text Available The Natural Path approach to chemical reaction kinetics was developed to bridge the considerable gap between the Mass Action mechanistic approach and the non-mechanistic irreversible thermodynamic approach. The Natural Path approach can correlate empirical kinetic data with a high degree precision, as least equal to that achievable by the Mass-Action rate equations, but without recourse mechanistic considerations. The reaction velocities arising from the particular rate equation chosen by kineticists to best represent the kinetic behavior of a chemical reaction are the natural outcome of the Natural Path approach. Moreover, by virtue of its thermodynamic roots, equilibrium thermodynamic functions can be extracted from reaction kinetic data with considerable accuracy. These results support the intrinsic validity of the Natural Path approach.

  12. Flow-Injection Responses of Diffusion Processes and Chemical Reactions

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov


    The technique of Flow-injection Analysis (FIA), now aged 25 years, offers unique analytical methods that are fast, reliable and consuming an absolute minimum of chemicals. These advantages together with its inherent feasibility for automation warrant the future applications of FIA as an attractive...... be used in the resolution of FIA profiles to obtain information about the content of interference’s, in the study of chemical reaction kinetics and to measure absolute concentrations within the FIA-detector cell....

  13. Knockout Reaction Mechanism for 6He+%Knockout Reaction Mechanism for 6He+

    Institute of Scientific and Technical Information of China (English)

    吕林辉; 叶沿林; 曹中鑫; 肖军; 江栋兴; 郑涛; 华辉; 李智焕; 葛俞成; 李湘庆; 楼建玲; 李阔昂; 李奇特; 乔锐; 游海波; 陈瑞九


    A knockout reaction experiment was carried out by using the 6He beam at 82.5 MeV/nucleon impinging on CH2 and C targets. The a core fragments at forward angles were detected in coincidence with the recoiled protons at larger angles. From this exclusive measure- ment the valence nucleon knockout mechanism and the core knockout mechanism are separated. This study provides a basis for the exclusive spectroscopic investigation of the exotic nuclei.

  14. Planarization mechanism of alkaline copper CMP slurry based on chemical mechanical kinetics (United States)

    Shengli, Wang; Kangda, Yin; Xiang, Li; Hongwei, Yue; Yunling, Liu


    The planarization mechanism of alkaline copper slurry is studied in the chemical mechanical polishing (CMP) process from the perspective of chemical mechanical kinetics. Different from the international dominant acidic copper slurry, the copper slurry used in this research adopted the way of alkaline technology based on complexation. According to the passivation property of copper in alkaline conditions, the protection of copper film at the concave position on a copper pattern wafer surface can be achieved without the corrosion inhibitors such as benzotriazole (BTA), by which the problems caused by BTA can be avoided. Through the experiments and theories research, the chemical mechanical kinetics theory of copper removal in alkaline CMP conditions was proposed. Based on the chemical mechanical kinetics theory, the planarization mechanism of alkaline copper slurry was established. In alkaline CMP conditions, the complexation reaction between chelating agent and copper ions needs to break through the reaction barrier. The kinetic energy at the concave position should be lower than the complexation reaction barrier, which is the key to achieve planarization.

  15. Planarization mechanism of alkaline copper CMP slurry based on chemical mechanical kinetics

    Institute of Scientific and Technical Information of China (English)

    Wang Shengli; Yin Kangda; Li Xiang; Yue Hongwei; Liu Yunling


    The planarization mechanism of alkaline copper slurry is studied in the chemical mechanical polishing (CMP) process from the perspective of chemical mechanical kinetics.Different from the international dominant acidic copper slurry,the copper slurry used in this research adopted the way of alkaline technology based on complexation.According to the passivation property of copper in alkaline conditions,the protection of copper film at the concave position on a copper pattern wafer surface can be achieved without the corrosion inhibitors such as benzotriazole (BTA),by which the problems caused by BTA can be avoided.Through the experiments and theories research,the chemical mechanical kinetics theory of copper removal in alkaline CMP conditions was proposed.Based on the chemical mechanical kinetics theory,the planarization mechanism of alkaline copper slurry was established.In alkaline CMP conditions,the complexation reaction between chelating agent and copper ions needs to break through the reaction barrier.The kinetic energy at the concave position should be lower than the complexation reaction barrier,which is the key to achieve planarization.

  16. Effects of incomplete mixing on chemical reactions under flow heterogeneities. (United States)

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


    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

  17. Reaction diffusion and solid state chemical kinetics handbook

    CERN Document Server

    Dybkov, V I


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

  18. Molecular codes in biological and chemical reaction networks. (United States)

    Görlich, Dennis; Dittrich, Peter


    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.

  19. Supersonic molecular beam experiments on surface chemical reactions. (United States)

    Okada, Michio


    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.

  20. Prediction of Rate Constants for Catalytic Reactions with Chemical Accuracy. (United States)

    Catlow, C Richard A


    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.

  1. Moment equations for chemical reactions on interstellar dust grains

    CERN Document Server

    Lipshtat, A; Lipshtat, Azi; Biham, Ofer


    While most chemical reactions in the interstellar medium take place in the gas phase, those occurring on the surfaces of dust grains play an essential role. Chemical models based on rate equations including both gas phase and grain surface reactions have been used in order to simulate the formation of chemical complexity in interstellar clouds. For reactions in the gas phase and on large grains, rate equations, which are highly efficient to simulate, are an ideal tool. However, for small grains under low flux, the typical number of atoms or molecules of certain reactive species on a grain may go down to order one or less. In this case the discrete nature of the opulations of reactive species as well as the fluctuations become dominant, thus the mean-field approximation on which the rate equations are based does not apply. Recently, a master equation approach, that provides a good description of chemical reactions on interstellar dust grains, was proposed. Here we present a related approach based on moment equ...

  2. Force-activated reactivity switch in a bimolecular chemical reaction at the single molecule level (United States)

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


    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.

  3. Multiscale stochastic simulations of chemical reactions with regulated scale separation

    Energy Technology Data Exchange (ETDEWEB)

    Koumoutsakos, Petros, E-mail: [Chair of Computational Science, Clausiusstrasse 33, ETH Zurich, CH-8092 (Switzerland); Feigelman, Justin [Chair of Computational Science, Clausiusstrasse 33, ETH Zurich, CH-8092 (Switzerland)


    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.

  4. NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics

    CERN Document Server

    Capellos, Christos


    This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys­ tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...

  5. Coriolis coupling and nonadiabaticity in chemical reaction dynamics. (United States)

    Wu, Emilia L


    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.

  6. Theoretical considerations of Flow Injection Analysis in the Absence of Chemical Reactions

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov


    The fundamental mechanism of flow injection analysis (FIA) is assumed to be simple dissusion and the response of the detector is included in a model description that provide information about the shape of the FIA peak in terms of, basically, five parameters. Two of the five parameters are associa...... that any deviation from the features of the present model and the results of a tentative chemical reaction with one of the test compounds, is related to chemical kinetics....

  7. A thermodynamic force generated by chemical gradient and adsorption reaction

    CERN Document Server

    Sugawara, Takeshi


    Biological units such as macromolecules, organelles, and cells are directed to a proper location under gradients of relevant chemicals. By considering a macroscopic element that has binding sites for a chemical adsorption reaction to occur on its surface, we show the existence of a thermodynamic force that is generated by the gradient and exerted on the element. By assuming local equilibrium and adopting the grand potential from thermodynamics, we derive a formula for such a thermodynamic force, which depends on the chemical potential gradient and Langmuir isotherm. The conditions under which the formula can be applied are demonstrated to hold in intracellular reactions. The role of the force in the partitioning of bacterial chromosome/plasmid during cell division is discussed.

  8. Single-molecule chemical reactions on DNA origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Rotaru, Alexandru


    as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position...... on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally......DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve...

  9. Carbonitriding reactions of diatomaceous earth: phase evolution and reaction mechanisms

    Directory of Open Access Journals (Sweden)



    Full Text Available The possibility of using diatomaceous earth as Si precursor for low temperature synthesis of non-oxide powders by carbothermal reduction-nitridation was studied. It was found that carbonitriding reactions produce phases of the Si–Al–O–N system. Already at 1300 °C, nanosized, non-oxide powders were obtained. The comparatively low reaction temperatures is attributred to the nano-porous nature of the raw material. The evolution of crystalline phases proceeded via many intermediate stages. The powders were characterized by X-ray and SEM investigations. The results showed that diatomaceous earth can be a very effective source for obtaining non-oxide powders.

  10. Two Experiments to Approach the Boltzmann Factor: Chemical Reaction and Viscous Flow (United States)

    Fazio, Claudio; Battaglia, Onofrio R.; Guastella, Ivan


    In this paper we discuss a pedagogical approach aimed at pointing out the role played by the Boltzmann factor in describing phenomena usually perceived as regulated by different mechanisms of functioning. Experimental results regarding some aspects of a chemical reaction and of the viscous flow of some liquids are analysed and described in terms…

  11. The mechanism of the modified Ullmann reaction

    NARCIS (Netherlands)

    Sperotto, Elena; Klink, Gerard P.M. van; Koten, Gerard van; Vries, Johannes G. de


    The copper-mediated aromatic nucleophilic substitution reactions developed by Fritz Ullmann and Irma Goldberg required stoichiometric amounts of copper and very high reaction temperatures. Recently, it was found that addition of relatively cheap ligands (diamines, aminoalcohols, diketones, diols) ma

  12. Insight into the Mechanism of the Michael Reaction. (United States)

    Giraldo, Carolina; Gómez, Sara; Weinhold, Frank; Restrepo, Albeiro


    The mechanism for the nucleophilic addition step of the Michael reaction between methanethiol as a model Michael donor and several α-substituted methyl acrylates (X=F, Cl, Me, H, CN, NO2 ) as model Michael acceptors is described in detail. We suggest a novel way to condense electrophilic Fukui functions at specific atoms in terms of the contributions from the atomic orbitals to the LUMO or, more generally, to the orbital controlling the reaction. This procedure correctly associates activation energies to local electrophilic Fukui indices for the cases treated in this work. The calculated reaction barriers strongly depend on the nature of the substituent. As a general rule, activation energies are governed by structural changes, although electronic factors are significant for electron-withdrawing groups. Nucleophilic addition to Michael receptors is best described as a highly nonsynchronous process, in which the geometry of the transition state comprises a nonplanar six-membered ring. Formation of the S⋅⋅⋅C bond, which defines the interaction between the reactants, progresses ahead of all other primitive processes in the early stages of the transformation. In view of our results, we postulate that highly complex chemical reactions, as is the case for the nucleophilic addition step studied herein, that involve cleavage/formation of a total of six bonds, lower their activation energies by favoring nonsynchronicity, that is, for these types of systems, primitive changes should advance at different rates.

  13. Heterogeneously Catalysed Chemical Reactions in Carbon Dioxide Medium

    DEFF Research Database (Denmark)

    Musko, Nikolai E.

    studies of catalytic chemical reactions in dense and supercritical carbon dioxide have been complemented by the theoretical calculations of phase equilibria using advanced thermodynamic models. In the recent years, the use of compressed carbon dioxide as innovative, non-toxic and non-flammable, cheap...... is discussed more extensively. Heterogeneously catalysed hydrogenation reactions are considered to be quite well studied and established. However, the catalyst performance can alter significantly when the reaction is performed in carbon dioxide medium. This effect was studied with the example of the selective...... the selective hydrogenation of unsaturated aldehydes in carbon dioxide medium. It was found that supported tungstosilicic acid catalysts and acidic resin Amberlyst-15 are very effective for performing aldol reactions. The positive influence of temperature and CO2-content on catalyst activity was studied...

  14. Reaction Networks For Interstellar Chemical Modelling: Improvements and Challenges

    CERN Document Server

    Wakelam, V; Herbst, E; Troe, J; Geppert, W; Linnartz, H; Oberg, K; Roueff, E; Agundez, M; Pernot, P; Cuppen, H M; Loison, J C; Talbi, D


    We survey the current situation regarding chemical modelling of the synthesis of molecules in the interstellar medium. The present state of knowledge concerning the rate coefficients and their uncertainties for the major gas-phase processes -- ion-neutral reactions, neutral-neutral reactions, radiative association, and dissociative recombination -- is reviewed. Emphasis is placed on those reactions that have been identified, by sensitivity analyses, as 'crucial' in determining the predicted abundances of the species observed in the interstellar medium. These sensitivity analyses have been carried out for gas-phase models of three representative, molecule-rich, astronomical sources: the cold dense molecular clouds TMC-1 and L134N, and the expanding circumstellar envelope IRC +10216. Our review has led to the proposal of new values and uncertainties for the rate coefficients of many of the key reactions. The impact of these new data on the predicted abundances in TMC-1 and L134N is reported. Interstellar dust p...

  15. Chemical research on red pigments after adverse reactions to tattoo. (United States)

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


    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.

  16. Effect of Chemicals on Chemical Mechanical Polishing of Glass Substrates

    Institute of Scientific and Technical Information of China (English)

    WANG Liang-Yong; ZHANG Kai-Liang; SONG Zhi-Tang; FENG Song-Lin


    @@ We investigate the effect of chemicals on chemical mechanical polishing (CMP) of glass substrates. Ceria slurry in an ultra-low concentration of 0.25wt.% is used and characterized by scanning electron microscopy. Three typical molecules, i.e. acetic acid, citric acid and sodium acrylic polymer, are adopted to investigate the effect on CMP performance in terms of material removal rate (MRR) and surface quality. The addition of sodium acrylic polymer shows the highest MRR as well as the best surface by atomic force microscopy after CMP, vhile the addition of citric acid shows the worst performance. These results reveal a mechanism that a long-chain molecule without any branches rather than small molecules and common molecules with ramose abundant-electron groups is better for the dispersion of the slurry and thus better for the CMP process.

  17. Mathematical description of the nonlinear chemical reactions with oscillatory inflow to the reaction field

    Indian Academy of Sciences (India)

    Aldona Krupska


    In this paper the arduous attempt to find a mathematical solution for the nonlinear autocatalytic chemical processes with a time-varying and oscillating inflow of reactant to the reaction medium has been taken. Approximate analytical solution is proposed. Numerical solutions and analytical attempts to solve the non-linear differential equation indicates a phase shift between the oscillatory influx of intermediate reaction reagent to the medium of chemical reaction and the change of its concentration in this medium. Analytical solutions indicate that this shift may be associated with the reaction rate constants 1 and 2 and the relaxation time . The relationship between the phase shift and the oscillatory flow of reactant seems to be similar to that obtained in the case of linear chemical reactions, as described previously, however, the former is much more complex and different. In this paper, we would like to consider whether the effect of forced phase shift in the case of nonlinear and non-oscillatory chemical processes occurring particularly in the living systems have a practical application in laboratory.

  18. Computational Analyses of Complex Flows with Chemical Reactions (United States)

    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

  19. The chemical, mechanical, and hydrological evolution of weathering granitoid (United States)

    Goodfellow, Bradley W.; Hilley, George E.; Webb, Samuel M.; Sklar, Leonard S.; Moon, Seulgi; Olson, Christopher A.


    Surprisingly few studies connect the chemical, mechanical, and hydrological evolution of rock as it weathers to saprolite and soil. We assess this coevolution in granodiorite from Monterey Peninsula, California, by measuring changes in bulk chemistry, mineralogy, volumetric strain, the oxidation state of Fe in biotite crystals, tensile strength, abrasion rate, connected porosity, and hydraulic conductivity in samples covering a range of weathering grades. We identify the oxidative dissolution of biotite as the key chemical reaction because of the volumetric expansion that accompanies formation of altered biotite and precipitation of ferrihydrite. We show how the associated accumulation of elastic strain produces an energy density that is sufficient to support rock fracturing over length scales equivalent to constituent crystals. The resulting intragranular and intergranular cracking profoundly reduces tensile strength and increases the abrasion rate, connected porosity, and hydraulic conductivity of the rock matrix. These changes increase the rate of plagioclase weathering, and ultimately the rock disintegrates into grus and clay. Major changes in rock properties can occur with only minor element leaching, and the threshold behavior of weathering that arises from the coevolution of chemical, hydrological, and mechanical properties may be difficult to capture using simplified weathering models that fail to incorporate these properties. Our results, which combine the mechanical and hydrological evolution of weathering rock with more common measurements of chemical changes, should help to more accurately model the effects of, and mechanical and hydrological feedbacks upon, chemical weathering of rock.

  20. Photo-induced chemical reaction of trans-resveratrol. (United States)

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


    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.

  1. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions (United States)

    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.

  2. Tribo-chemical mechanisms of copper chemical mechanical planarization (CMP) - Fundamental investigations and integrated modeling (United States)

    Tripathi, Shantanu

    inhibiting solutions, in particular to rule out capacitive charging beyond 1ms. Chronoamperometry of copper in acidic aqueous glycine solution containing the corrosion inhibitor benzotriazole (BTA) (a system that undergoes inhibition) displayed a very consistent current decay behavior at all potentials (current was inversely related to the square root of time). This, along with the scan rate dependent polarization data, indicated that the likely controlling step of the inhibition reaction was diffusion of BTA to the surface. EIS data indicated the presence of very thick inhibitor film at anodic potentials. In basic aqueous glycine solution, copper (a system that undergoes passivation, and is believed to induce mechanisms similar to those operating in weakly acidic hydrogen peroxide slurries) displayed similar chronoamperometric behavior for all anodic potentials for the first second or so. Thereafter, the current densities at active potentials settled to values around those expected from polarization curves, whereas the current densities at passive potentials continued to decline. Oxidized copper species typically formed at 'active' potentials were found to cause significant current decay at active potentials and at passive potentials before more protective passive films form. This was established from galvanostatic experiments; chronoamperometry behavior for different pre-step potentials indicating a role of passivation precursors; and distinctive EIS behavior at 'active' potentials. The second important component of the integrated tribo-chemical model, namely the mechanical properties of passive films on copper, was investigated using an environmental atomic force microscope (AFM). From the material removal response, the presence of a threshold abrasive force for removal of passive film was found. The removal per abrasive stroke was found to be less than an atomic layer, consistent with the prediction made by theoretical calculations on interaction frequency; this implies

  3. Reachability bounds for chemical reaction networks and strand displacement systems. (United States)

    Condon, Anne; Kirkpatrick, Bonnie; Maňuch, Ján


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

  4. Laser studies of chemical reaction and collision processes

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, G. [Columbia Univ., New York, NY (United States)


    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.

  5. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases. (United States)

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


    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.

  6. The mechanical and chemical equations of motion of muscle contraction (United States)

    Shiner, J. S.; Sieniutycz, Stanislaw


    Up to now no formulation of muscle contraction has provided both the chemical kinetic equations for the reactions responsible for the contraction and the mechanical equation of motion for the muscle. This has most likely been due to the lack of general formalisms for nonlinear systems with chemical-nonchemical coupling valid under the far from equilibrium conditions under which muscle operates physiologically. We have recently developed such formalisms and apply them here to the formulation of muscle contraction to obtain both the chemical and the mechanical equations. The standard formulation up to now has yielded only the dynamic equations for the chemical variables and has considered these to be functions of both time and an appropriate mechanical variable. The macroscopically observable quantities were then obtained by averaging over the mechanical variable. When attempting to derive the dynamics equations for both the chemistry and mechanics this choice of variables leads to conflicting results for the mechanical equation of motion when two different general formalisms are applied. The conflict can be resolved by choosing the variables such that both the chemical variables and the mechanical variables are considered to be functions of time alone. This adds one equation to the set of differential equations to be solved but is actually a simplification of the problem, since these equations are ordinary differential equations, not the partial differential equations of the now standard formulation, and since in this choice of variables the variables themselves are the macroscopic observables the procedure of averaging over the mechanical variable is eliminated. Furthermore, the parameters occurring in the equations at this level of description should be accessible to direct experimental determination.

  7. Simulation of underexpanded supersonic jet flows with chemical reactions

    Directory of Open Access Journals (Sweden)

    Fu Debin


    Full Text Available To achieve a detailed understanding of underexpanded supersonic jet structures influenced by afterburning and other flow conditions, the underexpanded turbulent supersonic jet with and without combustions are investigated by computational fluid dynamics (CFD method. A program based on a total variation diminishing (TVD methodology capable of predicting complex shocks is created to solve the axisymmetric expanded Navier–Stokes equations containing transport equations of species. The finite-rate ratio model is employed to handle species sources in chemical reactions. CFD solutions indicate that the structure of underexpanded jet is typically influenced by the pressure ratio and afterburning. The shock reflection distance and maximum value of Mach number in the first shock cell increase with pressure ratio. Chemical reactions for the rocket exhaust mostly exist in the mixing layer of supersonic jet flows. This tends to reduce the intensity of shocks existing in the jet, responding to the variation of thermal parameters.

  8. Simulation of underexpanded supersonic jet flows with chemical reactions

    Institute of Scientific and Technical Information of China (English)

    Fu Debin; Yu Yong; Niu Qinglin


    To achieve a detailed understanding of underexpanded supersonic jet structures influenced by afterburning and other flow conditions, the underexpanded turbulent supersonic jet with and without combustions are investigated by computational fluid dynamics (CFD) method. A program based on a total variation diminishing (TVD) methodology capable of predicting complex shocks is created to solve the axisymmetric expanded Navier-Stokes equations containing transport equations of species. The finite-rate ratio model is employed to handle species sources in chemical reactions. CFD solutions indicate that the structure of underexpanded jet is typically influenced by the pressure ratio and afterburning. The shock reflection distance and maximum value of Mach number in the first shock cell increase with pressure ratio. Chemical reactions for the rocket exhaust mostly exist in the mixing layer of supersonic jet flows. This tends to reduce the intensity of shocks existing in the jet, responding to the variation of thermal parameters.

  9. Tabletop imaging of structural evolutions in chemical reactions

    CERN Document Server

    Ibrahim, Heide; Beaulieu, Samuel; Schmidt, Bruno E; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Sanderson, Joseph; Schuurman, Michael S; Légaré, François


    The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using VUV light from a Free Electron Laser [Phys. Rev. Lett. 105, 263002 (2010)]. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond-breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and definitively quantitative ab initio trajectory simulations.

  10. Chemical Synthesis of Proanthocyanidins in Vitro and Their Reactions in Aging Wines

    Directory of Open Access Journals (Sweden)

    Qiu-Hong Pan


    Full Text Available Proanthocyanidins are present in many fruits and plant products like grapes and wine, and contribute to their taste and health benefits. In the past decades of years, substantial progresses has been achieved in the identification of composition and structure of proanthocyanidins, but the debate concerning the existence of an enzymatic or nonenzymatic mechanism for proanthocyanidin condensation still goes on. Substantial attention has been paid to elucidating the potential mechanism of formation by means of biomimetic and chemical synthesis in vitro. The present paper aims at summarizing the research status on chemical synthesis of proanthocyanidins, including non-enzymatic synthesis of proanthocyanidin precursors, chemical synthesis of proanthocyanidins with direct condensation of flavanols and stereoselective synthesis of proanthocyanidins. Proanthocyanidin-involved reactions in aging wines are also reviewed such as direct and indirect reactions among proanthocyanidins, flavanols and anthocyanins. Topics for future research in this field are also put forward in this paper.

  11. Implementation of a vibrationally linked chemical reaction model for DSMC (United States)

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


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  13. How is entropy production rate related to chemical reaction rate?

    CERN Document Server

    Banerjee, Kinshuk


    The entropy production rate is a key quantity in irreversible thermodynamics. In this work, we concentrate on the realization of entropy production rate in chemical reaction systems in terms of the experimentally measurable reaction rate. Both triangular and linear networks have been studied. They attain either thermodynamic equilibrium or a non-equilibrium steady state, under suitable external constraints. We have shown that the entropy production rate is proportional to the square of the reaction velocity only around equilibrium and not any arbitrary non-equilibrium steady state. This feature can act as a guide in revealing the nature of a steady state, very much like the minimum entropy production principle. A discussion on this point has also been presented.

  14. Reaction Mechanisms of Magnesium Potassium Phosphate Cement and its Application (United States)

    Qiao, Fei

    Magnesium potassium phosphate cement (MKPC) is a kind of cementitious binder in which the chemical bond is formed via a heterogeneous acid-base reaction between dead burned magnesia powder and potassium phosphate solution at room temperature. Small amount of boron compounds can be incorporated in the cement as a setting retarder. The final reaction product of MgO-KH2PO4-H 2O ternary system is identified as magnesium potassium phosphate hexahydrate, MgKPO4·6H2O. However, the mechanisms and procedures through which this crystalline product is formed and the conditions under which the crystallization process would be influenced are not yet clear. Understanding of the reaction mechanism of the system is helpful for developing new methodologies to control the rapid reaction process and furthermore, to adjust the phase assemblage of the binder, and to enhance the macroscopic properties. This study is mainly focused on the examination of the reaction mechanism of MKPC. In addition, the formulation optimization, microstructure characterization and field application in rapid repair are also systematically studied. The chemical reactions between magnesia and potassium dihydrogen phosphate are essentially an acid-base reaction with strong heat release, the pH and temperature variation throughout the reaction process could provide useful information to disclose the different stages in the reaction. However, it would be very difficult to conduct such tests on the cement paste due to the limited water content and fast setting. In the current research, the reaction mechanism of MKPC is investigated on the diluted MKPC system through monitoring the pH and temperature development, identification of the solid phase formed, and measurement of the ionic concentration of the solution. The reaction process can be explained as follows: when magnesia and potassium phosphate powder are mixed with water, phosphate is readily dissolved, which is instantly followed by the dissociation of

  15. Nonlinear chemical reaction between Na2S2O3 and Peroxide compound

    Institute of Scientific and Technical Information of China (English)

    高庆宇; 汪跃民; 王贵昌; 张松林; 臧雅茹; 赵学庄


    Kinetics of reaction between Na2S2O3 and peroxide compound ( H2O2 or Na2S2O8) in a batch reactor and in a continuous stirring tank reactor (CSTR) were studied.Steady oscillations in uncatalyzed reactions in a CSTR were first discovered.In Na2S2O3-H2O2-H2SO4 reaction system,Pt potential and pH of higher and lower flow rutes beyond oscillation flow rates were in around the same extreme values.The reaction catalyeed by Cu2+ corsist of the catalyzed oscillation process and the uncatalyzed osciliation one.On the basis of experiment,a reaction mechanism consisting of three stages was put forward.The three stages are H positive-feedback reactions,proton negative-feedba k (uncatalyzed negative-feedback and catalyzed negative-feedback) reactions and transitional reactions.The mechanism is able to explain reasonably the nonlinear chemical phenomena appearing in the thiosulfatc oxidation reaction by peroxide-compounds.

  16. A multipurpose reduced chemical-kinetic mechanism for methanol combustion (United States)

    Fernández-Tarrazo, Eduardo; Sánchez-Sanz, Mario; Sánchez, Antonio L.; Williams, Forman A.


    A multipurpose reduced chemical-kinetic mechanism for methanol combustion comprising 8 overall reactions and 11 reacting chemical species is presented. The development starts by investigating the minimum set of elementary reactions needed to describe methanol combustion with reasonable accuracy over a range of conditions of temperature, pressure, and composition of interest in combustion. Starting from a 27-step mechanism that has been previously tested and found to give accurate predictions of ignition processes for these conditions, it is determined that the addition of 11 elementary reactions taken from its basis (San Diego) mechanism extends the validity of the description to premixed-flame propagation, strain-induced extinction of non-premixed flames, and equilibrium composition and temperatures, giving results that compare favourably with experimental measurements and also with computations using the 247-step detailed San Diego mechanism involving 50 reactive species. Specifically, premixed-flame propagation velocities and extinction strain rates for non-premixed counterflow flames calculated with the 38-step mechanism show departures from experimental measurements and detailed-chemistry computations that are roughly on the order of 10%, comparable with expected experimental uncertainties. Similar accuracy is found in comparisons of autoignition times over the range considered, except at very high temperatures, under which conditions the computations tend to overpredict induction times for all of the chemistry descriptions tested. From this 38-step mechanism, the simplification is continued by introducing steady-state approximations for the intermediate species CH3, CH4, HCO, CH3O, CH2OH, and O, leading to an 8-step reduced mechanism that provides satisfactory accuracy for all conditions tested. The flame computations indicate that thermal diffusion has a negligible influence on methanol combustion in all cases considered and that a mixture-average species

  17. Reversible chemical reactions for single-color multiplexing microscopy. (United States)

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


    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.

  18. Ultrafast chemical reactions in shocked nitromethane probed with dynamic ellipsometry and transient absorption spectroscopy. (United States)

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


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

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

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, H.D.


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, H.D.


    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.

  1. Material removal mechanism of copper chemical mechanical polishing in a periodate-based slurry (United States)

    Cheng, Jie; Wang, Tongqing; He, Yongyong; Lu, Xinchun


    The material removal mechanism of copper in a periodate-based slurry during barrier layer chemical mechanical polishing (CMP) has not been intensively investigated. This paper presents a study of the copper surface film chemistry and mechanics in a periodate-based slurry. On this basis, the controlling factor of the copper CMP material removal mechanism is proposed. The results show that the chemical and electrochemical reaction products on the copper surface are complex and vary considerably as a function of the solution pH. Under acidic conditions (pH 4) the copper surface underwent strong chemical dissolution while the corrosion was mild and uniform under alkaline conditions (pH 11). The corrosion effect was the lowest in near neutral solutions because the surface was covered with non-uniform Cu(IO3)2·H2O/Cu-periodate/copper oxides films, which had better passivation effect. The surface film thickness and mechanical removal properties were studied by AES and AFM nano-scratch tests. Based on the combined surface film analysis and CMP experiment results, it can be concluded that the controlling factor during copper CMP in a periodate-based slurry is the chemical-enhanced mechanical removal of the surface films. The periodate-based slurry should be modified by the addition of corrosion inhibitors and complexing agents to achieve a good copper surface quality with moderate chemical dissolution.

  2. Cation Effect on Copper Chemical Mechanical Polishing

    Institute of Scientific and Technical Information of China (English)

    WANG Liang-Yong; LIU Bo; SONG Zhi-Tang; FENG Song-Lin


    We examine the effect of cations in solutions containing benzotriazole (BTA) and H2O2 on copper chemical mechanical polishing (CMP). On the base of atomic force microscopy (AFM) and material removal rate (MRR) results, it is found that ammonia shows the highest MRR as well as good surface after CMP, while KOH demon-strates the worst performance. These results reveal a mechanism that sma//molecules with lone-pairs rather than molecules with steric effect and common inorganic cations are better for copper CMP process, which is indirectly confirmed by open circuit potential (OCP).

  3. Cation Effect on Copper Chemical Mechanical Polishing (United States)

    Wang, Liang-Yong; Liu, Bo; Song, Zhi-Tang; Feng, Song-Lin


    We examine the effect of cations in solutions containing benzotriazole (BTA) and H2O2 on copper chemical mechanical polishing (CMP). On the base of atomic force microscopy (AFM) and material removal rate (MRR) results, it is found that ammonia shows the highest MRR as well as good surface after CMP, while KOH demonstrates the worst performance. These results reveal a mechanism that small molecules with lone-pairs rather than molecules with steric effect and common inorganic cations are better for copper CMP process, which is indirectly confirmed by open circuit potential (OCP).

  4. Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism. (United States)

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori


    The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an SN1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

  5. Chemical reaction network approaches to Biochemical Systems Theory. (United States)

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


    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.

  6. Chemical reaction optimization for solving shortest common supersequence problem. (United States)

    Khaled Saifullah, C M; Rafiqul Islam, Md


    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.

  7. Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas. (United States)

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

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

  8. Reaction mechanism for the thermal decomposition of BCl3/CH4/H2 gas mixtures. (United States)

    Reinisch, Guillaume; Vignoles, Gérard L; Leyssale, Jean-Marc


    This paper presents an ab initio study of the B/C/Cl/H gas phase mechanism, featuring 10 addition-elimination reactions involving BH(i)Cl(j) (i + j ≤ 3) species and a first description of the chemical interaction between the carbon-containing and boron-containing subsystems through the three reactions BCl(3) + CH(4) ⇌ BCl(2)CH(3) + HCl, BHCl(2) + CH(4) ⇌ BCl(2)CH(3) + H(2), and BCl(2) + CH(4) ⇌ BHCl(2) + CH(3). A reaction mechanism is then proposed and used to perform some illustrative equilibrium and kinetic calculations in the context of chemical vapor deposition (CVD) of boron carbide. Our results show that the new addition-elimination reaction paths play a crucial role by lowering considerably the activation barrier with respect to previous theoretical evaluations; they also confirm that BCl(2)CH(3) is an important species in the mechanism.

  9. Holistic Metrics for Assessment of the Greenness of Chemical Reactions in the Context of Chemical Education (United States)

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


    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…

  10. Study of Reaction Mechanism in Tracer Munitions (United States)


    Regression Rates (Furnished by Frankford Arsenal) 35 13 Calculated Heat Fluxes and Energy Partitions 43 4 I NOMENCLATURE B = preexponential factor... anhydride disproportionates in a fast step: N2 0 3 - 2 + NO (4) so that the resulting dioxide can react with more nitrite in another fast reaction: Sr

  11. Thermal energy storage. [by means of chemical reactions (United States)

    Grodzka, P. G.


    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.

  12. A quantum informational approach for dissecting chemical reactions

    CERN Document Server

    Duperrouzel, Corinne; Boguslawski, Katharina; Barcza, Gergerly; Legeza, Örs; Ayers, Paul W


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

  13. Modelling of structural effects on chemical reactions in turbulent flows

    Energy Technology Data Exchange (ETDEWEB)

    Gammelsaeter, H.R.


    Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.

  14. Spatially resolved chemical reaction monitoring using magnetic resonance imaging. (United States)

    Feindel, Kirk W


    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.

  15. Optimized reaction mechanism rate rules for ignition of normal alkanes

    KAUST Repository

    Cai, Liming


    The increasing demand for cleaner combustion and reduced greenhouse gas emissions motivates research on the combustion of hydrocarbon fuels and their surrogates. Accurate detailed chemical kinetic models are an important prerequisite for high fidelity reacting flow simulations capable of improving combustor design and operation. The development of such models for many new fuel components and/or surrogate molecules is greatly facilitated by the application of reaction classes and rate rules. Accurate and versatile rate rules are desirable to improve the predictive accuracy of kinetic models. A major contribution in the literature is the recent work by Bugler et al. (2015), which has significantly improved rate rules and thermochemical parameters used in kinetic modeling of alkanes. In the present study, it is demonstrated that rate rules can be used and consistently optimized for a set of normal alkanes including n-heptane, n-octane, n-nonane, n-decane, and n-undecane, thereby improving the predictive accuracy for all the considered fuels. A Bayesian framework is applied in the calibration of the rate rules. The optimized rate rules are subsequently applied to generate a mechanism for n-dodecane, which was not part of the training set for the optimized rate rules. The developed mechanism shows accurate predictions compared with published well-validated mechanisms for a wide range of conditions.

  16. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics. (United States)

    Shemesh, Dorit; Nizkorodov, Sergey A; Gerber, R Benny


    Photochemistry of carbonyl compounds is of major importance in atmospheric and organic chemistry. The photochemistry of cyclohexanone is studied here using on-the-fly molecular dynamics simulations on a semiempirical multireference configuration interaction potential-energy surface to predict the distribution of photoproducts and time scales for their formation. Rich photochemistry is predicted to occur on a picosecond time scale following the photoexcitation of cyclohexanone to the first singlet excited state. The main findings include: (1) Reaction channels found experimentally are confirmed by the theoretical simulations, and a new reaction channel is predicted. (2) The majority (87%) of the reactive trajectories start with a ring opening via C-Cα bond cleavage, supporting observations of previous studies. (3) Mechanistic details, time scales, and yields are predicted for all reaction channels. These benchmark results shed light on the photochemistry of isolated carbonyl compounds in the atmosphere and can be extended in the future to photochemistry of more complex atmospherically relevant carbonyl compounds in both gaseous and condensed-phase environments.

  17. Reaction Mechanism Investigation Using Vibrational Mode Analysis for the Multichannel Reaction of CH3O + CO

    Institute of Scientific and Technical Information of China (English)

    ZHOU,Zheng-Yu(周正宇); CHENG,Xue-Li(程学礼); GUO,Li(郭丽)


    On the basis of the computed results got by the Gaussian 94 package at B3LYP/6-311 + +G * * level, the reaction mechanism of CH3O radical with CO has been investigated thoroughly via the vibrational model analysis. And the relationships among the reactants, eight transition states, four intermediates and various products involved this multichannel reaction are elucidated. The vibrational mode analysis shows that the reaction mechanism is reliable.

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

    Energy Technology Data Exchange (ETDEWEB)

    Valentini, J.J. [Columbia Univ., New York, NY (United States)


    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.

  19. Tribology analysis of chemical-mechanical polishing

    Energy Technology Data Exchange (ETDEWEB)

    Runnels, S.R.; Eyman, L.M. (Sematech, Austin, TX (United States))


    To better understand the variation of material removal rate on a wafer during chemical-mechanical polishing (CMP), knowledge of the stress distribution on the wafer surface is required. The difference in wafer-surface stress distributions could be considerable depending on whether or not the wafer hydroplanes during polishing. This study analyzes the fluid film between the wafer and pad and demonstrates that hydroplaning is possible for standard CMP processes. The importance of wafer curvature, slurry viscosity, and rotation speed on the thickness of the fluid film is also demonstrated.

  20. Mechanical and Chemical Signaling in Angiogenesis

    CERN Document Server


    This volume of Studies in Mechanobiology, Tissue Engineering and Biomaterials describes the most recent advances in angiogenesis research at all biological length scales: molecular, cellular and tissue, in both in vivo and in vitro settings.  Angiogenesis experts from diverse fields including engineering, cell and developmental biology, and chemistry have contributed chapters which focus on the mechanical and chemical signals which affect and promote blood vessel growth. Specific emphasis is given to novel methodologies and biomaterials that have been developed and applied to angiogenesis research. 

  1. The Mechanism of Surface Chemical Kinetics of Dissolution of Minerals

    Institute of Scientific and Technical Information of China (English)

    谭凯旋; 张哲儒; 等


    This paper deals with the mechanism of dissolution reaction kinetics of minerals in aqueous solution based on the theory of surface chemistry.Surface chemical catalysis would lead to an obvous decrease in active energy of dissolution reaction of minerals.The dissolution rate of minerals is controlled by suface adsorption,surface exchange reaction and desorption,depending on pH of the solution and is directly proportional to δHn0+,When controlled by surface adsorption,i.e.,nθ=1,the dissolution rate will decrease with increasing pH;when controlled by surface exchane reaction,i.e.,nθ=0,the dissolution rate is independent of pH;when controlled by desorption,nθis a positive decimal between 0 and 1 in acidic solution and a negative decimal between-1 and 0 in alkaline solution.Dissolution of many minerals is controlled by surface adsorption and/or surface exchange reactions under acid conditions and by desorption under alkaline conditions.

  2. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.


    The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies....... for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems....

  3. A thermochemically derived global reaction mechanism for detonation application (United States)

    Zhu, Y.; Yang, J.; Sun, M.


    A 4-species 4-step global reaction mechanism for detonation calculations is derived from detailed chemistry through thermochemical approach. Reaction species involved in the mechanism and their corresponding molecular weight and enthalpy data are derived from the real equilibrium properties. By substituting these global species into the results of constant volume explosion and examining the evolution process of these global species under varied conditions, reaction paths and corresponding rates are summarized and formulated. The proposed mechanism is first validated to the original chemistry through calculations of the CJ detonation wave, adiabatic constant volume explosion, and the steady reaction structure after a strong shock wave. Good agreement in both reaction scales and averaged thermodynamic properties has been achieved. Two sets of reaction rates based on different detailed chemistry are then examined and applied for numerical simulations of two-dimensional cellular detonations. Preliminary results and a brief comparison between the two mechanisms are presented. The proposed global mechanism is found to be economic in computation and also competent in description of the overall characteristics of detonation wave. Though only stoichiometric acetylene-oxygen mixture is investigated in this study, the method to derive such a global reaction mechanism possesses a certain generality for premixed reactions of most lean hydrocarbon mixtures.

  4. Miscible viscous fingering involving viscosity changes of the displacing fluid by chemical reactions (United States)

    Nagatsu, Yuichiro; Iguchi, Chika; Matsuda, Kenji; Kato, Yoshihito; Tada, Yutaka


    In our previous study, we experimentally studied the effects of changes in the viscosity of the displaced more-viscous liquid by instantaneous reactions on miscible viscous fingering pattern [Y. Nagatsu, K. Matsuda, Y. Kato, and Y. Tada, "Experimental study on miscible viscous fingering involving viscosity changes induced by variations in chemical species concentrations due to chemical reactions," J. Fluid Mech. 571, 475 (2007)]. In the present study, experiments have been performed on the miscible viscous fingering involving changes in the viscosity of the displacing less-viscous liquid by instantaneous reactions in a radial Hele-Shaw cell. We have found that the shielding effect is suppressed and the fingers are widened when the viscosity is increased. As a result, the reaction makes the fingering pattern denser. In contrast, the shielding effect is enhanced, and the fingers are narrowed when the viscosity is decreased. As a result, the reaction makes the fingering pattern less dense. These results are essentially same as those obtained by the above-mentioned previous study. This shows that the effects of changes in the viscosity due to the instantaneous reactions are independent of whether the changes occur in the displaced liquid or in the displacing liquid. A mechanism for the independence is discussed.

  5. Understanding reaction mechanisms in organic chemistry from catastrophe theory applied to the electron localization function topology. (United States)

    Polo, Victor; Andres, Juan; Berski, Slawomir; Domingo, Luis R; Silvi, Bernard


    Thom's catastrophe theory applied to the evolution of the topology of the electron localization function (ELF) gradient field constitutes a way to rationalize the reorganization of electron pairing and a powerful tool for the unambiguous determination of the molecular mechanisms of a given chemical reaction. The identification of the turning points connecting the ELF structural stability domains along the reaction pathway allows a rigorous characterization of the sequence of electron pair rearrangements taking place during a chemical transformation, such as multiple bond forming/breaking processes, ring closure processes, creation/annihilation of lone pairs, transformations of C-C multiple bonds into single ones. The reaction mechanism of some relevant organic reactions: Diels-Alder, 1,3-dipolar cycloaddition and Cope rearrangement are reviewed to illustrate the potential of the present approach.

  6. Influence of oxygen on the chemical stage of radiobiological mechanism (United States)

    Barilla, Jiří; Lokajíček, Miloš V.; Pisaková, Hana; Simr, Pavel


    The simulation of the chemical stage of radiobiological mechanism may be very helpful in studying the radiobiological effect of ionizing radiation when the water radical clusters formed by the densely ionizing ends of primary or secondary charged particle may form DSBs damaging DNA molecules in living cells. It is possible to study not only the efficiency of individual radicals but also the influence of other species or radiomodifiers (mainly oxygen) being present in water medium during irradiation. The mathematical model based on Continuous Petri nets (proposed by us recently) will be described. It makes it possible to analyze two main processes running at the same time: chemical radical reactions and the diffusion of radical clusters formed during energy transfer. One may study the time change of radical concentrations due to the chemical reactions running during diffusion process. Some orientation results concerning the efficiency of individual radicals in DSB formation (in the case of Co60 radiation) will be presented; the influence of oxygen present in water medium during irradiation will be shown, too.

  7. The hunt for the dynamical resonances in chemical reaction dynamics: a perspective on historical advances

    Directory of Open Access Journals (Sweden)

    Yu Angyang


    Full Text Available The theoretical background and basic definition of the resonances in chemical reaction dynamics have been introduced in this article. The historical breakthrough in the experimental search for the reaction resonances has been reviewed in this report, with an emphasis on the crossed molecular beam apparatus. The research of the chemical reaction resonances has attracted many scientists’ attention from 80s of last century. The chemical reaction resonances in the F+H2 reaction were firstly observed by the researchers of the Chinese Academy of Sciences in 2006. Besides, the partial wave resonances in the chemical reactions have been observed for the first time in 2010.

  8. Low Energy Electrons as Probing Tool for Astrochemical Reaction Mechanisms (United States)

    Hendrik Bredehöft, Jan; Swiderek, Petra; Hamann, Thorben

    The complexity of molecules found in space varies widely. On one end of the scale of molecular complexity is the hydrogen molecule H2 . Its formation from H atoms is if not understood than at least thoroughly investigated[1]. On the other side of said spectrum the precursors to biopolymers can be found, such as amino acids[2,3], sugars[4], lipids, cofactors[5], etc, and the kerogen-like organic polymer material in carbonaceous meteorites called "black stuff" [6]. These have also received broad attention in the last decades. Sitting in the middle between these two extremes are simple molecules that are observed by radio astronomy throughout the Universe. These are molecules like methane (CH4 ), methanol (CH3 OH), formaldehyde (CH2 O), hydrogen cyanide (HCN), and many many others. So far more than 40 such species have been identified.[7] They are often used in laboratory experiments to create larger complex molecules on the surface of simulated interstellar dust grains.[2,8] The mechanisms of formation of these observed starting materials for prebiotic chemistry is however not always clear. Also the exact mechanisms of formation of larger molecules in photochemical experiments are largely unclear. This is mostly due to the very complex chemistry going on which involves many different radicals and ions. The creation of radicals and ions can be studied in detail in laboratory simulations. They can be created in a setup mimicking interstellar grain chemistry using slow electrons. There is no free electron radiation in space. What can be found though is a lot of radiation of different sorts. There is electromagnetic radiation (UV light, X-Rays, rays, etc.) and there is particulate radiation as well in the form of high energy ions. This radiation can provide energy that drives chemical reactions in the ice mantles of interstellar dust grains. And while the multitude of different kinds of radiation might be a little confusing, they all have one thing in common: Upon

  9. Revision of outcome and mechanism of a new multicomponent reaction. (United States)

    Carballares, Santiago; Espinosa, Juan F


    [reaction: see text] A recently reported multicomponent reaction (MCR) produces pyrido[1,2-a]pyrazines and not the previously described 1H-imidazol-4-yl-pyridines. This different structure is proposed on the basis of a new mechanism of formation and the spectroscopic data.

  10. Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations. (United States)

    Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino


    This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies.

  11. Chemical Reactions in the Processing of Mosi2 + Carbon Compacts (United States)

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


    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.

  12. Mass transfer in porous media with heterogeneous chemical reaction

    Directory of Open Access Journals (Sweden)

    Souza S.M.A.G.Ulson de


    Full Text Available In this paper, the modeling of the mass transfer process in packed-bed reactors is presented and takes into account dispersion in the main fluid phase, internal diffusion of the reactant in the pores of the catalyst, and surface reaction inside the catalyst. The method of volume averaging is applied to obtain the governing equation for use on a small scale. The local mass equilibrium is assumed for obtaining the one-equation model for use on a large scale. The closure problems are developed subject to the length-scale constraints and the model of a spatially periodic porous medium. The expressions for effective diffusivity, hydrodynamic dispersion, total dispersion and the Darcy's law permeability tensors are presented. Solution of the set of final equations permits the variations of velocity and concentration of the chemical species along the packed-bed reactors to be obtained.

  13. Mechanization of hydraulic testing of chemical equipment

    Energy Technology Data Exchange (ETDEWEB)

    Bannikov, M.T.; Fridman, R.N.; Petrovnin, A.I.


    The Institute VNIIPTKhimmash has worked out a comprehensive list of equipment for testing for strength and tightness containers and heat exchangers with jackets, with mixers, also of individual parts and subassemblies for this equipment. Points out that in the test stands developed for hydraulic testing of vessels both individual and centralized recirculating water supply can be used. Concludes that a reduction in labor consumption in hydraulic testing and in servicing of all the equipment used, an increase in the mechanization of this kind of chemical equipment, and the solution of the problem of standardization not only with regard to dimensions and parameters, but also with regard to the makes and types of the materials used, will make possible a considerable increase in labor productivity and product quality.

  14. Chemical Mechanical Planarization of Cu: Nanoscale Processes (United States)

    Arthur, Michael; Fishbeck, Kelly; Muessig, Kara; McDonald, James; Williams, Christine; White, Daniel; Koeck, Deborah; Perry, Scott; Galloway, Heather


    Interconnect lines in state of the art integrated circuits are made of copper in a process that requires the repeated planarization of the copper layer. During this process the material is subjected to an aqueous slurry containing active chemicals, corrosion inhibitors and abrasive particles. A model slurry buffered to pH2, pH4 and pH6, contained nitric acid, silica particles and benzotriazole (BTA) as a corrosion inhibitor. The degree of copper planarization was investigated as a function of slurry composition and pH using atomic force microscopy. Chemical surface changes can be explained by the effect of slurry composition on the charge at the material surface. This surface charge controls the amount of friction between the abrasive and the surface which, in turn, effects the global planarization of the material. Experiments using a macroscopic polishing system with AFM characterization along with the microscopic interaction of the AFM tip and sample provide insights into the fundamental mechanisms of a planarization process.

  15. Thermal Analysis for Monitoring Effects of Shock-Induced Physical, Mechanical, and Chemical Changes in Materials (United States)


    chemical reactions as a function of temperature. Since the DSC is at constant pressure, heat flow measured is equivalent to enthalpy changes: Here...mechanical activation; reactive materials; anaerobic reactions REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR/MONITOR’ of benefit to our other DoD supported work on understanding of shock-activation leading to reactions in energetic/reactive materials. The thermal

  16. Reaction Mechanism of the Multi-channel Decomposition Reactions of 1-Pentenyl Free Radicals

    Institute of Scientific and Technical Information of China (English)

    CHENG,Xue-Li; ZHAO,Yan-Yun; LI,Feng; LI,Li-Qing; TAO,Xiu-Jun


    The reactions of 1-pentenyl decomposition system have been studied extensively at the B3LYP/6-311++G** level with Gaussion 98 package. The potential energy surface with zero-point energy correction was drawn. All reaction channels were fully investigated with the vibrational mode analysis, frontier orbital analysis and electron population analysis to confirm the transition states and reveal the reaction mechanism.

  17. In Situ Environmental TEM in Imaging Gas and Liquid Phase Chemical Reactions for Materials Research. (United States)

    Wu, Jianbo; Shan, Hao; Chen, Wenlong; Gu, Xin; Tao, Peng; Song, Chengyi; Shang, Wen; Deng, Tao


    Gas and liquid phase chemical reactions cover a broad range of research areas in materials science and engineering, including the synthesis of nanomaterials and application of nanomaterials, for example, in the areas of sensing, energy storage and conversion, catalysis, and bio-related applications. Environmental transmission electron microscopy (ETEM) provides a unique opportunity for monitoring gas and liquid phase reactions because it enables the observation of those reactions at the ultra-high spatial resolution, which is not achievable through other techniques. Here, the fundamental science and technology developments of gas and liquid phase TEM that facilitate the mechanistic study of the gas and liquid phase chemical reactions are discussed. Combined with other characterization tools integrated in TEM, unprecedented material behaviors and reaction mechanisms are observed through the use of the in situ gas and liquid phase TEM. These observations and also the recent applications in this emerging area are described. The current challenges in the imaging process are also discussed, including the imaging speed, imaging resolution, and data management.

  18. Stochastic analysis of Chemical Reaction Networks using Linear Noise Approximation. (United States)

    Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca


    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.

  19. Bayesian inference of chemical kinetic models from proposed reactions

    KAUST Repository

    Galagali, Nikhil


    © 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.

  20. Theoretical Study of Sodium-Water Surface Reaction Mechanism (United States)

    Kikuchi, Shin; Kurihara, Akikazu; Ohshima, Hiroyuki; Hashimoto, Kenro

    Computational study of the sodium-water reaction at the gas (water) - liquid (sodium) interface has been carried out using the ab initio (first-principle) method. A possible reaction channel has been identified for the stepwise OH bond dissociations of a single water molecule. The energetics including the binding energy of a water molecule on the sodium surface, the activation energies of the bond cleavages, and the reaction energies, have been evaluated, and the rate constants of the first and second OH bond-breakings have been compared. It was found that the estimated rate constant of the former was much larger than the latter. The results are the basis for constructing the chemical reaction model used in a multi-dimensional sodium-water reaction code, SERAPHIM, being developed by Japan Atomic Energy Agency (JAEA) toward the safety assessment of the steam generator (SG) in a sodium-cooled fast reactor (SFR).

  1. Electron flow in reaction mechanisms--revealed from first principles. (United States)

    Knizia, Gerald; Klein, Johannes E M N


    The "curly arrow" of Robinson and Ingold is the primary tool for describing and rationalizing reaction mechanisms. Despite this approach's ubiquity and stellar success, its physical basis has never been clarified and a direct connection to quantum chemistry has never been found. Here we report that the bond rearrangements expressed by curly arrows can be directly observed in ab initio computations, as transformations of intrinsic bond orbitals (IBOs) along the reaction coordinate. Our results clarify that curly arrows are rooted in physical reality-a notion which has been challenged before-and show how quantum chemistry can directly establish reaction mechanisms in intuitive terms and unprecedented detail.

  2. Chemical Reaction and Flow Modeling in Fullerene and Nanotube Production (United States)

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


    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

  3. Polarization of molecular angular momentum in the chemical reactions Li + HF and F + HD. (United States)

    Krasilnikov, Mikhail B; Popov, Ruslan S; Roncero, Octavio; De Fazio, Dario; Cavalli, Simonetta; Aquilanti, Vincenzo; Vasyutinskii, Oleg S


    The quantum mechanical approach to vector correlation of angular momentum orientation and alignment in chemical reactions [G. Balint-Kurti and O. S. Vasyutinskii, J. Phys. Chem. A 113, 14281 (2009)] is applied to the molecular reagents and products of the Li + HF [L. Gonzalez-Sanchez, O. S. Vasyutinskii, A. Zanchet, C. Sanz-Sanz, and O. Roncero, Phys. Chem. Chem. Phys. 13, 13656 (2011)] and F + HD [D. De Fazio, J. Lucas, V. Aquilanti, and S. Cavalli, Phys. Chem. Chem. Phys. 13, 8571 (2011)] reactions for which accurate scattering information has become recently available through time-dependent and time-independent approaches. Application of the theory to two important particular cases of the reactive collisions has been considered: (i) the influence of the angular momentum polarization of reactants in the entrance channel on the spatial distribution of the products in the exit channel and (ii) angular momentum polarization of the products of the reaction between unpolarized reactants. In the former case, the role of the angular momentum alignment of the reactants is shown to be large, particularly when the angular momentum is perpendicular to the reaction scattering plane. In the latter case, the orientation and alignment of the product angular momentum was found to be significant and strongly dependent on the scattering angle. The calculation also reveals significant differences between the vector correlation properties of the two reactions under study which are due to difference in the reaction mechanisms. In the case of F + HD reaction, the branching ratio between HF and DF production points out interest in the insight gained into the detailed dynamics, when information is available either from exact quantum mechanical calculations or from especially designed experiments. Also, the geometrical arrangement for the experimental determination of the product angular momentum orientation and alignment based on a compact and convenient spherical tensor expression for

  4. Experimental investigations of mechanical and reaction responses for drop-weight impacted energetic particles (United States)

    Bao, Xiao-Wei; Wu, Yan-Qing; Wang, Ming-Yang; Huang, Feng-Lei


    Low-velocity drop-weight impact experiments on individual and multiple Cyclotetramethylene tetranitramine (HMX) energetic particles were performed using a modified drop-weight machine equipped with high-speed photography components. Multiple particles experienced more severe burning reactions than an individual particle. Comparisons between impacted salt and HMX particle show that jetting in HMX is mainly due to the motion of fragmented particles driven by gaseous reaction products. Velocity of jetting, flame propagation, and area expansion were measured via image processing, making it possible to quantify the chemical reaction or mechanical deformation violence at different stages.

  5. Investigation of opening switch mechanisms based on chemically reactive plasmas (United States)

    Lapatovich, W. P.; Piejak, R. B.; Proud, J. M.


    An investigation of discharge-induced chemical reactions resulting in high-density product vapors containing strongly attaching gases has been conducted to evaluate the feasibility and potential of such reactions in rapid opening plasma switches. This new concept of employing such reactions to limit and/or interrupt large currents on a microsecond time scale was studied in two element (electrodeless and electroded) devices and in three element (electroded) devices. Bimolecular and unimolecular reactions were considered. The plasma reaction between AlCl sub 3 and SiO sub 2 was studied. The electrical properties of one of the reaction products (SiCl sub 4) is reported.

  6. Importance of cytochromes in cyclization reactions: quantum chemical study on a model reaction of proguanil to cycloguanil. (United States)

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


    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.

  7. Quantum chemical aided prediction of the thermal decomposition mechanisms and temperatures of ionic liquids

    Energy Technology Data Exchange (ETDEWEB)

    Kroon, Maaike C. [Physical Chemistry and Molecular Thermodynamics, Department of Chemical Technology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft (Netherlands); Process Equipment, Department of Process and Energy, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft (Netherlands)], E-mail:; Buijs, Wim [Catalysis Engineering, Department of Chemical Technology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft (Netherlands); Peters, Cor J. [Physical Chemistry and Molecular Thermodynamics, Department of Chemical Technology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft (Netherlands); Witkamp, Geert-Jan [Process Equipment, Department of Process and Energy, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft (Netherlands)], E-mail:


    The long-term thermal stability of ionic liquids is of utmost importance for their industrial application. Although the thermal decomposition temperatures of various ionic liquids have been measured previously, experimental data on the thermal decomposition mechanisms and kinetics are scarce. It is desirable to develop quantitative chemical tools that can predict thermal decomposition mechanisms and temperatures (kinetics) of ionic liquids. In this work ab initio quantum chemical calculations (DFT-B3LYP) have been used to predict thermal decomposition mechanisms, temperatures and the activation energies of the thermal breakdown reactions. These quantum chemical calculations proved to be an excellent method to predict the thermal stability of various ionic liquids.

  8. Chemical Mechanism Solvers in Air Quality Models

    Directory of Open Access Journals (Sweden)

    John C. Linford


    Full Text Available The solution of chemical kinetics is one of the most computationally intensivetasks in atmospheric chemical transport simulations. Due to the stiff nature of the system,implicit time stepping algorithms which repeatedly solve linear systems of equations arenecessary. This paper reviews the issues and challenges associated with the construction ofefficient chemical solvers, discusses several families of algorithms, presents strategies forincreasing computational efficiency, and gives insight into implementing chemical solverson accelerated computer architectures.

  9. Functionalization of Hydrogenated Chemical Vapour Deposition-Grown Graphene by On-Surface Chemical Reactions. (United States)

    Drogowska, Karolina; Kovaříček, Petr; Kalbáč, Martin


    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.

  10. Numerical prediction of oblique detonation wave structures using detailed and reduced reaction mechanisms (United States)

    Thaker, A. A.; Chelliah, H. K.


    Modelling of the structure and the limiting flow turning angles of an oblique detonation wave, established by a two-dimensional wedge, requires the implementation of detailed chemical kinetic models involving a large number of chemical species. In this paper, a method of reducing the computational effort involved in simulating such high-speed reacting flows by implementing a systematically reduced reaction mechanism is presented. For a hydrogen - air mixture, starting with an elementary mechanism having eight species in 12 reactions, three alternate four-step reduced reaction mechanisms are developed by introducing the steady-state approximation for the reaction intermediates HO2, O and OH, respectively. Additional reduction of the computational effort is achieved by introducing simplifications to the thermochemical data evaluations. The influence of the numerical grid used in predicting the induction process behind the shock is also investigated. Comparisons of the induction zone predicted by two-dimensional oblique detonation wave calculations with that of a static reactor model (with initial conditions of the gas mixture specified by those behind the nonreactive oblique shock wave) are also presented. The reasonably good agreement between the three four-step reduced mechanism predictions and the starting mechanism predictions indicates that further reduction to a two-step mechanism is feasible for the physical flow time scales (corresponding to inflow Mach numbers of 8 - 10) considered here, and needs to be pursued in the future.

  11. Reaction mechanisms of ruthenium tetroxide mediated oxidations of organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Froehaug, Astrid Elisabeth


    This thesis reports a study of the mechanism of ruthenium tetroxide mediated oxidations of saturated hydrocarbons, ethers, alkenes and alcohols. Several methods were used. The RuO{sub 4}-mediated oxidations of adamantane and cis-decalin were studied in CCl{sub 4}-CH{sub 3}CN-H{sub 2}O and in acetone-water. The rate of reaction was found to be moderately influenced by the polarity of the solvent. Solvent properties other than the polarity were also found to influence the reaction rates. From the oxidations of adamantane and adamantane-1,3,5,7-d{sub 4} two primary kinetic deuterium isotope effects were found. These were comparable with the deuterium isotope effects found for the analogous oxidations of cis-decalin and cis-decalin-d{sub 18}. The results seem to exclude both a one step hydride abstraction reaction mechanism and a one step concerted mechanism, as well as a scheme where two such mechanisms compete. The observations may be explained by a two step reaction mechanism consisting of a pre-equilibrium with formation of a substrate-RuO{sub 4} complex followed by a concerted rate determining reaction. The RuO{sub 4}-mediated oxidation of ethers was of kinetic second order with a small enthalpy of activation and a large negative entropy of activation. Oxidation of cyclopropylmethyl methyl ether gave methyl cyclopropanecarboxylate, no rearranged products were observed. On RuO{sub 4} oxidations in CCl{sub 4} with NaIO{sub 4} as stoichiometric oxidant, no chlorinated products were observed. Several observations not in agreement with a hydride or a hydrogen abstraction mechanism may be explained by assuming that the reaction proceeds by either a concerted reaction or by a reversible oxidative addition of the ether to RuO{sub 4} followed by a slow concerted step. 228 refs., 9 figs., 27 tabs.

  12. Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions. (United States)

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


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

  13. Learning the mechanisms of chemical disequilibria (United States)

    Nicholson, Schuyler B.; Alaghemandi, Mohammad; Green, Jason R.


    When at equilibrium, large-scale systems obey thermodynamics because they have microscopic configurations that are typical. "Typical" states are a fraction of those possible with the majority of the probability. A more precise definition of typical states underlies the transmission, coding, and compression of information. However, this definition does not apply to natural systems that are transiently away from equilibrium. Here, we introduce a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation. While a gaseous mixture of hydrogen and oxygen combusts, reactant molecules transform through a variety of ephemeral species en route to the product, water. Out of the exponentially growing number of possible sequences of chemical species, we find that greater than 95% of the probability concentrates in less than 1% of the possible sequences. Overall, these results extend the notion of typicality across the nonequilibrium regime and suggest that typical sequences are a route to learning mechanisms from experimental measurements. They also open up the possibility of constructing ensembles for computing the macroscopic observables of systems out of equilibrium.

  14. Chemical Mechanical Planarization (CMP) for Microelectronic Applications

    Institute of Scientific and Technical Information of China (English)

    Li Yuzhuo


    Surface planarity is of paramount importance in microelectronics. Chemical Mechanical Polishing (CMP) is the most viable approach to address the planarity issues during the fabrication of advanced semiconductor devices. With the integration of copper as interconnect and low k materials as dielectric, the CMP community is facing an ever increasing demand on reducing defectivity without scarifying production throughput. Key issues in CMP today include reduction of surface defectivity and enhancement of planarization efficiency. More specifically, the polished surface should be free of defects such as scratches, pits, corrosion spots, and residue particles. To accomplish these goals, we have investigated a wide range of pathways including reduction of oversized particles,use of unique abrasives such as functionalized nanoparticles, and development of polishing solution without abrasive particles.In this presentation, some fundamental aspects of the CMP process will be given first.Several academic and industrial examples will be used to illustrate the issues and challenges during the implementation of various slurry designs into the CMP processes.

  15. Atherton–Todd reaction: mechanism, scope and applications

    Directory of Open Access Journals (Sweden)

    Stéphanie S. Le Corre


    Full Text Available Initially, the Atherton–Todd (AT reaction was applied for the synthesis of phosphoramidates by reacting dialkyl phosphite with a primary amine in the presence of carbon tetrachloride. These reaction conditions were subsequently modified with the aim to optimize them and the reaction was extended to different nucleophiles. The mechanism of this reaction led to controversial reports over the past years and is adequately discussed. We also present the scope of the AT reaction. Finally, we investigate the AT reaction by means of exemplary applications, which mainly concern three topics. First, we discuss the activation of a phenol group as a phosphate which allows for subsequent transformations such as cross coupling and reduction. Next, we examine the AT reaction applied to produce fire retardant compounds. In the last section, we investigate the use of the AT reaction for the production of compounds employed for biological applications. The selected examples to illustrate the applications of the Atherton–Todd reaction mainly cover the past 15 years.

  16. On the Reaction Mechanism of Br2 with OCS

    Institute of Scientific and Technical Information of China (English)

    Hai Tao YU; Hua ZHONG; Ming Xia LI; Hong Gang FU; Jia Zhong SUN


    The reaction mechanism of photochemical reaction between Br2 ( 1 ∑ ) and OCS ( 1 ∑ ) is predicted by means of theoretical methods. The calculated results indicate that the direct addition of Br2 to the CS bond of OCS molecule is more favorable in energy than the direct addition of Br2to the CO bond. Furthermore, the intermediate isomer syn-BrC(O)SBr is more stable thermodynamically and kinetically than anti-BrC(O)SBr. The original resultant anti-BrC(O)SBr formed in the most favorable reaction channel can easily isomerize into the final product syn-BrC(O)SBr with only 31.72 kJ/mol reaction barrier height. The suggested mechanism is in good agreement with previous experimental study.

  17. Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques (United States)

    Fernandez, Julio M.


    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

  18. Theoretical Study on the Dark Oxidation Reaction Mechanism of Ethers

    Institute of Scientific and Technical Information of China (English)

    WANG Gui-Xiu; ZHU Rong-Xiu; ZHANG Dong-Ju; LIU Cheng-Bu


    The dark oxidation reactions of ethers including aether, isopropyl ether, phenyl isopropyl ether, and benzyl isopropyl ether have been studied by using density functional theory calculations. The structures of initial contact charge transfer complexes (CCTCs), transition states and caged radical intermediates have been located at the B3LYP/6-31G (d) level. The bonding nature of ethers with triplet O2 in CCTCs has been analyzed, and the detailed mechanism of dark oxidation reactions of ether is presented clearly.

  19. Capillary Action may Cool Systems and Precisely balance Chemical Reactions (United States)

    Kriske, Richard


    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.

  20. Quantum Chemical Studies of the Substituent Effect on the Reaction of Carbonyl Oxime with Amine. (United States)

    Kaya, Yunus


    The reaction of the two different substitue carbonyl oximes (isonitrosoacetylnaphthaline, inanH and nitro-isonitrosoacetophenone, ninapH) with two different amines (1-phenylethanol amine, pea, and ethanol amine, ea) was carried out and characterized by elemental analyses, IR, and (1)H and (13)C NMR spectroscopic methods. As a result of these experimental studies, two different levels for all reactions were determined: (I) formation of imine oxime and (II) rearrangement of imine oxime or formation of amido alcohol. After a mechanism was suggested for all of these reactions, the reaction mechanism of carbonyl oxime with amine was first studied by means of the B3LYP/6-311G(d,p) method. Because of the deficiency of density functional theory (DFT) on dispersion effects, the wB97X-D/6-311G(d,p) method, which includes dispersion correction, was used to obtain the reaction heat and free energy barriers to explain why the formation (imine oxime) and unexpected rearrangement products (amido alcohol) occurred or did not occur. The statistical thermodynamic method was used to obtain the changes in thermodynamic properties of the studied molecules between 100 and 500 K. From a kinetic viewpoint, the slowest step of the reactions is the IN1-TS2-IN2 step, which determines the steps of the reaction kinetics. In addition, spectroscopic properties such as vibrational and NMR chemical shifts were studied for all of the molecules. The frontier molecular orbitals (FMOs), highest occupied molecular orbitals (HOMOs), and lowest unoccupied molecular orbitals (LUMOs) were monitored for all of the molecules.

  1. Mass transfer and chemical reaction in gas-liquid-liquid systems

    NARCIS (Netherlands)

    Brilman, Derk Willem Frederik


    Gas-liquid-liquid reaction systems may be encountered in several important fields of application as e.g. hydroformylation, alkylation, carboxylation, polymerisation, hydrometallurgy, biochemical processes and fine chemicals manufacturing. However, the reaction engineering aspects of these systems ha

  2. Influence of nonlinear chemical reactions on the transport coefficients in oscillatory Couette flow (United States)

    Barik, Swarup; Dalal, D. C.


    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.

  3. Chemical reactions between Venus' surface and atmosphere - An update. (Invited) (United States)

    Treiman, A. H.


    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

  4. Reaction mechanisms for on-surface synthesis of covalent nanostructures. (United States)

    Björk, J


    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

  5. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, W.M.


    The purpose of this review is to bring together and to correlate the wide variety of experimental studies that provide information on the reaction products and reaction mechanisms involved in the radiolysis of peptides, polypeptides and proteins (including chromosomal proteins) in both aqueous and solid-state systems. The comparative radiation chemistry of these systems is developed in terms of specific reactions of the peptide main-chain and the aliphatic, aromatic-unsaturated and sulfur-containing side-chains. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis and ESR spectroscopy is included. 147 refs.

  6. Colloid Aspects of Chemical-Mechanical Planarization

    Directory of Open Access Journals (Sweden)

    Matijević, E.


    Full Text Available The essential parts of interconnects for silicon based logic and memory devices consist of metal wiring (e.g. copper, a barrier metal (Ta, TaN, and of insulation (SiO2 , low-k polymer. The deposition of the conducting metal cannot be confined to trenches, resulting in additional coverage of Cu and Ta/TaN on the surface of the dielectrics, yielding an electrically conducting continuous but an uneven surface. The surplus metal must be removed until a perfectly flat surface consisting of electrically isolated metal lines is achieved with no imperfections. This task is accomplished by the chemical-mechanical planarization (CMP process, in which the wafer is polished with a slurry containing abrasives of finely dispersed particles in submicrometer to nanometer size. The slurries also contain dissolved chemicals to modify the surfaces to be planarized. Eventually the final product must be cleared of any adhered particles and debris left after polishing is completed. Obviously the entire process deals with materials and interactions which are the focal subjects of colloid and surface science, such as the natures of abrasive particles and their stability in the slurry, the properties of various surfaces and their modifications, adhesion and detachment of the particles and different methods for the characterization of constituents, as well as elucidation of the relevant interfacial phenomena. This review endeavors to describe the colloid approach to optimize the materials and processes in order to achieve desirable polish rates and final surfaces with no imperfections. Specifically, the effects of the composition, size, shape, and charge of abrasive particles on the polish process and the quality of planarized wafers is described in detail. Furthermore, the interactions of metal surfaces with oxidizing, chelating, and other species which affect the dissolution and surface modification of metal (copper surfaces are illustrated and related to the

  7. Detailed chemical kinetic oxidation mechanism for a biodiesel surrogate

    Energy Technology Data Exchange (ETDEWEB)

    Herbinet, O; Pitz, W J; Westbrook, C K


    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of methyl decanoate, a surrogate for biodiesel fuels. This model has been built by following the rules established by Curran et al. for the oxidation of n-heptane and it includes all the reactions known to be pertinent to both low and high temperatures. Computed results have been compared with methyl decanoate experiments in an engine and oxidation of rapeseed oil methyl esters in a jet stirred reactor. An important feature of this mechanism is its ability to reproduce the early formation of carbon dioxide that is unique to biofuels and due to the presence of the ester group in the reactant. The model also predicts ignition delay times and OH profiles very close to observed values in shock tube experiments fueled by n-decane. These model capabilities indicate that large n-alkanes can be good surrogates for large methyl esters and biodiesel fuels to predict overall reactivity, but some kinetic details, including early CO{sub 2} production from biodiesel fuels, can be predicted only by a detailed kinetic mechanism for a true methyl ester fuel. The present methyl decanoate mechanism provides a realistic kinetic tool for simulation of biodiesel fuels.

  8. Detailed chemical kinetic oxidation mechanism for a biodiesel surrogate

    Energy Technology Data Exchange (ETDEWEB)

    Herbinet, O; Pitz, W J; Westbrook, C K


    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of methyl decanoate, a surrogate for biodiesel fuels. This model has been built by following the rules established by Curran et al. for the oxidation of n-heptane and it includes all the reactions known to be pertinent to both low and high temperatures. Computed results have been compared with methyl decanoate experiments in an engine and oxidation of rapeseed oil methyl esters in a jet stirred reactor. An important feature of this mechanism is its ability to reproduce the early formation of carbon dioxide that is unique to biofuels and due to the presence of the ester group in the reactant. The model also predicts ignition delay times and OH profiles very close to observed values in shock tube experiments fueled by n-decane. These model capabilities indicate that large n-alkanes can be good surrogates for large methyl esters and biodiesel fuels to predict overall reactivity, but some kinetic details, including early CO2 production from biodiesel fuels, can be predicted only by a detailed kinetic mechanism for a true methyl ester fuel. The present methyl decanoate mechanism provides a realistic kinetic tool for simulation of biodiesel fuels.

  9. Chemical Reaction Between Polyvinyl Alcohol and Titanate Coupling Agent with X-Ray Photoelectron Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    LI Bei-xing; ZHANG Wen-sheng


    The chemical reaction between polyvinyl alcohol (PVA) and tri(dioctylpyrophosphoryloxy) isopropyl titanate (NDZ-201) was studied using X-ray photoelectron spectroscopy (XPS).The results show that some C-OH functional groups of PVA react with the titanate coupling agent to form CPVA-O-Ti-O-CPVA bond.The cross-linking of the PVA chains occurs through the formation of CPVA-O-Ti-O-CPVA bonds and produces a three dimensional hydrophobic polymer network.Accordingly,the mechanism is proposed that the titanate coupling agent improves the moisture sensitivity of high alumina cement/polyvinyl alcohol (HAC/PVA) based macro defect free (MDF) composite material.

  10. Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions. (United States)

    Cordes, Thorben; Blum, Suzanne A


    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.

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

    Cordes, Thorben; Blum, Suzanne A.


    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. Divergent reaction mechanisms in the aminofluorination of alkenes. (United States)

    Kong, Wangqing; Merino, Estíbaliz; Nevado, Cristina


    The aminofluorination of alkenes has become an attractive platform for the synthesis of β-amino-fluorinated compounds, valuable building blocks in medicinal and agricultural chemistry. The novel methodologies disclosed in recent years have unraveled a broad array of reaction mechanisms, so that the interest in these transformations transcends the mere synthetic aspects. This review aims to summarize the most relevant findings in this area attending at the nature of the fluorine source, and thus the specific mechanism operating in each of these transformations, namely electrophilic, nucleophilic, radical, and late transition metal-catalyzed reactions.

  13. Thermal degradation reaction mechanism of xylose: A DFT study (United States)

    Huang, Jinbao; He, Chao; Wu, Longqin; Tong, Hong


    The thermal degradation reaction mechanism of xylose as hemicellulose model compound was investigated by using density functional theory methods M062X with the 6-31++G(d,p) basis set. Eight possible pyrolytic reaction pathways were proposed and the standard kinetic and thermodynamic parameters in all reaction pathways were calculated at different temperatures. In reaction pathway (1), xylose is first transformed into acyclic containing-carbonyl isomer, and then the isomer further decomposes through four possible pyrolysis pathways (1-1)-(1-4). Pathways (2) and (3) depict an immediate ring-opening process through the simultaneous breaking of C-O and C-C bonds. Pathways (4)-(7) describe the pyrolysis processes of various anhydro-xyloses through a direct ring-opening process. Pathway (8) gives the evolutionary process of pyranones. The calculation results show that reaction pathways (1), (2) and (5) are the major reaction channels and reaction pathways (3), (4), and (6)-(8) are the competitive reaction channels in pyrolysis of xylose. The major products of xylose pyrolysis are low molecular products such as 2-furaldehyde, glycolaldehyde, acetaldehyde, methylglyoxal and acetone, and the main competitive products are formaldehyde, formic acid, acetic acid, CO2, CH4, acetol, pyranone, and so on.

  14. Reaction mechanism study of 7Li(7Li, 6He) reaction at above Coulomb barrier energies

    Indian Academy of Sciences (India)

    V V Parkar; V Jha; S Santra; B J Roy; K Ramachandran; A Shrivastava; K Mahata; A Chatterjee; S Kailas


    The elastic scattering and the 6He angular distributions were measured in 7Li + 7Li reaction at two energies, lab = 20 and 25 MeV. FRDWBA calculations have been performed to explain the measured 6He data. The calculations were very sensitive to the choice of the optical model potentials in entrance and exit channels. The one-step proton transfer was found to be the dominant reaction mechanism in 6He production.

  15. Defect-free surface of quartz glass polished in elastic mode by chemical impact reaction

    Institute of Scientific and Technical Information of China (English)

    彭文强; 关朝亮; 李圣怡


    Removal of brittle materials in the brittle or ductile mode inevitably causes damaged or strained surface layers containing cracks, scratches or dislocations. Within elastic deformation, the arrangement of each atom can be recovered back to its original position without any defects introduced. Based on surface hydroxylation and chemisorption theory, material removal mechanism of quartz glass in the elastic mode is analyzed to obtain defect-free surface. Elastic contact condition between nanoparticle and quartz glass surface is confirmed from the Hertz contact theory model. Atoms on the quartz glass surface are removed by chemical bond generated by impact reaction in the elastic mode, so no defects are generated without mechanical process. Experiment was conducted on a numerically controlled system for nanoparticle jet polishing, and one flat quartz glass was polished in the elastic mode. Results show that scratches on the sample surface are completely removed away with no mechanical defects introduced, and micro-roughness (Ra) is decreased from 1.23 nm to 0.47 nm. Functional group Ce—O—Si on ceria nanoparticles after polishing was detected directly and indirectly by FTIR, XRD and XPS spectra analysis from which the chemical impact reaction is validated.

  16. Reaction parameter study for the chemical synthesis of adsorbent silica gel

    Directory of Open Access Journals (Sweden)

    María Carolina Sáenz


    Full Text Available This article presents an appropriate set of reaction parameters (reaction temperature, sulphuric acid and sodium silicate reagent concentration for obtaining adsorbent silica gel (ASG using Colombian-produced raw materials. The core of ASG synthesis lies in sulphuric acid’s neutralisation reaction with sodium silicate. Their effect on final ASG moisture adsorption capacity was measured after changing such synthesis’ above–mentioned reaction parameters. Within the range of conditions studied, it was found that the highest adsorption capacity occurred by combining both low sodium silicate concentration with high temperatures or high sulphuric acid concentration and temperature. Synthesised ASG was also compared to a commercial product (Gel de sílice granulare con indicatore. Montedison group. Batch number 1684G100. Code number 453301 using adsorption capacity plots, BET areas, X–ray di-ffraction, mass and infrared spectrometry and mechanical strength measurements. Synthesised ASG presented larger specific surface areas but weaker mechanical strength than the commercial one. Likewise, all evaluated samples exhibited a low degree of molecular arrangement and conventional ASG chemical structure.

  17. Influence of chemical structure on hypersensitivity reactions induced by antiepileptic drugs: the role of the aromatic ring.

    NARCIS (Netherlands)

    Handoko, K.B.; Puijenbroek, E.P. van; Bijl, A.H.; Hermens, W.A.; Rijkom, JE Zwart-van; Hekster, Y.A.; Egberts, T.C.G.


    OBJECTIVE: Antiepileptic drugs (AEDs) can cause various 'idiosyncratic' hypersensitivity reactions, i.e. the mechanism by which AEDs induce hypersensitivity is unknown. The aim of this study was to assess whether the presence of an aromatic ring as a commonality in chemical structures of AEDs can ex

  18. Influence of chemical structure on hypersensitivity reactions induced by antiepileptic drugs : the role of the aromatic ring

    NARCIS (Netherlands)

    Handoko, Kim B; van Puijenbroek, Eugène P; Bijl, Annemarie H; Hermens, Walter A J J; Zwart-van Rijkom, Jeannette E F; Hekster, Yechiel A; Egberts, Toine C G


    OBJECTIVE: Antiepileptic drugs (AEDs) can cause various 'idiosyncratic' hypersensitivity reactions, i.e. the mechanism by which AEDs induce hypersensitivity is unknown. The aim of this study was to assess whether the presence of an aromatic ring as a commonality in chemical structures of AEDs can ex

  19. Reaction mechanism and reaction coordinates from the viewpoint of energy flow. (United States)

    Li, Wenjin; Ma, Ao


    Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

  20. Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies. (United States)

    Zinovjev, Kirill; Ruiz-Pernía, J Javier; Tuñón, Iñaki


    We present a combination of the string method and a path collective variable for the exploration of the free energy surface associated to a chemical reaction in condensed environments. The on-the-fly string method is employed to find the minimum free energy paths on a multidimensional free energy surface defined in terms of interatomic distances, which is a convenient selection to study bond forming/breaking processes. Once the paths have been determined, a reaction coordinate is defined as a measure of the advance of the system along these paths. This reaction coordinate can be then used to trace the reaction Potential of Mean Force from which the activation free energy can be obtained. This combination of methodologies has been here applied to the study, by means of Quantum Mechanics/Molecular Mechanics simulations, of the reaction catalyzed by guanidinoacetate methyltransferase. This enzyme catalyzes the methylation of guanidinoacetate by S-adenosyl-l-methionine, a reaction that involves a methyl transfer and a proton transfer and for which different reaction mechanisms have been proposed.

  1. Chemical and mechanical interactions of interstitials in V-5%Cr-5%Ti

    Energy Technology Data Exchange (ETDEWEB)

    DeVan, J.H.; DiStefano, J.R.; Hendricks, J.W. [Oak Ridge National Lab., TN (United States)] [and others


    A vanadium alloy structure with liquid lithium is the favored concept for an advanced breeding blanket for ITER. The objective of this task is to determine the kinetics of reactions of vanadium alloys with hydrogen and oxygen as a function of alloy composition and TMT. Gas-metal reaction studies of V-5Cr-5Ti were conducted to determine the kinetics of reactions with H{sub 2} and O{sub 2}, respectively, at 450-500{degree}C. Reaction rates were determined through wieght change measurements and chemical analyses, and effects on mechanical properties were evaluated by room temperature tensile tests.

  2. Formation of degradation compounds from lignocellulosic biomass in the biorefinery: sugar reaction mechanisms. (United States)

    Rasmussen, Helena; Sørensen, Hanne R; Meyer, Anne S


    The degradation compounds formed during pretreatment when lignocellulosic biomass is processed to ethanol or other biorefinery products include furans, phenolics, organic acids, as well as mono- and oligomeric pentoses and hexoses. Depending on the reaction conditions glucose can be converted to 5-(hydroxymethyl)-2-furaldehyde (HMF) and/or levulinic acid, formic acid and different phenolics at elevated temperatures. Correspondingly, xylose can follow different reaction mechanisms resulting in the formation of furan-2-carbaldehyde (furfural) and/or various C-1 and C-4 compounds. At least four routes for the formation of HMF from glucose and three routes for furfural formation from xylose are possible. In addition, new findings show that biomass monosaccharides themselves can react further to form pseudo-lignin and humins as well as a wide array of other compounds when exposed to high temperatures. Hence, several aldehydes and ketones and many different organic acids and aromatic compounds may be generated during hydrothermal treatment of lignocellulosic biomass. The reaction mechanisms are of interest because the very same compounds that are possible inhibitors for biomass processing enzymes and microorganisms may be valuable biobased chemicals. Hence a new potential for industrial scale synthesis of chemicals has emerged. A better understanding of the reaction mechanisms and the impact of the reaction conditions on the product formation is thus a prerequisite for designing better biomass processing strategies and forms an important basis for the development of new biorefinery products from lignocellulosic biomass as well.

  3. Mechanism and Kinetics Analysis of NO/SO2/N2/O2 Dissociation Reactions in Non-Thermal Plasma

    Institute of Scientific and Technical Information of China (English)

    WANG Xinliang; LI Tingting; WEI Dongxiang; WEI Yanli; GU Fan


    The kinetics mechanism of the dissociation reactions in a NO/SO2/N2/O2 system was investigated in consideration of energetic electrons' impacts on a non-thermal plasma. A model was derived from the Boltzmann equation and molecule collision theory to predict the dissociation reaction rate coefficients. Upon comparison with available literature, the model was confirmed to be acceptably accurate in general. Several reaction rate coefficients of the NO/SO2/N2/O2 dissociation system were derived according to the Arrhenius formula. The activation energies of each plasma reaction were calculated by quantum chemistry methods. The relation between the dissociation reaction rate coefficient and electron temperature was established to describe the importance of each reaction and to predict relevant processes of gaseous chemical reactions. The sensitivity of the mechanism of NO/SO2/N2/O2 dissociation reaction in a non-thermal plasma was also analysed.

  4. Probing isotope effects in chemical reactions using single ions

    CERN Document Server

    Staanum, Peter F; Wester, Roland; Drewsen, Michael


    Isotope effects in reactions between Mg+ in the 3p 2P3/2 excited state and molecular hydrogen at thermal energies are studied through single reaction events. From only ~250 reactions with HD, the branching ratio between formation of MgD+ and MgH+ is found to be larger than 5. From additional 65 reactions with H2 and D2 we find that the overall decay probability of the intermediate MgH2+, MgHD+ or MgD2+ complexes is the same. Our study shows that few single ion reactions can provide quantitative information on ion-neutral reactions. Hence, the method is well-suited for reaction studies involving rare species, e.g., rare isotopes or short-lived unstable elements.

  5. Physical Mechanism of Nuclear Reactions at Low Energies

    CERN Document Server

    Oleinik, V P; Arepjev, Yu.D


    The physical mechanism of nuclear reactions at low energies caused by spatial extension of electron is considered. Nuclear reactions of this type represent intra-electronic processes, more precisely, the processes occurring inside the area of basic localization of electron. Distinctive characteristics of these processes are defined by interaction of the own field produced by electrically charged matter of electron with free nuclei. Heavy nucleus, appearing inside the area of basic localization of electron, is inevitably deformed because of interaction of protons with the adjoining layers of electronic cloud, which may cause nuclear fission. If there occur "inside" electron two or greater number of light nuclei, an attractive force appears between the nuclei which may result in the fusion of nuclei. The intra-electronic mechanism of nuclear reactions is of a universal character. For its realization it is necessary to have merely a sufficiently intensive stream of free electrons, i.e. heavy electric current, an...

  6. Hydroxylation Reaction Mechanism for Nitrosodimethylamine by Oxygen Atom

    Institute of Scientific and Technical Information of China (English)

    LI Lan; LIN Xiao-yan; LI Zong-he


    The hydroxylation reaction mechanism of nitrosodimethylamine(NDMA)by oxygen atom was theoretically investigated at the B3LYP/6-31G** level.It has been found that the path of the oxydation of the C-H bond is easier than the path involving a Singlet/Triplet crossing.The study of the potential surface shows that both solvent effect at B3LYP/6-31G** level and different method at more credible MP2/6-311G** level in the gas phase have no effect on the hydroxylation reaction mechanism.The oxidation hydroxylation process of NDMA by O is exothermic reaction and easy to occur.

  7. Effect of Grain Size and Reaction Time in Characterisation of Aggregates for Alkali Silica Reaction Using Chemical Method

    Directory of Open Access Journals (Sweden)

    R.P. Pathak


    Full Text Available Concrete can deteriorate as a result of alkali aggregate reaction, an interaction between alkalis present in alkaline pore solution originating from the Portland cement and reactive minerals in certain types of aggregates. Potential reactivity of aggregates with regard to alkalis present in concrete mix can be determined by Mortar Bar method, Chemical Method and Petrographic analysis. Of these the chemical method though is quick and does not require a large quantity of material for testing yet have its own inherent limitations. It does not ensure completion of reaction as the observations are limited to 24hour only and also does not assess the effect of varying the combination of coarse and fine aggregates. A study on chemical method by allowing the reaction for a prolonged time up to 96 hours and also on different grain size ranged matrix was carried at Central Soil and Materials Research Station, New Delhi. Simultaneously the test results of the modified method are compared to the existing Mortar Bar method, Chemical Method and Petrographic analysis The outcome of the studies clearly reflects that the grain size play an important role in the reaction, the reaction time has a demarked impact on reactivity, in the cases having a high value of silica release the choice of reduction in alkalinity as an indicator of degree of reaction is not reliable, instead measuring remaining Na2O concentration in Sodium hydroxide solution after the reaction seems to be much more meaningful in justifying the silica release.

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

    DEFF Research Database (Denmark)

    Linneberg, Allan; Thyssen, Jacob Pontoppidan; Dirksen, Asger


    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...... 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...

  9. Separation of chemical reaction intermediates by metal-organic frameworks. (United States)

    Centrone, Andrea; Santiso, Erik E; Hatton, T Alan


    HPLC columns custom-packed with metal-organic framework (MOF) materials are used for the separation of four small intermediates and byproducts found in the commercial synthesis of an important active pharmaceutical ingredient in methanol. In particular, two closely related amines can be separated in the methanol reaction medium using MOFs, but not with traditional C18 columns using an optimized aqueous mobile phase. Infrared spectroscopy, UV-vis spectroscopy, X-ray diffraction, and thermogravimetric analysis are used in combination with molecular dynamic simulations to study the separation mechanism for the best-performing MOF materials. It is found that separation with ZIF-8 is the result of an interplay between the thermodynamic driving force for solute adsorption within the framework pores and the kinetics of solute diffusion into the material pores, while the separation with Basolite F300 is achieved because of the specific interactions between the solutes and Fe(3+) sites. This work, and the exceptional ability to tailor the porous properties of MOF materials, points to prospects for using MOF materials for the continuous separation and synthesis of pharmaceutical compounds.

  10. Reaction Mechanisms of the Initial Oligomerization of Aluminophosphate. (United States)

    Xiang, Yan; Xin, Liang; Deetz, Joshua D; Sun, Huai


    The mechanisms of aluminophosphate oligomerization were investigated using density functional theory with the SMD solvation model. Two aluminum species, Al(OH)4(-) and Al(H2O)6(3+), and four phosphorus species, H3PO4, H2PO4(-), HPO4(2-), and PO4(3-), were considered as the monomers for polycondensation reactions. It was found that the most favorable pathway to dimerization was a Lewis acid-base reaction: the aprotic oxygen of phosphoric acid (P═O) performs a nucleophilic attack on the central aluminum atom of Al(OH)4(-). Using this mechanism as a pattern, plausible dimerization mechanisms were investigated by varying the proticity and hydration of the phosphorus and aluminum monomers, respectively. The relative reaction rates of each mechanism were estimated under different pH conditions. The chain growth of aluminophosphates to trimers, tetramers, and pentamers and the cyclization of a linear tetramer were also investigated. For oligomerization reactions beyond dimer formation, it is found that cluster growth favors the addition of the phosphoric monomers rather than aluminum monomers.

  11. Non-allergic cutaneous reactions in airborne chemical sensitivity--a population based study. (United States)

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


    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.

  12. Thyroid disrupting chemicals: Mechanisms and mixtures (United States)

    Environmental contaminants are known to act as thyroid disrupting chemicals (TDCs). Broadly defined, TDCs are xenobiotics that alter the structure or function of the thyroid gland, alter regulatory enzymes associated with thyroid hormone (TH) homeostasis, or change circulating o...

  13. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    Energy Technology Data Exchange (ETDEWEB)

    Gorman, Brian P [Colorado School of Mines, Golden, CO (United States)


    Project Description: The general objective of the proposed research is to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, pCO2, and modest ranges in T and P. This will be accomplished by studying both reaction rates and solubility from changes in solution chemistry, and making nanoscale observations of calcite precipitate surface morphology and composition at the micro-to-nano-scale to provide an understanding of controlling reaction mechanisms and pathways. The specific objectives necessary to reach the general objective are: a) determination of how pCO2, Ca2+, ionic strength and “foreign” ions influence reaction rates; and b) investigate the influence of these parameters on apparent kinetic solubility from dissolution and precipitation reactions. This information will clearly be central to the construction of reliable reaction-transport models to predict reservoir and formation response to increased CO2 in saline waters. This program was initially collaborative with John Morse at Texas A&M, however his passing shortly after the beginning of this program resulted in abbreviated research time and effort. Summary of Results: Early studies using electron microscopy and spectroscopy indicated that carbonate precipitation from natural seawater (NSW) conditions onto aragonite substrates was mediated by a surface amorphous calcium carbonate layer. It was hypothesized that this ACC layer (observed after < 5days reaction time) was responsible for the abnormal reaction kinetics and also served as a metastable seed layer for growth of epitaxial aragonite. Further studies of the ACC formation mechanism indicated a strong dependence on the Mg concentration in solution. Subsequent studies at shorter times (10 hrs) on calcite substrates and in a wide range of supersaturation conditions did not indicate any ACC layer. Instead, an epitaxial layer by layer

  14. Mixing and chemical reaction in sheared and nonsheared homogeneous turbulence (United States)

    Leonard, Andy D.; Hill, James C.


    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.

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

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


    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.

  16. Method of operating a thermal engine powered by a chemical reaction (United States)

    Ross, J.; Escher, C.


    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.

  17. Method of operating a thermal engine powered by a chemical reaction (United States)

    Ross, John; Escher, Claus


    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.

  18. Motivational Factors Contributing to Turkish High School Students' Achievement in Gases and Chemical Reactions (United States)

    Kadioglu, Cansel; Uzuntiryaki, Esen


    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…

  19. Introducing Stochastic Simulation of Chemical Reactions Using the Gillespie Algorithm and MATLAB: Revisited and Augmented (United States)

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


    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. Mapping Students' Conceptual Modes When Thinking about Chemical Reactions Used to Make a Desired Product (United States)

    Weinrich, M. L.; Talanquer, V.


    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…

  1. Acid-Base Chemistry According to Robert Boyle: Chemical Reactions in Words as well as Symbols (United States)

    Goodney, David E.


    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…

  2. DFT study on mechanism of the classical Biginelli reaction

    Institute of Scientific and Technical Information of China (English)

    Jin Guang Ma; Ji Ming Zhang; Hai Hui Jiang; Wan Yong Ma; Jian Hua Zhou


    The condensation of benzaldehyde, urea, and ethyl acetoacetate according to the procedure described by Biginelli was investigated at the B3LYP/6-31G(d), B3LYP/6-31+G(d,p), and B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) levels to explore the reaction mechanism. According to the mechanism proposed by Kappe, structures of five intermediates were optimized and four transition states were found. The calculation results proved that the mechanism proposed by Kappe is right.

  3. A Novel Oscillating Chemical Reaction Using Ninhydrin as Single Organic Substrate

    Institute of Scientific and Technical Information of China (English)

    Fu Wei YANG; Jin Zhang GAO; Wu YANG; Kan Jun SUN


    A novel oscillating chemical reaction using ninhydrin as a single organic substrate was represented in this paper. It distinguished from the classically catalyzed BZ oscillating chemical reaction due to there was no active methene (CH2=) and/or enol structure in the ninhydrin molecule, which served as single organic substrate. This suggested that the substrates used in catalyzed BZ reaction were not always the organic compounds containing active methene (CH2=) and/or enol structure and bromination process in this kind of catalyzed chemical oscillating reaction was not also necessary.

  4. Reaction mechanisms in the 6Li+ 52Cr system

    Directory of Open Access Journals (Sweden)

    Pandey Bhawna


    Full Text Available Reactions induced by the weakly bound 6Li projectile interacting with the intermediate mass target 52Cr are investigated. The choice of this particular reaction in our study is because it is proposed as a surrogate reaction [6Li(52Cr, d56Fe*] for the measurement of 55Fe(n,p reaction cross-section, which has been found to be very important in fusion reactor studies. All the conditions which have to be satisfied for using the surrogate method have been checked. The energy of 6Li beam is selected in a way so as to get equivalent neutron energy in the region of 9-14 MeV, which is of primary interest in fusion reactor application. In the present work, statistical model calculations PACE (Projection-Angular-Momentum-Coupled-Evaporation, ALICE and Continuum-Discretized–Coupled-Channel (CDCC: FRESCO have been used to provide information for the 6Li + 52Cr system and the respective contributions of different reaction mechanisms. The present theoretical work is an important step in the direction towards studying the cross-section of the 55Fe(n, p55Mn reaction by surrogate method.

  5. Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD)

    KAUST Repository

    Quitterer, Felix


    The final step in the biosynthesis of the 22nd genetically encoded amino acid, pyrrolysine, is catalyzed by PylD, a structurally and mechanistically unique dehydrogenase. This catalyzed reaction includes an induced-fit mechanism achieved by major structural rearrangements of the N-terminal helix upon substrate binding. Different steps of the reaction trajectory are visualized by complex structures of PylD with substrate and product. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Chemical Synthesis Accelerated by Paper Spray: The Haloform Reaction (United States)

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


    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…

  7. Surface chemical reactions induced by molecules electronically-excited in the gas

    DEFF Research Database (Denmark)

    Petrunin, Victor V.


    and alignment are taking place, guiding all the molecules towards the intersections with the ground state PES, where transitions to the ground state PES will occur with minimum energy dissipation. The accumulated kinetic energy may be used to overcome the chemical reaction barrier. While recombination chemical...... be readily produced. Products of chemical adsorption and/or chemical reactions induced within adsorbates are aggregated on the surface and observed by light scattering. We will demonstrate how pressure and spectral dependencies of the chemical outcomes, polarization of the light and interference of two laser...... beams inducing the reaction can be used to distinguish the new process we try to investigate from chemical reactions induced by photoexcitation within adsorbed molecules and/or gas phase photolysis....

  8. Monitoring Chemical and Biological Electron Transfer Reactions with a Fluorogenic Vitamin K Analogue Probe. (United States)

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


    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.

  9. Preliminary analysis of chemical reaction under the radiation of electromagnetic wave

    Institute of Scientific and Technical Information of China (English)


    Microwave can be used to accelerate chemical reaction and improve the rate of production.Does microwave only act as a heating factor? Do there exist any specific effects? These questions are still holding a violent controversy.Here we will choose the Belousov- Zhabotinsky reaction,which is sensitive to surrounding effects,to study the influence of microwave on chemical reactions.Visible changes of periods have been observed.It appeares that there could have been specific effects of microwave.

  10. Reversible Diffusion-Limited Reactions: "Chemical Equilibrium" State and the Law of Mass Action Revisited


    Voituriez, R.; Moreau, M.; Oshanin, G.


    The validity of two fundamental concepts of classical chemical kinetics - the notion of "Chemical Equilibrium" and the "Law of Mass Action" - are re-examined for reversible \\textit{diffusion-limited} reactions (DLR), as exemplified here by association/dissociation $A+A \\rightleftharpoons B$ reactions. We consider a general model of long-ranged reactions, such that any pair of $A$ particles, separated by distance $\\mu$, may react with probability $\\omega_+(\\mu)$, and any $B$ may dissociate wit...

  11. A model for chemically-induced mechanical loading on MEMS

    DEFF Research Database (Denmark)

    Amiot, Fabien


    The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain, and displac......The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain...

  12. Numerical comparison of hydrogen-air reaction mechanisms for unsteady shockinduced combustion applications

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, P. Pradeep; Kim, Kui Soon; Oh, Se Jong; Choi, Jeong Yeol [Pusan National University, Busan (Korea, Republic of)


    An unsteady shock-induced combustion (SIC) is characterized by the regularly oscillating combustion phenomenon behind the shock wave supported by the blunt projectile flying around the speed of Chapman-Jouguet detonation wave. The SIC is the coupling phenomenon between the hypersonic flow and the chemical kinetics, but the effects of chemical kinetics have been rarely reported. We compared hydrogen-air reaction mechanisms for the shock-induced combustion to demonstrate the importance of considering the reaction mechanisms for such complex flows. Seven hydrogen-air reaction mechanisms were considered, those available publically and used in other researches. As a first step in the comparison of the hydrogen combustion, ignition delay time of hydrogen-oxygen mixtures was compared at various initial conditions. Laminar premixed flame speed was also compared with available experimental data and at high pressure conditions. In addition, half-reaction length of ZND (Zeldovich-Neumann-Doering) detonation structure accounts for the length scale in SIC phenomena. Oscillation frequency of the SIC is compared by running the time-accurate 3rd-order Navier-Stokes CFD code fully coupled with the detailed chemistry by using four levels of grid resolutions.

  13. Self-Organized Stationary Patterns in Networks of Bistable Chemical Reactions. (United States)

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


    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.

  14. Physical and chemical mechanisms in oxide-based resistance random access memory. (United States)

    Chang, Kuan-Chang; Chang, Ting-Chang; Tsai, Tsung-Ming; Zhang, Rui; Hung, Ya-Chi; Syu, Yong-En; Chang, Yao-Feng; Chen, Min-Chen; Chu, Tian-Jian; Chen, Hsin-Lu; Pan, Chih-Hung; Shih, Chih-Cheng; Zheng, Jin-Cheng; Sze, Simon M


    In this review, we provide an overview of our work in resistive switching mechanisms on oxide-based resistance random access memory (RRAM) devices. Based on the investigation of physical and chemical mechanisms, we focus on its materials, device structures, and treatment methods so as to provide an in-depth perspective of state-of-the-art oxide-based RRAM. The critical voltage and constant reaction energy properties were found, which can be used to prospectively modulate voltage and operation time to control RRAM device working performance and forecast material composition. The quantized switching phenomena in RRAM devices were demonstrated at ultra-cryogenic temperature (4K), which is attributed to the atomic-level reaction in metallic filament. In the aspect of chemical mechanisms, we use the Coulomb Faraday theorem to investigate the chemical reaction equations of RRAM for the first time. We can clearly observe that the first-order reaction series is the basis for chemical reaction during reset process in the study. Furthermore, the activation energy of chemical reactions can be extracted by changing temperature during the reset process, from which the oxygen ion reaction process can be found in the RRAM device. As for its materials, silicon oxide is compatible to semiconductor fabrication lines. It is especially promising for the silicon oxide-doped metal technology to be introduced into the industry. Based on that, double-ended graphene oxide-doped silicon oxide based via-structure RRAM with filament self-aligning formation, and self-current limiting operation ability is demonstrated. The outstanding device characteristics are attributed to the oxidation and reduction of graphene oxide flakes formed during the sputter process. Besides, we have also adopted a new concept of supercritical CO2 fluid treatment to efficiently reduce the operation current of RRAM devices for portable electronic applications.

  15. Fundamental study of mechanical and chemical degradation mechanisms of PEM fuel cell membranes (United States)

    Yoon, Wonseok

    One of the important factors determining the lifetime of polymer electrolyte membrane fuel cells (PEMFCs) is membrane degradation and failure. The lack of effective mitigation methods is largely due to the currently very limited understanding of the underlying mechanisms for mechanical and chemical degradations of fuel cell membranes. In order to understand degradation of membranes in fuel cells, two different experimental approaches were developed; one is fuel cell testing under open circuit voltage (OCV) with bi-layer configuration of the membrane electrode assemblies (MEAs) and the other is a modified gas phase Fenton's test. Accelerated degradation tests for polymer electrolyte membrane (PEM) fuel cells are frequently conducted under open circuit voltage (OCV) conditions at low relative humidity (RH) and high temperature. With the bi-layer MEA technique, it was found that membrane degradation is highly localized across thickness direction of the membrane and qualitatively correlated with location of platinum (Pt) band through mechanical testing, Infrared (IR) spectroscopy, fluoride emission, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy dispersive spectroscopy (EDS) measurement. One of the critical experimental observations is that mechanical behavior of membranes subjected to degradation via Fenton's reaction exhibit completely different behavior with that of membranes from the OCV testing. This result led us to believe that other critical factors such as mechanical stress may affect on membrane degradation and therefore, a modified gas phase Fenton's test setup was developed to test the hypothesis. Interestingly, the results showed that mechanical stress directly accelerates the degradation rate of ionomer membranes, implying that the rate constant for the degradation reaction is a function of mechanical stress in addition to commonly known factors such as temperature and humidity. Membrane degradation induced by

  16. Density Functional Study on the Reaction Mechanism for the Reaction of Ni+ with Ethane

    Institute of Scientific and Technical Information of China (English)

    ZHANG,Dong-Ju(张冬菊); LIU,Cheng-Bu(刘成卜); LIU,Yong-Jun(刘永军); HU,Hai-Quan(胡海泉)


    The mechanism of the reaction of Ni+ (2D) with ethane in the gas-phase was studied by using density functional theory. Both the B3LYP and BLYP functionals with standard all-electron basis sets are used to give the detailed information of the potential energy surface (PES) of [Ni, C2, H6 ] +. Tne mechanisms forming the products CH4 and H2 in the reaction of Ni+with ethane are proposed. The reductive eliminations of CH4and H2 are typical addition-elimination reactions. Each of the two reactions consists of two elementary steps: C-C or CH bond activations to form inserted species followed by isomerizations to form product-like intermediate. The rate determining steps for the elimination reatcions of forming CH4 and H2 are the isomerizations of the inserted species rather than C-C or C-H bond activations. The elimination reaction of forming H2 was found to be thermodynamically favored compared to that of CH4.

  17. Unraveling the reaction mechanisms governing methanol-to-olefins catalysis by theory and experiment. (United States)

    Hemelsoet, Karen; Van der Mynsbrugge, Jeroen; De Wispelaere, Kristof; Waroquier, Michel; Van Speybroeck, Veronique


    The conversion of methanol to olefins (MTO) over a heterogeneous nanoporous catalyst material is a highly complex process involving a cascade of elementary reactions. The elucidation of the reaction mechanisms leading to either the desired production of ethene and/or propene or undesired deactivation has challenged researchers for many decades. Clearly, catalyst choice, in particular topology and acidity, as well as the specific process conditions determine the overall MTO activity and selectivity; however, the subtle balances between these factors remain not fully understood. In this review, an overview of proposed reaction mechanisms for the MTO process is given, focusing on the archetypal MTO catalysts, H-ZSM-5 and H-SAPO-34. The presence of organic species, that is, the so-called hydrocarbon pool, in the inorganic framework forms the starting point for the majority of the mechanistic routes. The combination of theory and experiment enables a detailed description of reaction mechanisms and corresponding reaction intermediates. The identification of such intermediates occurs by different spectroscopic techniques, for which theory and experiment also complement each other. Depending on the catalyst topology, reaction mechanisms proposed thus far involve aromatic or aliphatic intermediates. Ab initio simulations taking into account the zeolitic environment can nowadays be used to obtain reliable reaction barriers and chemical kinetics of individual reactions. As a result, computational chemistry and by extension computational spectroscopy have matured to the level at which reliable theoretical data can be obtained, supplying information that is very hard to acquire experimentally. Special emphasis is given to theoretical developments that open new perspectives and possibilities that aid to unravel a process as complex as methanol conversion over an acidic porous material.

  18. A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure. (United States)

    Cammi, Roberto


    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.

  19. A new type of power energy for accelerating chemical reactions: the nature of a microwave-driving force for accelerating chemical reactions. (United States)

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


    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.

  20. A new type of power energy for accelerating chemical reactions: the nature of a microwave-driving force for accelerating chemical reactions (United States)

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


    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.

  1. Chemical photoallergy: photobiochemical mechanisms, classification, and risk assessments. (United States)

    Onoue, Satomi; Seto, Yoshiki; Sato, Hideyuki; Nishida, Hayato; Hirota, Morihiko; Ashikaga, Takao; Api, Anne Marie; Basketter, David; Tokura, Yoshiki


    Chemical photosensitivity can be elicited by exposure of the skin to various pharmaceutical substances, foods, cosmetics and other environmental chemicals, followed by exposure to sunlight. There are at least three types of chemical photosensitivity, i.e., photoirritancy (narrowly defined as phototoxicity), photogenotoxicity and photoallergenicity, and their clinical characteristics and mechanisms are quite different. Concerns about chemical photoallergy is increasing, and various studies have been made to clarify the photobiochemical characteristics of photoallergens and the mechanisms involved. Various methodologies, including in silico prediction models, photochemical assay systems, and in vitro phototoxicity prediction tools, have been developed to predict the photoallergenic potential of chemicals over the past few years. The aim of this manuscript is to review the clinical characteristics, pathogenetic mechanisms and photobiochemical features of photoallergens, with special emphasis on the current status about development of screening systems for predicting photoallergenic potential of chemicals.

  2. Vicher: A Virtual Reality Based Educational Module for Chemical Reaction Engineering. (United States)

    Bell, John T.; Fogler, H. Scott


    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…

  3. Reactions of a stable dialkylsilylene and their mechanisms

    Indian Academy of Sciences (India)

    Mitsuo Kira


    Various reactions for a stable dialkylsilylene, 2,2,5,5-tetrakis(trimethylsilyl)silacyclopentane-1,1-diyl (1), are summarized and their mechanisms are discussed. Silylene 1 isomerizes to the corresponding silaethene via the 1,2-trimethylsilyl migration. Reduction of 1 with alkali metals affords the corresponding radical anion 1.− with a relatively small 29Si hfs constant (2.99 mT) and a large g-factor (g = 2.0077) compared with those for trivalent silyl radicals. Photo-excitation of 1 generates the corresponding singlet excited state (11*) with the lifetime of 80.5 ns. The excited state reacts with C=C double bond compounds including benzene, naphthalene, and ()- and ()-2-butenes. Although the thermal reactions of 1 with haloalkanes occur via radical mechanisms, the insertion into O-H, Si-H and Si-Cl bonds proceeds concertedly via the threemembered cyclic transition states. The reaction of 1 with H2SiCl2 gives the Si-Cl insertion product exclusively, while the quantitative insertion to Si-H bond occurs when Me2SiHCl is used as a substrate. The origin of the rather unusual Si-H/Si-Cl selectivity is elucidated using DFT calculations. Silylene 1 adds to C=C, C≡C, and C=O bonds to afford the corresponding silacycles as stable compounds. The importance of the carbonyl silaylides during the reactions of silylenes with aldehydes and ketones is emphasized.

  4. Effects of Surfactants on the Rate of Chemical Reactions

    Directory of Open Access Journals (Sweden)

    B. Samiey


    Full Text Available Surfactants are self-assembled compounds that depend on their structure and electric charge can interact as monomer or micelle with other compounds (substrates. These interactions which may catalyze or inhibit the reaction rates are studied with pseudophase, cooperativity, and stoichiometric (classical models. In this review, we discuss applying these models to study surfactant-substrate interactions and their effects on Diels-Alder, redox, photochemical, decomposition, enzymatic, isomerization, ligand exchange, radical, and nucleophilic reactions.

  5. The Radical Pair Mechanism and the Avian Chemical Compass: Quantum Coherence and Entanglement

    CERN Document Server

    Zhang, Yiteng; Kais, Sabre


    We review the spin radical pair mechanism which is a promising explanation of avian navigation. This mechanism is based on the dependence of product yields on (1) the hyperfine interaction involving electron spins and neighboring nuclear spins and (2) the intensity and orientation of the geomagnetic field. One surprising result is that even at ambient conditions quantum entanglement of electron spins can play an important role in avian magnetoreception. This review describes the general scheme of chemical reactions involving radical pairs generated from singlet and triplet precursors; the spin dynamics of the radical pairs; and the magnetic field dependence of product yields caused by the radical pair mechanism. The main part of the review includes a description of the chemical compass in birds. We review: the general properties of the avian compass; the basic scheme of the radical pair mechanism; the reaction kinetics in cryptochrome; quantum coherence and entanglement in the avian compass; and the effects o...

  6. Automated Discovery of New Chemical Reactions and Accurate Calculation of Their Rates (United States)


    of the Search Space Thermochemistry Calculations. Even for a small hydrocarbon system, the number of reaction pathways which can be generated using... reaction is considered to be too endothermic to be interesting if the standard enthalpy of reaction (denoted as Hr0 in Tables 2-5) is higher than 20 kcal...AFRL-OSR-VA-TR-2015-0169 Automated discovery of new chemical reactions and accurate calculation of their rates William Green MASSACHUSETTS INSTITUTE

  7. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study. (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan


    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  8. Cutaneous reactions in nuclear, biological and chemical warfare

    Directory of Open Access Journals (Sweden)

    Arora Sandeep


    Full Text Available 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. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules. (United States)

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús


    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.

  10. Revealing a double-inversion mechanism for the F⁻+CH₃Cl SN2 reaction. (United States)

    Szabó, István; Czakó, Gábor


    Stereo-specific reaction mechanisms play a fundamental role in chemistry. The back-side attack inversion and front-side attack retention pathways of the bimolecular nucleophilic substitution (SN2) reactions are the textbook examples for stereo-specific chemical processes. Here, we report an accurate global analytic potential energy surface (PES) for the F(-)+CH₃Cl SN2 reaction, which describes both the back-side and front-side attack substitution pathways as well as the proton-abstraction channel. Moreover, reaction dynamics simulations on this surface reveal a novel double-inversion mechanism, in which an abstraction-induced inversion via a FH···CH₂Cl(-) transition state is followed by a second inversion via the usual [F···CH₃···Cl](-) saddle point, thereby opening a lower energy reaction path for retention than the front-side attack. Quasi-classical trajectory computations for the F(-)+CH₃Cl(ν1=0, 1) reactions show that the front-side attack is a fast direct, whereas the double inversion is a slow indirect process.

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  12. Understanding chemical binding using the Berlin function and the reaction force (United States)

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


    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.

  13. Formation of three N-acetyl-L-cysteine monoadducts and one diadduct by the reaction of S-(1,2-dichlorovinyl)-L-cysteine sulfoxide with N-acetyl-L-cysteine at physiological conditions: chemical mechanisms and toxicological implications. (United States)

    Barshteyn, Nella; Elfarra, Adnan A


    Previously, our laboratory has shown that S-(1,2-dichlorovinyl)-L-cysteine sulfoxide (DCVCS), a Michael acceptor produced by a flavin-containing monooxygenase 3 (FMO3)-mediated oxidation of S-(1,2-dichlorovinyl)-L-cysteine (DCVC), is a more potent nephrotoxicant than DCVC. In the present study, we characterized reactions of DCVCS with nucleophilic amino acids. DCVCS incubations with N-acetyl-L-cysteine (NAC) at pH 7.4 and 37 degrees C for 1 h resulted in the formation of three monoadducts and one diadduct characterized by LC/MS, 1H NMR, and 1H-detected heteronuclear single quantum correlation. The formation of all adducts (with relative ratios of 29, 31, 24, and 12%, respectively) was rapid and time-dependent; the half-lives of the two DCVCS diastereomers in the presence of NAC were 13.8 (diastereomer I) and 9.4 min (diastereomer II). Adducts 1 and 2 were determined to be diastereomers of S-[1-chloro-2-(N-acetyl-L-cystein- S-yl)vinyl]-L-cysteine sulfoxide formed by Michael addition of NAC to the terminal vinylic carbon of DCVCS followed by loss of HCl. Adduct 4 was determined to be S-[2-chloro-2-(N-acetyl-L-cystein- S-yl)vinyl]-L-cysteine sulfoxide formed from the initial Michael addition product followed by a less favorable loss of HCl and/or by a rearrangement of adduct 2 through the formation of a cyclic chloronium ion. The addition of another molecule of NAC to monoadducts 1, 2, or 4 resulted in the formation of the novel diadduct, S-[2,2-( N-acetyl-L-cystein-S-yl)vinyl]-L-cysteine sulfoxide (adduct 3), whose detection in relatively large amount suggests that DCVCS could act as a cross-linking agent. DCVCS was not reactive with N-acetyl-L-lysine or L-valinamide at similar incubation conditions. Collectively, the results suggest selective reactivity of DCVCS toward protein sulfhydryl groups. Furthermore, the cross-linking properties of DCVCS may in part explain its high nephrotoxic potency.

  14. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    Suleimanov, Yu.V.


    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+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  15. Predicting rare events in chemical reactions: Application to skin cell proliferation. (United States)

    Lee, Chiu Fan


    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.

  16. Diversity of Chemical Mechanisms in Thioredoxin Catalysis Revealed by Single-Molecule Force Spectroscopy (United States)

    Perez-Jimenez, Raul; Li, Jingyuan; Kosuri, Pallav; Sanchez-Romero, Inmaculada; Wiita, Arun P.; Rodriguez-Larrea, David; Chueca, Ana; Holmgren, Arne; Miranda-Vizuete, Antonio; Becker, Katja; Cho, Seung-Hyun; Beckwith, Jon; Gelhaye, Eric; Jacquot, Jean P.; Gaucher, Eric; Sanchez-Ruiz, Jose M.; Berne, Bruce J.; Fernandez, Julio M.


    Thioredoxins are oxido-reductase enzymes present in all organisms, catalyzing the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single molecule level. Here we use single molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different thioredoxin enzymes. While all Trxs show a characteristic Michaelis-Menten mechanism detected when the disulfide bond is stretched at low forces, two different chemical behaviors distinguish bacterial from eukaryotic-origin Trxs at high forces. Eukaryotic-origin Trxs reduce disulfide bonds through a single-electron transfer reaction (SET) whereas bacterial-origin Trxs exhibit both nucleophilic substitution (SN2) and SET reactions. A computational analysis of Trx structures identifies the evolution of the binding groove as an important factor controlling the chemistry of Trx catalysis. PMID:19597482

  17. Surface Nano-Structuring by Adsorption and Chemical Reactions


    Ken-ichi Tanaka


    Nano-structuring of the surface caused by adsorption of molecules or atoms and by the reaction of surface atoms with adsorbed species are reviewed from a chemistry viewpoint. Self-assembly of adsorbed species is markedly influenced by weak mutual interactions and the local strain of the surface induced by the adsorption. Nano-structuring taking place on the surface is well explained by the notion of a quasi-molecule provided by the reaction of surface atoms with adsorbed species. Self-assembl...

  18. Organoberyllium compounds and their chemical reactions. XI. Synthesis of diacetylhydrobenzoins

    Energy Technology Data Exchange (ETDEWEB)

    Lapkin, I.I.; Sinani, S.V.


    The authors previously determined that the reaction of aromatic aldehydes with acylhaloberyllium in ethyl acetate lead to the formation of stilbene. In this same vein they have found that the final products of this reaction can include not only stilbenes but also diacetylhydrobenzoin and that the product is determined by the nature of the solvent. In this paper they determine that while ethyl acetate indeed leads to the stilbene the use of an ether--diethyl or diisopropyl--leads to diacetylhydrobenzoin. NMR spectroscopy is used to ascertain the structure of the product.

  19. Reaction route graphs. III. Non-minimal kinetic mechanisms. (United States)

    Fishtik, Ilie; Callaghan, Caitlin A; Datta, Ravindra


    The concept of reaction route (RR) graphs introduced recently by us for kinetic mechanisms that produce minimal graphs is extended to the problem of non-minimal kinetic mechanisms for the case of a single overall reaction (OR). A RR graph is said to be minimal if all of the stoichiometric numbers in all direct RRs of the mechanism are equal to +/-1 and non-minimal if at least one stoichiometric number in a direct RR is non-unity, e.g., equal to +/-2. For a given mechanism, four unique topological characteristics of RR graphs are defined and enumerated, namely, direct full routes (FRs), empty routes (ERs), intermediate nodes (INs), and terminal nodes (TNs). These are further utilized to construct the RR graphs. One algorithm involves viewing each IN as a central node in a RR sub-graph. As a result, the construction and enumeration of RR graphs are reduced to the problem of balancing the peripheral nodes in the RR sub-graphs according to the list of FRs, ERs, INs, and TNs. An alternate method involves using an independent set of RRs to draw the RR graph while satisfying the INs and TNs. Three examples are presented to illustrate the application of non-minimal RR graph theory.

  20. Reaction dynamics. Extremely short-lived reaction resonances in Cl + HD (v = 1) → DCl + H due to chemical bond softening. (United States)

    Yang, Tiangang; Chen, Jun; Huang, Long; Wang, Tao; Xiao, Chunlei; Sun, Zhigang; Dai, Dongxu; Yang, Xueming; Zhang, Dong H


    The Cl + H2 reaction is an important benchmark system in the study of chemical reaction dynamics that has always appeared to proceed via a direct abstraction mechanism, with no clear signature of reaction resonances. Here we report a high-resolution crossed-molecular beam study on the Cl + HD (v = 1, j = 0) → DCl + H reaction (where v is the vibrational quantum number and j is the rotational quantum number). Very few forward scattered products were observed. However, two distinctive peaks at collision energies of 2.4 and 4.3 kilocalories per mole for the DCl (v' = 1) product were detected in the backward scattering direction. Detailed quantum dynamics calculations on a highly accurate potential energy surface suggested that these features originate from two very short-lived dynamical resonances trapped in the peculiar H-DCl (v' = 2) vibrational adiabatic potential wells that result from chemical bond softening. We anticipate that dynamical resonances trapped in such wells exist in many reactions involving vibrationally excited molecules.

  1. Chemical Principles Revisited. Redox Reactions and the Electropotential Axis. (United States)

    Vella, Alfred J.


    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)

  2. Arrangement for carrying out and studying chemical reactions

    NARCIS (Netherlands)

    Langeveld, A.D.; Makkee, M.; Moulijn, J.A.


    Abstract of NL 9102029 (A) Described is an arrangement for carrying out TAP experiments. Such an arrangement comprises a reaction chamber in which a very short-lived beam of molecules is directed at a target to produce a short-lived beam of intermediate-product molecules, and a vacuum chamber wher

  3. Theoretical studies of the dynamics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, A.F. [Argonne National Laboratory, IL (United States)


    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.

  4. Theoretical Studies of Chemical Reactions following Electronic Excitation (United States)

    Chaban, Galina M.


    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.

  5. Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds. (United States)

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


    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.

  6. Hypervelocity accelerators with electro-thermo-chemical reaction (United States)

    Ikuta, Kazunari


    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.


    Institute of Scientific and Technical Information of China (English)

    Bao-jun Qu


    The radical intermediates, the crosslink microstructures, and the reaction mechanism of benzophenone (BP)-photoinitiated crosslinking of low-density polyethylene (LDPE) and model compounds (MD) have been reviewed in detail.The spin-trapping electron spin resonance (ESR) spectra obtained from the LDPE/BP systems with spin-trap agents showthat two kinds of polymer radical intermediates are mainly formed: tertiary carbon and secondary carbon radicals. The spin-trapping ESR studies of MD/BP systems give further evidence that photocrosslinking reactions of PE predominantly takeplace at sites of tertiary carbon, secondary carbon, and especially allylic carbon when available. The high resolution 13C-NMR spectra obtained from LDPE and MD systems show that the crosslink microstructures have H- and Y-type links andthat their concentrations are of the same order. The fluorescence, ESR, 13C and 1H-NMR spectra from the PE and MDsystems demonstrate that the main photoreduction product of BP (PPB) is benzpinacol formed by the recombination of twodiphenylhydroxymethyl (K*) radical intermediates. Two new PPB products: an isomer of benzpinacol with quinoid structure,1-phenylhydroxymethylene-4-diphenylhydroxymethyl-2,5-cyclohexadiene and three kinds of a-alkyl-benzhydrols have beendetected and identified. These results provide new experimental evidence for elucidating the reaction mechanism in the BP-photoinitiated crosslinking of polyethylene.

  8. Drift and breakup of spiral waves in reaction-diffusion-mechanics systems. (United States)

    Panfilov, A V; Keldermann, R H; Nash, M P


    Rotating spiral waves organize excitation in various biological, physical, and chemical systems. They underpin a variety of important phenomena, such as cardiac arrhythmias, morphogenesis processes, and spatial patterns in chemical reactions. Important insights into spiral wave dynamics have been obtained from theoretical studies of the reaction-diffusion (RD) partial differential equations. However, most of these studies have ignored the fact that spiral wave rotation is often accompanied by substantial deformations of the medium. Here, we show that joint consideration of the RD equations with the equations of continuum mechanics for tissue deformations (RD-mechanics systems), yield important effects on spiral wave dynamics. We show that deformation can induce the breakup of spiral waves into complex spatiotemporal patterns. We also show that mechanics leads to spiral wave drift throughout the medium approaching dynamical attractors, which are determined by the parameters of the model and the size of the medium. We study mechanisms of these effects and discuss their applicability to the theory of cardiac arrhythmias. Overall, we demonstrate the importance of RD-mechanics systems for mathematics applied to life sciences.

  9. X-ray Microspectroscopy and Chemical Reactions in Soil Microsites

    Energy Technology Data Exchange (ETDEWEB)

    D Hesterberg; M Duff; J Dixon; M Vepraskas


    Soils provide long-term storage of environmental contaminants, which helps to protect water and air quality and diminishes negative impacts of contaminants on human and ecosystem health. Characterizing solid-phase chemical species in highly complex matrices is essential for developing principles that can be broadly applied to the wide range of notoriously heterogeneous soils occurring at the earth's surface. In the context of historical developments in soil analytical techniques, we describe applications of bulk-sample and spatially resolved synchrotron X-ray absorption spectroscopy (XAS) for characterizing chemical species of contaminants in soils, and for determining the uniqueness of trace-element reactivity in different soil microsites. Spatially resolved X-ray techniques provide opportunities for following chemical changes within soil microsites that serve as highly localized chemical micro- (or nano-)reactors of unique composition. An example of this microreactor concept is shown for micro-X-ray absorption near edge structure analysis of metal sulfide oxidation in a contaminated soil. One research challenge is to use information and principles developed from microscale soil chemistry for predicting macroscale and field-scale behavior of soil contaminants.

  10. Expanded utility of the native chemical ligation reaction. (United States)

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


    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.

  11. Influence of additives on microstructures, mechanical properties and shock-induced reaction characteristics of Al/Ni composites

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Wei; Zhang, Xianfeng, E-mail:; Wu, Yang; He, Yong; Wang, Chuanting; Guo, Lei


    Granular composites containing aluminum (Al) and nickel (Ni) are typical structural energetic materials, which possess ideal combination of both mechanical properties and energy release capability. The influence of two additives, namely Teflon (PTFE) and copper (Cu), on mechanical properties and shock-induced chemical reaction (SICR) characteristics of Al/Ni material system has been investigated. Three composites, namely Al/Ni, Al/Ni/PTFE and Al/Ni/Cu with same volumetric ratio of Al powder to Ni powder, were processed by means of static pressing. Scanning electron microscopy was used to study the microstructure of the mentioned three composites. Quasi static compression tests were also conducted to determine the mechanical properties and fracture behavior of the mentioned three composites. It was shown that the additives affected both compressive strength and fracture mode of the three composites. Impact initiation experiments on the mentioned three composites were performed to determine their shock-induced chemical reaction characteristics by considering pressure histories measured in the test chamber. The experimental results showed that the additives had significant effects on critical initiation velocity, reaction rate, reaction efficiency and post-reaction behavior. - Highlights: • .Al/Ni, Al/Ni/PTFE and Al/Ni/Cu were processed by means of static pressing. • .Microstructures, mechanical properties and shock-induced reactions were studied. • .Microstructures affect both compressive strength and fracture mode. • .Impact velocity is an important factor in shock-induced chemical characteristics. • .Each additive has significant effects on energy release behavior.

  12. Entropy-enthalpy compensation in chemical reactions and adsorption: an exactly solvable model. (United States)

    Freed, Karl F


    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.

  13. Mechanisms and chemical induction of aneuploidy in rodent germ cells

    Energy Technology Data Exchange (ETDEWEB)

    Mailhes, J B; Marchetti, F


    The objective of this review is to suggest that the advances being made in our understanding of the molecular events surrounding chromosome segregation in non-mammalian and somatic cell models be considered when designing experiments for studying aneuploidy in mammalian germ cells. Accurate chromosome segregation requires the temporal control and unique interactions among a vast array of proteins and cellular organelles. Abnormal function and temporal disarray among these, and others to be inidentified, biochemical reactions and cellular organelles have the potential for predisposing cells to aneuploidy. Although numerous studies have demonstrated that certain chemicals (mainly those that alter microtubule function) can induce aneuploidy in mammalian germ cells, it seems relevant to point out that such data can be influenced by gender, meiotic stage, and time of cell-fixation post-treatment. Additionally, a consensus has not been reached regarding which of several germ cell aneuploidy assays most accurately reflects the human condition. More recent studies have shown that certain kinase, phosphatase, proteasome, and topoisomerase inhibitors can also induce aneuploidy in rodent germ cells. We suggest that molecular approaches be prudently incorporated into mammalian germ cell aneuploidy research in order to eventually understand the causes and mechanisms of human aneuploidy. Such an enormous undertaking would benefit from collaboration among scientists representing several disciplines.

  14. BlenX-based compositional modeling of complex reaction mechanisms

    CERN Document Server

    Zámborszky, Judit; 10.4204/EPTCS.19.6


    Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model buildin...

  15. Contribution of ultrasonic traveling wave to chemical-mechanical polishing. (United States)

    Li, Liang; He, Qing; Zheng, Mian; Liu, Zheng


    The ultrasonic vibrators are introduced into the chemical-mechanical polishing devices, and in this polishing system, the ultrasonic vibrators generate ultrasonic traveling wave and keep coaxial with the polished silicon wafer rotating at given speed so as to compare the texture of the polished silicon wafers. And the experiments on the chemical-mechanical polishing with assisted ultrasonic vibration are accomplished in order to investigate the effect of the ultrasonic vibration on the chemical-mechanical polishing. Via comparing the roughness average of the two silicon wafers polished with assisted ultrasonic vibration and without assisted vibration, it is found that the morphology of the silicon wafer polished with assisted vibration is superior to that without assisted vibration, that is, this series of experiments indicate that the ultrasonic vibration is beneficial to the chemical-mechanical polishing. Aiming at understanding the contribution of the ultrasonic vibration to chemical-mechanical polishing in detail, the model of the chemical-mechanical polishing with the assisted ultrasonic vibration is built up, which establishes the relationship of the removal rate and the polishing variables such as the rotary speed of silicon wafers, the amplitude and the frequency of vibrators, the particle density of polishing slurry and the characteristics of polishing pad etc. This model not only could be used to explain the experimental results but also to illuminate the roles played by the polishing variables.

  16. Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence. (United States)

    de la Lande, Aurélien; Řezáč, Jan; Lévy, Bernard; Sanders, Barry C; Salahub, Dennis R


    Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.

  17. Effect of Coriolis coupling in chemical reaction dynamics. (United States)

    Chu, Tian-Shu; Han, Ke-Li


    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.

  18. A semiclassical non-adiabatic theory for elementary chemical reactions

    CERN Document Server

    Aubry, Serge


    Electron Transfer (ET) reactions are modeled by the dynamics of a quantum two-level system (representing the electronic state) coupled to a thermalized bath of classical harmonic oscillators (representing the nuclei degrees of freedom). Unlike for the standard Marcus theory, the complex amplitudes of the electronic state are chosen as reaction coordinates. Then, the dynamical equations at non vanishing temperature become those of an effective Hamiltonian submitted to damping terms and their associated Langevin random forces. The advantage of this new formalism is to extend the original theory by taking into account both ionic and covalent interactions. The standard theory is recovered only when covalent interactions are neglected. Increasing these covalent interactions from zero, the energy barrier predicted by the standard theory first depresses, next vanish (or almost vanish) and for stronger covalent interactions, covalent bond formation takes place of ET. In biochemistry, the standard Marcus theory often ...

  19. Quantum theory of chemical reactions in the presence of electromagnetic fields

    CERN Document Server

    Tscherbul, T V


    We present a theory for rigorous quantum scattering calculations of probabilities for chemical reactions of atoms with diatomic molecules in the presence of an external electric field. The approach is based on the fully uncoupled basis set representation of the total wave function in the space-fixed coordinate frame, the Fock-Delves hyperspherical coordinates and adiabatic partitioning of the total Hamiltonian of the reactive system. The adiabatic channel wave functions are expanded in basis sets of hyperangular functions corresponding to different reaction arrangements and the interactions with external fields are included in each chemical arrangement separately. We apply the theory to examine the effects of electric fields on the chemical reactions of LiF molecules with H atoms and HF molecules with Li atoms at low temperatures and show that electric fields may enhance the probability of chemical reactions and modify reactive scattering resonances by coupling the rotational states of the reactants. Our prel...

  20. Theory for Diffusion-Limited Oscillating Chemical Reactions

    CERN Document Server

    Bussemaker, H J


    A kinetic description of lattice-gas automaton models for reaction-diffusion systems is presented. It provides corrections to the mean-field rate equations in the diffusion-limited regime. When applied to the two-species Maginu model, the theory gives an excellent quantitative prediction of the effect of slow diffusion on the periodic oscillations of the average concentrations in a spatially homogeneous state.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Haw [Univ. of California, Berkeley, CA (United States)


    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

  2. Reformulation and solution of the master equation for multiple-well chemical reactions. (United States)

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


    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.

  3. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces. (United States)

    Faheem, Muhammad; Heyden, Andreas


    We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

  4. Concept Maps as a Tool for Teaching Organic Chemical Reactions. (United States)

    Šket, Barbara; Aleksij Glažar, Saša; Vogrinc, Janez


    The purpose of the research was to establish the impact of the application of a concept map in chemistry lessons on the effective solving of tasks with organic reactions content. In the first phase of the research, a concept map was produced representing the reactions of hydrocarbons, organic halogenated compounds and organic oxygen compounds, and in the second phase the produced concept map was introduced in lessons. Its impact was tested on a sample consisting of 186 students (average age of 17.8 years), who were divided into a control group (88 students) and an experimental group (98 students). Prior to the experiment, the two groups were equalised in terms of their level of development of formal logical thinking and their average grade in chemistry. A knowledge test, consisting of five problem tasks comprising multiple parts, was used as a quantitative instrument for measuring the impact of the applied concept map. The content of the knowledge test was selected on the basis of the chemistry lesson plan (reactions of organic oxygen compounds) for general upper secondary schools (in Slovenian: gimnazije). An analysis of the task solving showed statistically significant differences in the responses of the experimental group members and the control group members (experimental group M = 15.9; SD = 6.33; control group M = 13.6; SD = 7.93; p = 0.03). The produced concept map contributed to the more effective interrelation of concepts and, consequently, to more effective problem task solving.

  5. A discrete model to study reaction-diffusion-mechanics systems.

    Directory of Open Access Journals (Sweden)

    Louis D Weise

    Full Text Available This article introduces a discrete reaction-diffusion-mechanics (dRDM model to study the effects of deformation on reaction-diffusion (RD processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material. Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  6. A discrete model to study reaction-diffusion-mechanics systems. (United States)

    Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V


    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  7. Roles of interfacial reaction on mechanical properties of solder interfaces (United States)

    Liu, Pilin

    This study investigated roles of interfacial reaction in fracture and fatigue of solder interconnects. The interfacial reaction phases in the as-reflowed and after aging were examined by cross-sectional transmission electron microscopy (TEM) while interfacial mechanical properties were determined from a flexural peel fracture mechanics technique. Because of their widespread uses in microelectronic packaging, SnPb solder interfaces, and Bi-containing Pb-free solder interfaces were chosen as the subjects of this study. In the interfacial reaction study, we observed a complicated micro structural evolution during solid-state aging of electroless-Ni(P)/SnPb solder interconnects. In as-reflowed condition, the interfacial reaction produced Ni3Sn 4 and P-rich layers. Following overaging, the interfacial microstructure degenerated into a complex multilayer structure consisting of multiple layers of Ni-Sn compounds and transformed Ni-P phases. In SnPb solder interfacial system, fatigue study showed that the overaging of the high P electroless Ni-P/SnPb interconnects resulted in a sharp reduction in the fatigue resistance of the interface in the high crack growth rate regime. Fracture mechanism analysis indicated that the sharp drop in fatigue resistance was triggered by the brittle fracture of the Ni3Sn2 intermetallic phase developed at the overaged interface. The fatigue behavior was strongly dependent on P concentration in electroless Ni. Kirkendall voids were found in the interfacial region after aging, but they did not cause premature fracture of the solder interfaces. In Bi-containing solder interfacial system, we found that Bi segregated to the Cu-intermetallic interface during aging in SnBi/Cu interconnect. This caused serious embrittlement of Sn-Bi/Cu interface. Further aging induced numerous voids along the Cu3Sn/Cu interface. These interfacial voids were different from Kirkendall voids. Their formation was explained on basis of vacancy condensation at the

  8. Microstructure and Mechanical Properties of Reaction-Formed Joints in Reaction Bonded Silicon Carbide Ceramics (United States)

    Singh, M.


    A reaction-bonded silicon carbide (RB-SiC) ceramic material (Carborundum's Cerastar RB-SIC) has been joined using a reaction forming approach. Microstructure and mechanical properties of three types of reaction-formed joints (350 micron, 50-55 micron, and 20-25 micron thick) have been evaluated. Thick (approximately 350 micron) joints consist mainly of silicon with a small amount of silicon carbide. The flexural strength of thick joints is about 44 plus or minus 2 MPa, and fracture always occurs at the joints. The microscopic examination of fracture surfaces of specimens with thick joints tested at room temperature revealed the failure mode to be typically brittle. Thin joints (<50-55 micron) consist of silicon carbide and silicon phases. The room and high temperature flexural strengths of thin (<50-55 micron) reaction-formed joints have been found to be at least equal to that of the bulk Cerastar RB-SIC materials because the flexure bars fracture away from the joint regions. In this case, the fracture origins appear to be inhomogeneities inside the parent material. This was always found to be the case for thin joints tested at temperatures up to 1350C in air. This observation suggests that the strength of Cerastar RB-SIC material containing a thin joint is not limited by the joint strength but by the strength of the bulk (parent) materials.

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

    2015-06-28 Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A...Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...COMBUSTION CHEMISTRY (Briefing Charts) 5a. CONTRACT NUMBER In-House 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Ghanshyam L

  10. Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes. (United States)

    Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu


    A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

  11. Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition (United States)

    Grodzka, P.; Facemire, B.


    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.

  12. Allenes and computational chemistry: from bonding situations to reaction mechanisms. (United States)

    Soriano, Elena; Fernández, Israel


    The present review is focused on the application of computational/theoretical methods to the wide and rich chemistry of allenes. Special emphasis is made on the interplay and synergy between experimental and computational methodologies, rather than on recent developments in methods and algorithms. Therefore, this review covers the state-of-the-art applications of computational chemistry to understand and rationalize the bonding situation and vast reactivity of allenes. Thus, the contents of this review span from the most fundamental studies on the equilibrium structure and chirality of allenes to recent advances in the study of complex reaction mechanisms involving allene derivatives in organic and organometallic chemistry.

  13. Systematic lumping of complex tropospheric chemical mechanisms using a time-scale based approach

    Directory of Open Access Journals (Sweden)

    L. E. Whitehouse


    Full Text Available This paper presents a formal method of species lumping that can be applied automatically to intermediate compounds within detailed and complex tropospheric chemical reaction schemes. The method is based on grouping species with reference to their chemical lifetimes and reactivity structures. A method for determining the forward and reverse transformations between individual and lumped compounds is developed. Preliminary application to the Leeds Master Chemical Mechanism (MCMv2.0 has led to the removal of 734 species and 1777 reactions from the scheme, with minimal degradation of accuracy across a wide range of test trajectories relevant to polluted tropospheric conditions. The lumped groups are seen to relate to groups of peroxy acyl nitrates, nitrates, carbonates, oxepins, substituted phenols, oxeacids and peracids with similar lifetimes and reaction rates with OH. In combination with other reduction techniques, such as sensitivity analysis and the application of the quasi-steady state approximation (QSSA, a reduced mechanism has been developed that contains 35% of the number of species and 40% of the number of reactions compared to the full mechanism. This has led to a speed up of a factor of 8 in terms of computer calculation time within box model simulations.

  14. Dissipative structure of mechanically stimulated reaction; Kikaiteki reiki hanno ni okeru san`itsu kozo

    Energy Technology Data Exchange (ETDEWEB)

    Hida, M. [Okayama Univ., Okayama (Japan). Faculty of Engineering


    Recently various studies have been conducted concerning the state changes of materials obtained through mechanical alloying (MA) or mechano-chemical (MC) processing. What is noticeable is the quasi-steady state of almost all the materials obtained through various processes including MA and MC, and that the super cooling, supersaturating and high residue distortion realized under unbalanced conditions have not been clarified. In other words, the tracing capability to the external binding conditions is low. In this report, the appearance of the high temperature phase and high pressure phase obtained through MA or MC processing, the forming of amorphous, the mesomerism of the amorphous materials, the interesting phenomena generated by combination between the mechanical disturbance and chemical reactions were discussed with concrete examples, and a steady dissipative organization theory was approached from the viewpoint of dissipative structure development which is equal to the forming process of the quasi-steady phase. 34 refs., 2 figs.

  15. Reactions of Trimethylaluminium: Modelling the Chemical Degradation of Synthetic Lubricants. (United States)

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


    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.

  16. A New Formulation of the Lindemann Mechanism of Unimolecular Reactions

    Institute of Scientific and Technical Information of China (English)



    A new formulation of the Lindemann mechanism of unimolecular reactions in gaseous phase is presented, without the use of steady state hypothesis. It is hereby shown that the nature of applicability of steady state hypothesis in the regime of high reactant gas pressure is different from that in the regime of low gas pressure. In the former case it is an equilibrium approximation, while in the latter case it is a highly reactive intermediate approximation in no connection with a steady state. Furthermore for the latter case it is shown that in the classical formulation of Lindemann mecbRnism the use of steady state hypothesis is an ad hoc assumption. A highly reactive intermediate in the sense that its concentration is very small during the whole course of reaction is a necessary condition for the applicability of very reactive intermediate approximation. When the two distinctive nature of the applicability of steady state hypothesis is mlxed-up, wrong or useless conclusion may be arrived at. The only possible case of realizing a true steady state in a complex reaction is pointed out.

  17. Constructing and visualizing chemical reaction networks from pi-calculus models


    M. John; H.-J. Schulz; H. Schumann; A. M. Uhrmacher; Andrea Unger


    International audience; The pi-calculus, in particular its stochastic version the stochastic pi-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely unexplored how to transform a biochemical model expressed in the stochastic pi-calculus back into a set of meaningful reactions. To this end, we present a two step approach of first translating model states to reaction sets and then visualizing sequence...

  18. Development of a novel fingerprint for chemical reactions and its application to large-scale reaction classification and similarity. (United States)

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


    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.

  19. Students' Ideas about How and Why Chemical Reactions Happen: Mapping the Conceptual Landscape (United States)

    Yan, Fan; Talanquer, Vicente


    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…

  20. The Technology for Intensification of Chemical Reaction Process Envisaged in the "863" Plan

    Institute of Scientific and Technical Information of China (English)


    @@ It is learned from the Ministry of Science and Technology that in order to promote the shift of China's chemical industry toward an energy efficient and environmentally friendly product mode, the technology for intensification of chemical reaction processes has been included in the National "863" Project of the "Eleventh Five-Year Plan", and the application for research project proposals is to be accepted.

  1. Chemical mechanical polishing of freestanding GaN substrates

    Institute of Scientific and Technical Information of China (English)

    颜怀跃; 修向前; 刘战辉; 张荣; 华雪梅; 谢自力; 韩平; 施毅; 郑有炓


    Chemical mechanical polishing (CMP) has been used to produce smooth and scratch-free surfaces for GaN. In the aqueous solution of KOH, GaN is subjected to etching. At the same time, all surface irregularities, including etch pyramids, roughness after mechanical polishing and so on will be removed by a polishing pad. The experiments had been performed under the condition of different abrasive particle sizes of the polishing pad. Also the polishing results for different polishing times are analyzed, and chemical mechanical polishing resulted in an average root mean square (RMS) surface roughness of 0.565 nm, as measured by atomic force microscopy.

  2. Complete reaction mechanisms of mercury oxidation on halogenated activated carbon. (United States)

    Rungnim, Chompoonut; Promarak, Vinich; Hannongbua, Supa; Kungwan, Nawee; Namuangruk, Supawadee


    The reaction mechanisms of mercury (Hg) adsorption and oxidation on halogenated activated carbon (AC) have been completely studied for the first time using density functional theory (DFT) method. Two different halogenated AC models, namely X-AC and X-AC-X (X=Cl, Br, I), were adopted. The results revealed that HgX is found to be stable-state on the AC edge since its further desorption from the AC as HgX, or further oxidation to HgX2, are energetically unfavorable. Remarkably, the halide type does not significantly affect the Hg adsorption energy but it strongly affects the activation energy barrier of HgX formation, which obviously increases in the order HgIBr-AC>Cl-AC. Thus, the study of the complete reaction mechanism is essential because the adsorption energy can not be used as a guideline for the rational material design in the halide impregnated AC systems. The activation energy is an important descriptor for the predictions of sorbent reactivity to the Hg oxidation process.

  3. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

    Energy Technology Data Exchange (ETDEWEB)

    Lin, M.C. [Emory Univ., Atlanta, GA (United States)


    Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

  4. The mineralogic evolution of the Martian surface through time: Implications from chemical reaction path modeling studies (United States)

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


    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.

  5. Rate constants for chemical reactions in high-temperature nonequilibrium air (United States)

    Jaffe, R. L.


    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.

  6. On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

    CERN Document Server

    van der Schaft, Arjan; Jayawardhana, Bayu


    Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic equilibrium we derive a compact formulation exhibiting at the same time the structure of the complex graph and the stoichiometry of the network, and which admits a direct thermodynamical interpretation. This formulation allows us to easily characterize the set of equilibria and their stability properties. Furthermore, we develop a framework for interconnection of chemical reaction networks. Finally we discuss how the established framework leads to a new approach for model reduction.

  7. Quantum chemical study of the acrolein (CH2CHCHO) + OH + O2 reactions. (United States)

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


    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

  8. Heterogeneous nucleation - current transients under chemical reaction control

    CERN Document Server

    D'Ajello-Tettamanzy, P C; Kipervaser, Z G S


    Heterogeneous nucleation on catalytic surfaces plunged into a fluid is described through a stochastic model. To generate this non-equilibrium process we assume that the turn on of a electrostatic potential triggers a complex dynamics that includes a free Brownian motion, a reaction kinetic and a stimulated migration before the final adhesion of ions on the surface (electrode). At, when the potential is switched on, the spatial symmetry is broken and a two-stage process is developed. First the ion undergoes a change in its electrochemical character (at some region of the space) and then reacts at some specific points to stick together on the surface. The continuous addition of ions develops a material deposit connected to the current transient signals measured in electrochemical deposition processes. Unlike current models found in the literature, this procedure avoids the computation of the area covered by the diffusion zones, allowing a formalism skill to describe equally well the absorption of ions by channe...

  9. Research on the chemical mechanism in the polyacrylate latex modified cement system

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Min [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China); Wang, Rumin, E-mail: [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China); Zheng, Shuirong [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China); Northwestern Polytechnical University–East China University of Science and Technology Combined Research Institute of New High Speed Railway Materials (China); Farhan, Shameel; Yao, Hao; Jiang, Hao [The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi' an 710072 (China)


    In this paper, the chemical mechanism in the polyacrylate latex modified cement system was investigated by Fourier transform infrared spectra (FT-IR), X-ray photoelectron spectroscopy (XPS), gel permeation chromatography (GPC) and compact pH meter. All results have shown that the chemical reactions in the polyacrylate modified system can be divided into three stages. The hydration reactions of cement can produce large amounts of Ca(OH){sub 2} (calcium hydroxide) and lead the whole system to be alkali-rich and exothermic at the first stage. Subsequently, this environment can do great contributions to the hydrolysis of ester groups in the polyacrylate chains, resulting in the formation of carboxyl groups at the second stage. At the third stage, the final crosslinked network structure of the product was obtained by the reaction between the carboxyl groups in the polyacrylate latex chains and Ca(OH){sub 2}.

  10. Evaluation of the Chemical and Mechanical Properties of Hardening High-Calcium Fly Ash Blended Concrete

    Directory of Open Access Journals (Sweden)

    Wei-Jie Fan


    Full Text Available High-calcium fly ash (FH is the combustion residue from electric power plants burning lignite or sub-bituminous coal. As a mineral admixture, FH can be used to produce high-strength concrete and high-performance concrete. The development of chemical and mechanical properties is a crucial factor for appropriately using FH in the concrete industry. To achieve sustainable development in the concrete industry, this paper presents a theoretical model to systematically evaluate the property developments of FH blended concrete. The proposed model analyzes the cement hydration, the reaction of free CaO in FH, and the reaction of phases in FH other than free CaO. The mutual interactions among cement hydration, the reaction of free CaO in FH, and the reaction of other phases in FH are also considered through the calcium hydroxide contents and the capillary water contents. Using the hydration degree of cement, the reaction degree of free CaO in FH, and the reaction degree of other phases in FH, the proposed model evaluates the calcium hydroxide contents, the reaction degree of FH, chemically bound water, porosity, and the compressive strength of hardening concrete with different water to binder ratios and FH replacement ratios. The evaluated results are compared to experimental results, and good consistencies are found.

  11. Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins. (United States)

    Das, A K; Meuwly, M


    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.

  12. Study on the Reaction Mechanism of Naphthalene with Oxalyl Chloride

    Institute of Scientific and Technical Information of China (English)


    The reaction of naphthalene with oxalyl chloride in the presence of anhydrous AlCl3 was investigated. The homolog of dinaphthyl methanone can be obtained mainly from this reaction. Naphthalene conversion does not have evident correlation with the amount of AlCl3. The results show that the reaction proceeds via carbon cation electrophilic substitution reaction-free radical substitution reaction pathway.

  13. Systematic trends in photonic reagent induced reactions in a homologous chemical family. (United States)

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


    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.

  14. Thermally activated reaction–diffusion-controlled chemical bulk reactions of gases and solids

    Directory of Open Access Journals (Sweden)

    S. Möller


    Full Text Available The chemical kinetics of the reaction of thin films with reactive gases is investigated. The removal of thin films using thermally activated solid–gas to gas reactions is a method to in-situ control deposition inventory in vacuum and plasma vessels. Significant scatter of experimental deposit removal rates at apparently similar conditions was observed in the past, highlighting the need for understanding the underlying processes. A model based on the presence of reactive gas in the films bulk and chemical kinetics is presented. The model describes the diffusion of reactive gas into the film and its chemical interaction with film constituents in the bulk using a stationary reaction–diffusion equation. This yields the reactive gas concentration and reaction rates. Diffusion and reaction rate limitations are depicted in parameter studies. Comparison with literature data on tokamak co-deposit removal results in good agreement of removal rates as a function of pressure, film thickness and temperature.

  15. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures. (United States)

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


    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.

  16. Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications. (United States)

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


    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.

  17. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Theory and Practical Applications

    CERN Document Server

    Suleimanov, Yury V; Guo, Hua


    This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze theory and its connection to quantum transition state theory. We then focus on its practical application to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rates 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 rates. We also hope it will motivate further applications of RPMD to various chemical reactions.

  18. Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law (United States)

    Ge, Hao; Qian, Hong


    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.

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

    Otero, Toribio F


    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.

  20. Students' Dilemmas in Reaction Stoichiometry Problem Solving: Deducing the Limiting Reagent in Chemical Reactions (United States)

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


    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…

  1. Methanol synthesis on ZnO(0001{sup ¯}). IV. Reaction mechanisms and electronic structure

    Energy Technology Data Exchange (ETDEWEB)

    Frenzel, Johannes, E-mail:; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany)


    Methanol synthesis from CO and H{sub 2} over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(0001{sup ¯}) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving “near-surface” molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H{sub 2} stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are

  2. Methanol synthesis on ZnO(0001¯). IV. Reaction mechanisms and electronic structure. (United States)

    Frenzel, Johannes; Marx, Dominik


    Methanol synthesis from CO and H2 over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(0001¯) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving "near-surface" molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H2 stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are discussed based on extensive

  3. Methanol synthesis on ZnO(000overline{1}). IV. Reaction mechanisms and electronic structure (United States)

    Frenzel, Johannes; Marx, Dominik


    Methanol synthesis from CO and H2 over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(000overline{1}) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving "near-surface" molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H2 stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are discussed based on

  4. Two Optimization Methods to Determine the Rate Constants of a Complex Chemical Reaction Using FORTRAN and MATLAB

    Directory of Open Access Journals (Sweden)

    Abdel-Latif A. Seoud


    Full Text Available Problem statement: For chemical reactions, the determination of the rate constants is both very difficult and a time consuming process. The aim of this research was to develop computer programs for determining the rate constants for the general form of any complex reaction at a certain temperature. The development of such program can be very helpful in the control of industrial processes as well as in the study of the reaction mechanisms. Determination of the accurate values of the rate constants would help in establishing the optimum conditions of reactor design including pressure, temperature and other parameters of the chemical reaction. Approach: From the experimental concentration-time data, initial values of rate constants were calculated. Experimental data encountered several types of errors, including temperature variation, impurities in the reactants and human errors. Simulations of a second order consecutive irreversible chemical reaction of the saponification of diethyl ester were presented as an example of the complex reactions. The rate equations (system of simultaneous differential equations of the reaction were solved to get the analytical concentration versus time profiles. The simulation results were compared with experimental results at each measured point. All deviations between experimental and calculated values were squared and summed up to form a new function. This function was fed into a minimizer routine that gave the optimal rate constants. Two optimization techniques were developed using FORTRAN and MATLAB for accurately determining the rate constants of the reaction at certain temperature from the experimental data. Results: Results showed that the two proposed programs were very efficient, fast and accurate tools to determine the true rate constants of the reaction with less 1% error. The use of the MATLAB embedded subroutines for simultaneously solving the differential equations and minimization of the error function

  5. Valence shell charge concentration (VSCC) evolution: a tool to investigate the transformations within a VSCC throughout a chemical reaction. (United States)

    Cortés-Guzmán, Fernando; Gómez, Rosa María; Rocha-Rinza, Tomas; Sánchez-Obregón, María Azucena; Guevara-Vela, José Manuel


    Theoretical studies about reaction mechanisms are usually limited to the determination of the energetic paths that connect reactants, transition states, and products. Recently, our group proposed the structural evolution, which has provided insights about the molecular structure changes occurring along a reaction path. Structural evolution may be defined as the development of a chemical reaction system across the partitioning of the nuclear configuration space into a finite number of structural regions defined on account of the topology of a scalar field, e.g., the electron density. In this paper, we present a tool to investigate within the framework of the Quantum Theory of Atoms in Molecules the evolvement of the Valence Shell Charge Concentration, the VSCC evolution, which is the description of the changes of electron density concentrations and depletions around the bonding area of an atom. The VSCC evolution provides supplementary information to the structural evolution because it allows the analysis of valence shells within a structural region, i.e., a subset of R(Q) with the same connectivity among the atoms forming a molecule. This new approach constitutes also a complement to the Valence-Shell Electron Pair Repulsion (VSEPR) model because it gives an account of the adjustments of electron pairs in the valence shell of an atom across a chemical reaction. The insertion reaction in the hydroformylation reaction of ethylene, the reduction of cyclohexanone with lithium aluminum hydride, the oxidation of methanol with chlorochromate, and the bimolecular nucleophilic substitution of CH(3)F with F(-) are used as representatives examples of the application of the VSCC evolution. Overall, this paper shows how the VSCC evolution through an analysis of the modifications of local charge concentrations and depletions in individual steps of a chemical reaction gives new insights about these processes.

  6. Reduced chemical kinetic mechanisms for NOx emission prediction in biomass combustion

    DEFF Research Database (Denmark)

    Houshfar, Ehsan; Skreiberg, Øyvind; Glarborg, Peter;


    Because of the complex composition of biomass, the chemical mechanism contains many different species and therefore a large number of reactions. Although biomass gas‐phase combustion is fairly well researched and understood, the proposed mechanisms are still complex and need very long computational...... time and powerful hardware resources. A reduction of the mechanism for biomass volatile oxidation has therefore been performed to avoid these difficulties. The selected detailed mechanism in this study contains 81 species and 703 elementary reactions. Necessity analysis is used to determine which......‐ and low‐temperature range with 26 and 52 species, respectively. The modeling conditions are selected in a way to mimic values in the range of temperature 700–1400°C, excess air ratio 0.8–3.3, and four different residence times: 1, 0.1, 0.01, and 0.001 s, since these variables are the main affecting...

  7. Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms (United States)

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


    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.

  8. Chemical Reactions and Kinetics of the Carbon Monoxide Coupling in the Presence of Hydrogen

    Institute of Scientific and Technical Information of China (English)

    Fandong Meng; Genhui Xu; Zhenhua Li; Pa Du


    The chemical reactions and kinetics of the catalytic coupling reaction of carbon monoxide to diethyl oxalate were studied in the presence of hydrogen over a supported palladium catalyst in the gaseous phase at the typical coupling reaction conditions. The experiments were performed in a continuous flow fixed-bed reactor. The results indicated that hydrogen only reacts with ethyl nitrite to form ethanol, and kinetic studies revealed that the rate-determining step is the surface reaction of adsorbed hydrogen and the ethoxy radical (EtO-). A kinetic model is proposed and a comparison of the observed and calculated conversions showed that the rate expressions are of rather high confidence.

  9. Chemical and mechanical interactions of interstitials with vanadium alloys

    Energy Technology Data Exchange (ETDEWEB)

    DiStefano, J.R.; Chitwood, L.D.; DeVan, J.H. [Oak Ridge National Laboratory, TN (United States)


    Oxidation studies of V-4Cr-4Ti were conducted in air and reduced oxygen partial pressures (10{sup 4}, 10{sup -5} and 10{sup -6} torr). Reaction rates were determined by weight change measurements and chemical analyses. Mechanical properties after the exposures were determined by room temperature tensile tests. In air at 400 and 500{degrees}C, oxide films form on the surface. Initially, rates are high but decrease with time reaching similiar values to those found in oxygen partial pressures at 10{sup -4}, 10{sup -5}, and 10{sup -6} torr. At 400{degrees}C, oxygen pick-up followed a logarithmic function of time and was confined to regions near the surface. Little change in room temperature tensile properties was noted for oxygen increase up to 1500 ppm. Thermal cycling specimens from 400{degrees}C to room temperature up to 14 times had no apparent effect on oxidation rate or tensile properties. At 500{degrees}C, oxygen pick-up appeared to follow a parabolic relation with time. Rates were {approx} 10 times those at 400{degrees}C and correspondingly larger oxygen increases occurred when compared with the 400{degrees}C tests after similiar time periods. This resulted in a significant decrease in total elongation after 240 h. At reduced oxygen partial pressures, rates were measured for times <100 h. Data are relatively sparse but generally show a slightly higher initial rate before slowing. At 400{degrees}C increases to {approx}200 ppm oxygen were found with no effect on room temperature elongation. At 500{degrees}C increase in oxygen of 2400 ppm after 50h/10{sup -5} torr resulted in a decrease of around 25% in room temperature elongation. By comparison, exposure to air at 500{degrees}C for 12 h caused nearly the same results.

  10. Modeling regional secondary organic aerosol using the Master Chemical Mechanism (United States)

    Li, Jingyi; Cleveland, Meredith; Ziemba, Luke D.; Griffin, Robert J.; Barsanti, Kelley C.; Pankow, James F.; Ying, Qi


    A modified near-explicit Master Chemical Mechanism (MCM, version 3.2) with 5727 species and 16,930 reactions and an equilibrium partitioning module was incorporated into the Community Air Quality Model (CMAQ) to predict the regional concentrations of secondary organic aerosol (SOA) from volatile organic compounds (VOCs) in the eastern United States (US). In addition to the semi-volatile SOA from equilibrium partitioning, reactive surface uptake processes were used to simulate SOA formation due to isoprene epoxydiol, glyoxal and methylglyoxal. The CMAQ-MCM-SOA model was applied to simulate SOA formation during a two-week episode from August 28 to September 7, 2006. The southeastern US has the highest SOA, with a maximum episode-averaged concentration of ∼12 μg m-3. Primary organic aerosol (POA) and SOA concentrations predicted by CMAQ-MCM-SOA agree well with AMS-derived hydrocarbon-like organic aerosol (HOA) and oxygenated organic aerosol (OOA) urban concentrations at the Moody Tower at the University of Houston. Predicted molecular properties of SOA (O/C, H/C, N/C and OM/OC ratios) at the site are similar to those reported in other urban areas, and O/C values agree with measured O/C at the same site. Isoprene epoxydiol is predicted to be the largest contributor to total SOA concentration in the southeast US, followed by methylglyoxal and glyoxal. The semi-volatile SOA components are dominated by products from β-caryophyllene oxidation, but the major species and their concentrations are sensitive to errors in saturation vapor pressure estimation. A uniform decrease of saturation vapor pressure by a factor of 100 for all condensable compounds can lead to a 150% increase in total SOA. A sensitivity simulation with UNIFAC-calculated activity coefficients (ignoring phase separation and water molecule partitioning into the organic phase) led to a 10% change in the predicted semi-volatile SOA concentrations.

  11. A reaction mechanism for gasoline surrogate fuels for large polycyclic aromatic hydrocarbons

    KAUST Repository

    Raj, Abhijeet


    This work aims to develop a reaction mechanism for gasoline surrogate fuels (n-heptane, iso-octane and toluene) with an emphasis on the formation of large polycyclic aromatic hydrocarbons (PAHs). Starting from an existing base mechanism for gasoline surrogate fuels with the largest chemical species being pyrene (C 16H 10), this new mechanism is generated by adding PAH sub-mechanisms to account for the formation and growth of PAHs up to coronene (C 24H 12). The density functional theory (DFT) and the transition state theory (TST) have been adopted to evaluate the rate constants for several PAH reactions. The mechanism is validated in the premixed laminar flames of n-heptane, iso-octane, benzene and ethylene. The characteristics of PAH formation in the counterflow diffusion flames of iso-octane/toluene and n-heptane/toluene mixtures have also been tested for both the soot formation and soot formation/oxidation flame conditions. The predictions of the concentrations of large PAHs in the premixed flames having available experimental data are significantly improved with the new mechanism as compared to the base mechanism. The major pathways for the formation of large PAHs are identified. The test of the counterflow diffusion flames successfully predicts the PAH behavior exhibiting a synergistic effect observed experimentally for the mixture fuels, irrespective of the type of flame (soot formation flame or soot formation/oxidation flame). The reactions that lead to this synergistic effect in PAH formation are identified through the rate-of-production analysis. © 2011 The Combustion Institute.

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

    DEFF Research Database (Denmark)

    Berg, Nikolaj Drimer; Linneberg, Allan; Thyssen, Jacob Pontoppidan;


    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...... 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...

  13. On the moments of the Boltzmann's collision operator arising from chemical reactions (United States)

    Sarna, Neeraj; Torrilhon, Manuel


    For any study of microflows it is crucial to understand the collision dynamics of the molecules involved. In the present work we will discuss the collision dynamics of chemically reacting hard spheres(CRHS). The inability of the classical smooth inelastic hard spheres, which have been extensively used in the past to study granular gases, to describe the collision dynamics of chemically reacting hard spheres has been discussed. Using the model of rough inelastic hard spheres as a motivation, a new model has been proposed for chemically reacting hard spheres which has been further used to derive certain useful velocity transformations. A methodology to compute the moments of the Boltzmann's collision operator arising from chemical reactions, using Grad's distribution function, has been discussed in detail. Finally explicit expressions for the rates of the reaction have been obtained which contain contributions from higher order moment and thus can be used for non-equilibrium chemically reacting flows.

  14. Modeling of Chemical Reactions in Afterburning for the Reduction of N2O

    DEFF Research Database (Denmark)

    Gustavsson, Lennart; Glarborg, Peter; Leckner, Bo


    Full scale tests in a 12 MW fluidized bed combustor on reduction of N2O by secondary fuel injection are analyzed in terms a model that involves a detailed reaction mechanism for the gas phase chemistry as well as a description of gas-solid reactions.......Full scale tests in a 12 MW fluidized bed combustor on reduction of N2O by secondary fuel injection are analyzed in terms a model that involves a detailed reaction mechanism for the gas phase chemistry as well as a description of gas-solid reactions....

  15. BlenX-based compositional modeling of complex reaction mechanisms

    Directory of Open Access Journals (Sweden)

    Judit Zámborszky


    Full Text Available Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.

  16. Mechanism of heterogeneous reaction of carbonyl sulfide on magnesium oxide. (United States)

    Liu, Yongchun; He, Hong; Xu, Wenqing; Yu, Yunbo


    Heterogeneous reaction of carbonyl sulfide (OCS) on magnesium oxide (MgO) under ambient conditions was investigated by in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), quadrupole mass spectrometer (QMS), and density functional theory (DFT) calculations. It reveals that OCS can be catalytically hydrolyzed by surface hydroxyl on MgO to produce carbon dioxide (CO2) and hydrogen sulfide (H2S), and then H2S can be further catalytically oxidized by surface oxygen or gaseous oxygen on MgO to form sulfite (SO3(2-)) and sulfate (SO4(2-)). Hydrogen thiocarbonate (HSCO2-) was found to be the crucial intermediate. Surface hydrogen sulfide (HS), sulfur dioxide (SO2), and surface sulfite (SO3(2-)) were also found to be intermediates for the formation of sulfate. Furthermore, the surface hydroxyl contributes not only to the formation of HSCO2- but also to HSCO2- decomposition. On the basis of experimental results, the heterogeneous reaction mechanism of OCS on MgO was discussed.

  17. Mechanical reaction-diffusion model for bacterial population dynamics

    CERN Document Server

    Ngamsaad, Waipot


    The effect of mechanical interaction between cells on the spreading of bacterial population was investigated in one-dimensional space. A nonlinear reaction-diffusion equation has been formulated as a model for this dynamics. In this model, the bacterial cells are treated as the rod-like particles that interact, when contacting each other, through the hard-core repulsion. The repulsion introduces the exclusion process that causes the fast diffusion in bacterial population at high density. The propagation of the bacterial density as the traveling wave front in long time behavior has been analyzed. The analytical result reveals that the front speed is enhanced by the exclusion process---and its value depends on the packing fraction of cell. The numerical solutions of the model have been solved to confirm this prediction.

  18. Reaction mechanisms and staggering in S+Ni collisions (United States)

    D'Agostino, M.; Bruno, M.; Gulminelli, F.; Morelli, L.; Baiocco, G.; Bardelli, L.; Barlini, S.; Cannata, F.; Casini, G.; Geraci, E.; Gramegna, F.; Kravchuk, V. L.; Marchi, T.; Moroni, A.; Ordine, A.; Raduta, Ad. R.


    The reactions S32+Ni58 and S32+Ni64 are studied at 14.5 A MeV. After a selection of the collision mechanism, we show that important even-odd effects are present in the isotopic fragment distributions when the excitation energy is small. Close to the multifragmentation threshold this staggering appears hidden by the rapid variation of the production yields with the fragment size. Once this effect is accounted for, the staggering appears to be a universal feature of fragment production, slightly enhanced when the emission source is neutron poor. A closer look at the behavior of the production yields as a function of the neutron excess N-Z, reveals that odd-even effects cannot be explained by pairing effects in the nuclear masses alone, but depend in a more complex way on the de-excitation chain.

  19. Reaction mechanisms and staggering in S+Ni collisions

    Energy Technology Data Exchange (ETDEWEB)

    D' Agostino, M., E-mail: [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Bruno, M. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Gulminelli, F. [LPC (IN2P3-CNRS/Ensicaen et Universite), F-14076 Caen cedex (France); Morelli, L. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Baiocco, G. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); LPC (IN2P3-CNRS/Ensicaen et Universite), F-14076 Caen cedex (France); Bardelli, L. [INFN, Firenze (Italy); INFN, Catania (Italy); Barlini, S. [INFN, Firenze (Italy); Cannata, F. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Casini, G. [INFN, Firenze (Italy); Geraci, E. [Dipartimento di Fisica dell' Universita, Catania (Italy); INFN, Catania (Italy); Gramegna, F.; Kravchuk, V.L. [INFN, Laboratori Nazionali di Legnaro (Italy); Marchi, T. [INFN, Laboratori Nazionali di Legnaro (Italy); Dipartimento di Fisica dell' Universita, Padova (Italy); Moroni, A. [INFN, Milano (Italy); Ordine, A. [INFN, Napoli (Italy); Raduta, Ad.R. [NIPNE, Bucharest-Magurele, POB-MG6 (Romania)


    The reactions {sup 32}S+{sup 58}Ni and {sup 32}S+{sup 64}Ni are studied at 14.5 A MeV. After a selection of the collision mechanism, we show that important even-odd effects are present in the isotopic fragment distributions when the excitation energy is small. Close to the multifragmentation threshold this staggering appears hidden by the rapid variation of the production yields with the fragment size. Once this effect is accounted for, the staggering appears to be a universal feature of fragment production, slightly enhanced when the emission source is neutron poor. A closer look at the behavior of the production yields as a function of the neutron excess N-Z, reveals that odd-even effects cannot be explained by pairing effects in the nuclear masses alone, but depend in a more complex way on the de-excitation chain.

  20. [Reaction mechanism of cefotaxime with human serum albumin]. (United States)

    Liu, Luo-sheng; Wang, Xing-po; Zhao, Quan-qin; Zhang, Yu-yi


    The reaction mechanism of cefotaxime with human serum albumin (HSA) and the affinity between cefotaxime and beta-lactamase were investigated by spectrometry and spectrofluorimetry. The interaction dissociation constants of human serum albumin and cefotaxime were determined from a double reciprocal Lineweaver-Burk plot. The binding distance and transfer efficiency between cefotaxime and HSA were also obtained according to the theory of Förster non-radiation energy transfer. The result suggested that the main binding force between cefotaxime and HSA is electrostatic force interaction. The high beta-lactamase stability of cefotaxime may be correlative with its molecular structure. The antibiotic activity and valence are connected with transfer efficiency and dissociation constant. The effect of cefotaxime on the conformation of HSA was also analyzed using synchronous fluorescence spectrometry.