WorldWideScience

Sample records for chemical reaction system

  1. Chemical reactions in reverse micelle systems

    Science.gov (United States)

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

    1993-08-24

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

  2. 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

    2014-03-01

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

  3. Formal modeling of a system of chemical reactions under uncertainty.

    Science.gov (United States)

    Ghosh, Krishnendu; Schlipf, John

    2014-10-01

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

  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

    2011-07-01

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

  5. Reachability bounds for chemical reaction networks and strand displacement systems.

    Science.gov (United States)

    Condon, Anne; Kirkpatrick, Bonnie; Maňuch, Ján

    2014-01-01

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

  6. Chemical reaction network approaches to Biochemical Systems Theory.

    Science.gov (United States)

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

    2015-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, H.D.

    1991-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, H.D.

    1991-11-01

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

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

    Science.gov (United States)

    Kriske, Richard

    2011-10-01

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

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

    NARCIS (Netherlands)

    Brilman, Derk Willem Frederik

    1998-01-01

    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

  11. Translated chemical reaction networks.

    Science.gov (United States)

    Johnston, Matthew D

    2014-05-01

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

  12. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

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

    2016-01-01

    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....

  13. Microfluidic chemical reaction circuits

    Science.gov (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

    2012-06-26

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

  14. Mass Transfer with Chemical Reaction.

    Science.gov (United States)

    DeCoursey, W. J.

    1987-01-01

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

  15. Chemical burn or reaction

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/000059.htm 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. ...

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

    Science.gov (United States)

    Ge, Hao; Qian, Hong

    2017-01-01

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

  17. Chemical transport reactions

    CERN Document Server

    Schäfer, Harald

    2013-01-01

    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

  18. Fundamentals of chemical reaction engineering

    CERN Document Server

    Davis, Mark E

    2012-01-01

    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

  19. A modified next reaction method for simulating chemical systems with time dependent propensities and delays.

    Science.gov (United States)

    Anderson, David F

    2007-12-01

    Chemical reaction systems with a low to moderate number of molecules are typically modeled as discrete jump Markov processes. These systems are oftentimes simulated with methods that produce statistically exact sample paths such as the Gillespie algorithm or the next reaction method. In this paper we make explicit use of the fact that the initiation times of the reactions can be represented as the firing times of independent, unit rate Poisson processes with internal times given by integrated propensity functions. Using this representation we derive a modified next reaction method and, in a way that achieves efficiency over existing approaches for exact simulation, extend it to systems with time dependent propensities as well as to systems with delays.

  20. On the graph and systems analysis of reversible chemical reaction networks with mass action kinetics

    NARCIS (Netherlands)

    Rao, Shodhan; Jayawardhana, Bayu; Schaft, Arjan van der

    2012-01-01

    Motivated by the recent progresses on the interplay between the graph theory and systems theory, we revisit the analysis of reversible chemical reaction networks described by mass action kinetics by reformulating it using the graph knowledge of the underlying networks. Based on this formulation, we

  1. 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

    1997-04-01

    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.

  2. Speeding chemical reactions by focusing

    CERN Document Server

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

    2012-01-01

    We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, 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).

  3. Chemical kinetics of gas reactions

    CERN Document Server

    Kondrat'Ev, V N

    2013-01-01

    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

  4. A multi-time-scale analysis of chemical reaction networks: II. Stochastic systems.

    Science.gov (United States)

    Kan, Xingye; Lee, Chang Hyeong; Othmer, Hans G

    2016-11-01

    We consider stochastic descriptions of chemical reaction networks in which there are both fast and slow reactions, and for which the time scales are widely separated. We develop a computational algorithm that produces the generator of the full chemical master equation for arbitrary systems, and show how to obtain a reduced equation that governs the evolution on the slow time scale. This is done by applying a state space decomposition to the full equation that leads to the reduced dynamics in terms of certain projections and the invariant distributions of the fast system. The rates or propensities of the reduced system are shown to be the rates of the slow reactions conditioned on the expectations of fast steps. We also show that the generator of the reduced system is a Markov generator, and we present an efficient stochastic simulation algorithm for the slow time scale dynamics. We illustrate the numerical accuracy of the approximation by simulating several examples. Graph-theoretic techniques are used throughout to describe the structure of the reaction network and the state-space transitions accessible under the dynamics.

  5. Chemical Reactions at Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Michael Henderson and Nancy Ryan Gray

    2010-04-14

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

  6. The study of thermodynamic properties and transport properties of multicomponent systems with chemical reactions

    Directory of Open Access Journals (Sweden)

    Samujlov E.

    2013-04-01

    Full Text Available In case of system with chemical reaction the most important properties are heat conductivity and heat capacity. In this work we have considered the equation for estimate the component of these properties caused by chemical reaction and ionization processes. We have evaluated the contribution of this part in heat conductivity and heat capacity too. At the high temperatures contribution in heat conductivity from ionization begins to play an important role. We have created a model, which describe partial and full ionization of gases and gas mixtures. In addition, in this work we present the comparison of our result with experimental data and data from numerical simulation. We was used the data about transport properties of middle composition of Russian coals and the data of thermophysical properties of natural gas for comparison.

  7. Novel duplex vapor: Electrochemical method for silicon solar cells. [chemical reactor for a silicon sodium reaction system

    Science.gov (United States)

    Nanis, L.; Sanjurjo, A.; Sancier, K.

    1979-01-01

    The scaled up chemical reactor for a SiF4-Na reaction system is examined for increased reaction rate and production rate. The reaction system which now produces 5 kg batches of mixed Si and NaF is evaluated. The reactor design is described along with an analysis of the increased capacity of the Na chip feeder. The reactor procedure is discussed and Si coalescence in the reaction products is diagnosed.

  8. Performance and cost of energy transport and storage systems for dish applications using reversible chemical reactions

    Science.gov (United States)

    Schredder, J. M.; Fujita, T.

    1984-01-01

    The use of reversible chemical reactions for energy transport and storage for parabolic dish networks is considered. Performance and cost characteristics are estimated for systems using three reactions (sulfur-trioxide decomposition, steam reforming of methane, and carbon-dioxide reforming of methane). Systems are considered with and without storage, and in several energy-delivery configurations that give different profiles of energy delivered versus temperature. Cost estimates are derived assuming the use of metal components and of advanced ceramics. (The latter reduces the costs by three- to five-fold). The process that led to the selection of the three reactions is described, and the effects of varying temperatures, pressures, and heat exchanger sizes are addressed. A state-of-the-art survey was performed as part of this study. As a result of this survey, it appears that formidable technical risks exist for any attempt to implement the systems analyzed in this study, especially in the area of reactor design and performance. The behavior of all components and complete systems under thermal energy transients is very poorly understood. This study indicates that thermochemical storage systems that store reactants as liquids have efficiencies below 60%, which is in agreement with the findings of earlier investigators.

  9. Morphological stability criterion for a spherical crystallization front in a multicomponent system with chemical reactions

    Science.gov (United States)

    Kukushkin, S. A.; Osipov, A. V.; Redkov, A. V.

    2014-12-01

    The morphological stability of a spherical crystal growing from a multicomponent medium due to the chemical reaction has been investigated. The approach used in this study is applicable to the case where the chemical compound forming the crystal does not exist in a gaseous (dissolved) form (for example, GaN). The investigation has been performed according to the classical scheme by the expansion of an infinitesimal deviation of the crystallization front from the initial shape into a series with the subsequent calculation of the time dependence of the coefficients of the expansion. It has been found that there is a similarity of the stability criteria for single-component and multicomponent crystals. In a multicomponent system, the single-component supersaturation analog determining the stability of a particle is the affinity of the chemical reaction. It has been shown that the morphological stability can also depend on the formation of other phases on the surface of the initial crystal, which is excluded in a single-component medium.

  10. Chemical reaction and separation method

    NARCIS (Netherlands)

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

    2005-01-01

    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

  11. A Short Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility.

    Science.gov (United States)

    Warr, Wendy A

    2014-06-01

    This article is the text for a pedagogical lecture to be given at the Strasbourg Summer School in Chemoinformatics in June 2104. It covers a very wide range of reaction topics including structure and reaction representation, reaction centers, atom-to-atom mapping, reaction retrieval systems, computer-aided synthesis design, retrosynthesis, reaction prediction and synthetic feasibility. In the time available the coverage of each topic can only be cursory; the main usefulness of this article to the research community is the extensive bibliography.

  12. Chemical morphogenesis: recent experimental advances in reaction-diffusion system design and control.

    Science.gov (United States)

    Szalai, István; Cuiñas, Daniel; Takács, Nándor; Horváth, Judit; De Kepper, Patrick

    2012-08-06

    In his seminal 1952 paper, Alan Turing predicted that diffusion could spontaneously drive an initially uniform solution of reacting chemicals to develop stable spatially periodic concentration patterns. It took nearly 40 years before the first two unquestionable experimental demonstrations of such reaction-diffusion patterns could be made in isothermal single phase reaction systems. The number of these examples stagnated for nearly 20 years. We recently proposed a design method that made their number increase to six in less than 3 years. In this report, we formally justify our original semi-empirical method and support the approach with numerical simulations based on a simple but realistic kinetic model. To retain a number of basic properties of real spatial reactors but keep calculations to a minimal complexity, we introduce a new way to collapse the confined spatial direction of these reactors. Contrary to similar reduced descriptions, we take into account the effect of the geometric size in the confinement direction and the influence of the differences in the diffusion coefficient on exchange rates of species with their feed environment. We experimentally support the method by the observation of stationary patterns in red-ox reactions not based on oxihalogen chemistry. Emphasis is also brought on how one of these new systems can process different initial conditions and memorize them in the form of localized patterns of different geometries.

  13. Nonequilibrium Thermodynamic Formalism of Nonlinear Chemical Reaction Systems with Waage-Guldberg's Law of Mass Action

    CERN Document Server

    Ge, Hao

    2016-01-01

    Macroscopic entropy production $\\sigma^{(tot)}$ in the general nonlinear isothermal chemical reaction system with mass action kinetics is decomposed into a free energy dissipation and a house-keeping heat: $\\sigma^{(tot)}=\\sigma^{(fd)}+\\sigma^{(hk)}$; $\\sigma^{(fd)}=-\\rd A/\\rd t$, where $A$ is a generalized free enegy function. This yields a novel nonequilibrium free energy balance equation $\\rd A/\\rd t=-\\sigma^{(tot)}+\\sigma^{(hk)}$, which is on a par with celebrated entropy balance equation $\\rd S/\\rd t=\\sigma^{(tot)}+\\eta^{(ex)}$ where $\\eta^{(ex)}$ is the rate of entropy exchange with the environment.For kinetic system with complex balance,$\\sigma^{(fd)},\\sigma^{(hk)}\\ge 0$: $\\sigma^{(fd)}$ characterizes the irreversibility of a transient relaxation kinetics; while $\\sigma^{(hk)}$ is positive even in a steady state, representing irreversibility in open,driven chemical systems with a chemostat.For kinetic system withoutcomplex balance, negative $\\sigma^{(fd)}$ is a necessary condition for multistability, w...

  14. Methods and systems for carrying out a pH-influenced chemical and/or biological reaction

    Science.gov (United States)

    Stern, Michael C.; Simeon, Fritz; Hatton, Trevor Alan

    2016-04-05

    The present invention generally relates to methods and systems for carrying out a pH-influenced chemical and/or biological reaction. In some embodiments, the pH-influenced reaction involves the conversion of CO.sub.2 to a dissolved species.

  15. Methods and systems for carrying out a pH-influenced chemical and/or biological reaction

    Energy Technology Data Exchange (ETDEWEB)

    Eltayeb, Aly Eldeen O.; Stern, Michael C.; Hatton, Trevor Alan

    2017-02-14

    The present invention generally relates to methods and systems for carrying out a pH-influenced chemical and/or biological reaction. In some embodiments, the pH-influenced reaction involves the conversion of CO.sub.2 to a dissolved species.

  16. "Toward High School Biology": Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

    Science.gov (United States)

    Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better…

  17. A Novel Approach for Modeling Chemical Reaction in Generalized Fluid System Simulation Program

    Science.gov (United States)

    Sozen, Mehmet; Majumdar, Alok

    2002-01-01

    The Generalized Fluid System Simulation Program (GFSSP) is a computer code developed at NASA Marshall Space Flight Center for analyzing steady state and transient flow rates, pressures, temperatures, and concentrations in a complex flow network. The code, which performs system level simulation, can handle compressible and incompressible flows as well as phase change and mixture thermodynamics. Thermodynamic and thermophysical property programs, GASP, WASP and GASPAK provide the necessary data for fluids such as helium, methane, neon, nitrogen, carbon monoxide, oxygen, argon, carbon dioxide, fluorine, hydrogen, water, a hydrogen, isobutane, butane, deuterium, ethane, ethylene, hydrogen sulfide, krypton, propane, xenon, several refrigerants, nitrogen trifluoride and ammonia. The program which was developed out of need for an easy to use system level simulation tool for complex flow networks, has been used for the following purposes to name a few: Space Shuttle Main Engine (SSME) High Pressure Oxidizer Turbopump Secondary Flow Circuits, Axial Thrust Balance of the Fastrac Engine Turbopump, Pressurized Propellant Feed System for the Propulsion Test Article at Stennis Space Center, X-34 Main Propulsion System, X-33 Reaction Control System and Thermal Protection System, and International Space Station Environmental Control and Life Support System design. There has been an increasing demand for implementing a combustion simulation capability into GFSSP in order to increase its system level simulation capability of a liquid rocket propulsion system starting from the propellant tanks up to the thruster nozzle for spacecraft as well as launch vehicles. The present work was undertaken for addressing this need. The chemical equilibrium equations derived from the second law of thermodynamics and the energy conservation equation derived from the first law of thermodynamics are solved simultaneously by a Newton-Raphson method. The numerical scheme was implemented as a User

  18. Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems

    OpenAIRE

    2011-01-01

    The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form “by chance” within a sufficiently complex suite of molecules and reactions is one that we have investigated for a simple chemical reaction model based on polymer ligation and cleavage. In this paper, we extend this work in several further directions. In particular, we investigate in more detail the levels of cat...

  19. Sensitivity of chemical reaction networks: a structural approach 3. Regular multimolecular systems

    CERN Document Server

    Brehm, Bernhard

    2016-01-01

    We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions, multiple reaction products, nonmonotone rate functions, and non-closed autonomous systems. Our structural sensitivity analysis is based on the stoichiometry of the reaction network, only. It does not require numerical data on reaction rates. Instead, we impose mild and generic nondegeneracy conditions of algebraic type. From the structural data, only, we derive which steady-state concentrations are sensitive to, and hence influenced by, changes of any particular reaction rate - and which are not. We also establish transitivity properties for influences involving rate perturbations. This allows us to derive an influence graph which globally summarizes the influence pattern of the given network. The influence graph allows the computational, but meaningful, automatic identification ...

  20. Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems.

    Science.gov (United States)

    Hordijk, Wim; Kauffman, Stuart A; Steel, Mike

    2011-01-01

    The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form "by chance" within a sufficiently complex suite of molecules and reactions is one that we have investigated for a simple chemical reaction model based on polymer ligation and cleavage. In this paper, we extend this work in several further directions. In particular, we investigate in more detail the levels of catalysis required for a self-sustaining autocatalytic network to form. We study the size of chemical networks within which we might expect to find such an autocatalytic subset, and we extend the theoretical and computational analyses to models in which catalysis requires template matching.

  1. Required Levels of Catalysis for Emergence of Autocatalytic Sets in Models of Chemical Reaction Systems

    Directory of Open Access Journals (Sweden)

    Wim Hordijk

    2011-05-01

    Full Text Available The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form “by chance” within a sufficiently complex suite of molecules and reactions is one that we have investigated for a simple chemical reaction model based on polymer ligation and cleavage. In this paper, we extend this work in several further directions. In particular, we investigate in more detail the levels of catalysis required for a self-sustaining autocatalytic network to form. We study the size of chemical networks within which we might expect to find such an autocatalytic subset, and we extend the theoretical and computational analyses to models in which catalysis requires template matching.

  2. Learning to predict chemical reactions.

    Science.gov (United States)

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

    2011-09-26

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

  3. An automatic modeling system of the reaction mechanisms for chemical vapor deposition processes using real-coded genetic algorithms.

    Science.gov (United States)

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

    2011-09-01

    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.

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

    Science.gov (United States)

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

    2017-04-01

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

  5. Modelling Chemical Reasoning to Predict Reactions

    CERN Document Server

    Segler, Marwin H S

    2016-01-01

    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...

  6. Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation.

    Science.gov (United States)

    Mélykúti, Bence; Burrage, Kevin; Zygalakis, Konstantinos C

    2010-04-28

    The Chemical Langevin Equation (CLE), which is a stochastic differential equation driven by a multidimensional Wiener process, acts as a bridge between the discrete stochastic simulation algorithm and the deterministic reaction rate equation when simulating (bio)chemical kinetics. The CLE model is valid in the regime where molecular populations are abundant enough to assume their concentrations change continuously, but stochastic fluctuations still play a major role. The contribution of this work is that we observe and explore that the CLE is not a single equation, but a parametric family of equations, all of which give the same finite-dimensional distribution of the variables. On the theoretical side, we prove that as many Wiener processes are sufficient to formulate the CLE as there are independent variables in the equation, which is just the rank of the stoichiometric matrix. On the practical side, we show that in the case where there are m(1) pairs of reversible reactions and m(2) irreversible reactions there is another, simple formulation of the CLE with only m(1) + m(2) Wiener processes, whereas the standard approach uses 2(m(1) + m(2)). We demonstrate that there are considerable computational savings when using this latter formulation. Such transformations of the CLE do not cause a loss of accuracy and are therefore distinct from model reduction techniques. We illustrate our findings by considering alternative formulations of the CLE for a human ether a-go-go related gene ion channel model and the Goldbeter-Koshland switch.

  7. Reduction of chemical reaction models

    Science.gov (United States)

    Frenklach, Michael

    1991-01-01

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

  8. Controlling chemical reactions of a single particle

    CERN Document Server

    Ratschbacher, Lothar; Sias, Carlo; Köhl, Michael

    2012-01-01

    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...

  9. Kinematically complete chemical reaction dynamics

    Science.gov (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.

    2009-11-01

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

  10. Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation

    KAUST Repository

    Mélykúti, Bence

    2010-01-01

    The Chemical Langevin Equation (CLE), which is a stochastic differential equation driven by a multidimensional Wiener process, acts as a bridge between the discrete stochastic simulation algorithm and the deterministic reaction rate equation when simulating (bio)chemical kinetics. The CLE model is valid in the regime where molecular populations are abundant enough to assume their concentrations change continuously, but stochastic fluctuations still play a major role. The contribution of this work is that we observe and explore that the CLE is not a single equation, but a parametric family of equations, all of which give the same finite-dimensional distribution of the variables. On the theoretical side, we prove that as many Wiener processes are sufficient to formulate the CLE as there are independent variables in the equation, which is just the rank of the stoichiometric matrix. On the practical side, we show that in the case where there are m1 pairs of reversible reactions and m2 irreversible reactions there is another, simple formulation of the CLE with only m1 + m2 Wiener processes, whereas the standard approach uses 2 m1 + m2. We demonstrate that there are considerable computational savings when using this latter formulation. Such transformations of the CLE do not cause a loss of accuracy and are therefore distinct from model reduction techniques. We illustrate our findings by considering alternative formulations of the CLE for a human ether a-go-go related gene ion channel model and the Goldbeter-Koshland switch. © 2010 American Institute of Physics.

  11. Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics

    CERN Document Server

    Qian, Hong

    2016-01-01

    We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume $V$, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesoscopic scale. We introduce notions such as open, driven chemical systems, entropy production, free energy dissipation, etc. Then in the macroscopic limit, we illustrate how two new "laws", in terms of a generalized free energy of the mesoscopic stochastic dynamics, emerge. Detailed balance and complex balance are two special classes of "simple" nonlinear kinetics. Phase transition is intrinsically related to multi-stability...

  12. Apparent tunneling in chemical reactions

    DEFF Research Database (Denmark)

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

    2000-01-01

    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...

  13. 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

    2015-01-01

    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.

  14. Organic reaction systems: using microcapsules and microreactors to perform chemical synthesis.

    Science.gov (United States)

    Longstreet, Ashley R; McQuade, D Tyler

    2013-02-19

    The appetite for complex organic molecules continues to increase worldwide, especially in rapidly developing countries such as China, India, and Brazil. At the same time, the cost of raw materials and solvent waste disposal is also growing, making sustainability an increasingly important factor in the production of synthetic life-saving/improving compounds. With these forces in mind, our group is driven by the principle that how we synthesize a molecule is as important as which molecule we choose to synthesize. We aim to define alternative strategies that will enable more efficient synthesis of complex molecules. Drawing our inspiration from nature, we attempt to mimic (1) the multicatalytic metabolic systems within cells using collections of nonenzyme catalysts in batch reactors and (2) the serial synthetic machinery of fatty acid/polyketide biosynthesis using microreactor systems. Whether we combine catalysts in batch to prepare an active pharmaceutical ingredient (API) or use microreactors to synthesize small or polymeric molecules, we strive to understand the mechanism of each reaction while also developing new methods and techniques. This Account begins by examining our early efforts in the development of novel catalytic materials and characterization of catalytic systems and how these observations helped forge our current models for developing efficient synthetic routes. The Account progresses through a focused examination of design principles needed to develop multicatalyst systems using systems recently published by our group as examples. Our systems have been successfully applied to produce APIs as well as new synthetic methods. The multicatalyst section is then juxtaposed with our work in continuous flow multistep synthesis. Here, we discuss the design principles needed to create multistep continuous processes using examples from our recent efforts. Overall, this Account illustrates how multistep organic routes can be conceived and achieved using

  15. A higher-order numerical framework for stochastic simulation of chemical reaction systems.

    KAUST Repository

    Székely, Tamás

    2012-07-15

    BACKGROUND: In this paper, we present a framework for improving the accuracy of fixed-step methods for Monte Carlo simulation of discrete stochastic chemical kinetics. Stochasticity is ubiquitous in many areas of cell biology, for example in gene regulation, biochemical cascades and cell-cell interaction. However most discrete stochastic simulation techniques are slow. We apply Richardson extrapolation to the moments of three fixed-step methods, the Euler, midpoint and θ-trapezoidal τ-leap methods, to demonstrate the power of stochastic extrapolation. The extrapolation framework can increase the order of convergence of any fixed-step discrete stochastic solver and is very easy to implement; the only condition for its use is knowledge of the appropriate terms of the global error expansion of the solver in terms of its stepsize. In practical terms, a higher-order method with a larger stepsize can achieve the same level of accuracy as a lower-order method with a smaller one, potentially reducing the computational time of the system. RESULTS: By obtaining a global error expansion for a general weak first-order method, we prove that extrapolation can increase the weak order of convergence for the moments of the Euler and the midpoint τ-leap methods, from one to two. This is supported by numerical simulations of several chemical systems of biological importance using the Euler, midpoint and θ-trapezoidal τ-leap methods. In almost all cases, extrapolation results in an improvement of accuracy. As in the case of ordinary and stochastic differential equations, extrapolation can be repeated to obtain even higher-order approximations. CONCLUSIONS: Extrapolation is a general framework for increasing the order of accuracy of any fixed-step stochastic solver. This enables the simulation of complicated systems in less time, allowing for more realistic biochemical problems to be solved.

  16. Experimental Demonstrations in Teaching Chemical Reactions.

    Science.gov (United States)

    Hugerat, Muhamad; Basheer, Sobhi

    2001-01-01

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

  17. Atoms of multistationarity in chemical reaction networks

    CERN Document Server

    Joshi, Badal

    2011-01-01

    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...

  18. Chemical reactions at aqueous interfaces

    Science.gov (United States)

    Vecitis, Chad David

    2009-12-01

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

  19. Heat Integration of the Water-Gas Shift Reaction System for Carbon Sequestration Ready IGCC Process with Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Juan M. Salazara; Stephen E. Zitney; Urmila M. Diwekara

    2010-01-01

    Integrated gasification combined cycle (IGCC) technology has been considered as an important alternative for efficient power systems that can reduce fuel consumption and CO2 emissions. One of the technological schemes combines water-gas shift reaction and chemical-looping combustion as post gasification techniques in order to produce sequestration-ready CO2 and potentially reduce the size of the gas turbine. However, these schemes have not been energetically integrated and process synthesis techniques can be applied to obtain an optimal flowsheet. This work studies the heat exchange network synthesis (HENS) for the water-gas shift reaction train employing a set of alternative designs provided by Aspen energy analyzer (AEA) and combined in a process superstructure that was simulated in Aspen Plus (AP). This approach allows a rigorous evaluation of the alternative designs and their combinations avoiding all the AEA simplifications (linearized models of heat exchangers). A CAPE-OPEN compliant capability which makes use of a MINLP algorithm for sequential modular simulators was employed to obtain a heat exchange network that provided a cost of energy that was 27% lower than the base case. Highly influential parameters for the pos gasification technologies (i.e. CO/steam ratio, gasifier temperature and pressure) were calculated to obtain the minimum cost of energy while chemical looping parameters (oxidation and reduction temperature) were ensured to be satisfied.

  20. 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.

    1988-01-01

    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.

  1. Quantum Theory of Fast Chemical Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Light, John C

    2007-07-30

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

  2. Minimum Energy Pathways for Chemical Reactions

    Science.gov (United States)

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

    1995-01-01

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

  3. Neural Networks in Chemical Reaction Dynamics

    CERN Document Server

    Raff, Lionel; Hagan, Martin

    2011-01-01

    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. Measurement of Large Spiral and Target Waves in Chemical Reaction-Diffusion-Advection Systems: Turbulent Diffusion Enhances Pattern Formation

    Science.gov (United States)

    von Kameke, A.; Huhn, F.; Muñuzuri, A. P.; Pérez-Muñuzuri, V.

    2013-02-01

    In the absence of advection, reaction-diffusion systems are able to organize into spatiotemporal patterns, in particular spiral and target waves. Whenever advection is present that can be parametrized in terms of effective or turbulent diffusion D*, these patterns should be attainable on a much greater, boosted length scale. However, so far, experimental evidence of these boosted patterns in a turbulent flow was lacking. Here, we report the first experimental observation of boosted target and spiral patterns in an excitable chemical reaction in a quasi-two-dimensional turbulent flow. The wave patterns observed are ˜50 times larger than in the case of molecular diffusion only. We vary the turbulent diffusion coefficient D* of the flow and find that the fundamental Fisher-Kolmogorov-Petrovsky-Piskunov equation, vf∝D*, for the asymptotic speed of a reactive wave remains valid. However, not all measures of the boosted wave scale with D* as expected from molecular diffusion, since the wave fronts turn out to be highly filamentous.

  5. Toward High School Biology: Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems.

    Science.gov (United States)

    Herrmann-Abell, Cari F; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better foundation, we used research-based design principles and collaborated in the development of a curricular intervention that applies chemistry ideas to living and nonliving contexts. Six eighth grade teachers and their students participated in a test of the unit during the Spring of 2013. Two of the teachers had used an earlier version of the unit the previous spring. The other four teachers were randomly assigned either to implement the unit or to continue teaching the same content using existing materials. Pre- and posttests were administered, and the data were analyzed using Rasch modeling and hierarchical linear modeling. The results showed that, when controlling for pretest score, gender, language, and ethnicity, students who used the curricular intervention performed better on the posttest than the students using existing materials. Additionally, students who participated in the intervention held fewer misconceptions. These results demonstrate the unit's promise in improving students' understanding of the targeted ideas.

  6. Direct vacuum inlet system enabling highly sensitive in-situ analysis of chemical reaction products

    DEFF Research Database (Denmark)

    Trimarco, Daniel Bøndergaard; Scott, Søren Bertelsen; Pedersen, Thomas

    , a capillary maintaining a controlled flow over a pressure drop to ultra-high vacuum, and inlet and outlet channels for an inert make up gas. The use of a direct inlet enables orders of magnitude higher sensitivity than differentially pumped systems without a loss in time response for volatile products, while...

  7. Method and system for controlling chemical reactions between superconductors and metals in superconducting cables

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Tengming

    2016-11-15

    A method, system, and apparatus for fabricating a high-strength Superconducting cable comprises pre-oxidizing at least one high-strength alloy wire, coating at least one Superconducting wire with a protective layer, and winding the high-strength alloy wire and the Superconducting wire to form a high-strength Superconducting cable.

  8. 2005 Chemical Reactions at Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Cynthia M. Friend

    2006-03-14

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

  9. Chemical Reaction Networks for Computing Polynomials.

    Science.gov (United States)

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

    2017-01-20

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

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

    Science.gov (United States)

    Schultz, Emeric

    2008-01-01

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

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

    Science.gov (United States)

    Shinar, Guy; Feinberg, Martin

    2013-01-01

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

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

    Science.gov (United States)

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

    2014-03-11

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

  13. Suppression of Ostwald Ripening by Chemical Reactions

    Science.gov (United States)

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

    2015-03-01

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

  14. Chemical reactions in low-g

    Science.gov (United States)

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

    1978-01-01

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

  15. Entropy production in a chemical system involving an autocatalytic reaction in an isothermal, continuous stirred tank reactor

    Science.gov (United States)

    Yoshida, Nobuo

    1990-02-01

    The rate of entropy production due to chemical reaction is calculated for various combinations of parameter values in the cubic autocatalator model in an isothermal, continuous stirred tank reactor (CSTR) proposed by Gray and Scott and by Escher and Ross. Values of the entropy production averaged over periods of limit cycle oscillations are compared with those in coexistent unstable stationary states. It is found that in ranges of the residence time over which there are limit cycles, the entropy production in coexisting stationary states increases as the residence time is shortened, i.e., as the system is removed farther from thermodynamic equilibrium. The average entropy production over a limit cycle is less than that in the corresponding stationary state over wide ranges of parameter values, but not necessarily for the whole oscillatory region. More specifically, the former inequality always prevails in ranges where the entropy production of stationary states is larger, i.e., the residence time is shorter, but in some cases the inequality is reversed in ranges of lower magnitudes of the entropy production.

  16. Establishment of a finite element model for extracting chemical reaction kinetics in a micro-flow injection system with high throughput sampling.

    Science.gov (United States)

    Wu, Zeng-Qiang; Du, Wen-Bin; Li, Jin-Yi; Xia, Xing-Hua; Fang, Qun

    2015-08-01

    Numerical simulation can provide valuable insights for complex microfluidic phenomena coupling mixing and diffusion processes. Herein, a novel finite element model (FEM) has been established to extract chemical reaction kinetics in a microfluidic flow injection analysis (micro-FIA) system using high throughput sample introduction. To reduce the computation burden, the finite element mesh generation is performed with different scales based on the different geometric sizes of micro-FIA. In order to study the contribution of chemical reaction kinetics under non-equilibrium condition, a pseudo-first-order chemical kinetics equation is adopted in the numerical simulations. The effect of reactants diffusion on reaction products is evaluated, and the results demonstrate that the Taylor dispersion plays a determining role in the micro-FIA system. In addition, the effects of flow velocity and injection volume on the reaction product are also simulated. The simulated results agree well with the ones from experiments. Although gravity driven flow is used to the numerical model in the present study, the FEM model also can be applied into the systems with other driving forces such as pressure. Therefore, the established FEM model will facilitate the understanding of reaction mechanism in micro-FIA systems and help us to optimize the manifold of micro-FIA systems.

  17. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    Science.gov (United States)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  18. Modelling Chemical Reasoning to Predict Reactions

    OpenAIRE

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

    2016-01-01

    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...

  19. A Unified Theory of Chemical Reactions

    CERN Document Server

    Aubry, S

    2014-01-01

    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.

  20. Chemical Reaction Dynamics in Nanoscle Environments

    Energy Technology Data Exchange (ETDEWEB)

    Evelyn M. Goldfield

    2006-09-26

    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.

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

    OpenAIRE

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

    2014-01-01

    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...

  2. Reaction systems with precipitation

    Directory of Open Access Journals (Sweden)

    Marek Rogalski

    2015-04-01

    Full Text Available This article proposes expanding Reaction Systems of Ehrenfeucht and Rozenberg by incorporating precipitation reactions into it. This improves the computing power of Reaction Systems by allowing us to implement a stack. This addition enables us to implement a Deterministic Pushdown Automaton.

  3. Chemical potential and reaction electronic flux in symmetry controlled reactions.

    Science.gov (United States)

    Vogt-Geisse, Stefan; Toro-Labbé, Alejandro

    2016-07-15

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

  4. Chemical reactions in solvents and melts

    CERN Document Server

    Charlot, G

    1969-01-01

    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

  5. Integrated microfluidic system enabling (bio)chemical reactions with on-line MALDI-TOF mass spectrometry

    NARCIS (Netherlands)

    Brivio, Monica; Fokkens, Roel H.; Verboom, Willem; Reinhoudt, David N.; Tas, Niels R.; Goedbloed, Martijn; Berg, van den Albert

    2002-01-01

    A continuous flow micro total analysis system (μ-TAS) consisting of an on-chip microfluidic device connected to a matrix assisted laser desorption ionization [MALDI] time-of-flight [TOF] mass spectrometer (MS) as an analytical screening system is presented. Reaction microchannels and inlet/outlet re

  6. Flows and chemical reactions in heterogeneous mixtures

    CERN Document Server

    Prud'homme, Roger

    2014-01-01

    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

  7. Quantum dynamics of fast chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  8. Chemical-reaction model for Mexican wave

    Science.gov (United States)

    Nagatani, Takashi

    2003-05-01

    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.

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

    Science.gov (United States)

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

    2016-06-13

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

  10. Modeling of turbulent chemical reaction

    Science.gov (United States)

    Chen, J.-Y.

    1995-01-01

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

  11. Chemical kinetics and reaction dynamics

    CERN Document Server

    Houston, Paul L

    2006-01-01

    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 Reactions at Surfaces. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    None

    2003-02-21

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

  13. Explorations into Chemical Reactions and Biochemical Pathways.

    Science.gov (United States)

    Gasteiger, Johann

    2016-12-01

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

  14. Temperature waves in chemical reaction-diffusion-heat conduction systems with two ends respectively subject to Dirichlet and no-flux conditions

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Taking the Lindemann model as a sample system in which there exist chemical reactions, diffusion and heat conduction, we found the theoretical framework of linear stability analysis for a unidimensional nonhomogeneous two-variable system with one end subject to Dirichlet conditions, while the other end no-flux conditions. Furthermore, the conditions for the emergence of temperature waves are found out by the linear stabiliy analysis and verified by a diagram for successive steps of evolution of spatial profile of temperature during a period that is plotted by numerical simulations on a computer. Without doubt, these results are in favor of the heat balance in chemical reactor designs.

  15. Kinetic studies of elementary chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  16. Entropy Generation in a Chemical Reaction

    Science.gov (United States)

    Miranda, E. N.

    2010-01-01

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

  17. Chemical Reactions in Turbulent Mixing Flows

    Science.gov (United States)

    1989-10-15

    example, Levenspiel (1962). Eq. 27 would be necessary. A first guess is that it might scale with 6/z as it does for subsonic flow. i.e. -(r, s; M., -0 ) -(r...France), 45-63. KELLER. J. 0. and DAILY. J. W. (1985] "The Effect of Highly Exothermic Chemical Reaction on a Two-Dimensional Mixing Layer", LEVENSPIEL ...0. [19621 Chemical Reaction Engineering. An Introduc- ALAA J. 23(12), 1937-1945. tion to the Design of Chemical Reactors . (John Wiley). KERSTEIN. A

  18. Computed potential energy surfaces for chemical reactions

    Science.gov (United States)

    Walch, Stephen P.

    1994-01-01

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

  19. A new look at the chemical reaction

    Directory of Open Access Journals (Sweden)

    Johannes A.A.W. Elemans

    2009-07-01

    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.

  20. Chemical reactions confined within carbon nanotubes.

    Science.gov (United States)

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

    2016-08-22

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

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

    Science.gov (United States)

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

    2016-02-01

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

  2. Design of a New Concentration Series for the Orthogonal Sample Design Approach and Estimation of the Number of Reactions in Chemical Systems.

    Science.gov (United States)

    Shi, Jiajia; Liu, Yuhai; Guo, Ran; Li, Xiaopei; He, Anqi; Gao, Yunlong; Wei, Yongju; Liu, Cuige; Zhao, Ying; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2015-11-01

    A new concentration series is proposed for the construction of a two-dimensional (2D) synchronous spectrum for orthogonal sample design analysis to probe intermolecular interaction between solutes dissolved in the same solutions. The obtained 2D synchronous spectrum possesses the following two properties: (1) cross peaks in the 2D synchronous spectra can be used to reflect intermolecular interaction reliably, since interference portions that have nothing to do with intermolecular interaction are completely removed, and (2) the two-dimensional synchronous spectrum produced can effectively avoid accidental collinearity. Hence, the correct number of nonzero eigenvalues can be obtained so that the number of chemical reactions can be estimated. In a real chemical system, noise present in one-dimensional spectra may also produce nonzero eigenvalues. To get the correct number of chemical reactions, we classified nonzero eigenvalues into significant nonzero eigenvalues and insignificant nonzero eigenvalues. Significant nonzero eigenvalues can be identified by inspecting the pattern of the corresponding eigenvector with help of the Durbin-Watson statistic. As a result, the correct number of chemical reactions can be obtained from significant nonzero eigenvalues. This approach provides a solid basis to obtain insight into subtle spectral variations caused by intermolecular interaction.

  3. 基于化学反应算法的系统辨识%SYSTEM IDENTIFICATION USING CHEMICAL REACTION OPTIMISATION ALGORITHMS

    Institute of Scientific and Technical Information of China (English)

    何兴华; 周永华

    2016-01-01

    化学反应优化算法起源于化学反应过程中的能量变化的模拟。提出一种利用化学反应优化算法对系统进行辨识的方法。即通过建立连续系统和离散系统的传递函数结构模型,首先将系统辨识问题转化为数学上求取相关参数的全局最优估计问题,然后利用化学反应优化算法对该问题进行求解。最后给出仿真实例,并且与遗传算法进行了比较,结果表明该方法具有较好的效果,且兼具速度快、精度高等特点。%Chemical reaction optimisation algorithms are derived from simulating the energy changes in chemical reaction process.This paper shows how the chemical reaction optimisation algorithms be applied for system identification.That is,by building the transfer function structural model of continuous and discrete systems,first we convert the problem of system identification to a global optimal estimation problem of seeking the correlated parameters in mathematics,then we use chemical reaction optimisation algorithms to solve the problem.In end of the paper,we give some simulation examples and compare them with genetic algorithms.Results prove that our method has better effect,and has the features of both high speed and accuracy.

  4. Lycopene epoxides and apo-lycopenals formed by chemical reactions and autoxidation in model systems and processed foods.

    Science.gov (United States)

    Rodriguez, Evelyn B; Rodriguez-Amaya, Delia B

    2009-01-01

    To gain a better understanding of the reactions and the underlying mechanisms of the oxidative degradation of lycopene, the products formed by epoxidation with m-chloroperbenzoic acid (MCPBA), oxidative cleavage with KMnO(4), and autoxidation in low-moisture and aqueous model systems, under light exposure, at ambient temperature were identified. The presence of oxidation products was also verified in processed products (tomato juice, tomato paste, tomato puree, guava juice, "goiabada"). A total of 8 lycopene epoxides and a cyclolycopene diol were formed by the reaction of lycopene with MCPBA and 6 apo-lycopenals were produced with KMnO(4). Some of these oxidation products were not detected in the model systems and in the foods analyzed, but the acid-catalyzed rearrangement product 2,6-cyclolycopene-1,5-diol and apo-12'-lycopenal were found in all model and food systems and lycopene-1,2-epoxide and 2,6-cyclolycopene-1,5-epoxide were found in the model systems and in all but 1 ("goiabada") of the 5 foods analyzed. Other epoxides and apo-lycopenals were found in some systems. The inability to detect an intermediate product could be due to a fast turn over. Increased Z-isomerization was also observed and Z-isomers of the oxidation products were detected.

  5. Chemical memory reactions induced bursting dynamics in gene expression.

    Science.gov (United States)

    Tian, Tianhai

    2013-01-01

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

  6. Classification of Chemical Reactions: Stages of Expertise

    Science.gov (United States)

    Stains, Marilyne; Talanquer, Vicente

    2008-01-01

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

  7. Sequential identification of model parameters by derivative double two-dimensional correlation spectroscopy and calibration-free approach for chemical reaction systems.

    Science.gov (United States)

    Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

    2012-10-02

    A sequential identification approach by two-dimensional (2D) correlation analysis for the identification of a chemical reaction model, activation, and thermodynamic parameters is presented in this paper. The identification task is decomposed into a sequence of subproblems. The first step is the construction of a reaction model with the suggested information by model-free 2D correlation analysis using a novel technique called derivative double 2D correlation spectroscopy (DD2DCOS), which enables one to analyze intensities with nonlinear behavior and overlapped bands. The second step is a model-based 2D correlation analysis where the activation and thermodynamic parameters are estimated by an indirect implicit calibration or a calibration-free approach. In this way, a minimization process for the spectral information by sample-sample 2D correlation spectroscopy and kinetic hard modeling (using ordinary differential equations) of the chemical reaction model is carried out. The sequential identification by 2D correlation analysis is illustrated with reference to the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol. The reaction was investigated by FT-IR spectroscopy. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied by means of an integration of model-free and model-based 2D correlation analysis called a sequential identification approach. The study determined the enthalpy (ΔH = 15.25 kJ/mol) and entropy (TΔS = 13.20 kJ/mol) of C═O···H hydrogen bonding of diphenylurethane through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S) at equilibrium in the chemical reaction system.

  8. Plasmonic smart dust for probing local chemical reactions.

    Science.gov (United States)

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

    2013-04-10

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

  9. Modelling Chemical Reasoning to Predict and Invent Reactions.

    Science.gov (United States)

    Segler, Marwin H S; Waller, Mark P

    2016-11-11

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

  10. Chemical computing with reaction-diffusion processes.

    Science.gov (United States)

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

    2015-07-28

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

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

    Science.gov (United States)

    Fooshee, David; Andronico, Alessio; Baldi, Pierre

    2013-11-25

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

  12. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  13. Reaction diffusion and solid state chemical kinetics handbook

    CERN Document Server

    Dybkov, V I

    2010-01-01

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

  14. Study on a Bioethanol Solar Reforming System with the Solar Insolation Fluctuation in Consideration of Heat Chemical Reaction

    Science.gov (United States)

    Obara, Shin'ya; El-Sayed, Abeer Galal

    A bioethanol reforming system (FBSR) with a sunlight heat source is developed as a potential fuel supply system for distributed fuel cells. The temperature distribution of a catalyst layer in the reactor is not stable under conditions of unstable solar radiation and unstable outside air temperature; therefore, it is thought that the inversion rate of a reforming reaction will decrease. In this paper, heat transmission analysis was used in the catalyst layer of the reforming component of an FBSR, and temperature distribution, inversion rate, and process gas composition were investigated. Based on the results, the relationship between weather conditions and a hydrogen-generating rate was determined. When solar insolation was unstable, it turned out that the efficiency of the reforming component is reduced. Fluctuations of the solar insolation over a short period of time affect the hydrogen generating rate of an FBSR. Moreover, the amount of hydrogen production of an FBSR was simulated using meteorological data from a day in March and a day in August in a cold region (Sapporo). The analysis showed that efficiency of the reforming component exceeded 40% for both of the days.

  15. Flows and chemical reactions in homogeneous mixtures

    CERN Document Server

    Prud'homme, Roger

    2013-01-01

    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

  16. Molecular codes in biological and chemical reaction networks.

    Science.gov (United States)

    Görlich, Dennis; Dittrich, Peter

    2013-01-01

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

  17. From gas-phase to liquid-water chemical reactions: the fluorine atom plus water trimer system.

    Science.gov (United States)

    Li, Guoliang; Li, Qian-Shu; Xie, Yaoming; Schaefer, Henry F

    2015-09-14

    The potential energy profile for the F+(H2 O)3 →HF+(H2 O)2 OH reaction has been investigated using the "gold standard" CCSD(T) method with correlation-consistent basis sets up to cc-pVQZ. Four different reaction pathways have been found and these are related, both geometrically and energetically. The entrance complexes F⋅⋅⋅(H2 O)3 for all four reaction pathways are found lying ca. 7 kcal mol(-1) below the separated reactants F+(H2 O)3 . The four reaction barriers on their respective reaction coordinates lie ca. 4 kcal mol(-1) below the reactants. There are also corresponding exit complexes HF⋅⋅⋅(H2 O)2 OH, lying about 13 kcal mol(-1) below the separated products HF+(H2 O)2 OH. Compared with analogous F+(H2 O)2 and F+H2 O reactions, the F+(H2 O)3 reaction is somewhat similar to the former but qualitatively different from the latter. It may be reasonable to predict that the reactions between atomic fluorine and water tetramer (or even larger water clusters) may be similar to the F+(H2 O)3 reaction.

  18. Chemical reactions directed Peptide self-assembly.

    Science.gov (United States)

    Rasale, Dnyaneshwar B; Das, Apurba K

    2015-05-13

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

  19. Optimization of a Chemical Reaction Train

    Directory of Open Access Journals (Sweden)

    Bahar Sansar

    2010-01-01

    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.

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-01

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

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

    Science.gov (United States)

    Kayala, Matthew A; Baldi, Pierre

    2012-10-22

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

  3. Effect of Reaction Time and Temperature on Chemical, Structural, Optical, and Photoelectrical Properties of PbS Thin Films Chemically Deposited from the Pb(OAc)2-NaOH-TU-TEA Aqueous System

    Science.gov (United States)

    Castelo-González, O. A.; Sotelo-Lerma, M.; García-Valenzuela, J. A.

    2017-01-01

    Lead sulfide (PbS) thin films have been deposited on float glass substrates by the chemical bath deposition technique using a Pb(CH3COO)2-NaOH-(NH2)2CS-N(CH2CH2OH)3 definite aqueous system. The chemical and structural characteristics, as well as the variation of the optical and photoelectrical properties, were studied as functions of reaction time and temperature. For this purpose, the following characterization techniques were employed: x-ray diffraction analysis, x-ray photoelectron spectroscopy, ultraviolet-visible-near infrared spectrophotometry, and dark and light current measurements. Based on the results, it was observed that increase in the reaction temperature increased the deposition rate of the PbS thin film (associated with the cubic crystalline structure); increase of this parameter from 40°C to 70°C (with reaction time of 60 min) led to an increase of the thickness from ˜129 nm to ˜459 nm and the crystallite size ( D) from 15.3 nm to 20.2 nm; on the other hand, increase in temperature decreased the energy bandgap ( E g) from 1.66 eV to 0.51 eV and the relative photosensitivity factor ( S ph) from 0.468 to 0.032. A similar effect was obtained with increase of the reaction time for given temperature.

  4. Effect of Reaction Time and Temperature on Chemical, Structural, Optical, and Photoelectrical Properties of PbS Thin Films Chemically Deposited from the Pb(OAc)2-NaOH-TU-TEA Aqueous System

    Science.gov (United States)

    Castelo-González, O. A.; Sotelo-Lerma, M.; García-Valenzuela, J. A.

    2016-08-01

    Lead sulfide (PbS) thin films have been deposited on float glass substrates by the chemical bath deposition technique using a Pb(CH3COO)2-NaOH-(NH2)2CS-N(CH2CH2OH)3 definite aqueous system. The chemical and structural characteristics, as well as the variation of the optical and photoelectrical properties, were studied as functions of reaction time and temperature. For this purpose, the following characterization techniques were employed: x-ray diffraction analysis, x-ray photoelectron spectroscopy, ultraviolet-visible-near infrared spectrophotometry, and dark and light current measurements. Based on the results, it was observed that increase in the reaction temperature increased the deposition rate of the PbS thin film (associated with the cubic crystalline structure); increase of this parameter from 40°C to 70°C (with reaction time of 60 min) led to an increase of the thickness from ˜129 nm to ˜459 nm and the crystallite size (D) from 15.3 nm to 20.2 nm; on the other hand, increase in temperature decreased the energy bandgap (E g) from 1.66 eV to 0.51 eV and the relative photosensitivity factor (S ph) from 0.468 to 0.032. A similar effect was obtained with increase of the reaction time for given temperature.

  5. Chemical reaction due to stronger Ramachandran interaction

    Indian Academy of Sciences (India)

    Andrew Das Arulsamy

    2014-05-01

    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.

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

    Science.gov (United States)

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

    2016-03-02

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

  7. Law of localization in chemical reaction networks

    CERN Document Server

    Okada, Takashi

    2016-01-01

    In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone. 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.

  8. 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...

  9. Program Helps To Determine Chemical-Reaction Mechanisms

    Science.gov (United States)

    Bittker, D. A.; Radhakrishnan, K.

    1995-01-01

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

  10. Systematic Error Estimation for Chemical Reaction Energies

    CERN Document Server

    Simm, Gregor N

    2016-01-01

    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...

  11. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    Qian Xie; Tinker, Robert

    2006-01-01

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

  12. Chemical Reaction Optimization for Max Flow Problem

    Directory of Open Access Journals (Sweden)

    Reham Barham

    2016-08-01

    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.

  13. Supersonic molecular beam experiments on surface chemical reactions.

    Science.gov (United States)

    Okada, Michio

    2014-10-01

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

  14. Free convective heat transfer with hall effects, heat absorption and chemical reaction over an accelerated moving plate in a rotating system

    Science.gov (United States)

    Hussain, S. M.; Jain, J.; Seth, G. S.; Rashidi, M. M.

    2017-01-01

    The unsteady MHD free convective heat and mass transfer flow of an electrically conducting, viscous and incompressible fluid over an accelerated moving vertical plate in the presence of heat absorption and chemical reaction with ramped temperature and ramped surface concentration through a porous medium in a rotating system is studied, taking Hall effects into account. The governing equations are solved analytically with the help of Laplace transform technique. The unified closed-form expressions are obtained for fluid velocity, fluid temperature, species concentration, skin friction, Nusselt number and Sherwood numbers. The effects of various parameters on fluid velocity, fluid temperature and species concentration are discussed by graphs whereas numerical values of skin friction, Nusselt and Sherwood numbers are presented in tabular form for different values of pertinent flow parameters. The numerical results are also compared with free convective flow near ramped temperature plate with ramped surface concentration with the corresponding flow near isothermal plate with uniform surface concentration.

  15. 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.

    1994-10-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

  17. Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    2011-03-01

    Full Text Available In the era of personalized medical practice, understanding the genetic basis of patient-specific adverse drug reaction (ADR is a major challenge. Clozapine provides effective treatments for schizophrenia but its usage is limited because of life-threatening agranulocytosis. A recent high impact study showed the necessity of moving clozapine to a first line drug, thus identifying the biomarkers for drug-induced agranulocytosis has become important. Here we report a methodology termed as antithesis chemical-protein interactome (CPI, which utilizes the docking method to mimic the differences in the drug-protein interactions across a panel of human proteins. Using this method, we identified HSPA1A, a known susceptibility gene for CIA, to be the off-target of clozapine. Furthermore, the mRNA expression of HSPA1A-related genes (off-target associated systems was also found to be differentially expressed in clozapine treated leukemia cell line. Apart from identifying the CIA causal genes we identified several novel candidate genes which could be responsible for agranulocytosis. Proteins related to reactive oxygen clearance system, such as oxidoreductases and glutathione metabolite enzymes, were significantly enriched in the antithesis CPI. This methodology conducted a multi-dimensional analysis of drugs' perturbation to the biological system, investigating both the off-targets and the associated off-systems to explore the molecular basis of an adverse event or the new uses for old drugs.

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

    Indian Academy of Sciences (India)

    Aldona Krupska

    2015-06-01

    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.

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

    Science.gov (United States)

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

    2014-01-01

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

  20. Accelerated Stochastic Simulation of Large Chemical Systems

    Institute of Scientific and Technical Information of China (English)

    CHEN Xiao; AO Ling

    2007-01-01

    For efficient simulation of chemical systems with large number of reactions, we report a fast and exact algorithm for direct simulation of chemical discrete Markov processes. The approach adopts the scheme of organizing the reactions into hierarchical groups. By generating a random number, the selection of the next reaction that actually occurs is accomplished by a few successive selections in the hierarchical groups. The algorithm which is suited for simulating systems with large number of reactions is much faster than the direct method or the optimized direct method. For a demonstration of its efficiency, the accelerated algorithm is applied to simulate the reaction-diffusion Brusselator model on a discretized space.

  1. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; Elebeoba E. May; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

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

    Science.gov (United States)

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

    2012-05-01

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

  3. 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)

    1993-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

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

  5. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

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

    Science.gov (United States)

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

    2014-06-24

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

  7. Computational systems chemical biology.

    Science.gov (United States)

    Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  8. Flows and chemical reactions in an electromagnetic field

    CERN Document Server

    Prud'homme, Roger

    2014-01-01

    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

  9. [Recent results in research on oscillatory chemical reactions].

    Science.gov (United States)

    Poros, Eszter; Kurin-Csörgei, Krisztina

    2014-01-01

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

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

    CERN Document Server

    Banerjee, Kinshuk

    2013-01-01

    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.

  11. Chemical morphogenesis: turing patterns in an experimental chemical system.

    Science.gov (United States)

    Dulos, E; Boissonade, J; Perraud, J J; Rudovics, B; De Kepper, P

    1996-11-01

    Patterns resulting from the sole interplay between reaction and diffusion are probably involved in certain stages of morphogenesis in biological systems, as initially proposed by Alan Turing. Self-organization phenomena of this type can only develop in nonlinear systems (i.e. involving positive and negative feedback loops) maintained far from equilibrium. We present Turing patterns experimentally observed in a chemical system. An oscillating chemical reaction, the CIMA reaction, is operated in an open spatial reactor designed in order to obtain a pure reaction-diffusion system. The two types of Turing patterns observed, hexagonal arrays of spots and parallel stripes, are characterized by an intrinsic wavelength. We identify the origin of the necessary diffusivity between activator and inhibitor. We also describe a pattern growth mechanism by spot splitting that recalls cell division.

  12. Quantum mechanical calculations of vibrational population inversion in chemical reactions - Numerically exact L-squared-amplitude-density study of the H2Br reactive system

    Science.gov (United States)

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

    1988-01-01

    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.

  13. 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)

    1991-12-31

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

  14. Experimental investigation on moving chemical reaction boundary theory for weak-acid-strong-base system with background electrolyte KCl in large concentration.

    Science.gov (United States)

    Cao, C X; Zhou, S L; Qian, Y A; He, Y Z; Yang, L; Qu, Q S; Chen, W K

    2001-07-13

    In this report, the moving chemical reaction boundary (MCRB) was formed with the weak acid of acetic acid (HAc) and the strong alkali of NaOH, coupled with the excess of background electrolyte KCl. The experiments were compared with the predictions by the moving chemical reaction boundary equation (MCRBE). It is very interesting that (1) the experimental results are in good agreement with the predictions with the original MCRBE if the MCRB is an anodic moving boundary, (2) however, the experiments are extremely far away from the predictions with the original MCRBE if a cathodic moving boundary. Hence, the original MCRBE must be corrected under the later situation of cathodic moving MCRB. The corrected MCRBE was well quantitatively proved to be valid for the cathodic moving MNRB formed with the same electrolytes of HAc, NaOH and KCl.

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

    Science.gov (United States)

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

    2003-07-14

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

  16. 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)

    2015-12-31

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

  17. Negative Temperature Coefficient in Chemical Reactions

    Science.gov (United States)

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

    1984-05-01

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

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

    Science.gov (United States)

    Feindel, Kirk W

    2016-06-01

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

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

    Science.gov (United States)

    Kanehisa, Minoru

    2013-09-02

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

  20. Mesoscale simulations of shockwave energy dissipation via chemical reactions.

    Science.gov (United States)

    Antillon, Edwin; Strachan, Alejandro

    2015-02-28

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

  1. Fixed Points for Stochastic Open Chemical Systems

    CERN Document Server

    Malyshev, V A

    2011-01-01

    In the first part of this paper we give a short review of the hierarchy of stochastic models, related to physical chemistry. In the basement of this hierarchy there are two models --- stochastic chemical kinetics and the Kac model for Boltzman equation. Classical chemical kinetics and chemical thermodynamics are obtained as some scaling limits in the models, introduced below. In the second part of this paper we specify some simple class of open chemical reaction systems, where one can still prove the existence of attracting fixed points. For example, Michaelis\\tire Menten kinetics belongs to this class. At the end we present a simplest possible model of the biological network. It is a network of networks (of closed chemical reaction systems, called compartments), so that the only source of nonreversibility is the matter exchange (transport) with the environment and between the compartments. Keywords: chemical kinetics, chemical thermodynamics, Kac model, mathematical biology

  2. 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)

    2003-06-01

    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.

  3. 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)

    2015-12-31

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

  4. Chemical tailoring of teicoplanin with site-selective reactions.

    Science.gov (United States)

    Pathak, Tejas P; Miller, Scott J

    2013-06-05

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

  5. Non-equilibrium effects in high temperature chemical reactions

    Science.gov (United States)

    Johnson, Richard E.

    1987-01-01

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

  6. Communication: Control of chemical reactions using electric field gradients.

    Science.gov (United States)

    Deshmukh, Shivaraj D; Tsori, Yoav

    2016-05-21

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

  7. Communication: Control of chemical reactions using electric field gradients

    Science.gov (United States)

    Deshmukh, Shivaraj D.; Tsori, Yoav

    2016-05-01

    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

    Science.gov (United States)

    2014-05-16

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

    CERN Document Server

    Churchill, L R; Chapman, M S

    2010-01-01

    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$^{3+}$.

  10. Colloidal Assemblies Effect on Chemical Reactions.

    Science.gov (United States)

    1986-07-01

    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

  11. CHEMICAL REACTIONS SIMULATED BY GROUND-WATER-QUALITY MODELS.

    Science.gov (United States)

    Grove, David B.; Stollenwerk, Kenneth G.

    1987-01-01

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

  12. Automated Discovery of New Chemical Reactions and Accurate Calculation of Their Rates

    Science.gov (United States)

    2015-06-02

    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

  13. 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

    2007-01-01

    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.

  14. Physical Chemistry Chemical Kinetics and Reaction Mechanism

    CERN Document Server

    Trimm, Harold H

    2011-01-01

    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

  15. Electronic dissipation processes during chemical reactions on surfaces

    CERN Document Server

    Stella, Kevin

    2012-01-01

    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

  16. Quantifying chemical reactions by using mixing analysis.

    Science.gov (United States)

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

    2015-01-01

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

  17. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

    Science.gov (United States)

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

    2014-01-01

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

  18. Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

    Science.gov (United States)

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

    2014-11-12

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

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

    Science.gov (United States)

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

    2016-08-22

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

  20. Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

    Science.gov (United States)

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

    2011-01-01

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

  1. The Heck reaction in the production of fine chemicals

    NARCIS (Netherlands)

    Vries, Johannes G. de

    2001-01-01

    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

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

    Science.gov (United States)

    Cammi, Roberto

    2015-11-15

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

  3. Modeling Electric Double-Layers Including Chemical Reaction Effects

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

  4. Results of the 2010 Survey on Teaching Chemical Reaction Engineering

    Science.gov (United States)

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

    2012-01-01

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

  5. Chemical reactions on solid surfaces using molecular beam techniques

    Science.gov (United States)

    Palmer, R. L.

    1980-07-01

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

  6. On the Complexity of Reconstructing Chemical Reaction Networks

    DEFF Research Database (Denmark)

    Fagerberg, Rolf; Flamm, Christoph; Merkle, Daniel

    2013-01-01

    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...

  7. 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

    2009-01-01

    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 ...

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

    Science.gov (United States)

    Lee, Chiu Fan

    2010-08-01

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

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

    Science.gov (United States)

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

    2014-06-25

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

  10. Sequential Voronoi diagram calculations using simple chemical reactions

    CERN Document Server

    Costello, Ben de Lacy; Adamatzky, Andy

    2012-01-01

    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...

  11. The effect of carbon nanotubes on chiral chemical reactions

    Science.gov (United States)

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

    2013-02-01

    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.

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

    Science.gov (United States)

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

    2014-01-01

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

  13. Asymmetric chemical reactions by polarized quantum beams

    Science.gov (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

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

    Science.gov (United States)

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

    2015-10-01

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

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

    Science.gov (United States)

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

    1989-01-01

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

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

    OpenAIRE

    Deng, Lei

    2012-01-01

    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...

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2012-05-01

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

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

    Science.gov (United States)

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

    2012-09-24

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

  20. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-10-01

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

  2. The thermodynamic natural path in chemical reaction kinetics

    Directory of Open Access Journals (Sweden)

    Moishe garfinkle

    2000-01-01

    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.

  3. Vacuum Ultraviolet Photoionization of Complex Chemical Systems

    Science.gov (United States)

    Kostko, Oleg; Bandyopadhyay, Biswajit; Ahmed, Musahid

    2016-05-01

    Tunable vacuum ultraviolet (VUV) radiation coupled to mass spectrometry is applied to the study of complex chemical systems. The identification of novel reactive intermediates and radicals is revealed in flame, pulsed photolysis, and pyrolysis reactors, leading to the elucidation of spectroscopy, reaction mechanisms, and kinetics. Mass-resolved threshold photoelectron photoion coincidence measurements provide unprecedented access to vibrationally resolved spectra of free radicals present in high-temperature reactors. Photoionization measurements in water clusters, nucleic acid base dimers, and their complexes with water provide signatures of proton transfer in hydrogen-bonded and π-stacked systems. Experimental and theoretical methods to track ion-molecule reactions and fragmentation pathways in intermolecular and intramolecular hydrogen-bonded systems in sugars and alcohols are described. Photoionization of laser-ablated molecules, clusters, and their reaction products inform thermodynamics and spectroscopy that are relevant to astrochemistry and catalysis. New directions in coupling VUV radiation to interrogate complex chemical systems are discussed.

  4. Constructing and visualizing chemical reaction networks from pi-calculus models

    OpenAIRE

    M. John; H.-J. Schulz; H. Schumann; A. M. Uhrmacher; Andrea Unger

    2013-01-01

    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...

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

    Science.gov (United States)

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

    2014-09-01

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

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

    Science.gov (United States)

    Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca

    2016-11-01

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

  7. Quantum theory of chemical reactions in the presence of electromagnetic fields

    CERN Document Server

    Tscherbul, T V

    2008-01-01

    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...

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

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov

    2000-01-01

    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....

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

    Science.gov (United States)

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

    2016-12-22

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

  10. Variable elimination in chemical reaction networks with mass-action kinetics

    DEFF Research Database (Denmark)

    Feliu, Elisenda; Wiuf, C.

    2012-01-01

    We consider chemical reaction networks taken with mass-action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop an algebraic framework and procedure for linear elimination...

  11. Duality-based calculations for transition probabilities in stochastic chemical reactions

    Science.gov (United States)

    Ohkubo, Jun

    2017-02-01

    An idea for evaluating transition probabilities in chemical reaction systems is proposed, which is efficient for repeated calculations with various rate constants. The idea is based on duality relations; instead of direct time evolutions of the original reaction system, the dual process is dealt with. Usually, if one changes rate constants of the original reaction system, the direct time evolutions should be performed again, using the new rate constants. On the other hands, only one solution of an extended dual process can be reused to calculate the transition probabilities for various rate constant cases. The idea is demonstrated in a parameter estimation problem for the Lotka-Volterra system.

  12. New Method to Acquire Chemomechanical Parameters of Diverse Chemical Reactions

    Science.gov (United States)

    2011-01-30

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

    Science.gov (United States)

    Catlow, C Richard A

    2016-08-01

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

  14. Moment equations for chemical reactions on interstellar dust grains

    CERN Document Server

    Lipshtat, A; Lipshtat, Azi; Biham, Ofer

    2003-01-01

    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...

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

    Science.gov (United States)

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

    1993-01-01

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

  16. On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

    CERN Document Server

    van der Schaft, Arjan; Jayawardhana, Bayu

    2011-01-01

    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.

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

    CERN Document Server

    Capellos, Christos

    1986-01-01

    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...

  18. Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

    Science.gov (United States)

    Wu, Emilia L

    2010-12-01

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

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

    CERN Document Server

    Sugawara, Takeshi

    2009-01-01

    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.

  20. Single-molecule chemical reactions on DNA origami

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...

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

    Science.gov (United States)

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

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

  2. 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...

  3. 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

    2010-01-01

    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...

  4. Chemical research on red pigments after adverse reactions to tattoo.

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

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

    2015-03-15

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

  6. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions

    Science.gov (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.

  7. 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)

    2004-01-01

    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.

  8. Computational Analyses of Complex Flows with Chemical Reactions

    Science.gov (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

  9. The phase transition and classification of critical points in the multistability chemical reactions

    Institute of Scientific and Technical Information of China (English)

    ChunhuaZHANG; FugenWU; ChunyanWU; FaOU

    2000-01-01

    In this paper, we study the phase transition and classification of critical points in multistability chemical reaction systems. Referring to the spirit of Landau's theory of phase transitions, this paper deals with the varied transitions and critical phenomena in multistable chemical systems. It is demonstrated that the higher the order of the multistability,the wider the variety of phase transitions will be. A classification scheme of critical points according to the stability criterion and the thermodynamic potential continuity is suggested.It is useful for us to study critical phenomena especially in the non-equilibrium systems including the multi-stable chemical ones.

  10. Laser studies of chemical reaction and collision processes

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  11. Extending Horizon of Materials Processing with Solar Furnace Solar-synthesis of raw material powders (carbides and carbonitrides) and solar-sintering of ceramic powder compacts with novel prospects of introducing unstable chemical species into the reaction system

    Energy Technology Data Exchange (ETDEWEB)

    Guerra Rosa, L.; Cruz Fernandes, J.

    2002-07-01

    Solar furnace (SF) yielding high flux of concentrated solar beam has been used for our recent trial syntheses of carbides and carbonitrides of Si and d-group transition metals and, during the course of this series of preliminary work, we encountered several intriguing phenomena which cannot be interpreted in terms of available equilibrium phase relationships. These new evidences seem to indicate still unexploited potentiality of solar furnace as novel type of chemical reactor rather than mere ecological heat source replacing traditional electric furnace. Besides these raw materials powder synthesis experiments, we have been testing also potentiality of SF a reactor for sintering oxide and non-oxide ceramic powders and found that mechanical properties of the solar-sintered specimen were comparable to those of the counterpart manufactured by traditional industrial sintering process. As such, data gathered so far implicate great potentiality of SF as new type of chemical reactor. Introduction of unstable chemical species, such as non-graphitic carbon and NH{sub 3} gas with suppressed degree of dissociation, into the reaction system might further extend the range of producible materials in the SF. Thus, some review is also give concerning recent works involving usage of unstable chemical species emerging from a group of Osaka University. (Author) 35 refs.

  12. Simulation of underexpanded supersonic jet flows with chemical reactions

    Directory of Open Access Journals (Sweden)

    Fu Debin

    2014-06-01

    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.

  13. Simulation of underexpanded supersonic jet flows with chemical reactions

    Institute of Scientific and Technical Information of China (English)

    Fu Debin; Yu Yong; Niu Qinglin

    2014-01-01

    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.

  14. 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

    2014-01-01

    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.

  15. Implementation of a vibrationally linked chemical reaction model for DSMC

    Science.gov (United States)

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

    1994-01-01

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

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

    Science.gov (United States)

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

    2013-10-28

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-05-30

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

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

    Science.gov (United States)

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

    2016-09-01

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

  19. Growth and dispersal with inertia: Hyperbolic reaction-transport systems

    Science.gov (United States)

    Méndez, Vicenç; Campos, Daniel; Horsthemke, Werner

    2014-10-01

    We investigate the behavior of five hyperbolic reaction-diffusion equations most commonly employed to describe systems of interacting organisms or reacting particles where dispersal displays inertia. We first discuss the macroscopic or mesoscopic foundation, or lack thereof, of these reaction-transport equations. This is followed by an analysis of the temporal evolution of spatially uniform states. In particular, we determine the uniform steady states of the reaction-transport systems and their stability properties. We then address the spatiotemporal behavior of pure death processes. We end with a unified treatment of the front speed for hyperbolic reaction-diffusion equations with Kolmogorov-Petrosvskii-Piskunov kinetics. In particular, we obtain an exact expression for the front speed of a general class of reaction correlated random walk systems. Our results establish that three out of the five hyperbolic reaction-transport equations provide physically acceptable models of biological and chemical systems.

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

    Science.gov (United States)

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

    2014-08-04

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

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

    Science.gov (United States)

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

    2016-07-27

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

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

    Science.gov (United States)

    Danielson, Thomas; Savara, Aditya; Hin, Celine

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

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

    Science.gov (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.

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

    Science.gov (United States)

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

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

  5. Time-resolved imaging of purely valence-electron dynamics during a chemical reaction

    DEFF Research Database (Denmark)

    Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.

    2011-01-01

    Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...

  6. Numerical aspects of modelling of coupled chemical reactions and fluid flow in sedimentary basins

    Energy Technology Data Exchange (ETDEWEB)

    Holstad, Astrid

    1998-01-01

    Simulation of coupled chemical reactions and fluid flow in porous sedimentary basins, through long time periods, is a numerical challenge. In most models available today the equations representing such a physical problem are solved as PDEs (Partial Differential Equation) where efficient time-stepping with controlled error is very difficult. The DAE (Differential Algebraic Equation) system approach is used where robust adaptive time-stepping algorithms are available in solvers. In this report mathematical and numerical models are derived for coupled chemical reactions and fluid flow. The models have several interesting properties which are discussed. The performance of code is tested. 20 refs., 6 figs., 2 tabs.

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

    Science.gov (United States)

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

    2015-01-26

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

  8. Discrete formulation of mixed finite element methods for vapor deposition chemical reaction equations

    Institute of Scientific and Technical Information of China (English)

    LUO Zhen-dong; ZHOU Yan-jie; ZHU Jiang

    2007-01-01

    The vapor deposition chemical reaction processes, which are of extremely extensive applications, can be classified as a mathematical modes by the following governing nonlinear partial differential equations containing velocity vector,temperature field,pressure field,and gas mass field.The mixed finite element(MFE)method is employed to study the system of equations for the vapor deposition chemical reaction processes.The semidiscrete and fully discrete MFE formulations are derived.And the existence and convergence(error estimate)of the semidiscrete and fully discrete MFE solutions are deposition chemical reaction processes,the numerical solutions of the velocity vector,the temperature field,the pressure field,and the gas mass field can be found out simultaneonsly.Thus,these researches are not only of important theoretical means,but also of extremely extensive applied vistas.

  9. How to do an energy balance in the PRESENCE of chemical reaction - Part 1

    OpenAIRE

    Fernandez-Torres, Maria J.

    2013-01-01

    A solved example for the determination of the increment in enthalpy for the energy balances for open systems in the context of chemical engineering is presented. The example shows how to tackle this kind of problems when it has been decided not to make use of the enthalpy of the reaction. The substances elements will be used as reference state.

  10. How to do an energy balance in the PRESENCE of chemical reaction - part 2

    OpenAIRE

    Fernandez-Torres, Maria J.

    2013-01-01

    A solved example for the determination of the increment in enthalpy for the energy balances for open systems in the context of chemical engineering is presented. The example shows how to tackle this kind of problems when it has been decided to make use of the enthalpy of the reaction.

  11. Facilitating High School Students' Use of Multiple Representations to Describe and Explain Simple Chemical Reactions

    Science.gov (United States)

    Chandrasegaran, A. L.; Treagust, David F.; Mocerino, Mauro

    2011-01-01

    This study involved the evaluation of the efficacy of a planned instructional program to facilitate understanding of the macroscopic, submicroscopic and symbolic representational systems when describing and explaining chemical reactions by sixty-five Grade 9 students in a Singapore secondary school. A two-tier multiple-choice diagnostic instrument…

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

    Science.gov (United States)

    Khaled Saifullah, C M; Rafiqul Islam, Md

    2016-10-01

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

  13. Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas.

    Science.gov (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)

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

    Science.gov (United States)

    Suleimanov, Yury V; Green, William H

    2015-09-08

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

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

    CERN Document Server

    Suleimanov, Yury V

    2015-01-01

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

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

    Science.gov (United States)

    Krishnan, Raishma; Puri, Sanjay

    2015-11-01

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

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

    Science.gov (United States)

    Soliman, Sylvain

    2013-11-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Kustova, Elena V. [Department of Mathematics and Mechanics, Saint Petersburg State University, 198504 Universitetskiy pr., 28, Saint Petersburg (Russian Federation); Kremer, Gilberto M. [Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba (Brazil)

    2014-12-09

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

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

    Science.gov (United States)

    Kustova, Elena V.; Kremer, Gilberto M.

    2014-12-01

    In this work chemically reacting mixtures of viscous flows are analyzed within the framework of Boltzmann equation. By applying a modified Chapman-Enskog method to the system of Boltzmann equations general expressions for the rates of chemical reactions and vibrational energy transitions are determined as functions of two thermodynamic forces: the velocity divergence and the affinity. As an application chemically reacting mixtures of N2 across a shock wave are studied, where the first lowest vibrational states are taken into account. Here we consider only the contributions from the first four single quantum vibrational-translational energy transitions. It is shown that the contribution to the chemical reaction rate related to the affinity is much larger than that of the velocity divergence.

  1. Thermal energy storage. [by means of chemical reactions

    Science.gov (United States)

    Grodzka, P. G.

    1975-01-01

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

  2. A quantum informational approach for dissecting chemical reactions

    CERN Document Server

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

    2014-01-01

    We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected which allows us to monitor the interplay of back-bonding and $\\pi$-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.

  3. The precise condition of thermal runaway in microwave heating on chemical reaction

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The precise condition of thermal runaway in microwave heating on chemical reaction with a feedback control system is quantitatively studied. First, the precise condition of thermal runaway in engineering application is derived based on the principle of the feedback control system. Then, the temperature rising rates for 4 different kinds of reaction systems placed in the waveguide and irradiated by micro-wave with different input powers are simulated. Finally, the relationship, which is inattentive so far, between the thermal runaway and the sensor’s response time is discussed.

  4. The precise condition of thermal runaway in microwave heating on chemical reaction

    Institute of Scientific and Technical Information of China (English)

    HUANG KaMa; LU Bo

    2009-01-01

    The precise condition of thermal runaway in microwave heating on chemical reaction with a feedback control system is quantitatively studied. First, the precise condition of thermal runaway in engineering application is derived based on the principle of the feedback control system. Then, the temperature rising rates for 4 different kinds of reaction systems placed in the waveguide and irradiated by micro-wave with different input powers are simulated. Finally, the relationship, which is inattentive so far, between the thermal runaway and the sensor's response time is discussed.

  5. Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

    KAUST Repository

    Klingbeil, Guido

    2012-02-01

    We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system\\'s size. © 2006 IEEE.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gammelsaeter, H.R.

    1997-12-31

    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.

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

    Science.gov (United States)

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

    2016-01-22

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

  8. Reaction kinetics of fluorite in flow systems and surface chemistry

    Institute of Scientific and Technical Information of China (English)

    张荣华; 胡书敏

    1996-01-01

    The kinetic experiments of fluorite in water-HCl solution in an open-flow system at the temperatures ≤100℃ reveal that the variation of flow rate (U) can change the reaction rate orders from 0 to 2 or higher. In the far from equilibrium systems, the dissolution rates of fluorite in aqueous solutions have a zero order.The reaction rates are controlled by pH values of input solutions. In fact, the reaction rates are related to the concentrations of the active sites occupied by H+ on fluorite surface [SOH]. X-ray photospectroscopy observations on fluorite surface before and after reaction indicate that surface chemical processes control the reaction rates: Cl- cations attach on and enter into surface of fluorite besides H+ when fluorites react with HCl solutions, which affect the reaction rates.

  9. Galactic disks as reaction-diffusion systems

    CERN Document Server

    Smolin, L

    1996-01-01

    A model of a galactic disk is presented which extends the homogeneous one zone models by incorporating propagation of material and energy in the disk. For reasonable values of the parameters the homogeneous steady state is unstable to the development of inhomogeneities, leading to the development of spatial and temporal structure. At the linearized level a prediction for the length and time scales of the patterns is found. These instabilities arise for the same reason that pattern formation is seen in non-equilibrium chemical and biological systems, which is that the positive and negative feedback effects which govern the rates of the critical processes act over different distance scales, as in Turing's reaction-diffusion models. This shows that patterns would form in the disk even in the absence of gravitational effects, density waves, rotation, shear and external perturbations. These nonlinear effects may thus explain the spiral structure seen in the star forming regions of isolated flocculent galaxies.

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

    Science.gov (United States)

    Brogioli, Doriano

    2013-02-07

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  12. Chemical reactions modulated by mechanical stress: extended Bell theory.

    Science.gov (United States)

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

    2011-10-28

    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.

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

    Science.gov (United States)

    Buchachenko, Anatoly; Lawler, Ronald G

    2017-02-20

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

  14. Motif analysis for small-number effects in chemical reaction dynamics.

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-07

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  15. Motif analysis for small-number effects in chemical reaction dynamics

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-01

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  16. Thermodynamic Branch in the Chemical System Response to External Impact

    CERN Document Server

    Zilbergleyt, B

    2012-01-01

    The paper gives an account of a detailed investigation of the thermodynamic branch as a path of the chemical system deviation from its isolated thermodynamic equilibrium under an external impact. For a combination of direct and reverse reactions in the same chemical system, full thermodynamic branch is presented by an S-shaped curve, whose ends asymptotically achieve appropriate initial states, which, in turn, are logistic ends of the opposite reactions. The slope tangents of the steepest parts of the curves, the areas of the maximum rate of the shift growth vs. the external thermodynamic force, occurred to be directly proportional to the force and, simultaneously, linearly proportional to the thermodynamic equivalent of chemical reaction, which is the ratio between the amount in moles of any reaction participant, transformed in an isolated system, along the reaction way from its initial state to thermodynamic equilibrium, to its stoichiometric coefficient. The found linearity is valid for arbitrary combinati...

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

    Science.gov (United States)

    Gokoglu, Suleyman A.

    1988-01-01

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

  18. Nanoscale wear as a stress-assisted chemical reaction.

    Science.gov (United States)

    Jacobs, Tevis D B; Carpick, Robert W

    2013-02-01

    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.

  19. Computational singular perturbation analysis of stochastic chemical systems with stiffness

    Science.gov (United States)

    Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; Najm, Habib N.

    2017-04-01

    Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to not only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. The algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.

  20. The quantum dynamics of electronically nonadiabatic chemical reactions

    Science.gov (United States)

    Truhlar, Donald G.

    1993-01-01

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

  1. 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

    1997-01-01

    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.

  2. Numerical simulation of the interaction of transport, diffusion and chemical reactions in an urban plume

    Science.gov (United States)

    Vogel, Bernhard; Vogel, Heike; Fiedler, Franz

    1994-01-01

    A model system is presented that takes into account the main physical and chemical processes on the regional scale here in an area of 100x100 sq km. The horizontal gridsize used is 2x2 sq km. For a case study, it is demonstrated how the model system can be used to separate the contributions of the processes advection, turbulent diffusion, and chemical reactions to the diurnal cycle of ozone. In this way, typical features which are visible in observations and are reproduced by the numerical simulations can be interpreted.

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

    Directory of Open Access Journals (Sweden)

    Yu Angyang

    2015-06-01

    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.

  4. Theory for Diffusion-Limited Oscillating Chemical Reactions

    CERN Document Server

    Bussemaker, H J

    1997-01-01

    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.

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

    Science.gov (United States)

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

    1993-01-01

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

  6. Mass transfer in porous media with heterogeneous chemical reaction

    Directory of Open Access Journals (Sweden)

    Souza S.M.A.G.Ulson de

    2003-01-01

    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.

  7. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    Energy Technology Data Exchange (ETDEWEB)

    Ziaul Huque

    2007-08-31

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

  8. Bayesian inference of chemical kinetic models from proposed reactions

    KAUST Repository

    Galagali, Nikhil

    2015-02-01

    © 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.

  9. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

    Science.gov (United States)

    Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

    2015-11-12

    High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

  10. Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy

    Science.gov (United States)

    Piccini, GiovanniMaria; Alessio, Maristella

    2016-01-01

    Abstract The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude). PMID:27008460

  11. 微博与大学生思想政治教育间的化学反应体系%The Chemical Reaction System between Micro-blog and Ideological and Political Education of College Students

    Institute of Scientific and Technical Information of China (English)

    陈强

    2015-01-01

    “微”时代的潮流下,通过微博将现实中的客观存在、主观情感等信息投影到网络上,向周边辐射、影响、传播,形成一种类似化学反应式的传播体系,对当代大学生的思想政治教育产生深刻的影响。本文在化学反应式传播体系的反应方式和特点的基础上,提出了思政工作者积极利用该化学反应式体系思维方式开展思政教育的途径。%Under the trend of 'micro-era', the communication system of chemical reaction type is created by the radiation, influence, com-munication of information that included objective existence of reality and subjective emotion , which has a profound impact on the ideo-logical and political education of contemporary college students. The article states the responses and characteristics of this system, on this basis, offers some suitable ways using actively this type of thinking for ideological and political workers to carry out ideological and politi-cal education .

  12. Effect of Coriolis coupling in chemical reaction dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Han, Ke-Li

    2008-05-14

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

  13. A semiclassical non-adiabatic theory for elementary chemical reactions

    CERN Document Server

    Aubry, Serge

    2014-01-01

    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 ...

  14. From Steam Engines to Chemical Reactions: Gibbs’ Contribution to the Extension of the Second Law

    Directory of Open Access Journals (Sweden)

    Emilio Marco Pellegrino

    2016-04-01

    Full Text Available The present work analyzes the foundations of Gibbs’ thermodynamic equilibrium theory, with the general aim of understanding how the Second Law—as formulated by Clausius in 1865—has been embodied into Gibbs’ formal system and extended to processes involving chemical reactions. We show that Gibbs’ principle of maximal entropy (and minimal energy is the implicit expression of Clausius’ Second Law. In addition, by making explicit some implicit passages of Gibbs logical path, we provide an original formal justification of Gibbs’ principle. Finally we provide an analysis of how Gibbs’ principle—conceived for homogeneous isolated systems with fixed chemical composition—has come to be applied to systems entailing chemical transformations.

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

    Science.gov (United States)

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

    2004-01-01

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

  16. SYSTEMIC TOXIC REACTIONS TO LOCAL ANESTHETICS

    Science.gov (United States)

    Moore, Daniel C.; Green, John

    1956-01-01

    The topical use of anesthetic agents involves an element of risk. Systemic toxic reactions are rare, but they do occur and may result in death. When a reaction occurs from a topical application, it usually progresses rapidly to respiratory and cardiovascular collapse, and thus therapy must be instituted with more haste to avoid deaths. Fatal systemic toxic reactions from topically administered anesthetic drugs are, in effect, usually not due to well informed use of the drug but to misuse owing to less than complete understanding of absorption. Emphasis is placed on the causes, prophylaxis and treatment of severe systemic toxic reactions which follow the topical application of local anesthetic drugs. If systemic toxic reactions resulting from a safe dose of a local anesthetic agent are correctly treated, there will usually follow an uneventful recovery rather than a catastrophe. PMID:13343009

  17. Closed loop chemical systems for energy storage and transmission (chemical heat pipe). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Vakil, H.B.; Flock, J.W.

    1978-02-01

    The work documents the anlaysis of closed loop chemical systems for energy storage and transmission, commonly referred to as the Chemical Heat Pipe (CHP). Among the various chemical reaction systems and sources investigated, the two best systems were determined to be the high temperature methane/steam reforming reaction (HTCHP) coupled to a Very High Temperature Gas Cooled Reactor (VHTR) and the lower temperature, cyclohexane dehydrogenation reaction (LTCHP) coupled to existing sources such as coal or light water reactors. Solar and other developing technologies can best be coupled to the LTCHP. The preliminary economic and technical analyses show that both systems could transport heat at an incremental cost of approximately $1.50/GJ/160 km (in excess of the primary heat cost of $2.50/GJ), at system efficiencies above 80%. Solar heat can be transported at an incremental cost of $3/GJ/160 km. The use of the mixed feed evaporator concept developed in this work contributes significantly to reducing the transportation cost and increasing the efficiency of the system. The LTCHP shows the most promise of the two systems if the technical feasibility of the cyclic closed loop chemical reaction system can be established. An experimental program for establishing this feasibility is recommended. Since the VHTR is several years away from commercial demonstration and the HTCHP chemical technology is well developed, future HTCHP programs should be aimed at VHTR and interface problems.

  18. A new halogen-free chemical oscillator: the reaction between permanganate ion and ninhydrin in a continuously stirred tank reactor

    Science.gov (United States)

    Treindl, Ľudovít; Nagy, Arpád

    1987-07-01

    The reaction between permanganate ion and ninhydrin in the presence of phosphoric acid in aqueous solution shows sustained oscillations in a continuously stirred tank reactor (CSTR). It exhibits a kinetic bistability between an oscillatory and a stationary state. Our new oscillating system seems to be a second permanganate chemical oscillator, thus broadening the small group of non-halogen-based chemical oscillators.

  19. Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

    Science.gov (United States)

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

    1994-01-01

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

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

    Science.gov (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)

  1. 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

    2007-01-01

    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.

  2. Acceleration of convective dissolution by chemical reaction in a Hele-Shaw cell.

    Science.gov (United States)

    Cherezov, Ilia; Cardoso, Silvana S S

    2016-09-14

    New laboratory experiments quantify the destabilising effect of a second-order chemical reaction on the fingering instability of a diffusive boundary layer in a Hele-Shaw cell. We show that, for a given chemical system, the dynamics of such a reactive boundary layer is fully determined by two dimensionless groups, Da/Ra(2), which measures the timescale for convection compared to those for reaction and diffusion, and CBo', which reflects the excess of the environmental reactant species relative to the diffusing solute. Results of a systematic study varying CBo' in the range 0-0.1 are presented. It is shown that the chemical reaction increases the growth rate of a perturbation and favours small wavelengths compared to the inert system. A higher concentration of CBo' not only accelerates the onset of convection, but crucially also increases the transport of the solute by up to 150% compared to the inert system. This increase in solute transfer has important practical implications, such as in the storage of carbon dioxide in saline aquifers.

  3. Unsteady Bioconvection Squeezing Flow in a Horizontal Channel with Chemical Reaction and Magnetic Field Effects

    Directory of Open Access Journals (Sweden)

    Qingkai Zhao

    2017-01-01

    Full Text Available The time-dependent mixed bioconvection flow of an electrically conducting fluid between two infinite parallel plates in the presence of a magnetic field and a first-order chemical reaction is investigated. The fully coupled nonlinear systems describing the total mass, momentum, thermal energy, mass diffusion, and microorganisms equations are reduced to a set of ordinary differential equations via a set of new similarity transformations. The detailed analysis illustrating the influences of various physical parameters such as the magnetic, squeezing, and chemical reaction parameters and the Schmidt and Prandtl numbers on the distributions of temperature and microorganisms as well as the skin friction and the Nusselt number is presented. The conclusion is drawn that the flow field, temperature, and chemical reaction profiles are significantly influenced by magnetic parameter, heat generation/absorption parameter, and chemical parameter. Some examples of potential applications of such bioconvection could be found in pharmaceutical industry, microfluidic devices, microbial enhanced oil recovery, modeling oil, and gas-bearing sedimentary basins.

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

    Science.gov (United States)

    Drogowska, Karolina; Kovaříček, Petr; Kalbáč, Martin

    2017-03-23

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

  5. A thermodynamical framework for chemically reacting systems

    Science.gov (United States)

    Kannan, K.; Rajagopal, K. R.

    2011-04-01

    In this paper, we develop a thermodynamic framework that is capable of describing the response of viscoelastic materials that are undergoing chemical reactions that takes into account stoichiometry. Of course, as a special sub-case, we can also describe the response of elastic materials that undergo chemical reactions. The study generalizes the framework developed by Rajagopal and co-workers to study the response of a disparate class of bodies undergoing entropy producing processes. One of the quintessential feature of this framework is that the second law of thermodynamics is formulated by introducing Gibbs' potential, which is the natural way to study problems involving chemical reactions. The Gibbs potential-based formulation also naturally leads to implicit constitutive equations for the stress tensor. Another feature of the framework is that the constraints due to stoichiometry can also be taken into account in a consistent manner. The assumption of maximization of the rate of entropy production due to dissipation, heat conduction, and chemical reactions is invoked to determine an equation for the evolution of the natural configuration κ p( t)( B), the heat flux vector and a novel set of equations for the evolution of the concentration of the chemical constituents. To determine the efficacy of the framework with regard to chemical reactions, those occurring during vulcanization, a challenging set of chemical reactions, are chosen. More than one type of reaction mechanism is considered and the theoretically predicted distribution of mono, di and polysulfidic cross-links agree reasonably well with available experimental data.

  6. Chemically Assisted Photocatalytic Oxidation System

    Science.gov (United States)

    Andino, Jean; Wu, Chang-Yu; Mazyck, David; Teixeira, Arthur A.

    2009-01-01

    The chemically assisted photocatalytic oxidation system (CAPOS) has been proposed for destroying microorganisms and organic chemicals that may be suspended in the air or present on surfaces of an air-handling system that ventilates an indoor environment. The CAPOS would comprise an upstream and a downstream stage that would implement a tandem combination of two partly redundant treatments. In the upstream stage, the air stream and, optionally, surfaces of the air-handling system would be treated with ozone, which would be generated from oxygen in the air by means of an electrical discharge or ultraviolet light. In the second stage, the air laden with ozone and oxidation products from the first stage would be made to flow in contact with a silica-titania photocatalyst exposed to ultraviolet light in the presence of water vapor. Hydroxyl radicals generated by the photocatalytic action would react with both carbon containing chemicals and microorganisms to eventually produce water and carbon dioxide, and ozone from the first stage would be photocatalytically degraded to O2. The net products of the two-stage treatment would be H2O, CO2, and O2.

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

    Science.gov (United States)

    Cordes, Thorben; Blum, Suzanne A

    2013-12-01

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

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

    Science.gov (United States)

    Cordes, Thorben; Blum, Suzanne A.

    2013-12-01

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

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

    Science.gov (United States)

    Maeda, Satoshi; Ohno, Koichi; Morokuma, Keiji

    2013-03-21

    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.

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

    Science.gov (United States)

    Barik, Swarup; Dalal, D. C.

    2016-10-01

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

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

    Science.gov (United States)

    Treiman, A. H.

    2013-12-01

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

  12. Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach.

    Science.gov (United States)

    van Roekel, Hendrik W H; Rosier, Bas J H M; Meijer, Lenny H H; Hilbers, Peter A J; Markvoort, Albert J; Huck, Wilhelm T S; de Greef, Tom F A

    2015-11-07

    Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

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

    Science.gov (United States)

    Vorotilin, V. P.

    2017-01-01

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

  14. Reactions of small molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Wittig, C. [Univ. of Southern California, Los Angeles, CA (United States)

    1993-12-01

    This DOE program remains focused on small molecular systems relevant to combustion. Though a number of experimental approaches and machines are available for this research, the authors` activities are centered around the high-n Rydberg time-of-flight (HRTOF) apparatus in this laboratory. One student and one postdoc carry out experiments with this machine and also engage in small intra-group collaborations involving shared equipment. This past year was more productive than the previous two, due to the uninterrupted operation of the HRTOF apparatus. Results were obtained with CH{sub 3}OH, CH{sub 3}SH, Rg-HX complexes, HCOOH, and their deuterated analogs where appropriate. One paper is in print, three have been accepted for publication, and one is under review. Many preliminary results that augur well for the future were obtained with other systems such as HNO{sub 3}, HBr-HI complexes, toluene, etc. Highlights from the past year are presented below that display some of the features of this program.

  15. Parametric spatiotemporal oscillation in reaction-diffusion systems.

    Science.gov (United States)

    Ghosh, Shyamolina; Ray, Deb Shankar

    2016-03-01

    We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

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

    Science.gov (United States)

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

    2017-01-01

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

  17. Chemical reaction path modeling of hydrothermal processes on Mars: Preliminary results

    Science.gov (United States)

    Plumlee, Geoffrey S.; Ridley, W. Ian

    1992-01-01

    Hydrothermal processes are thought to have had significant roles in the development of surficial mineralogies and morphological features on Mars. For example, a significant proportion of the Martian soil could consist of the erosional products of hydrothermally altered impact melt sheets. In this model, impact-driven, vapor-dominated hydrothermal systems hydrothermally altered the surrounding rocks and transported volatiles such as S and Cl to the surface. Further support for impact-driven hydrothermal alteration on Mars was provided by studies of the Ries crater, Germany, where suevite deposits were extensively altered to montmorillonite clays by inferred low-temperature (100-130 C) hydrothermal fluids. It was also suggested that surface outflow from both impact-driven and volcano-driven hydrothermal systems could generate the valley networks, thereby eliminating the need for an early warm wet climate. We use computer-driven chemical reaction path calculation to model chemical processes which were likely associated with postulated Martian hydrothermal systems.

  18. Modeling Complex Chemical Systems: Problems and Solutions

    Science.gov (United States)

    van Dijk, Jan

    2016-09-01

    Non-equilibrium plasmas in complex gas mixtures are at the heart of numerous contemporary technologies. They typically contain dozens to hundreds of species, involved in hundreds to thousands of reactions. Chemists and physicists have always been interested in what are now called chemical reduction techniques (CRT's). The idea of such CRT's is that they reduce the number of species that need to be considered explicitly without compromising the validity of the model. This is usually achieved on the basis of an analysis of the reaction time scales of the system under study, which identifies species that are in partial equilibrium after a given time span. The first such CRT that has been widely used in plasma physics was developed in the 1960's and resulted in the concept of effective ionization and recombination rates. It was later generalized to systems in which multiple levels are effected by transport. In recent years there has been a renewed interest in tools for chemical reduction and reaction pathway analysis. An example of the latter is the PumpKin tool. Another trend is that techniques that have previously been developed in other fields of science are adapted as to be able to handle the plasma state of matter. Examples are the Intrinsic Low Dimension Manifold (ILDM) method and its derivatives, which originate from combustion engineering, and the general-purpose Principle Component Analysis (PCA) technique. In this contribution we will provide an overview of the most common reduction techniques, then critically assess the pros and cons of the methods that have gained most popularity in recent years. Examples will be provided for plasmas in argon and carbon dioxide.

  19. Probing isotope effects in chemical reactions using single ions

    CERN Document Server

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

    2008-01-01

    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.

  20. Moment estimation for chemically reacting systems by extended Kalman filtering

    NARCIS (Netherlands)

    Ruess, J; Milias-Argeitis, A; Summers, S; Lygeros, J

    2011-01-01

    In stochastic models of chemically reacting systems that contain bimolecular reactions, the dynamics of the moments of order up to n of the species populations do not form a closed system, in the sense that their time-derivatives depend on moments of order n + 1. To close the dynamics, the moments o

  1. 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

    2016-04-01

    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.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...

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

    Science.gov (United States)

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

    2011-06-01

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

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

    Science.gov (United States)

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

    2015-04-14

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

  5. Self-similar fast-reaction limits for reaction-diffusion systems on unbounded domains

    Science.gov (United States)

    Crooks, E. C. M.; Hilhorst, D.

    2016-08-01

    We present a unified approach to characterising fast-reaction limits of systems of either two reaction-diffusion equations, or one reaction-diffusion equation and one ordinary differential equation, on unbounded domains, motivated by models of fast chemical reactions where either one or both reactant(s) is/are mobile. For appropriate initial data, solutions of four classes of problems each converge in the fast-reaction limit k → ∞ to a self-similar limit profile that has one of four forms, depending on how many components diffuse and whether the spatial domain is a half or whole line. For fixed k, long-time convergence to these same self-similar profiles is also established, thanks to a scaling argument of Kamin. Our results generalise earlier work of Hilhorst, van der Hout and Peletier to a much wider class of problems, and provide a quantitative description of the penetration of one substance into another in both the fast-reaction and long-time regimes.

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

    Science.gov (United States)

    Leonard, Andy D.; Hill, James C.

    1992-01-01

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

  7. Effects of gel properties produced by chemical reactions on viscous fingering

    Science.gov (United States)

    Ujiie, Tomohiro; Nagatsu, Yuichiro; Ban, Mitsumasa; Iwata, Shuichi; Kato, Yoshihito; Tada, Yutaka

    2011-11-01

    We have experimentally investigated viscous fingering with chemical reaction producing gel. Here, two systems were employed. In one system, sodium polyacrylate (SPA) solution and ferric ion solution were used as the more and less viscous liquids, respectively. In another system, xthantan gum (XG) solution and the ferric ion solution were used as the more and less viscous liquids, respectively. For high concentration of ferric ion, viscous fingering pattern was changed into spiral pattern in the former system, whereas into fracture pattern in the latter system. We consider that the difference in the change of the patterns in the two systems will be caused by the difference in the properties of the gels. Therefore, we have measured the rheological properties of the gels by means of a rheometer. We have found that the gel in the former case is more elastic. Furthermore, we have discussed the relationship between the measured rheological properties and the observed spiral or fracturing patterns.

  8. Coupling sample paths to the partial thermodynamic limit in stochastic chemical reaction networks

    CERN Document Server

    Levien, Ethan

    2016-01-01

    We present a new technique for reducing the variance in Monte Carlo estimators of stochastic chemical reaction networks. Our method makes use of the fact that many stochastic reaction networks converge to piecewise deterministic Markov processes in the large system-size limit. The statistics of the piecewise deterministic process can be obtained much more efficiently than those of the exact process. By coupling sample paths of the exact model to the piecewise deterministic process we are able to reduce the variance, and hence the computational complexity of the Monte Carlo estimator. In addition to rigorous results concerning the asymptotic behavior of our method, numerical simulations are performed on some simple biological models suggesting that significant computational gains are made for even moderate system-sizes.

  9. Method of operating a thermal engine powered by a chemical reaction

    Science.gov (United States)

    Ross, J.; Escher, C.

    1988-06-07

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

  10. 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)

    2010-02-01

    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.

  11. Method of operating a thermal engine powered by a chemical reaction

    Science.gov (United States)

    Ross, John; Escher, Claus

    1988-01-01

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

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

    Science.gov (United States)

    Kadioglu, Cansel; Uzuntiryaki, Esen

    2008-01-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

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

    Science.gov (United States)

    Weinrich, M. L.; Talanquer, V.

    2015-01-01

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

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

    Science.gov (United States)

    Goodney, David E.

    2006-01-01

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

  16. Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension.

    Science.gov (United States)

    Greene, Samuel M; Shan, Xiao; Clary, David C

    2016-06-28

    Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives are obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.

  17. 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

    2006-01-01

    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.

  18. Chemical Pattern Formation in Far-From Systems.

    Science.gov (United States)

    Pearson, John Evan

    The diffusive instability was proposed as a mechanism for pattern formation in chemical systems, in the context of biological morphogenesis, by Alan Turing in 1952. The instability gives rise to a chemical pattern with an intrinsic "chemical wavelength" that is independent of the system size. Since 1952, the diffusive instability, or Turing bifurcation, has been invoked to explain pattern formation in a variety of fields. To date there has been no unambiguous observation of such an instability. Model studies of the instability are usually carried out on systems containing two variables. Such works do not address issues that are of fundamental importance in experimental studies. How does one go about finding Turing bifurcations in systems with many parameters and for which the chemical kinetics are only partially known? What is the chemical wavelength? Turing bifurcations cannot occur in systems with all diffusion coefficients exactly equal. How unequal must the diffusion coefficients be for a system to undergo a Turing bifurcation?. Reacting and diffusing systems obey a partial -differential equation which is a sum of a diffusion term and a reaction term. Dropping the diffusion term results in an ordinary differential equation describing the reaction kinetics in a well-mixed system. In this dissertation it is shown that, for systems with an arbitrary number of variables, Turing bifurcations can occur with diffusion coefficients arbitrarily close to equal, provided the corresponding well-mixed system is sufficiently close to a point of coalescence of Hopf and saddle-node bifurcations. Since the bifurcation set can be obtained directly from experiments, one does not need a detailed microscopic theory of the reaction kinetics. Similarly, the chemical wavelength can be estimated from experimental measurements without knowledge of the reaction kinetics.

  19. Systemic allergic reaction to pine nuts.

    Science.gov (United States)

    Nielsen, N H

    1990-02-01

    This case report describes a systemic reaction due to ingestion of pine nuts, confirmed by an open, oral provocation test. Skin prick testing with the aqueous allergen revealed an immediate positive prick test, and histamine release from basophil leukocytes to the aqueous allergen was demonstrated. Radioallergosorbent test demonstrated specific IgE antibodies to pine nuts. In a review of medical literature, we found no reports of either oral provocation tests confirming a systemic reaction due to ingestion of pine nuts or demonstration of specific IgE antibodies.

  20. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions.

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  1. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B.

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

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

    Science.gov (United States)

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

    2016-01-01

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

  3. Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

    Science.gov (United States)

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

    1994-01-01

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

  4. Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: controlling single E-coli β-galactosidase enzyme catalysis through the elementary reaction steps.

    Science.gov (United States)

    Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

    2013-12-28

    In this work, we develop an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the elementary reaction propensities. The method is akin to the microscopic formulation of the dissipation function in terms of the Kullback-Leibler distance of phase space trajectories in Hamiltonian system. The formalism is applied to a single oligomeric enzyme kinetics at chemiostatic condition that leads the reaction system to a nonequilibrium steady state, characterized by a positive total entropy production rate. Analytical expressions are derived, relating the individual reaction contributions towards the total entropy production rate with experimentally measurable reaction velocity. Taking a real case of Escherichia coli β-galactosidase enzyme obeying Michaelis-Menten kinetics, we thoroughly analyze the temporal as well as the steady state behavior of various thermodynamic quantities for each elementary reaction. This gives a useful insight in the relative magnitudes of various energy terms and the dissipated heat to sustain a steady state of the reaction system operating far-from-equilibrium. It is also observed that, the reaction is entropy-driven at low substrate concentration and becomes energy-driven as the substrate concentration rises.

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

    DEFF Research Database (Denmark)

    Petrunin, Victor V.

    2011-01-01

    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....

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

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    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.

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

    OpenAIRE

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

    2004-01-01

    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...

  8. Chemical Tracking Systems: Not Your Usual Global Positioning System!

    Science.gov (United States)

    Roy, Ken

    2007-01-01

    The haphazard storing and tracking of chemicals in the laboratory is a serious safety issue facing science teachers. To get control of your chemicals, try implementing a "chemical tracking system". A chemical tracking system (CTS) is a database of chemicals used in the laboratory. If implemented correctly, a CTS will reduce purchasing costs,…

  9. A weak comparison principle for reaction-diffusion systems

    CERN Document Server

    Valero, José

    2012-01-01

    In this paper we prove a weak comparison principle for a reaction-diffusion system without uniqueness of solutions. We apply the abstract results to the Lotka-Volterra system with diffusion, a generalized logistic equation and to a model of fractional-order chemical autocatalysis with decay. Morever, in the case of the Lotka-Volterra system a weak maximum principle is given, and a suitable estimate in the space of essentially bounded functions $L^{\\infty}$ is proved for at least one solution of the problem.

  10. A Weak Comparison Principle for Reaction-Diffusion Systems

    Directory of Open Access Journals (Sweden)

    José Valero

    2012-01-01

    Full Text Available We prove a weak comparison principle for a reaction-diffusion system without uniqueness of solutions. We apply the abstract results to the Lotka-Volterra system with diffusion, a generalized logistic equation, and to a model of fractional-order chemical autocatalysis with decay. Moreover, in the case of the Lotka-Volterra system a weak maximum principle is given, and a suitable estimate in the space of essentially bounded functions L∞ is proved for at least one solution of the problem.

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

    Science.gov (United States)

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

    2016-04-27

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

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

    Science.gov (United States)

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

    2016-04-01

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

  13. Harmonic versus subharmonic patterns in a spatially forced oscillating chemical reaction.

    Science.gov (United States)

    Hammele, Martin; Zimmermann, Walter

    2006-06-01

    The effects of a spatially periodic forcing on an oscillating chemical reaction as described by the Lengyel-Epstein model are investigated. We find a surprising competition between two oscillating patterns, where one is harmonic and the other subharmonic with respect to the spatially periodic forcing. The occurrence of a subharmonic pattern is remarkable as well as its preference up to rather large values of the modulation amplitude. For small modulation amplitudes we derive from the model system a generic equation for the envelope of the oscillating reaction that includes an additional forcing contribution, compared to the amplitude equations known from previous studies in other systems. The analysis of this amplitude equation allows the derivation of analytical expressions even for the forcing corrections to the threshold and to the oscillation frequency, which are in a wide range of parameters in good agreement with the numerical analysis of the complete reaction equations. In the nonlinear regime beyond threshold, the subharmonic solutions exist in a finite range of the control parameter that has been determined by solving the reaction equations numerically for various sets of parameters.

  14. Chemical reactions induced by oscillating external fields in weak thermal environments

    CERN Document Server

    Craven, Galen T; Hernandez, Rigoberto

    2015-01-01

    Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally varying external field, the transition state that the reaction must pass through during the transformation from reactant to product is no longer a fixed geometric structure, but is instead time-dependent. For a periodically forced model reaction, we develop a recrossing-free dividing surface that is attached to a transition state trajectory [T. Bartsch, R. Hernandez, and T. Uzer, Phys. Rev. Lett. 95, 058301 (2005)]. We have previously shown that for single-mode sinusoidal driving, the stability of the time-varying transition state directly determines the reaction rate [G. T. Craven, T. Bartsch, and R. Hernandez, J. Chem. Phys. 141, 041106 (2014)]. Here, we extend our previous work to the case of multi-mode driving waveforms. Excellent agreement is observed between the rates pred...

  15. Heat and mass transfer in unsteady rotating fluid flow with binary chemical reaction and activation energy.

    Directory of Open Access Journals (Sweden)

    Faiz G Awad

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

  16. A finite difference method for estimating second order parameter sensitivities of discrete stochastic chemical reaction networks.

    Science.gov (United States)

    Wolf, Elizabeth Skubak; Anderson, David F

    2012-12-14

    We present an efficient finite difference method for the approximation of second derivatives, with respect to system parameters, of expectations for a class of discrete stochastic chemical reaction networks. The method uses a coupling of the perturbed processes that yields a much lower variance than existing methods, thereby drastically lowering the computational complexity required to solve a given problem. Further, the method is simple to implement and will also prove useful in any setting in which continuous time Markov chains are used to model dynamics, such as population processes. We expect the new method to be useful in the context of optimization algorithms that require knowledge of the Hessian.

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

    Science.gov (United States)

    Bell, John T.; Fogler, H. Scott

    1996-01-01

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

  18. Saponification reaction system: a detailed mass transfer coefficient determination.

    Science.gov (United States)

    Pečar, Darja; Goršek, Andreja

    2015-01-01

    The saponification of an aromatic ester with an aqueous sodium hydroxide was studied within a heterogeneous reaction medium in order to determine the overall kinetics of the selected system. The extended thermo-kinetic model was developed compared to the previously used simple one. The reaction rate within a heterogeneous liquid-liquid system incorporates a chemical kinetics term as well as mass transfer between both phases. Chemical rate constant was obtained from experiments within a homogeneous medium, whilst the mass-transfer coefficient was determined separately. The measured thermal profiles were then the bases for determining the overall reaction-rate. This study presents the development of an extended kinetic model for considering mass transfer regarding the saponification of ethyl benzoate with sodium hydroxide within a heterogeneous reaction medium. The time-dependences are presented for the mass transfer coefficient and the interfacial areas at different heterogeneous stages and temperatures. The results indicated an important role of reliable kinetic model, as significant difference in k(L)a product was obtained with extended and simple approach.

  19. Effects of Surfactants on the Rate of Chemical Reactions

    Directory of Open Access Journals (Sweden)

    B. Samiey

    2014-01-01

    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.

  20. ENGINEERED BARRIER SYSTEM: PHYSICAL AND CHEMICAL ENVIRONMENT

    Energy Technology Data Exchange (ETDEWEB)

    R. Jarek

    2005-08-29

    The purpose of this model report is to describe the evolution of the physical and chemical environmental conditions within the waste emplacement drifts of the repository, including the drip shield and waste package surfaces. The resulting seepage evaporation and gas abstraction models are used in the total system performance assessment for the license application (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. This report develops and documents a set of abstraction-level models that describe the engineered barrier system physical and chemical environment. Where possible, these models use information directly from other reports as input, which promotes integration among process models used for TSPA-LA. Specific tasks and activities of modeling the physical and chemical environment are included in ''Technical Work Plan for: Near-Field Environment and Transport In-Drift Geochemistry Model Report Integration'' (BSC 2005 [DIRS 173782], Section 1.2.2). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system reports. To be consistent with other project documents that address features, events, and processes (FEPs), Table 6.14.1 of the current report includes updates to FEP numbers and FEP subjects for two FEPs identified in the technical work plan (TWP) governing this report (BSC 2005 [DIRS 173782]). FEP 2.1.09.06.0A (Reduction-oxidation potential in EBS), as listed in Table 2 of the TWP (BSC 2005 [DIRS 173782]), has been updated in the current report to FEP 2.1.09.06.0B (Reduction-oxidation potential in Drifts; see Table 6.14-1). FEP 2.1.09.07.0A (Reaction kinetics in EBS), as listed in Table 2 of the TWP (BSC 2005 [DIRS 173782]), has been updated in the current report to FEP 2.1.09.07.0B (Reaction kinetics in Drifts; see Table 6.14-1). These deviations from the TWP are justified because they improve integration with FEPs

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

    Science.gov (United States)

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

    2016-09-12

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

  2. Cutaneous reactions in nuclear, biological and chemical warfare

    Directory of Open Access Journals (Sweden)

    Arora Sandeep

    2005-03-01

    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.

  3. Effects of Chemical Reaction on Dissipative Radiative MHD Flow through a Porous Medium over a Nonisothermal Stretching Sheet

    Directory of Open Access Journals (Sweden)

    S. Mohammed Ibrahim

    2014-01-01

    Full Text Available The steady two-dimensional radiative MHD boundary layer flow of an incompressible, viscous, electrically conducting fluid caused by a nonisothermal linearly stretching sheet placed at the bottom of fluid saturated porous medium in the presence of viscous dissipation and chemical reaction is studied. The governing system of partial differential equations is converted to ordinary differential equations by using the similarity transformations, which are then solved by shooting method. The dimensionless velocity, temperature, and concentration are computed for different thermophysical parameters, namely, the magnetic parameter, permeability parameter, radiation parameter, wall temperature parameter, Prandtl number, Eckert number, Schmidt number, and chemical reaction.

  4. 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

    2009-08-01

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

  5. Understanding chemical binding using the Berlin function and the reaction force

    Science.gov (United States)

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

    2012-06-01

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

  6. Determination of the interfacial area of a continuous integrated mixer/separator (CINC) using a chemical reaction method

    NARCIS (Netherlands)

    Schuur, B.; Jansma, W. J.; Winkelman, J. G. M.; Heeres, H. J.

    2008-01-01

    The effect of the liquid flow rates (18-100 mL/min) and rotor frequency (30-60 Hz) on the interfacial area of a liquid-liquid system in a CINC-V02 continuous integrated mixer/separator have been studied using a chemical reaction method. Topical specific interfacial areas were in the range of 3.2 x 1

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

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

    We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  8. Surface Nano-Structuring by Adsorption and Chemical Reactions

    OpenAIRE

    Ken-ichi Tanaka

    2010-01-01

    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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1987-08-10

    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.

  10. Control of Convective Dissolution by Chemical Reactions: General Classification and Application to CO2 Dissolution in Reactive Aqueous Solutions

    Science.gov (United States)

    Loodts, V.; Thomas, C.; Rongy, L.; De Wit, A.

    2014-09-01

    In partially miscible two-layer systems within a gravity field, buoyancy-driven convective motions can appear when one phase dissolves with a finite solubility into the other one. We investigate the influence of chemical reactions on such convective dissolution by a linear stability analysis of a reaction-diffusion-convection model. We show theoretically that a chemical reaction can either enhance or decrease the onset time of the convection, depending on the type of density profile building up in time in the reactive solution. We classify the stabilizing and destabilizing scenarios in a parameter space spanned by the solutal Rayleigh numbers. As an example, we experimentally demonstrate the possibility to enhance the convective dissolution of gaseous CO2 in aqueous solutions by a classical acid-base reaction.

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

    Science.gov (United States)

    Vella, Alfred J.

    1990-01-01

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

  12. Arrangement for carrying out and studying chemical reactions

    NARCIS (Netherlands)

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

    1993-01-01

    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

  13. Theoretical studies of the dynamics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  14. Theoretical Studies of Chemical Reactions following Electronic Excitation

    Science.gov (United States)

    Chaban, Galina M.

    2003-01-01

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

  15. Weakly bound systems, continuum effects, and reactions

    CERN Document Server

    Jaganathen, Y; Ploszajczak, M

    2012-01-01

    Structure of weakly bound/unbound nuclei close to particle drip lines is different from that around the valley of beta stability. A comprehensive description of these systems goes beyond standard Shell Model and demands an open quantum system description of the nuclear many-body system. We approach this problem using the Gamow Shell Model which provides a fully microscopic description of bound and unbound nuclear states, nuclear decays, and reactions. We present in this paper the first application of the GSM for a description of the elastic and inelastic scattering of protons on 6He.

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

    Science.gov (United States)

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

    2016-10-10

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

  17. Hypervelocity accelerators with electro-thermo-chemical reaction

    Science.gov (United States)

    Ikuta, Kazunari

    1991-08-01

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

  18. X-ray Microspectroscopy and Chemical Reactions in Soil Microsites

    Energy Technology Data Exchange (ETDEWEB)

    D Hesterberg; M Duff; J Dixon; M Vepraskas

    2011-12-31

    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.

  19. Expanded utility of the native chemical ligation reaction.

    Science.gov (United States)

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

    2004-10-04

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

  20. Enzymes as modular catalysts for redox half-reactions in H2-powered chemical synthesis: from biology to technology

    Science.gov (United States)

    Reeve, Holly A.; Ash, Philip A.; Park, HyunSeo; Huang, Ailun; Posidias, Michalis; Tomlinson, Chloe; Lenz, Oliver

    2017-01-01

    The present study considers the ways in which redox enzyme modules are coupled in living cells for linking reductive and oxidative half-reactions, and then reviews examples in which this concept can be exploited technologically in applications of coupled enzyme pairs. We discuss many examples in which enzymes are interfaced with electronically conductive particles to build up heterogeneous catalytic systems in an approach which could be termed synthetic biochemistry. We focus on reactions involving the H+/H2 redox couple catalysed by NiFe hydrogenase moieties in conjunction with other biocatalysed reactions to assemble systems directed towards synthesis of specialised chemicals, chemical building blocks or bio-derived fuel molecules. We review our work in which this approach is applied in designing enzyme-modified particles for H2-driven recycling of the nicotinamide cofactor NADH to provide a clean cofactor source for applications of NADH-dependent enzymes in chemical synthesis, presenting a combination of published and new work on these systems. We also consider related photobiocatalytic approaches for light-driven production of chemicals or H2 as a fuel. We emphasise the techniques available for understanding detailed catalytic properties of the enzymes responsible for individual redox half-reactions, and the importance of a fundamental understanding of the enzyme characteristics in enabling effective applications of redox biocatalysis. PMID:28062838

  1. Enzymes as modular catalysts for redox half-reactions in H2-powered chemical synthesis: from biology to technology.

    Science.gov (United States)

    Reeve, Holly A; Ash, Philip A; Park, HyunSeo; Huang, Ailun; Posidias, Michalis; Tomlinson, Chloe; Lenz, Oliver; Vincent, Kylie A

    2017-01-15

    The present study considers the ways in which redox enzyme modules are coupled in living cells for linking reductive and oxidative half-reactions, and then reviews examples in which this concept can be exploited technologically in applications of coupled enzyme pairs. We discuss many examples in which enzymes are interfaced with electronically conductive particles to build up heterogeneous catalytic systems in an approach which could be termed synthetic biochemistry We focus on reactions involving the H(+)/H2 redox couple catalysed by NiFe hydrogenase moieties in conjunction with other biocatalysed reactions to assemble systems directed towards synthesis of specialised chemicals, chemical building blocks or bio-derived fuel molecules. We review our work in which this approach is applied in designing enzyme-modified particles for H2-driven recycling of the nicotinamide cofactor NADH to provide a clean cofactor source for applications of NADH-dependent enzymes in chemical synthesis, presenting a combination of published and new work on these systems. We also consider related photobiocatalytic approaches for light-driven production of chemicals or H2 as a fuel. We emphasise the techniques available for understanding detailed catalytic properties of the enzymes responsible for individual redox half-reactions, and the importance of a fundamental understanding of the enzyme characteristics in enabling effective applications of redox biocatalysis.

  2. Suppression of viscous fingering instability by a chemical reaction producing gel

    Science.gov (United States)

    Nagatsu, Yuichiro; Kanbara, Toshizo; Taniguchi, Masafumi

    2016-11-01

    Viscous fingering (VF) is a well-known hydrodynamic instability which is observed when a more viscous fluid is displaced by another less viscous one in porous media or Hele-Shaw cell. In such a situation, the interface between two fluids formed finger-like patterns. Recently, several techniques for suppress VF instability has been developed, which include time-dependent injection, addition of permeability gradient, and use of viscoelastic plates of Hele-Shaw cell. Here, we demonstrate our trial to suppress VF by chemical reaction producing gel. We have succeeded to find a system of solutions and reaction in which the reaction producing a gel is able to completely suppress VF. In addition, we have performed rheological measurement of the gel produced at the reactive interface. The VF experiment and the rheological measurement have been performed by varying concentrations of the reactants. We show the storage modulus (G') of the gel, which corresponds to elastic response to small amplitude oscillatory shear, is responsible for the ability of suppression of VF in the present reactive system.

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

    Science.gov (United States)

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

    2016-12-21

    We report herein the design, synthesis, and characterization of a two-segment fluorogenic analogue of vitamin K, B-VKQ, prepared by coupling vitamin K3, also known as menadione (a quinone redox center), to a boron-dipyrromethene (BODIPY) fluorophore (a lipophilic reporter segment). Oxidation-reduction reactions, spectroelectrochemical studies, and enzymatic assays conducted in the presence of DT-diaphorase illustrate that the new probe shows reversible redox behavior on par with that of vitamin K, provides a high-sensitivity fluorescence signal, and is compatible with biological conditions, opening the door to monitor remotely (i.e., via imaging) redox processes in real time. In its oxidized form, B-VKQ is non-emissive, while upon reduction to the hydroquinone form, B-VKQH2, BODIPY fluorescence is restored, with emission quantum yield values of ca. 0.54 in toluene. Density functional theory studies validate a photoinduced electron transfer intramolecular switching mechanism, active in the non-emissive quinone form and deactivated upon reduction to the emissive dihydroquinone form. Our results highlight the potential of B-VKQ as a fluorogenic probe to study electron transfer and transport in model systems and biological structures with optimal sensitivity and desirable chemical specificity. Use of such a probe may enable a better understanding of the role that vitamin K plays in biological redox reactions ubiquitous in key cellular processes, and help elucidate the mechanism and pathological significance of these reactions in biological systems.

  4. Computer aided design, analysis and experimental investigation of membrane assisted batch reaction-separation systems

    DEFF Research Database (Denmark)

    Mitkowski, Piotr Tomasz; Buchaly, Carsten; Kreis, Peter;

    2009-01-01

    Membrane assisted batch reaction operation offers an interesting option for equilibrium limited reaction systems in chemical and biochemical manufacturing by selective removal of one of the products and thereby increasing the product yield. The design of such hybrid systems need to take into acco...... and separation functionalities and to design/analyse the hybrid scheme. The generated hybrid scheme has been validated through experiments involving an esterification reaction....

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

    CERN Document Server

    1986-01-01

    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...

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

    Science.gov (United States)

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

    2013-11-21

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

  7. Concept Maps as a Tool for Teaching Organic Chemical Reactions.

    Science.gov (United States)

    Šket, Barbara; Aleksij Glažar, Saša; Vogrinc, Janez

    2015-01-01

    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.

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

    Science.gov (United States)

    2015-06-28

    ghanshyam.vaghjiani@us.af.mil 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

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

    Science.gov (United States)

    Grodzka, P.; Facemire, B.

    1977-01-01

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

  10. Feasibility Study of Venus Surfuce Cooling Using Chemical Reactions with the Atmosphere

    Science.gov (United States)

    Evans, Christopher

    2013-01-01

    A literature search and theoretical analysis were conducted to investigate the feasibility of cooling a craft on Venus through chemical reformation of materials from the atmosphere. The core concept was to take carbon dioxide (CO2) from the Venus atmosphere and chemically reform it into simpler compounds such as carbon, oxygen, and carbon monoxide. This process is endothermic, taking energy from the surroundings to produce a cooling effect. A literature search was performed to document possible routes for achieving the desired reactions. Analyses indicated that on Venus, this concept could theoretically be used to produce cooling, but would not perform as well as a conventional heat pump. For environments other than Venus, the low theoretical performance limits general applicability of this concept, however this approach to cooling may be useful in niche applications. Analysis indicated that environments with particular atmospheric compositions and temperatures could allow a similar cooling system to operate with very good performance. This approach to cooling may also be useful where the products of reaction are also desirable, or for missions where design simplicity is valued. Conceptual designs for Venus cooling systems were developed using a modified concept, in which an expendable reactant supply would be used to promote more energetically favorable reactions with the ambient CO2, providing cooling for a more limited duration. This approach does not have the same performance issues, but the use of expendable supplies increases the mass requirements and limits the operating lifetime. This paper summarizes the findings of the literature search and corresponding analyses of the various cooling options

  11. Feasibility Study of Venus Surface Cooling Using Chemical Reactions with the Atmosphere

    Science.gov (United States)

    Evans, Christopher

    2013-01-01

    A literature search and theoretical analysis were conducted to investigate the feasibility of cooling a craft on Venus through chemical reformation of materials from the atmosphere. The core concept was to take carbon dioxide (CO2) from the Venus atmosphere and chemically reform it into simpler compounds such as carbon, oxygen, and carbon monoxide. This process is endothermic, taking energy from the surroundings to produce a cooling effect. A literature search was performed to document possible routes for achieving the desired reactions. Analyses indicated that on Venus, this concept could theoretically be used to produce cooling, but would not perform as well as a conventional heat pump. For environments other than Venus, the low theoretical performance limits general applicability of this concept, however this approach to cooling may be useful in niche applications. Analysis indicated that environments with particular atmospheric compositions and temperatures could allow a similar cooling system to operate with very good performance. This approach to cooling may also be useful where the products of reaction are also desirable, or for missions where design simplicity is valued. Conceptual designs for Venus cooling systems were developed using a modified concept, in which an expendable reactant supply would be used to promote more energetically favorable reactions with the ambient CO2, providing cooling for a more limited duration. This approach does not have the same performance issues, but the use of expendable supplies increases the mass requirements and limits the operating lifetime. This paper summarizes the findings of the literature search and corresponding analyses of the various cooling options.

  12. Thermodynamics of chemical systems far from equilibrium

    Energy Technology Data Exchange (ETDEWEB)

    Ross, J. (Stanford Univ., CA (USA)); Garcia-Colin, L.S. (UAM-Iztapalapa, Postal (Mexico))

    1989-03-09

    A critique is presented of some recent work in this and other journals on the relation of thermodynamics to the mass action law of kinetics. For most chemical reactions, the thermodynamic variables change on the same time scale as the progress variable and there is no need for an extended thermodynamics.

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

    Science.gov (United States)

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

    2017-01-01

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

  14. 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

    2014-01-01

    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.

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

    Science.gov (United States)

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

    2003-12-01

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

  16. Enzyme efficiency: An open reaction system perspective

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Kinshuk, E-mail: kb36@rice.edu [Department of Chemistry, University of Calcutta, Rajabazar Science College Campus, Kolkata 700 009 (India); Bhattacharyya, Kamal, E-mail: pchemkb@gmail.com [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Kolkata 700 009 (India)

    2015-12-21

    A measure of enzyme efficiency is proposed for an open reaction network that, in suitable form, applies to closed systems as well. The idea originates from the description of classical enzyme kinetics in terms of cycles. We derive analytical expressions for the efficiency measure by treating the network not only deterministically but also stochastically. The latter accounts for any significant amount of noise that can be present in biological systems and hence reveals its impact on efficiency. Numerical verification of the results is also performed. It is found that the deterministic equation overestimates the efficiency, the more so for very small system sizes. Roles of various kinetics parameters and system sizes on the efficiency are thoroughly explored and compared with the standard definition k{sub 2}/K{sub M}. Study of substrate fluctuation also indicates an interesting efficiency-accuracy balance.

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

    Science.gov (United States)

    Cerar, Janez

    2015-01-01

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

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

    Science.gov (United States)

    Yan, Fan; Talanquer, Vicente

    2015-01-01

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

  19. The Technology for Intensification of Chemical Reaction Process Envisaged in the "863" Plan

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ 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.

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

    Science.gov (United States)

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

    2015-01-02

    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. Rate constants for chemical reactions in high-temperature nonequilibrium air

    Science.gov (United States)

    Jaffe, R. L.

    1986-01-01

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

  2. Heterogeneous nucleation - current transients under chemical reaction control

    CERN Document Server

    D'Ajello-Tettamanzy, P C; Kipervaser, Z G S

    2002-01-01

    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...

  3. Analytical solution of steady-state equations for chemical reaction networks with bilinear rate laws.

    Science.gov (United States)

    Halász, Adám M; Lai, Hong-Jian; McCabe Pryor, Meghan; Radhakrishnan, Krishnan; Edwards, Jeremy S

    2013-01-01

    True steady states are a rare occurrence in living organisms, yet their knowledge is essential for quasi-steady-state approximations, multistability analysis, and other important tools in the investigation of chemical reaction networks (CRN) used to describe molecular processes on the cellular level. Here, we present an approach that can provide closed form steady-state solutions to complex systems, resulting from CRN with binary reactions and mass-action rate laws. We map the nonlinear algebraic problem of finding steady states onto a linear problem in a higher-dimensional space. We show that the linearized version of the steady-state equations obeys the linear conservation laws of the original CRN. We identify two classes of problems for which complete, minimally parameterized solutions may be obtained using only the machinery of linear systems and a judicious choice of the variables used as free parameters. We exemplify our method, providing explicit formulae, on CRN describing signal initiation of two important types of RTK receptor-ligand systems, VEGF and EGF-ErbB1.

  4. Hazardous chemical tracking system (HAZ-TRAC)

    Energy Technology Data Exchange (ETDEWEB)

    Bramlette, J D; Ewart, S M; Jones, C E

    1990-07-01

    Westinghouse Idaho Nuclear Company, Inc. (WINCO) developed and implemented a computerized hazardous chemical tracking system, referred to as Haz-Trac, for use at the Idaho Chemical Processing Plant (ICPP). Haz-Trac is designed to provide a means to improve the accuracy and reliability of chemical information, which enhances the overall quality and safety of ICPP operations. The system tracks all chemicals and chemical components from the time they enter the ICPP until the chemical changes form, is used, or becomes a waste. The system runs on a Hewlett-Packard (HP) 3000 Series 70 computer. The system is written in COBOL and uses VIEW/3000, TurboIMAGE/DBMS 3000, OMNIDEX, and SPEEDWARE. The HP 3000 may be accessed throughout the ICPP, and from remote locations, using data communication lines. Haz-Trac went into production in October, 1989. Currently, over 1910 chemicals and chemical components are tracked on the system. More than 2500 personnel hours were saved during the first six months of operation. Cost savings have been realized by reducing the time needed to collect and compile reporting information, identifying and disposing of unneeded chemicals, and eliminating duplicate inventories. Haz-Trac maintains information required by the Superfund Amendment Reauthorization Act (SARA), the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) and the Occupational Safety and Health Administration (OSHA).

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

    Science.gov (United States)

    Das, A K; Meuwly, M

    2016-01-01

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

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

    Science.gov (United States)

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

    2013-08-29

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

  7. Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence.

    Science.gov (United States)

    de la Lande, Aurélien; Řezáč, Jan; Lévy, Bernard; Sanders, Barry C; Salahub, Dennis R

    2011-03-23

    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.

  8. Thermally activated reaction–diffusion-controlled chemical bulk reactions of gases and solids

    Directory of Open Access Journals (Sweden)

    S. Möller

    2015-01-01

    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.

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

    Science.gov (United States)

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

    2015-12-01

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

  10. Method to reduce chemical background interference in atmospheric pressure ionization liquid chromatography-mass spectrometry using exclusive reactions with the chemical reagent dimethyl disulfide.

    Science.gov (United States)

    Guo, Xinghua; Bruins, Andries P; Covey, Thomas R

    2007-06-01

    The interference of chemical background ions (chemical noise) has been a problem since the inception of mass spectrometry. We present here a novel method to reduce the chemical noise in LC-MS based on exclusive gas-phase reactions with a reactive collision gas in a triple-quadrupole mass spectrometer. Combined with the zero neutral loss (ZNL) scan of a triple-quadrupole mass spectrometer, the reactive chemical noise ions can be removed because of shifts of mass-to-charge ratios from the original background ions. The test on various classes of compounds with different functional groups indicates a generic application of this technique in LC-MS. The preliminary results show that a reduction of the level of LC-MS base-peak chromatographic baseline by a factor up to 40 and an improvement of the signal-to-noise ratio by a factor up to 5-10 are achieved on both commercial and custom-modified triple-quadrupole LC-MS systems. Application is foreseen in both quantitative and qualitative trace analysis. It is expected that this chemical noise reduction technique can be optimized on a dedicated mass spectrometric instrumentation which incorporates both a chemical reaction cell for noise reduction and a collision stage for fragmentation.

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

    Science.gov (United States)

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

    2016-11-03

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

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

    CERN Document Server

    Suleimanov, Yury V; Guo, Hua

    2016-01-01

    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.

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

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

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

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

    Science.gov (United States)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2016-02-09

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

  16. Separation of chemical reaction intermediates by metal-organic frameworks.

    Science.gov (United States)

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

    2011-08-22

    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.

  17. Chemical Stimulation of Engineered Geothermal Systems

    Energy Technology Data Exchange (ETDEWEB)

    Rose, Peter, E.

    2008-08-08

    The objective of this project is to design, develop and demonstrate methods for the chemical stimulation of candidate EGS reservoirs as well as the chemical treatment of mineral-scaled wellbores. First, a set of candidate chemical compounds capable of dissolving calcite was identified. A series of tests was then performed on each candidate in order to screen it for thermal stability and reactivity towards calcite. A detailed analysis was then performed on each compound that emerged from the screening tests in order to characterize its decay kinetics and reaction kinetics as functions of temperature and chemical composition. From among the compounds emerging from the laboratory studies, one compounds was chosen for a field experiment in order to verify the laboratory predictions.

  18. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    Science.gov (United States)

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach.

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

    Science.gov (United States)

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

    1989-02-01

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

  20. 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

    2002-01-01

    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.

  1. Accelerated stochastic and hybrid methods for spatial simulations of reaction-diffusion systems

    OpenAIRE

    Rossinelli, D; Bayati, B; Koumoutsakos, P.

    2008-01-01

    Spatial distributions characterize the evolution of reaction-diffusion models of several physical, chemical, and biological systems. We present two novel algorithms for the efficient simulation of these models: Spatial т-Leaping (Sт -Leaping), employing a unified acceleration of the stochastic simulation of reaction and diffusion, and Hybrid т-Leaping (Hт-Leaping), combining a deterministic diffusion approximation with a т-Leaping acceleration of the stochastic reactions. The algorithms are v...

  2. Chemical reaction and heat source effects on MHD oscillatory flow in an irregular channel

    Directory of Open Access Journals (Sweden)

    P.V. Satya Narayana

    2016-12-01

    Full Text Available This paper investigates the effect of heat and mass transfer on MHD oscillatory flow in an asymmetric wavy channel with chemical reaction and heat source. The unsteadiness in the flow is due to an oscillatory pressure gradient across the ends of the channel. A magnetic field of uniform strength is applied in the direction perpendicular to the channel. However, the induced magnetic field is neglected due to the assumption of small magnetic Reynolds number. The temperature difference of the channel is also assumed high enough to induce heat transfer due to radiation. The governing equations are solved analytically by regular perturbation method. The analytical results are evaluated numerically and then are presented graphically to discuss the effects of different parameters entering into the problem. It is observed that the heat transport of a system is more increased in oscillatory flow than in ordinary conduction.

  3. Axisymmetric mixed convective MHD flow over a slender cylinder in the presence of chemically reaction

    Directory of Open Access Journals (Sweden)

    Prasad K.V.

    2016-02-01

    Full Text Available The present analysis is focused on the study of the magnetic effect on coupled heat and mass transfer by mixed convection boundary layer flow over a slender cylinder in the presence of a chemical reaction. The buoyancy effect due to thermal diffusion and species diffusion is investigated. Employing suitable similarity transformations, the governing equations are transformed into a system of coupled non-linear ordinary differential equations and are solved numerically via the implicit, iterative, second order finite difference method. The numerical results obtained are compared with the available results in the literature for some special cases and the results are found to be in excellent agreement. The velocity, temperature, and the concentration profiles are presented graphically and analyzed for several sets of the pertinent parameters. The pooled effect of the thermal and mass Grashof number is to enhance the velocity and is quite the opposite for temperature and the concentration fields.

  4. Radiation and chemical reaction effects on MHD flow along a moving vertical porous plate

    Directory of Open Access Journals (Sweden)

    Ramana Reddy G.V.

    2016-02-01

    Full Text Available This paper presents an analysis of the effects of magnetohydrodynamic force and buoyancy on convective heat and mass transfer flow past a moving vertical porous plate in the presence of thermal radiation and chemical reaction. The governing partial differential equations are reduced to a system of self-similar equations using the similarity transformations. The resultant equations are then solved numerically using the fourth order Runge-Kutta method along with the shooting technique. The results are obtained for the velocity, temperature, concentration, skin-friction, Nusselt number and Sherwood number. The effects of various parameters on flow variables are illustrated graphically, and the physical aspects of the problem are discussed.

  5. Chemical reaction effect on MHD free convective surface over a moving vertical plate through porous medium

    Directory of Open Access Journals (Sweden)

    R.S. Tripathy

    2015-09-01

    Full Text Available An attempt has been made to study the heat and mass transfer effect in a boundary layer flow of an electrically conducting viscous fluid subject to transverse magnetic field past over a moving vertical plate through porous medium in the presence of heat source and chemical reaction. The governing non-linear partial differential equations have been transformed into a two-point boundary value problem using similarity variables and then solved numerically by fourth order Runge–Kutta fourth order method with shooting technique. Graphical results are discussed for non-dimensional velocity, temperature and concentration profiles while numerical values of the skin friction, Nusselt number and Sherwood number are presented in tabular form for various values of parameters controlling the flow system.

  6. Chemical Reactions Catalyzed by Metalloporphyrin-Based Metal-Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Kelly Aparecida Dias de Freitas Castro

    2013-06-01

    Full Text Available The synthetic versatility and the potential application of metalloporphyrins (MP in different fields have aroused researchers’ interest in studying these complexes, in an attempt to mimic biological systems such as cytochrome P-450. Over the last 40 years, synthetic MPs have been mainly used as catalysts for homogeneous or heterogeneous chemical reactions. To employ them in heterogeneous catalysis, chemists have prepared new MP-based solids by immobilizing MP onto rigid inorganic supports, a strategy that affords hybrid inorganic-organic materials. More recently, materials obtained by supramolecular assembly processes and containing MPs as building blocks have been applied in a variety of areas, like gas storage, photonic devices, separation, molecular sensing, magnets, and heterogeneous catalysis, among others. These coordination polymers, known as metal-organic frameworks (MOFs, contain organic ligands or complexes connected by metal ions or clusters, which give rise to a 1-, 2- or 3-D network. These kinds of materials presents large surface areas, Brønsted or redox sites, and high porosity, all of which are desirable features in catalysts with potential use in heterogeneous phases. Building MOFs based on MP is a good way to obtain solid catalysts that offer the advantages of bioinspired systems and zeolitic materials. In this mini review, we will adopt a historical approach to present the most relevant MP-based MOFs applicable to catalytic reactions such as oxidation, reduction, insertion of functional groups, and exchange of organic functions.

  7. Chemical reactions catalyzed by metalloporphyrin-based metal-organic frameworks.

    Science.gov (United States)

    Nakagaki, Shirley; Ferreira, Gabriel Kaetan Baio; Ucoski, Geani Maria; Dias de Freitas Castro, Kelly Aparecida

    2013-06-21

    The synthetic versatility and the potential application of metalloporphyrins (MP) in different fields have aroused researchers' interest in studying these complexes, in an attempt to mimic biological systems such as cytochrome P-450. Over the last 40 years, synthetic MPs have been mainly used as catalysts for homogeneous or heterogeneous chemical reactions. To employ them in heterogeneous catalysis, chemists have prepared new MP-based solids by immobilizing MP onto rigid inorganic supports, a strategy that affords hybrid inorganic-organic materials. More recently, materials obtained by supramolecular assembly processes and containing MPs as building blocks have been applied in a variety of areas, like gas storage, photonic devices, separation, molecular sensing, magnets, and heterogeneous catalysis, among others. These coordination polymers, known as metal-organic frameworks (MOFs), contain organic ligands or complexes connected by metal ions or clusters, which give rise to a 1-, 2- or 3-D network. These kinds of materials presents large surface areas, Brønsted or redox sites, and high porosity, all of which are desirable features in catalysts with potential use in heterogeneous phases. Building MOFs based on MP is a good way to obtain solid catalysts that offer the advantages of bioinspired systems and zeolitic materials. In this mini review, we will adopt a historical approach to present the most relevant MP-based MOFs applicable to catalytic reactions such as oxidation, reduction, insertion of functional groups, and exchange of organic functions.

  8. Quantitative real-time monitoring of chemical reactions by autosampling flow injection analysis coupled with atmospheric pressure chemical ionization mass spectrometry.

    Science.gov (United States)

    Zhu, Zhenqian; Bartmess, John E; McNally, Mary Ellen; Hoffman, Ron M; Cook, Kelsey D; Song, Liguo

    2012-09-04

    Although qualitative and/or semiquantitative real-time monitoring of chemical reactions have been reported with a few mass spectrometric approaches, to our knowledge, no quantitative mass spectrometric approach has been reported so far to have a calibration valid up to molar concentrations as required by process control. This is mostly due to the absence of a practical solution that could well address the sample overloading issue. In this study, a novel autosampling flow injection analysis coupled with an atmospheric pressure chemical ionization mass spectrometry (FIA/APCI-MS) system, consisting of a 1 μL automatic internal sample injector, a postinjection splitter with 1:10 splitting ratio, and a detached APCI source connected to the mass spectrometer using a 4.5 in. long, 0.042 in. inner diameter (ID) stainless-steel capillary, was thus introduced. Using this system together with an optional FIA solvent modifier, e.g., 0.05% (v/v) isopropylamine, a linear quantitative calibration up to molar concentration has been achieved with 3.4-7.2% relative standard deviations (RSDs) for 4 replicates. As a result, quantitative real-time monitoring of a model reaction was successfully performed at the 1.63 M level. It is expected that this novel autosampling FIA/APCI-MS system can be used in quantitative real-time monitoring of a wide range of reactions under diverse reaction conditions.

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

    DEFF Research Database (Denmark)

    Berg, Nikolaj Drimer; Linneberg, Allan; Thyssen, Jacob Pontoppidan;

    2011-01-01

    Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. The aetiology is unknown, but chemical related respiratory symptoms have been found associated with positive patch test. The purpose of this study was to investigate...... the relationship between cutaneous reactions from patch testing and self-reported severity of chemical sensitivity to common airborne chemicals. A total of 3460 individuals participating in a general health examination, Health 2006, were patch tested with allergens from the European standard series and screened...... 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...

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

    Science.gov (United States)

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

    2015-06-01

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

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

    Science.gov (United States)

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

    2015-06-25

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

  12. On the moments of the Boltzmann's collision operator arising from chemical reactions

    Science.gov (United States)

    Sarna, Neeraj; Torrilhon, Manuel

    2016-11-01

    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.

  13. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  14. Radiation Reaction in a Bent Focusing System

    Science.gov (United States)

    Huang, Zhirong; Chen, Pisin; Ruth, Ronald D.

    1996-05-01

    We have shown that in a straight, continuous focusing channel the radiation reaction is different from that in a bending magnet. Quantum excitation to the transverse action is absent in this focusing system, and the radiation damping is faster in the transverse direction than in the longitudinal one. In this talk we study the effect of radiation in a combined-function system, where both focusing and bending fields are present. In one case where the bending dominates over the focusing, we recover the result of standard synchrotron radiation damping in storage rings. In the other case where the focusing dominates over the bending, we find that the lack of quantum excitation and the asymmetric damping found in a straight focusing channel still hold. In addition, the possibility of designing a focusing-dominated damping ring to demonstrate and apply this effect is discussed.

  15. Distribution in flowing reaction-diffusion systems

    KAUST Repository

    Kamimura, Atsushi

    2009-12-28

    A power-law distribution is found in the density profile of reacting systems A+B→C+D and 2A→2C under a flow in two and three dimensions. Different densities of reactants A and B are fixed at both ends. For the reaction A+B, the concentration of reactants asymptotically decay in space as x-1/2 and x-3/4 in two dimensions and three dimensions, respectively. For 2A, it decays as log (x) /x in two dimensions. The decay of A+B is explained considering the effect of segregation of reactants in the isotropic case. The decay for 2A is explained by the marginal behavior of two-dimensional diffusion. A logarithmic divergence of the diffusion constant with system size is found in two dimensions. © 2009 The American Physical Society.

  16. Soil chemical sensor and precision agricultural chemical delivery system and method

    Energy Technology Data Exchange (ETDEWEB)

    Colburn, J.W. Jr.

    1991-07-23

    A real time soil chemical sensor and precision agricultural chemical delivery system includes a plurality of ground-engaging tools in association with individual soil sensors which measure soil chemical levels. The system includes the addition of a solvent which rapidly saturates the soil/tool interface to form a conductive solution of chemicals leached from the soil. A multivalent electrode, positioned within a multivalent frame of the ground-engaging tool, applies a voltage or impresses a current between the electrode and the tool frame. A real-time soil chemical sensor and controller senses the electrochemical reaction resulting from the application of the voltage or current to the leachate, measures it by resistivity methods, and compares it against pre-set resistivity levels for substances leached by the solvent. Still greater precision is obtained by calibrating for the secondary current impressed through solvent-less soil. The appropriate concentration is then found and the servo-controlled delivery system applies the appropriate amount of fertilizer or agricultural chemicals substantially in the location from which the soil measurement was taken. 5 figures.

  17. A low power sub- μW chemical gilbert cell for ISFET differential reaction monitoring.

    Science.gov (United States)

    Kalofonou, Melpomeni; Toumazou, Christofer

    2014-08-01

    This paper presents a low power current-mode method for monitoring differentially derived changes in pH from ion-sensitive field-effect transistor (ISFET) sensors, by adopting the Chemical Gilbert Cell. The fabricated system, with only a few transistors, achieves differential measurements and therefore drift minimisation of continuously recorded pH signals obtained from biochemical reactions such as DNA amplification in addition to combined gain tunability using only a single current. Experimental results are presented, demonstrating the capabilities of the front-end at a microscopic level through integration in a lab-on-chip (LoC) setup combining a microfluidic assembly, suitable for applications that require differential monitoring in small volumes, such as DNA detection where more than one gene needs to be studied. The system was designed and fabricated in a typical 0.35 μ m CMOS process with the resulting topology achieving good differential pH sensitivity with a measured low power consumption of only 165 nW due to weak inversion operation. A tunable gain is demonstrated with results confirming 15.56 dB gain at 20 nA of ISFET bias current and drift reduction of up to 100 times compared to a single-ended measurement is also reported due to the differential current output, making it ideal for robust, low-power chemical measurement.

  18. Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy.

    Science.gov (United States)

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

    2015-10-14

    Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes. We also consider the entanglement developed using adiabatic electronic basis, providing a novel way for interpreting effects of the breakdown of the Born-Oppenheimer (BO) approximation. We consider: (i) BO entanglement in the ground-state wavefunction relevant to equilibrium thermodynamics, (ii) BO entanglement associated with low-energy wavefunctions relevant to infrared and tunneling spectroscopies, (iii) BO entanglement in high-energy eigenfunctions relevant to chemical reaction processes, and (iv) BO entanglement developed during reactive wavepacket dynamics. A two-state single-mode diabatic model descriptive of a wide range of chemical phenomena is used for this purpose. The entanglement developed by BO breakdown correlates simply with the diameter of the cusp introduced by the BO approximation, and a hierarchy appears between the various BO-breakdown correction terms, with the first-derivative correction being more important than the second-derivative correction which is more important than the diagonal correction. This simplicity is in contrast to the complexity of BO-breakdown effects on thermodynamic, spectroscopic, and kinetic properties. Further, processes poorly treated at the BO level that appear adequately treated using the Born-Huang adiabatic approximation are found to have properties that can only be described using a non-adiabatic description. For the entanglement developed between diabatic electronic states and the nuclear motion

  19. Research and development of utilization technology of solar thermal system for industrial and other use. Research and development of key technology (energy conversion on technology using chemical reactions); Sangyoyo nado solar system jitsuyoka gijutsu kaihatsu. Yoso gijutsu no kenkyu (kagaku energy henkan gijutsu no kenkyu)

    Energy Technology Data Exchange (ETDEWEB)

    Takita, M. [New Energy and Industrial Technology Development Organization, Tokyo (Japan)

    1994-12-01

    Described herein are the results of the FY1994 research program for energy conversion technology using chemical reactions by the aid of solar energy. The demonstration runs were conducted by a bench-scale unit, which was operated stably for 100h, to produce promising results. The catalyst exhibits stable performance, without showing a sign of deactivation. It is found that the heat pump system works well, without being interfered with accumulated by-products. A heat of approximately 2,100kcal/h is recovered. It is confirmed that steam of 150{degree}C and 200{degree}C is generated from hot water of 80{degree}C and 95{degree}C, respectively. The bench-scale runs show a thermal efficiency of around 10%, which is lower than the target level. However, the runs with hydrogen-occluding alloy attain a process thermal efficiency of 30%. The system in which solar collector and chemical heat pump units are combined is evaluated with respect to its economic efficiency and operability for its eventual commercialization. 6 figs., 2 tabs.

  20. Piecewise linear and Boolean models of chemical reaction networks.

    Science.gov (United States)

    Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir

    2014-12-01

    Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] appears in practice, it is not well understood. We provide a mathematical analysis of this limit and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed-form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator.

  1. Piecewise linear and Boolean models of chemical reaction networks

    Science.gov (United States)

    Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir

    2014-01-01

    Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions (xn/(Jn + xn)). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent n is large. However, while the case of small constant J appears in practice, it is not well understood. We provide a mathematical analysis of this limit, and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator. PMID:25412739

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

    Science.gov (United States)

    Barreto, Rodrigo Egydio

    2017-02-01

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

  3. Linear-noise approximation and the chemical master equation agree up to second-order moments for a class of chemical systems.

    Science.gov (United States)

    Grima, Ramon

    2015-10-01

    It is well known that the linear-noise approximation (LNA) agrees with the chemical master equation, up to second-order moments, for chemical systems composed of zero and first-order reactions. Here we show that this is also a property of the LNA for a subset of chemical systems with second-order reactions. This agreement is independent of the number of interacting molecules.

  4. 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)

    1999-11-01

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

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

    Science.gov (United States)

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

    2016-10-01

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

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

    Science.gov (United States)

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

    2009-12-01

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

  7. Combustion chemical vapor desposited coatings for thermal barrier coating systems

    Energy Technology Data Exchange (ETDEWEB)

    Hampikian, J.M.; Carter, W.B. [Georgia Institute of Technology, Atlanta, GA (United States)

    1995-10-01

    The new deposition process, combustion chemical vapor deposition, shows a great deal of promise in the area of thermal barrier coating systems. This technique produces dense, adherent coatings, and does not require a reaction chamber. Coatings can therefore be applied in the open atmosphere. The process is potentially suitable for producing high quality CVD coatings for use as interlayers between the bond coat and thermal barrier coating, and/or as overlayers, on top of thermal barrier coatings.

  8. 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

    2010-01-01

    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

  9. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

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

    Science.gov (United States)

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

    2016-03-01

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

  11. A Hybrid Mutation Chemical Reaction Optimization Algorithm for Global Numerical Optimization

    Directory of Open Access Journals (Sweden)

    Ransikarn Ngambusabongsopa

    2015-01-01

    Full Text Available This paper proposes a hybrid metaheuristic approach that improves global numerical optimization by increasing optimal quality and accelerating convergence. This algorithm involves a recently developed process for chemical reaction optimization and two adjustment operators (turning and mutation operators. Three types of mutation operators (uniform, nonuniform, and polynomial were combined with chemical reaction optimization and turning operator to find the most appropriate framework. The best solution among these three options was selected to be a hybrid mutation chemical reaction optimization algorithm for global numerical optimization. The optimal quality, convergence speed, and statistical hypothesis testing of our algorithm are superior to those previous high performance algorithms such as RCCRO, HP-CRO2, and OCRO.

  12. A novel Chemical Reaction Optimization based Higher order Neural Network (CRO-HONN for nonlinear classification

    Directory of Open Access Journals (Sweden)

    Janmenjoy Nayak

    2015-09-01

    Full Text Available In this paper, a Chemical Reaction Optimization (CRO based higher order neural network with a single hidden layer called Pi–Sigma Neural Network (PSNN has been proposed for data classification which maintains fast learning capability and avoids the exponential increase of number of weights and processing units. CRO is a recent metaheuristic optimization algorithm inspired by chemical reactions, free from intricate operator and parameter settings such as other algorithms and loosely couples chemical reactions with optimization. The performance of the proposed CRO-PSNN has been tested with various benchmark datasets from UCI machine learning repository and compared with the resulting performance of PSNN, GA-PSNN, PSO-PSNN. The methods have been implemented in MATLAB and the accuracy measures have been tested by using the ANOVA statistical tool. Experimental results show that the proposed method is fast, steady and reliable and provides better classification accuracy than others.

  13. CHEMICAL REACTION EFFECTS ON FLOW PAST AN EXPONENTIALLY ACCELERATED VERTICAL PLATE WITH VARIABLE TEMPERATURE

    Directory of Open Access Journals (Sweden)

    R. Muthucumaraswamy

    2010-12-01

    Full Text Available An analysis is performed to study the unsteady flow past an exponentially accelerated infinite vertical plate with variable temperature and uniform mass diffusion, in the presence of a homogeneous chemical reaction of first-order. The plate temperature is raised linearly with time and the concentration level near the plate is raised uniformly. The dimensionless governing equations are solved using the Laplace transform. The velocity profiles are studied for different physical parameters such as the chemical reaction parameter, thermal Grashof number, mass Grashof number, a, and time. It is observed that the velocity increases with increasing values of a or t. But the trend is just the reverse in the chemical reaction parameter.

  14. Chaos in a chemical system

    Science.gov (United States)

    Srivastava, R.; Srivastava, P. K.; Chattopadhyay, J.

    2013-07-01

    Chaotic oscillations have been observed experimentally in dual-frequency oscillator OAP - Ce+4-BrO- 3-H2SO4 in CSTR. The system shows variation of oscillating potential and frequencies when it moves from low frequency to high frequency region and vice-versa. It was observed that system bifurcate from low frequency to chaotic regime through periode-2 and period-3 on the other hand system bifurcate from chaotic regime to high frequency oscillation through period-2. It was established that the observed oscillations are chaotic in nature on the basis of next amplitude map and bifurcation sequences.

  15. Valence shell charge concentration (VSCC) evolution: a tool to investigate the transformations within a VSCC throughout a chemical reaction.

    Science.gov (United States)

    Cortés-Guzmán, Fernando; Gómez, Rosa María; Rocha-Rinza, Tomas; Sánchez-Obregón, María Azucena; Guevara-Vela, José Manuel

    2011-11-17

    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.

  16. Acoustic imaging for diagnostics of chemically reacting systems

    Science.gov (United States)

    Ramohalli, K.; Seshan, P.

    1983-01-01

    The concept of local diagnostics, in chemically reacting systems, with acoustic imaging is developed. The elements of acoustic imaging through ellipsoidal mirrors are theoretically discussed. In a general plan of the experimental program, the first system is chosen in these studies to be a simple open jet, non premixed turbulent flame. Methane is the fuel and enriched air is the oxidizer. This simple chemically reacting flow system is established at a Reynolds number (based on cold viscosity) of 50,000. A 1.5 m diameter high resolution acoustic mirror with an f-number of 0.75 is used to map the acoustic source zone along the axis of the flame. The results are presented as acoustic power spectra at various distances from the nozzle exit. It is seen that most of the reaction intensity is localized in a zone within 8 diameters from the exit. The bulk reactions (possibly around the periphery of the larger eddies) are evenly distributed along the length of the flame. Possibilities are seen for locally diagnosing single zones in a multiple cluster of reaction zones that occur frequently in practice. A brief outline is given of the future of this work which will be to apply this technique to chemically reacting flows not limited to combustion.

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

    Science.gov (United States)

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

    2016-03-17

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

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

    Science.gov (United States)

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

    2017-02-01

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

  19. Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies

    Science.gov (United States)

    Abel zur Wiesch, Pia; Cohen, Ted

    2017-01-01

    Identifying optimal dosing of antibiotics has proven challenging—some antibiotics are most effective when they are administered periodically at high doses, while others work best when minimizing concentration fluctuations. Mechanistic explanations for why antibiotics differ in their optimal dosing are lacking, limiting our ability to predict optimal therapy and leading to long and costly experiments. We use mathematical models that describe both bacterial growth and intracellular antibiotic-target binding to investigate the effects of fluctuating antibiotic concentrations on individual bacterial cells and bacterial populations. We show that physicochemical parameters, e.g. the rate of drug transmembrane diffusion and the antibiotic-target complex half-life are sufficient to explain which treatment strategy is most effective. If the drug-target complex dissociates rapidly, the antibiotic must be kept constantly at a concentration that prevents bacterial replication. If antibiotics cross bacterial cell envelopes slowly to reach their target, there is a delay in the onset of action that may be reduced by increasing initial antibiotic concentration. Finally, slow drug-target dissociation and slow diffusion out of cells act to prolong antibiotic effects, thereby allowing for less frequent dosing. Our model can be used as a tool in the rational design of treatment for bacterial infections. It is easily adaptable to other biological systems, e.g. HIV, malaria and cancer, where the effects of physiological fluctuations of drug concentration are also poorly understood. PMID:28060813

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

    Science.gov (United States)

    Freed, Karl F

    2011-02-24

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

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

    Science.gov (United States)

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

    2017-02-22

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

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

    Science.gov (United States)

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

    2010-03-01

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

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

    Science.gov (United States)

    Johnson, Erik C B; Kent, Stephen B H

    2006-05-24

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

  4. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    Science.gov (United States)

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

    2016-05-17

    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

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

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov

    2000-01-01

    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....

  6. Power optimization of chemically driven heat engine based on first and second order reaction kinetic theory and probability theory

    Science.gov (United States)

    Zhang, Lei; Chen, Lingen; Sun, Fengrui

    2016-03-01

    The finite-time thermodynamic method based on probability analysis can more accurately describe various performance parameters of thermodynamic systems. Based on the relation between optimal efficiency and power output of a generalized Carnot heat engine with a finite high-temperature heat reservoir (heat source) and an infinite low-temperature heat reservoir (heat sink) and with the only irreversibility of heat transfer, this paper studies the problem of power optimization of chemically driven heat engine based on first and second order reaction kinetic theory, puts forward a model of the coupling heat engine which can be run periodically and obtains the effects of the finite-time thermodynamic characteristics of the coupling relation between chemical reaction and heat engine on the power optimization. The results show that the first order reaction kinetics model can use fuel more effectively, and can provide heat engine with higher temperature heat source to increase the power output of the heat engine. Moreover, the power fluctuation bounds of the chemically driven heat engine are obtained by using the probability analysis method. The results may provide some guidelines for the character analysis and power optimization of the chemically driven heat engines.

  7. Quantum Theory of Rearrangement Collisions with Applications to Elementary Chemical Reactions.

    Science.gov (United States)

    Bowers, Mark Steven

    A three-dimensional, quantum mechanical, coupled channel distorted wave approximation is developed for calculating cross sections for rearrangement collisions between an atom and a diatomic molecule based on the transition (T matrix) formulation of molecular scattering. In this approximation, both entrance and exit channel wave functions are calculated from the inelastic vibrational and rotational close-coupling approximation, and these wave functions are used in the calculation of the T matrix elements for rearrangement. This method allows for the internal states of both the target and product molecule to be dynamically coupled following the motion of the atom, and the wave functions for the exit and entrance channel have the proper asymptotic behavior. Therefore, this method is capable of yielding more accurate results than those from most of the T matrix schemes employed so far. An efficient computational procedure for calculating cross sections is given utilizing parity conservation and by reducing the six-dimensional integral over complex-valued functions to a real-valued three-dimensional integral. Cross sections calculated from this method are presented for the isotopic reactions H+H(,2), D+H(,2), H+H(,2), and Mu+H(,2) using the most accurate available potential surface for energies in the threshold regions of these reactions, and these are compared to other theoretical results when possible. The calculated cross sections for the H+H(,2) reaction are found to be in excellent agreement with the converged close coupling results. Rate constants obtained from the cross sections show the same temperature dependence and are of the same order of magnitude as experimental results; however, the present results are about a factor of 2-3 smaller than the experimental values at lower temperatures for all systems studied. The results of this study indicate that the present method is capable of correctly predicting all reaction attributes of the elementary chemical

  8. Oligonucleotide-templated chemical reactions: pushing the boundaries of a nature-inspired process.

    Science.gov (United States)

    Percivalle, Claudia; Bartolo, Jean-François; Ladame, Sylvain

    2013-01-07

    Widespread in nature, oligonucleotide-templated reactions of phosphodiester bond formation have inspired chemists who are now applying this elegant strategy to the catalysis of a broad range of otherwise inefficient reactions. This review highlights the increasing diversity of chemical reactions that can be efficiently catalysed by an oligonucleotide template, using Watson-Crick base-pairing to bring both reagents in close enough proximity to react, thus increasing significantly their effective molarity. The applications of this elegant concept for nucleic acid sensing and controlled organic synthesis will also be discussed.

  9. Systems metabolic engineering for chemicals and materials.

    Science.gov (United States)

    Lee, Jeong Wook; Kim, Tae Yong; Jang, Yu-Sin; Choi, Sol; Lee, Sang Yup

    2011-08-01

    Metabolic engineering has contributed significantly to the enhanced production of various value-added and commodity chemicals and materials from renewable resources in the past two decades. Recently, metabolic engineering has been upgraded to the systems level (thus, systems metabolic engineering) by the integrated use of global technologies of systems biology, fine design capabilities of synthetic biology, and rational-random mutagenesis through evolutionary engineering. By systems metabolic engineering, production of natural and unnatural chemicals and materials can be better optimized in a multiplexed way on a genome scale, with reduced time and effort. Here, we review the recent trends in systems metabolic engineering for the production of chemicals and materials by presenting general strategies and showcasing representative examples.

  10. Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress.

    Science.gov (United States)

    Chodak, Marcin; Gołębiewski, Marcin; Morawska-Płoskonka, Justyna; Kuduk, Katarzyna; Niklińska, Maria

    Reaction of soil bacteria to drought and rewetting stress may depend on soil chemical properties. The objectives of this study were to test the reaction of different bacterial phyla to drought and rewetting stress and to assess the influence of different soil chemical properties on the reaction of soil bacteria to this kind of stress. The soil samples were taken at ten forest sites and measured for pH and the contents of organic C (Corg) and total N (Nt), Zn, Cu, and Pb. The samples were kept without water addition at 20 - 30 °C for 8 weeks and subsequently rewetted to achieve moisture equal to 50 - 60 % of their maximum water-holding capacity. Prior to the drought period and 24 h after the rewetting, the structure of soil bacterial communities was determined using pyrosequencing of 16S rRNA genes. The drought and rewetting stress altered bacterial community structure. Gram-positive bacterial phyla, Actinobacteria and Firmicutes, increased in relative proportion after the stress, whereas the Gram-negative bacteria in most cases decreased. The largest decrease in relative abundance was for Gammaproteobacteria and Bacteroidetes. For several phyla the reaction to drought and rewetting stress depended on the chemical properties of soils. Soil pH was the most important soil property influencing the reaction of a number of soil bacterial groups (including all classes of Proteobacteria, Bacteroidetes, Acidobacteria, and others) to drought and rewetting stress. For several bacterial phyla the reaction to the stress depended also on the contents of Nt and Corg in soil. The effect of heavy metal pollution was also noticeable, although weaker compared to other chemical soil properties. We conclude that soil chemical properties should be considered when assessing the effect of stressing factors on soil bacterial communities.

  11. O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

    Science.gov (United States)

    Slanger, T. G.; Black, G.

    1978-01-01

    The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

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

    Science.gov (United States)

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

    2017-01-01

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

  13. A quantum chemical study on hydrogen radical reactions with methane and silane

    Science.gov (United States)

    Sato, Kota; Kojima, Kuniharu; Kawasaki, Masashi; Matsuzaki, Yoshio; Hirano, Tsuneo; Nakano, Masatake; Koinuma, Hideomi

    1989-03-01

    A quantum chemical study on the reaction of CH4 , CF4 , SiH4 , and SiF4 with a hydrogen radical is performed on the basis of an ab initio molecular orbital calculation to predict the photochemical reactivity of methane, silane, and their analogues. The transition state geometry of the reactions is determined by employing a 3-21G basis set. The total energies of reactant molecules at the initial, transition, and final states are calculated by employing a 6-31G** basis set. The exponential parts of the rate constants of these reactions determined from these energies on the basis of the transition state theory are in good agreement with the experimentally obtained relative rates of the reaction. The present calculation was consistent with the experimental results of photochemical reactions for methane and silane derivatives.

  14. On the impedance of galvanic cells XXVIII. The frequency-dependence of the electrode admittance for systems with first-order homogeneous chemical reactions and reactant adsorption occurring simultaneously

    NARCIS (Netherlands)

    Sluyters-Rehbach, M.; Sluyters, J.H.

    1969-01-01

    Equations are derived for the interfacial admittance of an electrode at which the electrode reaction O+neR occurs assuming that the charge transfer is infinitely fast and that either O or R is involved in a first-order homogeneous reaction delivering the substance Y, or that both O and R are involve

  15. Magnetohydrodynamic flow of a Casson fluid over an exponentially inclined permeable stretching surface with thermal radiation and chemical reaction

    Directory of Open Access Journals (Sweden)

    P. Bala Anki Reddy

    2016-06-01

    Full Text Available This article investigates the theoretical study of the steady two-dimensional MHD convective boundary layer flow of a Casson fluid over an exponentially inclined permeable stretching surface in the presence of thermal radiation and chemical reaction. The stretching velocity, wall temperature and wall concentration are assumed to vary according to specific exponential form. Velocity slip, thermal slip, solutal slip, thermal radiation, chemical reaction and suction/blowing are taken into account. The proposed model considers both assisting and opposing buoyant flows. The non-linear partial differential equations of the governing flow are converted into a system of coupled non-linear ordinary differential equations by using the similarity transformations, which are then solved numerically by shooting method with fourth order Runge–Kutta scheme. The numerical solutions for pertinent parameters on the dimensionless velocity, temperature, concentration, skin friction coefficient, the heat transfer coefficient and the Sherwood number are illustrated in tabular form and are discussed graphically.

  16. Volatile emission in dry seeds as a way to probe chemical reactions during initial asymptomatic deterioration

    Science.gov (United States)

    The nature and kinetics of reactions in dry seeds determines how long they survive. We used gas chromatography to assay volatile organic compounds (VOC) emitted from seeds of three unrelated species as a means to non-invasively probe chemical changes during very dry, dry and humid (15, 33 and 75% RH...

  17. Turkish, Indian, and American Chemistry Textbooks Use of Inscriptions to Represent "Types of Chemical Reactions"

    Science.gov (United States)

    Aydin, Sevgi; Sinha, Somnath; Izci, Kemal; Volkmann, Mark

    2014-01-01

    The purpose of this study was to investigate inscriptions used in "Types of Chemical Reactions" topic in Turkish, Indian, and American chemistry textbooks. We investigated both the types of inscriptions and how they were used in textbooks to support learning. A conceptual analysis method was employed to determine how those textbooks use…

  18. Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds

    Directory of Open Access Journals (Sweden)

    Triviño Juan C

    2010-04-01

    Full Text Available Abstract Background Global studies of the protein repertories of organisms are providing important information on the characteristics of the protein space. Many of these studies entail classification of the protein repertory on the basis of structure and/or sequence similarities. The situation is different for metabolism. Because there is no good way of measuring similarities between chemical reactions, there is a barrier to the development of global classifications of "metabolic space" and subsequent studies comparable to those done for protein sequences and structures. Results In this work, we propose a vectorial representation of chemical reactions, which allows them to be compared and classified. In this representation, chemical compounds, reactions and pathways may be represented in the same vectorial space. We show that the representation of chemical compounds reflects their physicochemical properties and can be used for predictive purposes. We use the vectorial representations of reactions to perform a global classification of the reactome of the model organism E. coli. Conclusions We show that this unsupervised clustering results in groups of enzymes more coherent in biological terms than equivalent groupings obtained from the EC hierarchy. This hierarchical clustering produces an optimal set of 21 groups which we analyzed for their biological meaning.

  19. Molecular Modeling as a Self-Taught Component of a Conventional Undergraduate Chemical Reaction Engineering Course

    Science.gov (United States)

    Rothe, Erhard W.; Zygmunt, William E.

    2016-01-01

    We inserted a self-taught molecular modeling project into an otherwise conventional undergraduate chemical-reaction-engineering course. Our objectives were that students should (a) learn with minimal instructor intervention, (b) gain an appreciation for the relationship between molecular structure and, first, macroscopic state functions in…

  20. Mapping Students' Modes of Reasoning When Thinking about Chemical Reactions Used to Make a Desired Product

    Science.gov (United States)

    Weinrich, M. L.; Talanquer, V.

    2016-01-01

    The central goal of this study was to analyze the complexity of students' explanations about how and why chemical reactions happen in terms of the types of causal connections students built between expressed concepts and ideas. We were particularly interested in characterizing differences in the types of reasoning applied by students with…

  1. Using Drawing Technology to Assess Students' Visualizations of Chemical Reaction Processes

    Science.gov (United States)

    Chang, Hsin-Yi; Quintana, Chris; Krajcik, Joseph

    2014-01-01

    In this study, we investigated how students used a drawing tool to visualize their ideas of chemical reaction processes. We interviewed 30 students using thinking-aloud and retrospective methods and provided them with a drawing tool. We identified four types of connections the students made as they used the tool: drawing on existing knowledge,…

  2. Two Experiments to Approach the Boltzmann Factor: Chemical Reaction and Viscous Flow

    Science.gov (United States)

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

    2012-01-01

    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…

  3. The Effective Concepts on Students' Understanding of Chemical Reactions and Energy

    Science.gov (United States)

    Ayyildiz, Yildizay; Tarhan, Leman

    2012-01-01

    The purpose of this study was to determine the relationship between the basic concepts related to the unit of "Chemical Reactions and Energy" and the sub-concepts underlying for meaningful learning of the unit and to investigate the effectiveness of them on students' learning achievements. For this purpose, the basic concepts of the unit…

  4. Impact of supersonic and subsonic aircraft on ozone: Including heterogeneous chemical reaction mechanisms

    Science.gov (United States)

    Kinnison, Douglas E.; Wuebbles, Donald J.

    1994-01-01

    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.

  5. Stepwise chemical reaction strategy for highly sensitive electrochemiluminescent detection of dopamine.

    Science.gov (United States)

    Zhang, Lei; Cheng, Yan; Lei, Jianping; Liu, Yueting; Hao, Qing; Ju, Huangxian

    2013-08-20

    A stepwise chemical reaction strategy based on the specific recognition of boronic acid to diol, and N-hydroxysuccinimide (NHS) ester to amine group, was designed to construct a "signal on" electrochemiluminescence (ECL) platform for highly sensitive detection of dopamine. A boronic acid-functionalized pyrene probe was synthesized and was self-assembled on the sidewalls of carbon nanotubes via π-π stacking interactions as capture probes on a glassy carbon electrode. Meanwhile, 3,3'-dithiodipropionic acid di(N-hydroxysuccinimide ester) (DSP)-functionalized CdTe quantum dots (QDs) were designed as signal probes and characterized with transmission electron microscopy and spectroscopic techniques. Upon stepwise chemical reaction of dopamine with boronic acid and then DSP-QDs, the QDs were captured on the electrode as ECL emitters for signal readout, leading to an ultralow background signal. By using O2 as an endogenous coreactant, the "signal on" ECL method was employed to quantify the concentration of dopamine from 50 pM to 10 nM with a detection limit of 26 pM. Moreover, the stepwise chemical reaction-based biosensor showed high specificity against cerebral interference and was successfully applied in the detection of dopamine in cerebrospinal fluid samples. The stepwise chemical reaction strategy should be a new concept for the design of highly selective analytical methods for the detection of small biomolecules.

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

    Science.gov (United States)

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

    2014-04-10

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

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

    Science.gov (United States)

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

    1984-01-01

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

  8. Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

    Directory of Open Access Journals (Sweden)

    Mukherjee Srabani

    2003-01-01

    Full Text Available During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP. Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches.

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

    Science.gov (United States)

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

    2016-08-18

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

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

    Directory of Open Access Journals (Sweden)

    Qiu-Hong Pan

    2008-12-01

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-09-01

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

  12. Balanced biochemical reactions: a new approach to unify chemical and biochemical thermodynamics.

    Directory of Open Access Journals (Sweden)

    Antonio Sabatini

    Full Text Available A novel procedure is presented which, by balancing elements and electric charge of biochemical reactions which occur at constant pH and pMg, allows assessing the thermodynamics properties of reaction Δ(rG'⁰, Δ(rH'⁰, Δ(rS'⁰ and the change in binding of hydrogen and magnesium ions of these reactions. This procedure of general applicability avoids the complex calculations required by the use of the Legendre transformed thermodynamic properties of formation Δ(fG'⁰, Δ(fH'⁰ and Δ(fS'⁰ hitherto considered an obligatory prerequisite to deal with the thermodynamics of biochemical reactions. As a consequence, the term "conditional" is proposed in substitution of "Legendre transformed" to indicate these thermodynamics properties. It is also shown that the thermodynamic potential G is fully adequate to give a criterion of spontaneous chemical change for all biochemical reactions and then that the use of the Legendre transformed G' is unnecessary. The procedure proposed can be applied to any biochemical reaction, making possible to re-unify the two worlds of chemical and biochemical thermodynamics, which so far have been treated separately.

  13. Chemical reactions at metallic and metal/semiconductor interfaces stimulated by pulsed laser annealing

    Science.gov (United States)

    Petit, E. J.; Caudano, R.

    1992-01-01

    Multilayer Al/Sb thin films have been evaporated on GaSb single crystals in ultra-high vacuum and pulsed-laser irradiated in-situ above the energy density threshold for surface melting. Superficial and interfacial chemical reactions have been characterized in-situ by Auger electron spectroscopy; and later, by X-ray photoelectron spectroscopy profiling, Rutherford backscattering spectrometry and scanning electron microscopy. The chemical reaction between the Al and Sb films is considered as a model reaction for laser-assisted synthesis of high-purity intermetallic compounds. The observation of a strong interfacial reaction between the melted film and the substrate is also a subject of great concern for optical data recording and laser alloying of ohmic contacts on semiconductors. We show that a suitable choice of the substrate and adding a low surface tension element into the metallic film can improve its stability during melting, and prevent inhomogeneous reaction and formation of holes, cracks and particles. Finally, other solutions are suggested to improve the control of these reactions.

  14. Miscible viscous fingering involving viscosity changes of the displacing fluid by chemical reactions

    Science.gov (United States)

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

    2010-02-01

    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.

  15. Unusual reaction paths of SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-: Quantum chemical calculations

    Science.gov (United States)

    Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.

    2013-11-01

    Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.

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

    Science.gov (United States)

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

    2014-10-30

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

  17. A general paradigm to model reaction-based biogeochemical processes in batch systems

    Science.gov (United States)

    Fang, Yilin; Yeh, Gour-Tsyh; Burgos, William D.

    2003-04-01

    This paper presents the development and illustration of a numerical model of reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions. The objective is to provide a general paradigm for modeling reactive chemicals in batch systems, with expectations that it is applicable to reactive chemical transport problems. The unique aspects of the paradigm are to simultaneously (1) facilitate the segregation (isolation) of linearly independent kinetic reactions and thus enable the formulation and parameterization of individual rates one reaction by one reaction when linearly dependent kinetic reactions are absent, (2) enable the inclusion of virtually any type of equilibrium expressions and kinetic rates users want to specify, (3) reduce problem stiffness by eliminating all fast reactions from the set of ordinary differential equations governing the evolution of kinetic variables, (4) perform systematic operations to remove redundant fast reactions and irrelevant kinetic reactions, (5) systematically define chemical components and explicitly enforce mass conservation, (6) accomplish automation in decoupling fast reactions from slow reactions, and (7) increase the robustness of numerical integration of the governing equations with species switching schemes. None of the existing models to our knowledge has included these scopes simultaneously. This model (BIOGEOCHEM) is a general computer code to simulate biogeochemical processes in batch systems from a reaction-based mechanistic standpoint, and is designed to be easily coupled with transport models. To make the model applicable to a wide range of problems, programmed reaction types include aqueous complexation, adsorption-desorption, ion-exchange, oxidation-reduction, precipitation-dissolution, acid-base reactions, and microbial mediated reactions. In addition, user-specified reaction types can be programmed into the model. Any reaction can be treated as fast/equilibrium or slow

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

    CERN Document Server

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

    2011-01-01

    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...

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

    Science.gov (United States)

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

    2015-02-11

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

  20. Review and analysis of high temperature chemical reactions and the effect of non-equilibrium conditions

    Science.gov (United States)

    Johnson, R. E.

    1986-01-01

    Chemical reactions at high temperatures have been considered extensively because of their importance to the heating effects on re-entry of space vehicles. Data on these reactions however, are not abundant and even when found there are discrepancies in data collected by various investigators. In particular, data for recombination reactions are calculated from the dissociation reactions or vice versa through the equilibrium constant. This involves the use of the principle of detailed balancing. This principle is discussed in reference to conditions where it is valid as well as to those where it is not valid. Related topics that merit further study or for which applicable information was available are briefly mentioned in an appendix to this report.