Treatment Of Chemical Reactions Research Articles

Exploiting the quantum mechanically derived force field for functional materials simulations

The computational design of functional materials relies heavily on large-scale atomistic simulations. Such simulations are often problematic for conventional classical force fields, which require tedious and time-consuming parameterization of interaction parameters. The problem can be solved using a quantum mechanically derived force field (QMDFF)—a system-specific force field derived directly from the first-principles calculations. We present a computational approach for atomistic simulations of complex molecular systems, which include the treatment of chemical reactions with the empirical valence bond approach. The accuracy of the QMDFF is verified by comparison with the experimental properties of liquid solvents. We illustrate the capabilities of our methodology to simulate functional materials in several case studies: chemical degradation of material in organic light-emitting diode (OLED), polymer chain packing, material morphology of organometallic photoresists. The presented methodology is fast, accurate, and highly automated, which allows its application in diverse areas of materials science.

Development of a hybrid model to quantify the single and double strand breaks following the iron 57 de-excitation

The therapeutic utility of certain Auger emitters such as iodine-125 depends on their position within the cell nucleus. Or diagnostically, and to maintain as low as possible cell damage, it is preferable to have radionuclide localized outside the cell or at least the core. One solution to this problem is to consider markers capable of conveying anticancer drugs to the tumor site regardless of their location within the human body. The objective of this study is to simulate the impact of a complex such as bleomycin on single and double strand breaks in the DNA molecule. Indeed, this simulation consists of the following transactions: Construction of BLM -Fe- DNA complex, simulation of the electron’s transport from the metastable state excitation of Fe 57 by the Monte Carlo method, treatment of chemical reactions in the considered environment by the diffusion equation. For physical, physico-chemical and finally chemical steps, the geometry of the complex is considered as a sphere of 50 nm centered on the binding site , and the mathematical method used is called step by step based on Monte Carlo codes.

Vortices generation in the reactive flow on the evaporative surface

Vortices generation and flow dynamics are investigated by a numerical calculation with LES methodology on the evaporative surface including chemical reactions. For simplicity, fuel is radially injected from the surface in order to decouple pyrolysis of solid fuel from the governing equation and consideration of heat transfer balance. Nevertheless its simple treatment of chemical reactions and fuel pyrolysis, numerical results captured very fundamental understandings in terms of averaged temperature, velocity profile, and mixture fraction distribution. Results showed that a well-defined turbulent velocity profile at the inlet becomes twisted and highly wrinkled in the downstream reaching the maximum velocity at far above the surface, where the flame is located. And the thickness of boundary layer increases in the downstream due to the enhanced interaction of axial flow and mass injection from the surface. Also, chemical reaction appears highly active and partially concentrated along the plane where flow condition is in stoichiometric. In particular, flame front locates at the surface where mixture fraction Z equals to 0.07. Flame front severely wrinkles in the downstream by the interaction with turbulences in the flow. Partial reactions on the flame front contribute to produce hot spots periodically in the downstream attaining the max temperature at the center of each spot. This may take the role of additional unsteady heat generations and pressure perturbations in the downstream. Future study will focus on the evolution of hot spots and pressure perturbations in the post chamber of lab scale hybrid rocket motors.

Teaching chemical change modeling to Tunisian students: an “expanded chemistry triplet” for analyzing teachers' discourse

Through a comparative analysis of the chemical content of three teachers' discourse; we propose to give answers to the question: “how is the connection between the experiential level and the generally accepted representation of the three levels of chemistry presented by teachers to Tunisian students, during their first contact with chemical change modeling”. We chose to perform the analysis using an “expanded chemistry triplet” to represent the different levels and their possible connections to the elements of knowledge taught. These elements of knowledge, called facets, included definitions, representations and rules used by the teachers to convey the meaning. While there was some difference in priorities between the three teachers with regard to teaching content, the connection between the experiential field and the three levels of representation of chemistry was only partially taught by all. It is the description, the interpretation and the representation of objects and events of the experiential field at the macroscopic level that are strongly in the majority. On the other hand, interest in the sub-microscopic level and clarification of the procedures to implement for the quantitative treatment of chemical reactions seems insufficient. The responsibility is thus left to the students to acquire a large amount of knowledge and expertise. These observations led us to formulate proposals for improving the teaching of chemical reactions and teacher training.

A fully-coupled flow-reactive-transport formulation based on element conservation, with application to CO2 storage simulations

A numerical simulation framework for coupled multiphase flow, multicomponent transport and geochemical reactions in porous media is presented. The approach is an element-based formulation that combines the compositional modeling capabilities used in oil reservoir simulation with the treatment of chemical reactions used in groundwater modeling. The procedure employs a conservative finite-volume method with a fully-implicit treatment in time in order to preserve the nonlinear coupling of flow, transport, reactions, and mass transfer across phases. Phase behavior is described using cubic equations of state. In this framework, all the governing equations and associated constraints are cast in discrete residual form, such that any variable, or coefficient, can depend on any other variable in the problem. Prior to linearization, which is applied to construct the Jacobian matrix, no algebraic or analytic manipulation need be performed to reduce the nonlinear sets of equations and unknowns. Once the complete Jacobian matrix is assembled, a series of algebraic reductions (Schur complements), of the type used in compositional reservoir simulation, are performed to reduce the number of discrete equations that must be solved simultaneously. A GMRES solution strategy with CPR (Constrained Pressure Residual) preconditioning is applied to solve the reduced linear system. We demonstrate the formulation using two CO2 sequestration problems, one of which involves chemical reactions. The simulations demonstrate the efficiency and applicability of the overall procedure for modeling the long-term fate of sequestered CO2.

A numerical evaluation of global oceanic emissions of α-pinene and isoprene

Abstract. A numerical evaluation of global oceanic emissions of α-pinene and isoprene based on both "bottom-up" and "top-down" methods is presented. We infer that the global "bottom-up" oceanic emissions of α-pinene and isoprene are 0.013 TgC yr−1 and 0.32 TgC yr−1, respectively. By constraining global chemistry model simulations with the shipborne measurement of Organics over the Ocean Modifying Particles in both Hemispheres summer cruise, we derived the global "top-down" oceanic α-pinene source of 29.5 TgC yr−1 and isoprene source of 11.6 TgC yr−1. Both the "bottom-up" and "top-down" values are subject to large uncertainties. The incomplete understanding of the in-situ phytoplankton communities and their range of emission potentials significantly impact the estimated global "bottom-up" oceanic emissions, while the estimated total amounts of the global "top-down" oceanic sources can be influenced by emission parameterizations, model and input data spatial resolutions, boundary layer mixing processes, and the treatments of chemical reactions. The global oceanic α-pinene source and its impact on organic aerosol formation is significant based on "top-down" method, but is negligible based on "bottom-up" approach. Our research highlights the importance of carrying out further research (especially measurements) to resolve the large offset in the derived oceanic organic emission based on two different approaches.

Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: A ubiquinol complex in solution

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schrodinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schrodinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes in this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems.

A Novel Radiation Exposure Control Apparatus For Microwave Assisted Chemical Reactions

A radiation exposure control apparatus is used for microwave (2.45 GHz) treatment of chemical reactions in controlled and reproducible conditions. A spectrophotometer has been interfaced with the microwave set-up in order to monitor the reaction evolution in situ. Both numerical and experimental dosimetries are carried out in order to evaluate the field distribution within the sample. Finally, particular working conditions are suggested.

A coupled reactive chemical transport model:: mixing cell model with two solid phases and its application

A research tool for modeling the reactive flow and transport of groundwater contaminants in a one-dimensional scheme is presented. The use of a mixing cell concept with two solid phases for hydrological transport, and the incorporation of chemical reactions, recoil processes and phase transformation of minerals are some features of the model that make it a versatile research tool for the modeling of a wide variety of laboratory and field experiments. The treatment of chemical reactions is general so that the model can deal with aqueous complexation, adsorption, ion exchange, precipitation reaction, and decay reaction. The model has been applied to the analysis of uranium data obtained from the weathered zone of Koongarra uranium ore deposit in Australia, which illustrates some of these features.

The modeling of chemical reactions and thermochemical nonequilibrium in particle simulation computations

The treatment of chemical reactions and nonequilibrium energy exchange in Direct Simulation Monte Carlo calculations is examined. Details of a Maximum Entropy chemical reaction model are presented that is based on the classical scheme devised by Levine and Bernstein. Data are given for all of the significant reactions that occur in hypersonic reentry flight into the atmospheres of the Earth, Mars, and Venus. The method is an extension of that described and used previously by the authors (Gallis and Harvey [J. Fluid Mech. 312, 149 (1996); AIAA J. 34(7), 1378 (1996)]) and now includes carbon dioxide/nitrogen and ionic reactions. The model allows an appropriate dependence of each reaction on its controlling energy mode and avoids inappropriate use of equilibrium distributions to determine the reaction probabilities and post-collision energy reallocation. Sample flow solutions are given and comparisons are made with results obtained using continuum solvers.

Premixed Laminar Flames in Impinging Flows

The flat laminar flames arising from the flow of reactants from a jet against a wall are analyzed. If the velocity of the reactants exiting from the jet is suitably high, the flame is adjacent to the wall; this is the case treated in previous studies. However, if either the jet velocity is reduced and/or the chemical kinetics enhanced, the flame is separated from the wall. Here both cases are systematically treated. As a consequence of the generality dealt with a large number of thermo-chemical and aerothermodynamic parameters are shown to be significant in characterizing these flames but two asymptotic analyses simplify their description; one relates to the treatment of chemical reactions and results in a thin reaction zone surrounded by chemically inert regions. The second applies when the Reynolds number is large and separates the flow into one or two viscous regions and one or two inviscid regions. Either when the rate of strain is large and the flame adjacent to the wall or when the Reynolds number is small, heat transfer to the wall is shown to influence the behavior of the flame. Comparison is made with data on the axial velocity in a flame displaced from a separation streamline which can be interpreted as a wall within the context of the present analysis.

Semi-classical treatment of chemical reactions

Abstract We investigate the full 3D semi-classical method for treating chemical reactions in hyperspherical coordinates. Two degrees of freedom are treated quantum mechanically, but the full classical dynamics is included for the remaining degrees of freedom. The method has been used for obtaining cross-sections for the reactions D + H2 → DH + H and D+ + H2 → DH+ + H, DH + H+, D + H2+. A new projection technique for rotationally averaged cross sections is suggested.

THEORETICAL STUDIES OF CHEMICAL REACTIONS IN A LASER FIELD

Semiclassical and quantum mechanical approaches for describing the F + H -*• HF + H reaction in a laser field are summarized. For a laser-assisted reaction where the molecular system forms a van der Waals complex, such as He + T 0, a theory which combines radiative resonance formation with predissociation is suggested. During the past decade, both theory and experiment have indicated that laser radiation can significantly modify the dynamics of a molecular collision process, where the radiation need not be resonant with the asymptotic energy levels of the collision system. The collision process which is perhaps of most interest to chemists is the chexn-Lcat fina.cJxon, where bonds are broken and new bonds are formed. In this paper we discuss several theoretical treatments of chemical reactions in a laser field. We shall begin in Section II with a study of the F + H„ •* HF + H reaction and its isotopic variants. Our main focus will be on semiclassical techniques, although quantum mechanical techniques will also be mentioned. We shall look at effects due to the variation of the laser intensity and frequency, isotopic substitution and the variation of the collision energy. We shall then turn in Section III to a laser-assisted reaction where the molecular system forms a van der Waals complex, such as the He + I„ collision system. Our interest here is in^resonance formation, whereby the laser intensity can be low (less than a kW/cm ). The mechanism which we shall consider is one where the van der Waals complex is converted to products by laser-induced predissociation. Section III is the Summary. I. Semiclassical and quantum mechanical approaches In this section, we review some of the theoretical results which we have obtained for the collinear chemical reaction

Relativistic thermodynamics of fluids. I

In 1953, Stueckelberg and Wanders derived the basic laws of relativistic linear nonequilibrium thermodynamics for chemically reacting fluids from the relativistic local conservation laws for energy-momentum and the local laws of production of substances and of non-negative entropy production by the requirement that the corresponding currents (assumed to depend linearly on the first derivatives of the state variables) should not be independent. Generalizing their method, we determine the most general allowed form of the energy-momentum tensor T αβ and of the corresponding rate of entropy production under the same restriction on the currents. The problem of expressing this rate in terms of thermodynamic forces and fluxes is discussed in detail; it is shown that the number of independent forces is not uniquely determined by the theory, and several possibilities are explored. A number of possible new cross effects are found, all of which persist in the Newtonian (low-velocity) limit. The treatment of chemical reactions is incorporated into the formalism in a consistent manner, resulting in a derivation of the law for rate of production, and in relating this law to transport processes differently than suggested previously. The Newtonian limit is discussed in detail to establish the physical interpretation of the various terms of T αβ . In this limit, the interpretation hinges on that of the velocity field characterizing the fluid. If it is identified with the average matter velocity following from a consideration of the number densities, the usual local conservation laws of Newtonian nonequilibrium thermodynamics are obtained, including that of mass. However, a slightly different identification allows conversion of mass into energy even in this limit, and thus a macroscopic treatment of nuclear or elementary particle reactions. The relation of our results to previous work is discussed in some detail.

A quasi-one-dimensional treatment of chemical reactions in turbulent wakes of hypersonic objects

A quasi-one-dimensional treatment of chemical reactions in turbulent wakes of hypersonic objects