An efficient molecular dynamics simulation method for calculating the diffusion-influenced reaction rates

We present a molecular dynamics (MD) simulation method for calculating the diffusion-influenced reaction rates in the limit of low reactant concentrations. To calculate the reaction rate coefficient, we use MD trajectories of a nonreactive equilibrium system that are initiated with a pair of reactant molecules in reactive configuration. Hence reaction systems involving complicated reactant molecules with geometrically restricted reactivities can be treated with comparable efficiency as the simple hard-sphere reaction system. Compared to the similar MD method proposed by Van Beijeren, Dong, and Bocquet [J. Chem. Phys. 114, 6265 (2001)], the present method has a couple of advantages. First, reactions involving more general sink functions can be treated. Second, more accurate results can be obtained when the reaction probability upon collision is less than unity. As an application, we investigate the effects of nondiffusive dynamics and hydrodynamic interaction of reactants on the reaction rate.     

The Claus Reaction: VI. The Reaction Mechanism over a Sn–Mo Oxide Catalyst

Based on the comparison of reactant conversions in pulses on the stationary surface of the catalyst, the Claus reaction is found to occur via a stepwise mechanism. The nature of interaction of the SO₂ and H₂S molecules with the catalyst surface was studied by FTIR and UV–VIS spectroscopy and the reactivity of the adsorbed species was studied in situ. The intermediate adsorbed reactant species are determined. A scheme of the reaction mechanism over the Sn–Mo oxide catalyst is discussed.     

Effect of reactant size on discrete stochastic chemical kinetics

This paper is aimed at understanding what happens to the propensity functions (rates) of bimolecular chemical reactions when the volume occupied by the reactant molecules is not negligible compared to the containing volume of the system. For simplicity our analysis focuses on a one-dimensional gas of N hard-rod molecules, each of length l. Assuming these molecules are distributed randomly and uniformly inside the real interval [0,L] in a nonoverlapping way, and that they have Maxwellian distributed velocities, the authors derive an expression for the probability that two rods will collide in the next infinitesimal time dt. This probability controls the rate of any chemical reaction whose occurrence is initiated by such a collision. The result turns out to be a simple generalization of the well-known result for the point molecule case l=0: the system volume L in the formula for the propensity function in the point molecule case gets replaced by the "free volume" L-Nl. They confirm the result in a series of one-dimensional molecular dynamics simulations. Some possible wider implications of this result are discussed.     

Cavity Catalysis by Cooperative Vibrational Strong Coupling of Reactant and Solvent Molecules

Here, we report the catalytic effect of vibrational strong coupling (VSC) on the solvolysis of para‐nitrophenyl acetate (PNPA), which increases the reaction rate by an order of magnitude. This is observed when the microfluidic Fabry–Perot cavity in which the VSC is generated is tuned to the C=O vibrational stretching mode of both the reactant and solvent molecules. Thermodynamic experiments confirm the catalytic nature of VSC in the system. The change in the reaction rate follows an exponential relation with respect to the coupling strength of the solvent, indicating a cooperative effect between the solvent molecules and the reactant. Furthermore, the study of the solvent kinetic isotope effect clearly shows that the vibrational overlap of the C=O vibrational bands of the reactant and the strongly coupled solvent molecules is critical for the catalysis in this reaction. The combination of cooperative effects and cavity catalysis confirms the potential of VSC as a new frontier in chemistry.     

Autocatalysis and self-inhibition: coupled kinetic phenomena in the chlorite-tetrathionate reaction

The initial rate of formation of chlorine dioxide in the chlorite-tetrathionate reaction changes in an unusual fashion. The formal kinetic order of both reactants varies over a very wide range. Moreover, chlorite ion behaves not just as a simple reactant, but also as a self-inhibitor. A five-step scheme, derived from an eight-step mechanism, is proposed in which the autocatalytic formation of HOCl plays a central role in accounting for this kinetic behavior.     

溶液反应机理与动力学-2：影响因素与动力学方程的一般形式

对引起溶液反应与气相反应速率差异的因素进行了分析。指出大量溶剂分子的存在,并不会导致反应物分子之间的碰撞频率大幅度降低。除影响反应物活度和起催化作用之外,溶剂化和微观粘度是影响溶液反应速率的主要因素。微观粘度的影响可正可负,可能存在"负粘度"效应。基于简单碰撞理论和过渡态理论,给出了溶液反应速率公式的一般形式,可以综合活化能和微观粘度的影响。该方法可以比较合理地解释一些实验现象。     

Method of kinetic analysis of photodegradation: nifedipine in solutions

A rate equation for photodegradation was derived from Lambert-Beer's law and Grotthus-Draper's law: -dc/dt=k1(1-exp(-(k2c+k3(c0-c))))k2c/(k2c+k3(c0-c)) where c is the concentration of reactant, c0 is the initial concentration of reactant, t is time, k1 is the rate constant, and k2 and k3 are the absorption coefficient of reactant and its photodegradation product, respectively. In a case where the photodegradation products have no photoabsorption, k3 assumes the value of zero in the above general equation. In a case where the photodegradation products have the same spectrum and molar absorptivity as that of the reactant, k3 assumes the value of k2, and hence the photodegradation is not a first-order reaction; however, the equation itself gives the pseudo-first-order reaction rate equation. In a case where the concentration of reactant is high enough, the equation approaches a zero-order reaction rate equation. The photodegradation rate of nifedipine in solutions under a germicidal lamp, near an ultraviolet fluorescent lamp and a fluorescent lamp was analyzed using the above equation. The photodegradation rate was directly proportional to the amount of light absorbed, and fitted well with the equation. The above theoretical equation was substantiated by the photodegradation of nifedipine, and hence is expected to apply to other photosensitive drugs.     

Automatic determination of reaction mappings and reaction center information. 1. The imaginary transition state energy approach

Chemical reactions transform the reactant molecules by deleting existing and forming new bonds. The identification of these so-called reacting bonds is important for studying the reaction mechanism and for applications in metabolomics, e.g. for interpreting substrate labeling experiments. Here, we introduce an approach which suggests the simplest possible reaction center at the heavy atom level, with high accuracy. In contrast to current methods the approach is motivated by a simple theoretical model based on a crude approximation of the reaction energetics, and takes the complete reacting system into account. Finally, it recovers all optimal solutions to the problem while removing all symmetry-related, redundant solutions. We apply the method on the complete KEGG database of biochemical reactions, and compare our approach with previous methods. The resulting reaction centers are represented as imaginary transition states, which are molecule-like representations of reaction mechanisms. We provide the statistics of the calculations on the KEGG database and discuss some examples for the different types of alternative solutions found.     

Microimaging of Transient Concentration Profiles of Reactant and Product Molecules during Catalytic Conversion in Nanoporous Materials

Microimaging by IR microscopy is applied to the recording of the evolution of the concentration profiles of reactant and product molecules during catalytic reaction, notably during the hydrogenation of benzene to cyclohexane by nickel dispersed within a nanoporous glass. Being defined as the ratio between the reaction rate in the presence of and without diffusion limitation, the effectiveness factors of catalytic reactions were previously determined by deliberately varying the extent of transport limitation by changing a suitably chosen system parameter, such as the particle size and by comparison of the respective reaction rates. With the novel options of microimaging, effectiveness factors become accessible in a single measurement by simply monitoring the distribution of the reactant molecules over the catalyst particles.     

循环流动固定床光催化反应器动力学数学模拟

以甲基橙为模型反应物,研究了连续循环固定床光催化反应器的动力学过程.根据光催化氧化过程特点,分析并建立了准一级反应动力学方程,对该反应系统的动力学过程进行动态数学模拟,用四阶Runge-Kutta法进行数值计算,结果表明数学模拟与实验数据相吻合.在该光催化反应体系中,处理量增加时实际反应速率常数k基本不变,而表观反应速率常数kapp变小,二者之间关系与反应器体积对处理量体积比（γ）密切相关;反应速率常数受起始浓度影响很大,在15～150 μmol•L－1浓度范围内,lnk=－0.48ln[c0]＋1.42;反应速率常数与光强的关系为k∝I0.5;反应速率常数受溶液pH值的影响也很大.     

Acid-catalyzed hydrolysis of triacylglycerols obeys monoexponential kinetics

The acid-catalyzed hydrolyses of triacetyl-glycerol and of tributyryl-glycerol take place following a simple monoexponential kinetic scheme. The result can be interpreted as all three ester groups reacting with approximately the same specific rate. This observation reported in 1920 is unusual, because the intrinsic reactivities of primary and secondary esters are different, and because as far as the reaction proceeds, the remaining ester groups have neighboring hydroxyl groups, which undoubtly alter the reactivity of the reaction centers, relative to the situation in the initial reactant structure. The phenomenom can be explained by considering that local solvation effects due to neighboring hydrophylic groups remain unchanged as the transition-state complex is formed in all three stages of the reaction. © John Wiley & Sons, Inc.     

Molecular-dynamics simulations for nonclassical kinetics of diffusion-controlled bimolecular reactions

Molecular-dynamics simulations are presented for the diffusion-controlled bimolecular reaction A+B<==>C in two and three dimensions. The reactants and solvent molecules are modeled as spheres interacting via continuous potential-energy functions. The interaction potential between two reactants contains a deep well that results in a reaction. When the solvent concentration is low and the reactant dynamics is essentially ballistic, the system reaches equilibrium rapidly, and the reaction follows classical kinetics with exponential decay to the equilibrium. When the solvent concentration is high the particles enter the normal diffusion regime quickly and nonclassical behavior is observed, i.e., the reactant concentrations approach equilibrium as t(-d/2) where d is the dimensionality of space. When the reaction well depth is large, however, the reaction becomes irreversible within the simulation time. In this case the reactant concentrations decay as t(-d/4). Interestingly this behavior is also observed at intermediate times for reversible reactions.     

Applicability of two-membrane reactors for reversible gas phase reaction. Effects of flow patterns and inerts

The objective of this study is a comparative analysis of single and two-membrane reactor performances for isothermal reversible gas phase reaction. The effects of flow patterns (ideal mixing, cocurrent and countercurrent plug flow) and the presence of inert components were investigated. It is shown by simulation that for the pure reactant feed in absence of inerts, the performance of a two-membrane reactor is not significantly affected by the flow patterns, providing the pressure ratio is kept close to zero. Concerning the conversion efficiency in the case when the reactant is the slowest permeating component, the advantage of a two-membrane reactor is evident, it being least significant for countercurrent plug flow. In the presence of inerts in the separation zone, the advantage of a two-membrane reactor is maintained, while it is diminished by increasing inert flow rate in the reaction zone.     

The generalized transition state method

Current theories of unimolecular reaction rates are based on the transition state method which replaces internal reactant dynamics by an assumption of internal equilibrium. The present work is devoted to the development of generalized transition state method which allows effects such as nonergodicity and non-exponential decay to be accounted for within a simple theoretical framework. The derivation is quantum mechanical and not limited by any weak perturbation assumption. An effective hamiltonian is constructed for the reactant dynamics. The loss of amplitude due to reaction is accounted for by a dissipative term in the hamiltonian which is obtained on a phenomenological basis. The diagonalization of the hamiltonian allows the decay of reactant state to be predicted. The decay information is then used to set up a non-markovian master equation which in turn yields the rate coefficient for the reaction. The accuracy of the method is tested in one-dimensional model calculations in which particular attention is paid to decay by quantum mechanical tunneling through a potential barrier.     

Molecular beam measurements of small specific rate constants for unimolecular reactions

The investigation of unimolecular reactions with small rate constants is difficult owing to competing processes (inelastic collisions and bimolecular reactions) and the diffusion of reactant and product molecules out of the detection volume. For this reason, a new experimental approach for the measurement of specific rate constants in a molecular beam experiment has been exploited; instead of monitoring the temporal change of intensity as in a cell experiment, we monitor the spatial change along the molecular beam axis after laser excitation. For a given particle velocity the flight path between excitation and detection region defines the reaction time. By varying the distance the specific rate constant can be determined directly both from the decrease in the number density of reactant molecules as well as from the increase in product molecules. As a model system, the laser-induced (λ = 193 nm) photodissociation of mesitylene (trimethylbenzene) is studied. Previous experiments on the specific rate constant of mesitylene at this excitation energy differ between each other by about a factor of ten. By combining the new results with measurements at higher excitation energies, rate constants over a range of two orders of magnitude are now available for this reaction. The differences between the various experimental results are discussed within the framework of a statistical theory.     

GAS-PHASE PHOTOCATALYTIC OXIDATION OF CHCl CCl_2 AND Ph Me BY SUPPORTED TITANIA

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Electrical bias dependent photochemical functionalization of diamond surfaces

Diamond is an excellent substrate for many sensing and electronic applications because of its outstanding stability in biological and aqueous environments. When the diamond surface is H-terminated, it can be covalently modified with organic alkenes using wet photochemical methods that are surface-mediated and initiated by the ejection of electrons from the diamond. To develop a better understanding of the photochemical reaction mechanism, we examine the effect of applying an electrical bias to the diamond samples during the photochemical reaction. Applying a 1 V potential between two diamond electrodes significantly increases the rate of functionalization of the negative electrode. Cyclic voltammetry and electrochemical impedance measurements show that the 1 V potential induces strong downward band-bending within the diamond film of the negative electrode. At higher voltages a Faradaic current is observed, with no further acceleration of the functionalization rate. We attribute the bias-dependent changes in rate to a field effect, in which the applied potential induces a strong downward band-bending on the negative electrode and facilitates the ejection of electrons into the adjacent fluid of reactant organic alkenes. We also demonstrate the ability to directly photopattern the surface with reactant molecules on length scales of <25 microm, the smallest we have measured, using simple photomasking techniques.     

Scanning electrochemical microscopy #54. Application to the study of heterogeneous catalytic reactions-hydrogen peroxide decomposition

A scanning electrochemical microscopy (SECM) approach for the analysis of heterogeneous catalytic reactions at solid-liquid interfaces is described and applied. In this scheme, reactant, generated at a tip, undergoes a reaction (e.g., disproportionation) at the substrate. The theoretical background for this study, performed by digital simulations using a finite difference method, considers a chemical reaction at the substrate with general stoichiometry. In this case, the fraction of regenerated mediator (nu(S)) may differ with respect to a substrate reaction that is the reverse of the tip reaction, resulting in an asymmetric mediator loop. Simulated tip current transients and approach curves at different values of the kinetic rate constant for reactions where nu(S) < 1 were used to analyze this new SECM situation. This approach was used to study the catalytic decomposition of hydrogen peroxide (HO2- --> 1/2O2 + OH-), where nu(S) = 0.5, on supported catalysts. A gold-mercury amalgam tip was used to quantitatively reduce dissolved O2 (mediator) to HO2-, which was decomposed back to oxygen at the catalyst substrate. Rate constants for the decomposition reaction on immobilized catalase and Pt particles were measured at different pH values by the correlation of experimental approach curves with the theoretical dependencies.     

Analytical solution of nonlinear diffusion processes in modified electrode

The system of coupled nonlinear diffusion equations are solved analytically for the transport and kinetics of electrons and reactant in the layer of a modified electrode. Analytical expressions of concentrations of mediator and substrate are presented using Homotopy perturbation method. A simple expression of electrochemical rate constant K _ME⁺ is also obtained for all values of reaction parameters. The available limiting case results are compared with our results and are found to be in good agreement.