动力学方程控制表面反应的模拟模型和方法

提出了动力学方程控制表面反应的模拟模型和方法.该模型从最基本的质量作用定律出发,获得表面反应的动力学方程.而表面反应通过格子模拟反应器进行.通过表面催化样板反应"CO表面催化氧化"检验了该模拟模型和方法,与实验结果吻合.该模型可在其它复杂的表面催化反应体系中推广应用.     

A multiscale model for kinetics of formation and disintegration of spherical micelles

Dynamics of self-assembly and structural transitions in surfactant systems often involve a large span of length and time scales. A comprehensive understanding of these processes requires development of models connecting phenomena taking place on different scales. In this paper, we develop a multiscale model for formation and disintegration of spherical nonionic micelles. The study is performed under the assumption that the dominant mechanism of micelle formation (disintegration) is a stepwise addition (removal) of single monomers to (from) a surfactant aggregate. Different scales of these processes are investigated using a combination of coarse-grained molecular dynamics simulations, analytical and numerical solution of stochastic differential equations, and a numerical solution of kinetic equations. The removal of a surfactant from an aggregate is modeled by a Langevin equation for a single reaction coordinate, the distance between the centers of mass of the surfactant and the aggregate, with parameters obtained from a series of constrained molecular dynamics simulations. We demonstrate that the reverse process of addition of a surfactant molecule to an aggregate involves at least two additional degrees of freedom, orientation of the surfactant molecule and micellar microstructure. These additional degrees of freedom play an active role in the monomer addition process and neglecting their contribution leads to qualitative discrepancies in predicted surfactant addition rates. We propose a stochastic model for the monomer addition which takes the two additional degrees of freedom into account and extracts the model parameters from molecular dynamics simulations. The surfactant addition rates are determined from Brownian dynamics simulations of this model. The obtained addition and removal rates are then incorporated into the kinetic model of micellar formation and disintegration.     

The influence of solvation and finite temperatures on theWittig reaction: A theoretical study

The effects of the solvent and finite temperature (entropy) on the Wittig reaction are studied by using density functional theory in combination with molecular dynamics and a continuum solvation model. Standard gas-phase zero-temperature calculations are found to give similar results to previous studies. Gas-phase dynamics simulations allow the free energy profile of the reaction to be calculated through thermodynamic integration. The free energy profile is found to have a significant entropic barrier to the addition step of the reaction where only a small barrier was present in the potential energy curve. The introduction of the solvent dimethyl sulfoxide causes a change in the structure of the intermediate from the oxaphosphetane structure to the dipolar betaine structure. The overall reaction energy is changed only slightly. When the effects of both entropy and the solvent are included a significant entropic barrier to the addition reaction is obtained and the predicted intermediate again has the betaine structure.     

Independent trajectory implementation of the semiclassical Liouville method: application to multidimensional reaction dynamics

We describe an independent trajectory implementation of semiclassical Liouville method for simulating quantum processes using classical trajectories. In this approach, a single ensemble of trajectories describes all semiclassical density matrix elements of a coupled electronic state problem, with the ensemble evolving classically under a single reference Hamiltonian chosen on the basis of physical grounds. In this paper, we introduce an additional uncoupled trajectory approximation, allowing the members of the ensemble to evolve independently of one another and eliminating the major computational costs of our previous coupled trajectory implementation. The accuracy of the method is demonstrated for model one-dimensional problems. In addition, the approach is applied to the chemical reaction dynamics of a collinear triatomic system, yielding excellent agreement with exact calculations. This method allows molecular dynamics involving coupled electronic surfaces to be modeled with essentially the same effort as classical molecular dynamics and ensemble averaging.     

Dynamic and reversible self-assembly of photoelectrochemical complexes based on lipid bilayer disks, photosynthetic reaction centers, and single-walled carbon nanotubes

An aqueous solution containing photosynthetic reaction centers (RCs), membrane scaffold proteins (MSPs), phospholipids, and single-walled carbon nanotubes (SWCNTs) solubilized with the surfactant sodium cholate (SC) reversibly self-assembles into a highly ordered structure upon dialysis of the latter. The resulting structure is photoelectrochemically active and consists of 4-nm-thick lipid bilayer disks (nanodisks, NDs) arranged parallel to the surface of the SWCNT with the RC housed within the bilayer such that its hole injecting site faces the nanotube surface. The structure can be assembled and disassembled autonomously with the addition or removal of surfactant. We model the kinetic and thermodynamic forces that drive the dynamics of this reversible self-assembly process. The assembly is monitored using spectrofluorimetry during dialysis and subsequent surfactant addition and used to fit a kinetic model to determine the forward and reverse rate constants of ND and ND-SWCNT formation. The calculated ND and ND-SWCNT forward rate constants are 79 mM(-1) s(-1) and 5.4 × 10(2) mM(-1) s(-1), respectively, and the reverse rate constants are negligible over the dialysis time scale. We find that the reaction is not diffusion-controlled since the ND-SWCNT reaction, which consists of entities with smaller diffusion coefficients, has a larger reaction rate constant. Using these rate parameters, we were able to develop a kinetic phase diagram for the formation of ND-SWCNT complexes, which indicates an optimal dialysis rate of approximately 8 × 10(-4) s(-1). We also fit the model to cyclic ND-SWCNT assembly and disassembly experiments and hence mimic the thermodynamic forces used in regeneration processes detailed previously. Such forces may form the basis of both synthetic and natural photoelectrochemical complexes capable of dynamic component replacement and repair.     

On the origin of altered diastereomeric ratios for anionic versus neutral reaction conditions in the oxy-Cope/ene reaction: an interplay of experiment and computational modeling

We report herein a detailed investigation into the reaction mechanism for a sequential oxy-Cope/ene reaction under anionic conditions. With DFT calculations and ab initio molecular dynamics simulations, the observed diastereoselectivity is shown to be the result of an isomerization of the enolate olefin, which would evidently not occur under neutral conditions. The potential energy surface was thoroughly mapped out for the reaction pathways and the proposed mechanism confirmed the different product distributions observed under neutral and anionic oxy-Cope conditions. In addition, other possible pathways are shown to be higher in energy and experimental evidence is given that supports the olefin-isomerization pathway.     

Dichlorocarbene addition to cyclopropenes: a computational study

Reaction paths for addition of dichlorocarbene to 1,2-disubstituted cyclopropenes were calculated using hybrid density functional theory (B3LYP/6-31G) in the gas phase and in the presence of a continuum solvation model corresponding to acetonitrile. In both the gas phase and acetonitrile, :CCl2-cyclopropene addition follows an asymmetric, non-least-motion approach. Barriers to addition range from 0 to 2 kcal/mol. The reactions proceed in concerted fashion in both the gas phase and solution to yield 1,3-dienes or bicyclobutanes. The reaction pathway on this complex potential energy surface of this reaction appears to bifurcate, and the product distribution is believed to be controlled by reaction dynamics. At the present level of theory, there appears to be no minimum on the potential energy surface corresponding to a dipolar intermediate.     

Hybrid molecular dynamics simulations of living filaments

We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.     

Oscillatory dynamics protect enzymes and possibly cells against toxic substances

We have used the oscillating peroxidase-oxidase (PO) reaction as a model system to study how oscillatory dynamics may affect the influence of toxic reaction intermediates on enzyme stability. In the peroxidase-oxidase reaction reactive intermediates, such as hydrogen peroxide, superoxide, and hydroxyl radical are formed. Such intermediates inactivate many cellular macromolecules such as proteins and nucleic acids. These reaction intermediates also react with peroxidase itself to form an inactive enzyme. The fact that the PO reaction shows bistability between an oscillatory and a steady state gives us a unique possibility to compare such inactivation when the system is in one of these two states. We show that inactivation of peroxidase is slower when the system is in an oscillatory state, and using numerical simulations we provide evidence that oscillatory dynamics lower the average concentration of the reactive intermediates.     

Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch

In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.     

Reaction coordinates and transition pathways of rare events via forward flux sampling

A new approach is developed for identifying suitable reaction coordinates to describe the progression of rare events in complex systems. The method is based on the forward flux sampling (FFS) technique and standard least-square estimation (LSE) and it is denoted as FFS-LSE. The FFS algorithm generates trajectories for the transition between stable states as chains of partially connected paths, which can then be used to obtain "on-the-fly" estimates for the committor probability to the final region, p(B). These p(B) data are then used to screen a set of candidate collective properties for an optimal order parameter (i.e., reaction coordinate) that depends on a few relevant variables. LSE is used to find the coefficients of the proposed reaction coordinate model and an analysis of variance is used to determine the significant terms in the model. The method is demonstrated for several test systems, including the folding of a lattice protein. It is shown that a simple approximation to p(B) via a model linear on energy and number of native contacts is sufficient to describe the intrinsic dynamics of the protein system and to ensure an efficient sampling of pathways. In addition, since the p(B) surface found from the FFS-LSE approach leads to the identification of the transition state ensemble, mechanistic details of the dynamics of the system can be readily obtained during a single FFS-type simulation without the need to perform additional committor simulations.     

Quantum force molecular dynamics study of the reaction of O atoms with HOCO

The reaction of HOCO with O atoms has been studied using a direct ab initio dynamics approach based on the scaling all correlation UCCD/D95(d,p) method. Ab initio calculations point to two possible reaction mechanisms for the O+HOCO-->OH+CO2 reaction. They are a direct hydrogen abstraction and an oxygen addition reaction through a short-lived HOC(O)O intermediate. The dynamics results show that only the addition mechanism is important under the conditions considered here. The lifetime of the HOC(O)O complex is predicted to be 172+/-15 fs. This is typical of a direct and fast radical-radical reaction. At room temperature, the calculated thermal rate coefficient is 1.44 x 10(-11) cm(3) mol(-1) s(-1) and its temperature dependence is rather weak. The two kinds of reactive trajectories are illustrated in detail.     

Period-doubling and chaotic oscillations in the ferroin-catalyzed Belousov-Zhabotinsky reaction in a CSTR

The ferroin-catalyzed Belousov-Zhabotinsky(BZ) reaction,the oxidation of malonic acid by acidic bromate,is the most commonly investigated chemical system for understanding spatial pattern forma-tion. Various oscillatory behaviors were found from such as mixed-mode and simple period-doubling oscillations and chaos on both Pt electrode and Br-ISE at high flow rates to mixed-mode oscillations on Br-ISE only at low flow rates. The complex dynamic behaviors were qualitatively reproduced with a two-cycle coupling model proposed initially by Gy?rgyi and Field. This investigation offered a proper medium for studying pattern formation under complex temporal dynamics. In addition,it also shows that complex oscillations and chaos in the BZ reaction can be extended to other bromate-driven nonlinear reaction systems with different metal catalysts.     

The femtosecond dynamics of electron transfer in a modified photosynthesis reaction center: Quantum, classical, and kinetic analyses

The dynamics of electron transfer in a modified photosynthesis reaction center in which electron transfer from the bridge to the acceptor is blocked is considered. A microscopic model of the process is suggested. Within this model, the diabatic electronic states of the donor and bridge are described by one-dimensional displaced harmonic oscillators. The dynamics of the population of electronic states is calculated by the quantum method of wave packets and classical and kinetic modeling. The suggested model is used to study the qualitative dependence of the dynamics of electron transfer on the nonadiabatic interaction potential. The parameters of the model are determined by comparing the experimental and calculated absorption spectra of the product of electron transfer. It is shown that kinetic models can be used to approximately describe the dynamics of electron transfer in reaction centers. The boundaries of the applicability of the kinetic method are considered.     

Period-doubling and chaotic oscillations the ferroin-catalyzed Belousov-Zhabotinsky reaction in a CSTR

The ferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction, the oxidation of malonic acid by acidic bromate, is the most commonly investigated chemical system for understanding spatial pattern formation. Various oscillatory behaviors were found from such as mixed-mode and simple period-doubling oscillations and chaos on both Pt electrode and Br-ISE at high flow rates to mixed-mode oscillations on Br-ISE only at Iow flow rates. The complex dynamic behaviors were qualitatively reproduced with a two-cycle coupling model proposed initially by Gy(o)rgyi and Field. This investigation offered a proper medium for studying pattern formation under complex temporal dynamics. In addition, it also shows that complex oscillations and chaos in the BZ reaction can be extended to other bromate-driven nonlinear reaction systems with different metal catalysts.     

Excited state dynamics and catalytic mechanism of the light-driven enzyme protochlorophyllide oxidoreductase

The reduction of protochlorophyllide (Pchlide) to chlorophyllide, catalysed by the enzyme protochlorophyllide oxidoreductase (POR), is the penultimate step in the chlorophyll biosynthetic pathway and is a key light-driven reaction that triggers a profound transformation in plant development. As POR is light-activated it can provide new information on the way in which light energy can be harnessed to power enzyme reactions. Consequently, POR presents a unique opportunity to study catalysis at low temperatures and on ultrafast timescales, which are not usually accessible for the majority of enzymes. Recent advances in our understanding of the catalytic mechanism of POR illustrate why it is an important model for studying enzyme catalysis and reaction dynamics. The reaction involves the addition of one hydride and one proton, and catalysis is initiated by the absorption of light by the Pchlide substrate. As the reaction involves the Pchlide excited state, a variety of ultrafast spectroscopic measurements have shown that significant parts of the reaction occur on the picosecond timescale. A number of excited state Pchlide species, including an intramolecular charge transfer complex and a hydrogen bonded intermediate, are proposed to be required for the subsequent hydride and proton transfers, which occur on the microsecond timescale. Herein, we review spectroscopic investigations, with a particular focus on time-resolved transient absorption and fluorescence experiments that have been used to study the excited state dynamics and catalytic mechanism of POR.     

A simple picture for the rotational enhancement of the rate for the F + HCl --> HF + Cl reaction: a dynamical study using a new ab initio potential energy surface

Quantum scattering calculations for the reaction F + HCl --> HF + Cl are performed on a new ground-state ab initio potential energy surface. The reagent rotation is found to have a dramatic effect on the reaction probability. Furthermore, the exit channel rotational thresholds leave a strong imprint on the reaction probabilities and even on the cumulative reaction probability. A very simple vibrationally adiabatic model is shown to account for most aspects of the reaction dynamics. In this model, the fast vibrational motion is adiabatically eliminated leaving the key reaction dynamics represented by a reduced atom + rotor collision. The shape of the adiabatic potential surface immediately yields to a simple and intuitive interpretation for the rotational enhancement of the rate. The rotational enhancement is shown to be an effect of the entrance channel dynamics of the atom-rotor problem.