Molecular dynamics simulation description

Progress in the theoretical description of reaction rates in solution of course correlates strongly with that in other theoretical disciplines, in particular those which have profited most from the enonnous advances in computing power such as quantum chemistry and equilibrium as well as non-equilibrium statistical mechanics of liquid solutions where Monte Carlo and molecular dynamics simulations in many cases have taken on the traditional role of experunents, as they allow the detailed investigation of the influence of intra- and intemiolecular potential parameters on the microscopic dynamics not accessible to measurements in the laboratory. No attempt, however, will be made here to address these areas in more than a cursory way, and the interested reader is referred to the corresponding chapters of the encyclopedia. 

The principal idea behind the CSP approach is to use input from Classical Molecular Dynamics simulations, carried out for the process of interest as a first preliminary step, in order to simplify a quantum mechanical calculation, implemented in a subsequent, second step. This takes advantage of the fact that classical dynamics offers a reasonable description of many properties of molecular systems, in particular of average quantities. More specifically, the method uses classical MD simulations in order to determine effective... 

The flat interface model employed by Marcus does not seem to be in agreement with the rough picture obtained from molecular dynamics simulations [19,21,64-66]. Benjamin examined the main assumptions of work terms [Eq. (19)] and the reorganization energy [Eq. (18)] by MD simulations of the water-DCE junction [8,19]. It was found that the electric field induced by both liquids underestimates the effect of water molecules and overestimates the effect of DCE molecules in the case of the continuum approach. However, the total field as a function of the charge of the reactants is consistent in both analyses. In conclusion, the continuum model remains as a good approximation despite the crude description of the liquid-liquid boundary. 

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. 

Demchenko AP, Yesylevskyy SO (2009) Nanoscopic description of biomembrane electrostatics results of molecular dynamics simulations and fluorescence probing. Chem Phys Lipids 160(2) 63-84... 

This sequence of states is a discrete representation of the continuous dynamical trajectory starting from zo at time t = 0 and ending at z at time t = . Such a discrete trajectory may, for instance, result from a molecular dynamics simulation, in which the equations of motion of the system are integrated in small time steps. A trajectory can also be viewed as a high-dimensional object whose description includes time as an additional variable. Accordingly, the discrete states on a trajectory are also called time slices. 

One example of the use of semiempirical methodology is provided in an article detailing a molecular-dynamics simulation of the beta domain of metallothionein with a semiempirical treatment of the metal core.73 The beta domain of rat liver metallothionein-2 contains three-metal centers. In this study, three molecular variants with different metal contents—(1) three cadmium ions, (2) three zinc ions, and (3) one cadmium ion and two zinc ions—were investigated using a conventional molecular dynamics simulation, as well as a simulation with a semiempirical quantum chemical description (MNDO and MNDO/d) of the metal core embedded in a classical environment. For the purely classical simulations, the standard GROMOS96 force-field parameters were used, and parameters were estimated for cadmium. The results of both kinds of simulations were compared to each other... 

This volume of Modem Aspects covers a wide spread of topics presented in an authoritative, informative and instructive manner by some internationally renowned specialists. Professors Politzer and Dr. Murray provide a comprehensive description of the various theoretical treatments of solute-solvent interactions, including ion-solvent interactions. Both continuum and discrete molecular models for the solvent molecules are discussed, including Monte Carlo and molecular dynamics simulations. The advantages and drawbacks of the resulting models and computational approaches are discussed and the impressive progress made in predicting the properties of molecular and ionic solutions is surveyed. 

The complications for fhe fheoretical description of proton fransporf in the interfacial region befween polymer and water are caused by the flexibility of fhe side chains, fheir random distributions at polymeric aggregates, and their partial penetration into the bulk of water-filled pores. The importance of an appropriate flexibilify of hydrated side chains has been explored recently in extensive molecular modeling studies. Continuum dielectric approaches and molecular dynamics simulations have been utilized to explore the effects of sfafic inferfacial charge distributions on proton mobility in single-pore environments of Molecular level simulations were employed... 

TvaroSka, KoS r and Hricovini in this book). One way to account for the effect of solvent on conforxnation might be to represent the molecule without environmental influences, and then explicitly include the solvent or other environmental molecules in the calculation. While avoiding built-in influences of environment is a satisfying concept, it is difficult to obtain by experiment parameters that lack those influences. Several methods have been used to study solvation effects, including continuum descriptions (24) and the explicit treatment of solvent molecules in Monte Carlo and molecular dynamics simulation. 

The problem of linking atomic scale descriptions to continuum descriptions is also a nontrivial one. We will emphasize here that the problem cannot be solved by heroic extensions of the size of molecular dynamics simulations to millions of particles and that this is actually unnecessary. Here we will describe the use of atomic scale calculations for fixing boundary conditions for continuum descriptions in the context of the modeling of static structure (capacitance) and outer shell electron transfer. Though we believe that more can be done with these approaches, several kinds of electrochemical problems—for example, those associated with corrosion phenomena and both inorganic and biological polymers—will require approaches that take into account further intermediate mesoscopic scales. There is less progress to report here, and our discussion will be brief. 

Ray Kapral came to Toronto from the United States in 1969. His research interests center on theories of rate processes both in systems close to equilibrium, where the goal is the development of a microscopic theory of condensed phase reaction rates,89 and in systems far from chemical equilibrium, where descriptions of the complex spatial and temporal reactive dynamics that these systems exhibit have been developed.90 He and his collaborators have carried out research on the dynamics of phase transitions and critical phenomena, the dynamics of colloidal suspensions, the kinetic theory of chemical reactions in liquids, nonequilibrium statistical mechanics of liquids and mode coupling theory, mechanisms for the onset of chaos in nonlinear dynamical systems, the stochastic theory of chemical rate processes, studies of pattern formation in chemically reacting systems, and the development of molecular dynamics simulation methods for activated chemical rate processes. His recent research activities center on the theory of quantum and classical rate processes in the condensed phase91 and in clusters, and studies of chemical waves and patterns in reacting systems at both the macroscopic and mesoscopic levels. 

Note that the water molecules are not aligned into a rigid, ordered structure in practice all of the molecules are moving rapidly and randomly. Molecular dynamics simulations represent all of the intermolecular interactions with classical potentials, generating forces and acceleration via Newton s laws. Such simulations give very good descriptions of many of the properties of bulk solutions. 

Kramers idea was to give a more realistic description of the dynamics in the reaction coordinate by including dynamical effects of the solvent. Instead of giving a deterministic description, which is only possible in a large-scale molecular dynamics simulation, he proposed to give a stochastic description of the motion similar to that of the Brownian motion of a heavy particle in a solvent. From the normal coordinate analysis of the activated complex, a reduced mass pi has been associated with the motion in the reaction coordinate, so the proposal is to describe the motion in that coordinate as that of a Brownian particle of mass g in the solvent. 

The development of multiscale simulation techniques that involve the atomistic modeling of various structures and processes still remains at its early stage. There are many problems to be solved associated with more accurate and detailed description of these structures and processes. These problems include the development of efficient and fast methods for quantum calculations at the atomistic level, the development of transferable interatomic potentials (especially, reactive potentials) for molecular dynamic simulations, and the development of strategies for the application of multiscale simulation methods to other important processes and materials (optical, magnetic, sensing, etc.). 

The main advantage of the MFA is that it permits one to dramatically reduce the computational requisites associated with the study of solvent effects. This allows one to focus attention on the solute description, and it consequently becomes possible to use calculation levels similar to those usually employed in the study of systems and processes in the gas phase. Furthermore, in the case of ASEP/MD this high level description of the solute is combined with a detailed description of the solvent structure obtained from molecular dynamics simulations. Thanks to these features ASEP/MD [8] enables the study of systems and processes where it is necessary to have simultaneously a good description of the electron correlation of the solute and the explicit consideration of specific solute-solvent interactions, such as for VIS-UV spectra [9] or chemical reactivity [10]. 

In its current formulation the ASEP/MD method introduces a dual representation of the solute molecule. At each cycle of the ASEP/MD calculation, the solute charge distribution is updated using quantum mechanics but during the molecular dynamics simulations the solute charge distribution is represented by a set of fixed point charges. The use of an inadequate set of charges in the solute description can introduce errors into the estimation of the solvent structure, and hence of the solute s properties... 

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