Molecular dynamics computation

In Fig. III-7 we show a molecular dynamics computation for the density profile and pressure difference P - p across the interface of an argonlike system [66] (see also Refs. 67, 68 and citations therein). Similar calculations have been made of 5 in Eq. III-20 [69, 70]. Monte Carlo calculations of the density profile of the vapor-liquid interface of magnesium how stratification penetrating about three atomic diameters into the liquid [71]. Experimental measurement of the transverse structure of the vapor-liquid interface of mercury and gallium showed structures that were indistinguishable from that of the bulk fluids [72, 73]. 

Gain G and Pasquarello A 1993 First-principles molecular dynamics Computer Simulation in Chemioal Physios vol 397 NATO ASI Series C ed M P Allen and D J Tildesley (Dordrecht Kluwer) pp 261-313... 

Creveld, L., Amadei, A., Van Schaik, C., Pepermans, R., De Vlieg, J., Berendsen, H.J.C. Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations. Submitted (1998). 

J. A. McCammon, B. M. Pettitt, and L. R. Scott. Ordinary differential equa tions of molecular dynamics. Computers Math. Applic., 28 319-326, 1994. 

Listed is a collection of general-purpose molecular dynamics computer simulation packages for the study of molecular systems. The packages include a wide variety of functionalities for the analysis and simulation of biomolecules. In addition, they contain integrated force fields. 

GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecules http //igc.ethz.ch/gromos/weicome.htmi GROMACS (GROningen MAchine for Chemical Simulations) http //rugmdO. chem. rug.ni/ gmx/... 

M. L. Berkowitz, I.-C. Yeh, E. Spohr. Structure of water at the water/metal interface. Molecular dynamics computer simulations. In A. Wieckowski, ed. Interfacial Electrochemistry. New York Marcel Dekker, 1999, (in press). 

M. Kroger, R. Makhloufi. Wormlike micelles under shear flow A microscopic model studied by nonequihbrium molecular dynamics computer simulations. Phys Rev E 55 2531-2536, 1996. 

The only feasible procedure at the moment is molecular dynamics computer simulation, which can be used since most systems are currently essentially controlled by classical dynamics even though the intermolecular potentials are often quantum mechanical in origin. There are indeed many intermolecular potentials available which are remarkably reliable for most liquids, and even for liquid mixtures, of scientific and technical importance. However potentials for the design of membranes and of the interaction of fluid molecules with membranes on the atomic scale are less well developed. 

The industrialist should take note of the utility of molecular dynamics computer simulation in this field and of the rapid developments in progress. 

M. Menon and R. E. AUen, New technique for molecular-dynamics computer simulations Hellmann- Feynman theorem and subspace Hamiltonian approach , Phys. Rev. B33 7099 (1986) Simulations of atomic processes at semiconductor surfaces General method and chemisorption on GaAs(llO) , ibid B38 6196 (1988). 

Garofalini, S.H. (1990) Molecular dynamics computer simulations of silica surface structure and adsorption of water molecules, J. Non-Cryst. Solids, 120, 1. 

Nakano A (1997) Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics. Comput Phys Commun 104(l-3) 59-69... 

Engberts, Molecular dynamics computer simulation of the hydration of two simple organic solutes. Comparison with the simulation of an empty cavity, Mol. Phys. 53 1517 (1984). 

The two avenues above recalled, namely ab-initio computations on clusters and Molecular Dynamics on one hand and continuum model on the other, are somewhat bridged by those techniques where the solvent is included in the hamiltonian at the electrostatic level with a discrete representation [13,17], It is important to stress that quantum-mechanical computations imply a temperature of zero K, whereas Molecular Dynamics computations do include temperature. As it is well known, this inclusion is of paramount importance and allows also the consideration of entropic effects and thus free-energy, essential parameters in any reaction. 

We have reviewed above the GH approach to reaction rate constants in solution, together with simple models that give a deeper perspective on the reaction dynamics and various aspects of the generalized frictional influence on the rates. The fact that the theory has always been found to agree with Molecular Dynamics computer simulation results for realistic models of many and varied reaction types gives confidence that it may be used to analyze real experimental results. 

Supercritical water (SCW) presents a unique combination of aqueous and non-aqueous character, thus being able to replace an organic solvent in certain kinds of chemical synthesis. In order to allow for a better understanding of the particular properties of SCW and of its influence on the rate of chemical reactions, molecular dynamics computer simulations were used to determine the free energy of the SN2 substitution reaction of Cl- and CH3C1 in SCW as a function of the reaction coordinate [216]. The free energy surface of this reaction was compared with that for the gas-phase and ambient water (AW) [248], In the gas phase, an ion-dipole complex and a symmetric transition... 

CT, 1999, pp. 441—451. The Dynamics of Non-Crystalline Silica Insight from Molecular Dynamics Computer Simulations. 

This review examines the new understanding that molecular dynamics computer simulations have provided regarding the structure and dy-... 

The microscopic structure of water at the solution/metal interface has been the focus of a large body of literature, and excellent reviews have been published summarizing the extensive knowledge gained from experiments, statistical mechanical theories of varied sophistication, and Monte Carlo and molecular dynamics computer simulations. To keep this chapter to a reasonable size, we limit ourselves to a brief summary of the main results and to a sample of the type of information that can be gained from computer simulations. 

The interfacial pair correlation functions are difficult to compute using statistical mechanical theories, and what is usually done is to assume that they are equal to the bulk correlation function times the singlet densities (the Kirkwood superposition approximation). This can be then used to determine the singlet densities (the density and the orientational profile). Molecular dynamics computer simulations can in... 

An important aspect of the study of water under electrochemical conditions is that one is able to continuously modify the charge on the metal surface and thus apply a well-defined external electric field, which can have a dramatic effect on adsorption and on chemical reactions. Here we briefly discuss the effect of the external electric field on the properties of water at the solution/metal interface obtained from molecular dynamics computer simulations. A general discussion of the theoretical and experi-... 

The calculations of the stmcture of water between charged flat walls show that the density profile becomes asymmetric and that there is enhanced structuring. This enhanced structuring is intimately connected with the possibility of a continuous phase transition in quasi two-dimensional systems, a subject of recent intense interest. ° Most of the molecular dynamics computer simulations on the effects of an external field have been carried out in an attempt to clarify the field-induced restructuring of water molecules at the metal surface, for which recent experimental data have become available. ... 

The main goal of the molecular dynamics computer simulation of ionic solvation and adsorption on a metal surface has been to test the above model and to provide more quantitative information about the different factors that influence the structure of hydrated ions at the interface. Unfortunately, most of the experimental information about these issues has been obtained from indirect measurements such as capacity and current-potential plots, although in recent years in situ experimental techniques have begun to provide an accurate test of the above model. For a recent review of experimental techniques and the theory of ionic adsorption at the water/metal interface, see the excellent paper by Philpott. ... 

Although our knowledge of the structure of the electric double layer is based on experimental data collected at finite electrolyte concentrations, understanding the structure of the electric double layer at the microscopic level must begin with knowledge of the structure of a single solvated ion at the interface. This information has been obtained in recent years from molecular dynamics computer simulations. 

The theoretical modeling of electron transfer reactions at the solution/metal interface is challenging because, in addition to the difficulties associated with the quantitative treatment of the water/metal surface and of the electric double layer discussed earlier, one now needs to consider the interactions of the electron with the metal surface and the solvated ions. Most theoretical treatments have focused on electron-metal coupling, while representing the solvent using the continuum dielectric media. In keeping with the scope of this review, we limit our discussion to subjects that have been adi essed in recent years using molecular dynamics computer simulations. 

Figure 12. The rate of the electron transfer reaction Fe + e Fe in the nonadiabatic limit. The dotted line is the result of molecular dynamics computer simulations [Eqs. (27) and (28)] and the solid line corresponds to Eqs. (29)-(31). (Adapted from Ref 163.)...

Although this chapter would not be complete without a discussion of the contribution of molecular dynamics computer simulation to the study of electrochemical processes at the liquid/liquid interface, this subject has been extensively reviewed recently, and so here we limit ourselves to a complete listing of the publications in this area. 

Following the early studies on the pure interface, chemical and electrochemical processes at the interface between two immiscible liquids have been studied using the molecular dynamics method. The most important processes for electrochemical research involve charge transfer reactions. Molecular dynamics computer simulations have been used to study the rate and the mechanism of ion transfer across the water/1,2-dichloroethane interface and of ion transfer across a simple model of a liquid/liquid interface, where a direct comparison of the rate with the prediction of simple diffusion models has been made. ° ° Charge transfer of several types has also been studied, including the calculations of free energy curves for electron transfer reactions at a model liquid/liquid... 

In addition to the development of new methods, new applications of molecular dynamics computer simulation are also needed in order to make comparisons with experimental results. In particular, more complicated chemical reactions, beyond the relatively simple electron transfer reaction, could be studied. Examples include the study of chemical adsorption, hydrogen evolution reactions, and chemical modification of the electrode surface. All of the above directions and opportunities promise to keep this area of research very active ... 

Central to the understanding of surface-related phenomena has been the study of gas-surface reactions. A comprehensive understanding of these reactions has proven challenging because of the intrinsic many-body nature of surface dynamics. In terms of theoretical methods, this complexity often forces us either to treat complex realistic systems using approximate approaches, or to treat simple systems with realistic approaches. When one is interested in studying processes of technological importance, the latter route is often the most fruitful. One theoretical technique which embodies the many-body aspect of the dynamics of surface chemistry (albeit in a very approximate manner) is molecular dynamics computer simulation. 

Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, et al. 1999. NAMD2 greater scalability for parallel molecular dynamics. Comput Phys 151 283-312. 

In Figure 1 we compare our numerical solutions with the molecular dynamics computer simulations of Thompson, et al. (7). In this comparison we use liquid and vapor densities obtained from the simulation studies. In the next section we obtain the required boundary values by approximate evaluation of vapor-liquid equilibrium for a small system. 

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