Dynamical Processes in Solution

Chong, Song

doi:10.1007/1-4020-2590-4_5

Cited by 3 publications

(4 citation statements)

References 78 publications

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“…Consequently, and in contrast to MD, RISM does not provide any information about the solvent dynamics of a system, but yields the equilibrium statistical mechanical distribution of solvent particles around a given solute. It should be noted that there has been a non-equilibrium statistical mechanical theory, the generalized Langevin equation in the interaction site model formalism (using the solutions from the equilibrium RISM theory as initial conditions in the time evolution), that does provide full statistical microscopic information about solvent dynamics [38-40]. The conformational degrees of freedom of a solute molecule can be accounted for in the hybrid approaches coupling RISM with Monte Carlo (MC) [41], or 3D-RISM with MD [42, 43].…”

Section: Introductionmentioning

confidence: 99%

“…It should be noted that there has been a nonequilibrium statistical mechanical theory, the generalized Langevin equation in the interaction site model formalism (using the solutions from the equilibrium RISM theory as initial conditions in the time evolution), that does provide full statistical microscopic information about solvent dynamics. [38][39][40] The conformational degrees of freedom of a solute molecule can be accounted for in the hybrid approaches coupling RISM with Monte Carlo (MC) 41 or 3D-RISM with MD. 42,43 RISM was combined with the multicanonical and simulated annealing MC methods 44,45 for predicting conformations of biomolecules stabilized by a solvent.…”

Section: Introductionmentioning

confidence: 99%

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Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

et al. 2010

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Water plays a unique role in all living organisms. Not only is it nature's ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules like proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces like the hydrophobic effect are relevant. Computational methods like molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are indeed the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods, MD simulations and the three-dimensional reference interaction site model with the KovalenkoHirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH, and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

et al. 2010

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“…Therefore, dynamic quantities such as collision cross sections or Green's functions as in, for example, the linear response theory, 52,53 the Chapman-Enskog line of kinetic theory, 54 or the mode coupling theory do not enter into the potential energy contribution part of the shear viscosity. [55][56][57] Consequently, from the computational standpoint the present density fluctuation theory formula for shear viscosity and the concomitant self-diffusion coefficient are rather easily computable by means of relatively minor computational resources readily available at present. This is an important advantage of the density fluctuation theory results for transport coefficients presented in this work.…”

Section: Discussionmentioning

confidence: 99%

“…This is an important advantage of the density fluctuation theory results for transport coefficients presented in this work. It is, probably, helpful to note that the aforementioned alternative theories [52][53][54][55][56][57] have not so far yielded the density and temperature dependences of transport coefficients to the extent presented in this work.…”

Section: Discussionmentioning

confidence: 99%

Modified Free Volume Theory of Self-Diffusion and Molecular Theory of Shear Viscosity of Liquid Carbon Dioxide

Nasrabad

Laghaei

2005

J. Phys. Chem. B

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In previous work on the density fluctuation theory of transport coefficients of liquids, it was necessary to use empirical self-diffusion coefficients to calculate the transport coefficients (e.g., shear viscosity of carbon dioxide). In this work, the necessity of empirical input of the self-diffusion coefficients in the calculation of shear viscosity is removed, and the theory is thus made a self-contained molecular theory of transport coefficients of liquids, albeit it contains an empirical parameter in the subcritical regime. The required self-diffusion coefficients of liquid carbon dioxide are calculated by using the modified free volume theory for which the generic van der Waals equation of state and Monte Carlo simulations are combined to accurately compute the mean free volume by means of statistical mechanics. They have been computed as a function of density along four different isotherms and isobars. A Lennard-Jones site-site interaction potential was used to model the molecular carbon dioxide interaction. The density and temperature dependence of the theoretical self-diffusion coefficients are shown to be in excellent agreement with experimental data when the minimum critical free volume is identified with the molecular volume. The self-diffusion coefficients thus computed are then used to compute the density and temperature dependence of the shear viscosity of liquid carbon dioxide by employing the density fluctuation theory formula for shear viscosity as reported in an earlier paper (J. Chem. Phys. 2000, 112, 7118). The theoretical shear viscosity is shown to be robust and yields excellent density and temperature dependence for carbon dioxide. The pair correlation function appearing in the theory has been computed by Monte Carlo simulations.

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Site-site memory equation approach in study of density/pressure dependence of translational diffusion coefficient and rotational relaxation time of polar molecular solutions: Acetonitrile in water, methanol in water, and methanol in acetonitrile

Kobryn

Yamaguchi

Hirata

2005

The Journal of Chemical Physics

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We present results of the theoretical study and numerical calculation of the dynamics of molecular liquids based on the combination of the memory equation formalism and the reference interaction site model (RISM). Memory equations for the site-site intermediate scattering functions are studied in the mode-coupling approximation for the first-order memory kernels, while equilibrium properties such as site-site static structure factors are deduced from RISM. The results include the temperature-density (pressure) dependence of translational diffusion coefficients D and orientational relaxation times tau for acetonitrile in water, methanol in water, and methanol in acetonitrile--all in the limit of infinite dilution. Calculations are performed over the range of temperatures and densities employing the extended simple point charge model for water and optimized site-site potentials for acetonitrile and methanol. The theory is able to reproduce qualitatively all main features of temperature and density dependences of D and tau observed in real and computer experiments. In particular, anomalous behavior, i.e, the increase in mobility with density, is observed for D and tau of methanol in water, while acetonitrile in water and methanol in acetonitrile do not show deviations from the ordinary behavior. The variety exhibited by the different solute-solvent systems in the density dependence of the mobility is interpreted in terms of the two competing origins of friction, which interplay with each other as density increases: the collisional and dielectric frictions which, respectively, increase and decrease with increasing density.

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Dynamical Processes in Solution

Cited by 3 publications

References 78 publications

Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

Modified Free Volume Theory of Self-Diffusion and Molecular Theory of Shear Viscosity of Liquid Carbon Dioxide

Site-site memory equation approach in study of density/pressure dependence of translational diffusion coefficient and rotational relaxation time of polar molecular solutions: Acetonitrile in water, methanol in water, and methanol in acetonitrile

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