Molecular dynamics simulations of aqueous NaCl and KCl solutions: Effects of ion concentration on the single-particle, pair, and collective dynamical properties of ions and water molecules

Dynamics of ionic and hydrophobic solutes in water-methanol mixtures of varying composition

We have carried out a series of molecular-dynamics simulations of water-methanol mixtures containing either an ionic or a neutral atomic solute to investigate the effects of composition of the mixture on the diffusion of these solutes. Altogether, we have considered 17 different systems of varying composition ranging from pure water to pure methanol. The diffusion coefficients of ionic solutes are found to show nonideal behavior with variation of composition of the solvent mixture. The extent of nonideality of the solute diffusion is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and methanol molecules in these mixtures and is attributed to the enhanced stability of the hydrogen bonds and formation of interspecies complexes in the mixtures. The neutral solute shows characteristics of hydrophobic solvation and its diffusion decreases monotonically with increase of methanol concentration. The present simulation results are compared with those of experiments wherever available.

A molecular dynamics simulation of the electrical conductivity behaviors of highly concentrated liquid ammoniates NaI∙αNH3: Comparison with experimental measurements

In this paper, we present a molecular dynamics simulation study devoted to the calculation of the electrical conductivities of highly concentrated liquid electrolytes as a function of their dilution. As an illustration, we give the first such study of the ammoniate NaIalphaNH(3). The theoretical results are presented together with experimental data obtained at 293 K, and show that the calculated conductivities are in agreement with the experimental values in the whole salt dilution range provided that correlations between the species in the solution are taken into account. Indeed, the usual Nernst-Einstein relation is a crude approximation to calculate accurately the conductivities in such high concentrated electrolytes.

On the coupling between molecular diffusion and solvation shell exchange

The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li(+) and Na(+) ions, and for liquid argon. First, two methods are proposed which allow, by means of simulation, to extract the quantitative speed-up in diffusion induced by the exchange events. Second, it is shown by simple kinematic considerations that the instantaneous velocity of the solute conditions to a considerable extent the character of the exchanges. Analytic formulas are derived which quantitatively estimate this effect, and which are of general applicability to molecular diffusion in any thermal fluid. Despite the simplicity of the kinematic considerations, they are shown to well describe many aspects of solvent exchange/diffusion coupling features for nontrivial systems.

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncertainty reflect the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity. We discuss possible implications on the computation of potential of mean force and effective potentials.

Hydrogen bonds in aqueous electrolyte solutions: statistics and dynamics based on both geometric and energetic criteria

We have investigated the statistics and dynamics of hydrogen bonds in a concentrated aqueous electrolyte solution and also in pure water by means of molecular dynamics simulations. Both geometric and energetic definitions are employed for the existence of a hydrogen bond. The present study extends our earlier work on the structure and dynamics of hydrogen bonds where only the geometric definition was used [A. Chandra, Phys. Rev. Lett. 85, 768 (2000)]. In the presence of ions, like the earlier results for geometric definition, the energetic definition is also found to give a lower number of hydrogen bonds per water molecule and a wider distribution, a slightly faster rate of breaking and a slower rate of structural relaxation of hydrogen bonds. The results are explained in terms of a decrease of the potential of mean force between water molecules, an enhanced population of hydrogen bonded water pairs in the vicinity of the dividing surface that separates the hydrogen bonded and nonbonded states and an increase of the friction on translational and rotational motion of water molecules in the presence of ions.

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation

For the structure and function of proteins, the pH of the solution is one of the determining parameters. Current molecular dynamics (MD) simulations account for the solution pH only in a limited way by keeping each titratable site in a chosen protonation state. We present an algorithm that generates trajectories at a Boltzmann distributed ensemble of protonation states by a combination of MD and Monte Carlo (MC) simulation. The algorithm is useful for pH-dependent structural studies and to investigate in detail the titration behavior of proteins. The method is tested on the acidic residues of the protein hen egg white lysozyme. It is shown that small structural changes may have a big effect on the pK(A) values of titratable residues.