Including diverging electrostatic potential in 3D-RISM theory: The charged wall case.

Although three-dimensional site-site molecular integral equations of liquids are a powerful tool of the modern theoretical chemistry, their applications to the problem of characterizing the electrical double layer originating at the solid-liquid interface with a macroscopic substrate are severely limited by the fact that an infinitely extended charged plane generates a divergent electrostatic potential. Such potentials cannot be treated within the standard 3D-Reference Interaction Site Model equation solution framework since it leads to functions that are not Fourier transformable. In this paper, we apply a renormalization procedure to overcome this obstacle. We then check the validity and numerical accuracy of the proposed computational scheme on the prototypical gold (111) surface in contact with water/alkali chloride solution. We observe that despite the proposed method requires, to achieve converged charge densities, a higher spatial resolution than that suited to the estimation of biomolecular solvation with either 3D-RISM or continuum electrostatics approaches, it still is computationally efficient. Introducing the electrostatic potential of an infinite wall, which is periodic in 2 dimensions, we avoid edge effects, permit a robust integration of Poisson's equation, and obtain the 3D electrostatic potential profile for the first time in such calculations. We show that the potential within the electrical double layer presents oscillations which are not grasped by the Debye-Hückel and Gouy-Chapman theories. This electrostatic potential deviates from its average of up to 1-2 V at small distances from the substrate along the lateral directions. Applications of this theoretical development are relevant, for example, for liquid scanning tunneling microscopy imaging.

Implicit solvent methods for free energy estimation.

Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described.

Extraction of site-site bridge functions and effective pair potentials from simulations of polar molecular liquids.

We develop an efficient method to extract site-site bridge functions from molecular simulations. The method is based on the inverse solution of the reference site interaction model. Using the exact long-range asymptotics of site-site direct correlation functions defined by the site-site Ornstein-Zernike equations, we regularize the ill-posed inverse problem, and then calculate site-site bridge functions and effective pair potentials for ambient water, methanol, and ethanol. We have tested the proposed algorithm and checked its performance. Our study has revealed various peculiarities of the site-site bridge functions, such as long-range behavior, strong dependence on the electrostatic interactions. Using the obtained data, we have calculated thermodynamic properties of the solvents, namely, isothermal compressibility, internal energy, and Kirkwood-Buff integrals. The obtained values are in excellent agreement not only with molecular simulations but also with available experimental data. Further extensions of the method are discussed.

On the characterization of inhomogeneity of the density distribution in supercritical fluids via molecular dynamics simulation and data mining analysis.

We combined molecular dynamics simulation and DBSCAN algorithm (Density Based Spatial Clustering of Application with Noise) in order to characterize the local density inhomogeneity distribution in supercritical fluids. The DBSCAN is an algorithm that is capable of finding arbitrarily shaped density domains, where domains are defined as dense regions separated by low-density regions. The inhomogeneity of density domain distributions of Ar system in sub- and supercritical conditions along the 50 bar isobar is associated with the occurrence of a maximum in the fluctuation of number of particles of the density domains. This maximum coincides with the temperature, Tα, at which the thermal expansion occurs. Furthermore, using Voronoi polyhedral analysis, we characterized the structure of the density domains. The results show that with increasing temperature below Tα, the increase of the inhomogeneity is mainly associated with the density fluctuation of the border particles of the density domains, while with increasing temperature above Tα, the decrease of the inhomogeneity is associated with the core particles.

Detailed insight into the hydrogen bonding interactions in acetone-methanol mixtures. A molecular dynamics simulation and Voronoi polyhedra analysis study.

Voronoi polyhedra (VP) analysis of mixtures of acetone and methanol is reported on the basis of molecular dynamics computer simulations, performed at 300 K and 1 bar. The composition of the systems investigated covers the entire range from neat acetone to neat methanol. Distribution of the volume, reciprocal volume and asphericity parameter of the VP as well as that of the area of the individual VP faces and of the radius of the empty voids located between the molecules are calculated. To investigate the tendency of the like molecules to self-associate the analyses are repeated by disregarding one of the two components. The self-aggregates of the disregarded component thus turn into large empty voids, which are easily detectable in VP analysis. The obtained results reveal that both molecules show self-association, but this behavior is considerably stronger among the acetone than among the methanol molecules. The strongest self-association of the acetone and methanol molecules is found in their mole fraction ranges of 02-0.5 and 0.5-0.6, respectively. The caging effect around the methanol molecules is found to be stronger than around acetones. Finally, the local environment of the acetone molecules turns out to be more spherical than that of the methanols, not only in the respective neat liquids, but also in their mixtures.

Assessment of the potential models of acetone/CO2 and ethanol/CO2 mixtures by computer simulation and thermodynamic integration in liquid and supercritical states.

Binary mixtures of CO(2) with ethanol and with acetone are studied by computer simulation, including extensive free energy calculations done by the method of thermodynamic integration, at 313 K, i.e., above the critical point of CO(2) in the entire composition range. The calculations are repeated with three different models of acetone and ethanol, and two models of CO(2). Comparisons of the molar volume of the different systems as well as of the change of their molar volume accompanying the mixing of the two components with experimental data reveal that, among the model pairs tested, the best results are obtained if both components are described by the Transferable Potentials for Phase Equilibria (TraPPE) force field. Around the ethanol/acetone mole fraction of 0.05 all ethanol/CO(2) and almost all acetone/CO(2) model pairs considered predict the existence of a sharp maximum of the molar volume. Due to the lack of experimental data in this composition range, however, these predictions cannot be verified/falsified yet. Most of the model pairs considered also predict limited miscibility of these compounds, as seen from the positive values of the free energy change accompanying their mixing, and the miscibility gap is located at the same composition range as the aforementioned molar volume maximum.