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.

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.

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.

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.

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.

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.