Homogeneous crystallization of the Lennard-Jones liquid. Structural analysis based on Delaunay simplices method

The crystallization process of a simple liquid upon slow cooling has been modeled by the Monte-Carlo method. The model contains 10,000 Lennard-Jones atoms in the model box with periodic boundary conditions. The model structure is investigated at different stages of crystallization using Delaunay simplices. The simplex belonging to one or another particular crystal structure was determined by the shape of the given simplex taking into account the shape of its neighboring simplices. Simplices typical of the fcc and hcp crystal structures, as well as of polytetrahedral aggregates, not typical of crystals, were studied. The analysis has shown that the “precursors” of a hcp structure are strongly dominating over the “precursors” of a fcc structure in liquid phase before the beginning of crystallization. When crystallization starts, small embryos of the fcc structure are observed; the simplices peculiar to hcp are present at that in great amount, but they are distributed over the sample more uniformly. As crystallization proceeds, the portion of the fcc phase grows faster than hcp. However, no unified crystal appears in our case of slow cooling of the model. A complex polycrystalline structure containing crystalline regions with multiple twinning, pentagonal prisms and elements of icosahedral structures arises instead.     

Large-scale and long-term correlations in collective motions of atoms of liquid argon. Computer simulation

The correlation coefficients of displacements of pairs of neighboring particles located in spheres of a given radius have been studied within the molecular dynamics models of liquid argon including 50000 and 500000 atoms. Atoms separated by distances of about ten diameters from each other are correlated and correlations last nanoseconds. A size effect has been revealed: correlations increase with the size of the model. All these properties indicate that mesoscopic supramolecular structures exist in a liquid.     

Visualization of vortex movements in a molecular dynamics model of liquid argon

A method was proposed to visualize collective displacements of particles in diffusion motion in liquids. Using this method, in molecular dynamics models of liquid argon, groups of collectively moving atoms were detected, which had the shape of long curved flows, often appearing as vortex-like structures. These structures are revealed only by considering movements of atoms over long time intervals, on the order of tens and hundreds of picoseconds, and over long distances, on the order of tens of nanometers.     

Culation of partial molar volume and its components for molecular dynamics models of dilute solutions

This paper is a review of our recent computational studies of volumetric characteristics using computer models of dilute solutions. Partial molar volume (PMV) and its components are calculated for simple and complex molecules in water (methane, noble gases, surfactants, polypeptides). Advantages and disadvantages of various computational methods are discussed. It is proposed to use the Voronoi-Delaunay technique to determine the reasonable boundary between a solute molecule and solvent molecules and to identify the PMV components related to the molecule, the boundary layer, and the solvent. It is noted that the observed increase in PMV with temperature for large molecules is due to an increase in the volume of voids in the boundary layer, i.e., due to the “thermal volume.” In this case, the solvent gives a negative contribution to the PMV. In contrast, for simple molecules (methane), the contribution from the solvent is positive and is the main factor in the increase in the PMV, which is associated with a specific change in water structure around a spherical hydrophobic particle outside the boundary layer. For surfactant molecules, the contribution from the solvent changes sign (from negative to positive) with increasing temperature.     

Ionic liquid matrices for MALDI mass spectrometry of lignin

Analytical and Bioanalytical Chemistry - The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the study of lignin is still extremely limited due to its low...     

Simulation of glycyrrhizic acid associates with cholesterol in methanol

There are experimental evidences that in the methanol solution of glycyrrhizic acid (GA) and cholesterol, the cholesterol molecules have two different types of the environment. One corresponds to free molecules and another corresponds to the molecules associated with GA. However, the nature of these associates remains unclear. The all-atom molecular dynamics simulation of GA solutions in methanol is performed. It is shown that, contrary to aqueous solutions, GA in methanol does not form small stable clusters, even in the presence of cholesterol. The arising associates do not have distinct structures and exist for no longer than dozens of nanoseconds. The concentrations of these clusters and their stability constants are estimated. It is necessary to assume the existence of larger-scale associates to explain the experimental data.     

On the origin of the high density of liquid cyclohexane

Cyclohexane and 2,3-dimethylbutane molecules are the most compact among saturated C6-hydrocarbons. They have a similar size and are arranged in the liquid phase like atoms in simple liquids. However, the cyclohexane density is higher approximately by 20% than that of 2,3-dimethylbutane. The reasons of this distinction are discussed. It can be explained within the concepts of the physics of simple liquids. According to them, a small variation of the radius of a particle hard core or the pair interaction energy can lead to appreciable changes in the structure and density of a liquid. The obtained results give grounds to discard the explanations based exclusively on the features of the shape of the given molecules.     

Statistical verification of crystallization in hard sphere packings under densification

The performance of various structure characteristics in the task of indicating structural peculiarities in packings of hard spheres is investigated. Various characteristics based on Voronoi polyhedra, spherical harmonics, and Delaunay simplices are considered together with the pair correlation function and the mean number of r-close triples. They are applied to a set of hard sphere packings of density φ from 0.62 to 0.72. It turns out that all used structure characteristics are able to indicate changes of order from non-crystalline to crystalline packings. However, not all of them are sensitive enough to indicate different stages of structure transformation under densification. The characteristics based on Delaunay simplices turn out to be the most sensitive for this purpose. For the models considered three principal structure classes are found: packings of densities lower than the known critical value 0.64 showing a non-crystalline behavior; packings with considerable crystalline regions for φ up to 0.66–0.67; rather complete crystals although with numerous defects for φ above 0.67.