A. V. Anikeenko

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.

Polytetrahedral order and chemical short-range order in metallic melts

The reasons are investigated for the prepeak and the asymmetry of the second peak in the structure factor curve that are observed in a variety of metallic melts. The prepeak is observed as an additional maximum in the left wing of the main peak of the structure factor for multicomponent melts and is attributed to their chemical short-range order (CSRO). The asymmetry of the second peak in the structure factor, which is usually explained by the “icosahedral” (polytetrahedral) order in the melt, is observed both for multicomponent systems and for pure metals. However, some aluminum alloys with transition metals exhibit the two features simultaneously, which requires an explanation. An X-ray diffraction study of the liquid ternary Al66.6Mn16.7Co16.7 alloy is performed at 1393 K and that of liquid copper at 1353 K, 1403 K, and 1553 K. The reverse Monte Carlo (RMC) method is used to derive structural models of these and other melts. Structural analysis of these melts is conducted using Delaunay simplices. A theoretical simulation of CSRO is performed in the model of liquid aluminum, the structure factor of which does not have these features. It is discussed that CSRO can exist in a melt regardless of the presence of the polytetrahedral order.

Visualization of collective vortex-like motions in a computer model of liquid argon

Visualization pictures of collective motion of particles are presented, showing the existence of mesoscopic (of the order of tens of angstroms) vortex-like motions at time intervals of at least hundreds of picoseconds in molecular dynamics models of liquid argon.

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.

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.

Structure of Aqueous Solutions of Trimethylaminoxide, Urea, and Their Mixture

Aqueous solutions of natural osmolytes (trimethylaminoxide (TMAO), urea, and their mixture) at relatively small (biologically relevant) concentrations are analyzed by the all-atom molecular dynamics simulation. In the recent work (Smolin N. et al. PCCP. 2017. 19. P. 6345) it has been noted that in the protein hydration shell the fraction of TMAO molecules is much smaller than that of urea. The urea addition causes a further decrease in the TMAO fraction in the protein hydration shell. This work shows that in binary solutions urea fraction at urea molecules is always larger than the bulk urea concentration. At the same time, the TMAO fraction near TMAO is the same as in the bulk. In ternary solutions, TMAO and urea behave the same as the binary ones, i.e. they do not noticeably affect each other. This means that the behavior of TMAO and urea molecules in the protein hydration shell is associated with protein rather than their interaction with each other.

Visualization of the collective vortex-like motions in liquid argon and water: Molecular dynamics simulation

We propose a new measure of collectivity of molecular motion in the liquid: the average vector of displacement of the particles, ⟨ΔR⟩, which initially have been localized within a sphere of radius Rsph and then have executed the diffusive motion during a time interval Δt. The more correlated the motion of the particles is, the longer will be the vector ⟨ΔR⟩. We visualize the picture of collective motions in molecular dynamics (MD) models of liquids by constructing the ⟨ΔR⟩ vectors and pinning them to the sites of the uniform grid which divides each of the edges of the model box into equal parts. MD models of liquid argon and water have been studied by this method. Qualitatively, the patterns of ⟨ΔR⟩ vectors are similar for these two liquids but differ in minor details. The most important result of our research is the revealing of the aggregates of ⟨ΔR⟩ vectors which have the form of extended flows which sometimes look like the parts of vortices. These vortex-like clusters of ⟨ΔR⟩ vectors have the mesoscopic size (of the order of 10 nm) and persist for tens of picoseconds. Dependence of the ⟨ΔR⟩ vector field on parameters Rsph, Δt, and on the model size has been investigated. This field in the models of liquids differs essentially from that in a random-walk model.We propose a new measure of collectivity of molecular motion in the liquid: the average vector of displacement of the particles, ⟨ΔR⟩, which initially have been localized within a sphere of radius Rsph and then have executed the diffusive motion during a time interval Δt. The more correlated the motion of the particles is, the longer will be the vector ⟨ΔR⟩. We visualize the picture of collective motions in molecular dynamics (MD) models of liquids by constructing the ⟨ΔR⟩ vectors and pinning them to the sites of the uniform grid which divides each of the edges of the model box into equal parts. MD models of liquid argon and water have been studied by this method. Qualitatively, the patterns of ⟨ΔR⟩ vectors are similar for these two liquids but differ in minor details. The most important result of our research is the revealing of the aggregates of ⟨ΔR⟩ vectors which have the form of extended flows which sometimes look like the parts of vortices. These vortex-like clusters of ⟨ΔR⟩ vectors have the mesoscop...

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.