Studying the mechanism of phase separation in aqueous solutions of globular proteins via molecular dynamics computer simulations.

Proteins are the most abundant biomacromolecules in living cells, where they perform vital roles in virtually every biological process. To maintain their function, proteins need to remain in a stable (native) state. Inter- and intramolecular interactions in aqueous protein solutions govern the fate of proteins, as they can provoke their unfolding or association into aggregates. The initial steps of protein aggregation are difficult to capture experimentally, therefore we used molecular dynamics simulations in this study. We investigated the initial phase of aggregation of two different lysozymes, hen egg-white (HEWL) and T4 WT* lysozyme and also human lens γ-D crystallin by using atomistic simulations. We monitored the phase stability of their aqueous solutions by calculating time-dependent density fluctuations. We found that all proteins remained in their compact form despite aggregation. With an extensive analysis of intermolecular residue-residue interactions we discovered that arginine is of paramount importance in the initial stage of aggregation of HEWL and γ-D crystallin, meanwhile lysine was found to be the most involved amino acid in forming initial contacts between T4 WT* molecules.

Water structure near the surface of Weyl semimetals as catalysts in photocatalytic proton reduction.

In this work, second-generation Car-Parrinello-based mixed quantum-classical mechanics molecular dynamics simulations of small nanoparticles of NbP, NbAs, TaAs, and 1T-TaS2 in water are presented. The first three materials are topological Weyl semimetals, which were recently discovered to be active catalysts in photocatalytic water splitting. The aim of this research was to correlate potential differences in the water structure in the vicinity of the nanoparticle surface with the photocatalytic activity of these materials in light induced proton reduction. The results presented herein allow explaining the catalytic activity of these Weyl semimetals: the most active material, NbP, exhibits a particularly low water coordination near the surface of the nanoparticle, whereas for 1T-TaS2, with the lowest catalytic activity, the water structure at the surface is most ordered. In addition, the photocatalytic activity of several organic and metalorganic photosensitizers in the hydrogen evolution reaction was experimentally investigated with NbP as the proton reduction catalyst. Unexpectedly, the charge of the photosensitizer plays a decisive role for the photocatalytic performance.

Structure and Stability of Long Rod-like Dodecyltrimethylammonium Chloride Micelles in Solutions of Hydroxybenzoates: A Molecular Dynamics Simulation Study.

The relative position of the hydroxylic and carboxylic groups in the isomeric hydroxybenzoate (HB) anions is experimentally known to have a large impact on the thermodynamics of micellization of cationic surfactants, such as dodecyltrimethylammonium chloride (DTAC), and on the structure of the resulting micelles. To understand the effect of the different isomers on the molecular level, we employed atomistic molecular dynamics simulations to study systems containing infinitely long cylindrical DTAC micelles in aqueous solutions of the sodium salts of all three isomers of HB at a temperature and a pressure of 298.15 K and 1 atm. In all studied systems, the number of DTAC unimers is identical to the number of HB anions. At this concentration, the initially cylindrical micelles remain stable, irrespective of the nature of the isomer, whereas micelles rapidly disintegrated in the absence of HB anions. The HB isomers decrease the line density of unimers along the micellar axis and its concomitant thickness in the order o-HB > m-HB > p-HB. It is further observed that o-HB anions penetrate more deeply into the micellar core, induce a more ordered internal structure of the micelle, and are oriented more strongly than the other two isomers. In addition, the ortho isomer shows two different preferential orientations with respect to the radial direction of the cylindrical micelle; it can either be incorporated almost completely into the micelle or it can be attached through hydrogen bonding to one of those o-HB anions that are already incorporated into the micelle, and thus stick out of the micellar surface.

Ion mobility and clustering of sodium hydroxybenzoates in aqueous solutions: a molecular dynamics simulation study.

The relative position of the hydroxylic and the carboxylic group in the isomeric hydroxybenzoate (HB) anions is known to have a large impact on transport properties of this species. It also influences crucially the self-organisation of cationic surfactants. In this article a systematic investigation of aqueous solutions of the ortho, meta, and para isomers of the HB anion is presented. Molecular dynamics simulations of all three HB isomers were conducted for two different concentrations at 298.15 K and using two separate water models. From the resulting trajectories we calculated the self-diffusion coefficient of each isomer. According to the calculated self-diffusion coefficients, isomers were ranked in the order o-HB > m-HB > p-HB at both concentrations for both the used SPC and SPC/E water models, which agrees very well with the experiment. The structural analysis revealed that at lower concentration, where the tendency for dimerisation or cluster formation is low, hydrogen bonding with water determines the mobility of the HB anion. o-HB forms the least hydrogen bonds and is therefore the most mobile, and p-HB, which forms the most hydrogen bonds with water, is the least mobile isomer. At higher concentration the formation of clusters also needs to be considered. The ortho isomer predominantly forms dimers with 2 hydrogen bonds per dimer between one OH and one carboxylate group of each anion. m-HB mostly forms clusters of sizes around 5 and p-HB forms clusters of sizes even larger than 10, which can be either rings or chains.

An Investigation of Ion-Pairing of Alkali Metal Halides in Aqueous Solutions Using the Electrical Conductivity and the Monte Carlo Computer Simulation Methods.

The ion pairing is, in very dilute aqueous solutions, of rather small importance for solutions' properties, which renders its precise quantification quite a laborious task. Here we studied the ion pairing of alkali halides in water by using the precise electric conductivity measurements in dilute solutions, and in a wide temperature range. The low-concentration chemical model was used to analyze the results, and to estimate the association constant of different alkali halide salts. It has been shown that the association constant is related to the solubility of salts in water and produces a 'volcano relationship', when plotted against the difference between the free energy of hydration of the corresponding individual ions. The computer simulation, using the simple MB+dipole water model, were used to interprete the results, to find a microscopic basis for Collins' law of matching water affinities.