A study of a model rod-like polyelectrolyte molecule immersed into a monovalent or divalent electrolyte is presented. Results for the local concentration profile, mean electrostatic potential, charge distribution function and ζ−potential are obtained from hypernetted-chain/mean spherical approximation (HNC/MSA) theory and compared with molecular dynamics (MD) simulations. As a particular case, the parameters of the polyelectrolyte molecule are mapped to those of a DNA molecule. Both, HNC/MSA and MD, predict the occurrence of overcharging, which is not present in the Poisson-Boltzmann theory. Futher an excellent qualitative, and in some cases quantitative, agreement between HNC/MSA and MD is found. Oscillations observed in the mean electrostatic potential, local concentration profiles, as well as the curvature of the ζ-potential are discussed in terms of the observed overcharging effect. Particularly interesting results are a very non-monotonic behavior of the ζ-potential, as a function of the rod charge density, and the overcharging by monovalent counterions.

Methane hydrates are crystalline structures composed of cages of hydrogenbonded water molecules in which methane molecules are trapped. The nucleation mechanisms of crystallization are not fully resolved, as they cannot be accessed experimentally. For methane hydrates most of the reported simulations on the phenomena capture some of the basic elements of the full structure. In few reports, formation of crystalline structures is reached by imposing very high pressure, or dynamic changes of temperature, or a pre-existing hydrate structure. In a series of nanoscale molecular dynamics simulations of supersaturated water−methane mixtures, we find that the order of the crystalline structure increases by decreasing subcooling. Crystalline structures I and II form and coexist at moderate temperatures. Crystallization initiates from the spontaneous formation of an amorphous cluster wherein structures I, II, and other ordered defects emerge. We observe the transient coexistence of sI and sII in agreement with experiments. Our simulations are carried out at high methane supersaturation. This condition dramatically reduces the nucleation time and allows simulating nucleation at moderate subcooling. Moderate temperatures drive hydrates to more ordered structures.

We study the inhomogeneous primitive model macroion solution next to a charged wall, through an integral equations theory. We report a new class of oVercharging, which refers to the adsorption of an effective charge onto a like-charged wall. In addition, macroions produce surface charge reversal, charge inversion, and layering. The role of electrostatic and excluded volume correlations, on these effects, is discussed. It is argued that electrostatic and the steric repulsive interactions give rise to depletion forces which produce macroion adsorption, even if the wall or the macroparticle are uncharged or if the wall and macroions are like charged. By consideration of two limit cases of the inhomogeneous primitive model, the role of the small ion and macroion short-range correlations is separately examined. Across the paper, the agreement is discussed of our results with computer simulations and with experimental results.

The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water−amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.