Solvation thermodynamics from cavity shapes of amino acids.

According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution.

The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (>2σ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.

Model Folded Hydrophobic Polymers Reside in Highly Branched Voids.

By using advanced data analysis techniques, we characterize the shape of the voids surrounding model polymers of different sizes in water, observed in molecular dynamics simulations. We find that even when the model polymer is folded, the voids are extremely rough, with branches that can extend to over 1 nm away from the polymer. Water molecules in contact with the void retain close-to-bulk properties in terms of local structure. The branches disappear, and the voids start resembling the quasispherical shape predicted by dewetting theory only when they surround particles with a radius ∼1 nm, well above the size occupied by a folded hydrophobic polymer. Our results provide fresh insights into the microscopic origins of the vapor-like interfaces underlying dewetting and drying transitions.

Graphyne-3: a highly efficient candidate for separation of small gas molecules from gaseous mixtures.

Two-dimensional nanosheets, such as the general family of graphenes have attracted considerable attention over the past decade, due to their excellent thermal, mechanical, and electrical properties. We report on the result of a study of separation of gaseous mixtures by a model graphyne-3 membrane, using extensive molecular dynamics simulations and density functional theory. Four binary and one ternary mixtures of H[Formula: see text], CO[Formula: see text], CH[Formula: see text] and C[Formula: see text]H[Formula: see text] were studied. The results indicate the excellence of graphyne-3 for separation of small gas molecules from the mixtures. In particular, the H[Formula: see text] permeance through the membrane is on the order of [Formula: see text] gas permeation unit, by far much larger than those in other membranes, and in particular in graphene. To gain deeper insights into the phenomenon, we also computed the density profiles and the residence times of the gases near the graphyne-3 surface, as well as their interaction energies with the membrane. The results indicate clearly the tendency of H[Formula: see text] to pass through the membrane at high rates, leaving behind C[Formula: see text]H[Formula: see text] and larger molecules on the surface. In addition, the possibility of chemisorption is clearly ruled out. These results, together with the very good mechanical properties of graphyne-3, confirm that it is an excellent candidate for separating small gas molecules from gaseous mixtures, hence opening the way for its industrial use.