How are water’s material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth’s living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies—water’s solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions—hydroxide and protons—diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water’s molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water’s orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.

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Water plays a central role in the structures and properties of biomolecules--proteins, nucleic acids, and membranes--and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global properties-water's thermodynamics, phase diagram, and solvation properties, for example-and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water.

Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible protein-protein aggregation in salt solutions. We treat proteins as hard spheres having square-well-energy binding sites, using Wertheim's thermodynamic perturbation theory. The necessary condition required for such modeling to be realistic is that proteins in solution during the experiment remain in their compact form. Within this limitation our model gives accurate liquid-liquid coexistence curves for lysozyme and γ IIIa-crystallin solutions in respective buffers. It provides good fits to the cloudpoint curves of lysozyme in buffer-salt mixtures as a function of the type and concentration of salt. It than predicts full coexistence curves, osmotic compressibilities, and second virial coefficients under such conditions. This treatment may also be relevant to protein crystallization.phase separation | protein aggregation | Hofmeister series P rotein molecules can aggregate with each other. This process is important in many ways (1). First, a key step in developing biotech drugs-which are mostly mABs-is to formulate proteins so that they do not aggregate. This is because good shelflife requires long-term solution stability, and because patient compliance requires liquids having low viscosities. The importance of such formulations comes from the fact that the world market for protein biologicals is about the same size as for smartphones. Second, protein aggregation in the cell plays a key role in protein condensation diseases, such as Alzheimer's, Parkinson's, Huntington's, and others. Third, much of structural biology derives from the 100,000 protein structures in the Protein Data Bank, a resource that would not have been possible without protein crystals, a particular state of protein aggregation. Also, it is not yet possible to rationally design the conditions for proteins to crystallize.However, protein aggregation is poorly understood. Atomistic-level molecular simulations are not practical for studying multiprotein interactions as a function of concentration, and in liquid solutions that are themselves fairly complicated-that account for salts of different types and concentrations as well as other ligands, excipients, stabilizers, or metabolites. So, a traditional approach is to adapt colloid theories, such as the DerjaguinLandau-Verwey-Overbeek (DLVO) (2) theory. In those treatments, proteins are represented as spheres that interact through spherically symmetric van der Waals and electrostatic interactions in salt water, using a continuum representation of solvent and a Debye-Hückel screening for salts. DLVO often gives correct trends for the pH and salt concentration dependencies. However, DLVO does not readily account for protein sequence-structure properties, salt bridges (which are commonly the "glue" holding protein crystals together), explicit waters in general, or Hofmeister effects, where different salts have widely different powers of protein precipitation...

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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.

Disordered porous materials filled with liquid or solution may be considered as partly-quenched, i.e., as systems in which some of the degrees of freedom are quenched and others annealed. In such cases, the statistical-mechanical averages used to calculate the system's thermodynamical properties become double ensemble averages: first over the annealed degrees of freedom and then over all possible values of the quenched variables. In this respect, the quenched-annealed systems differ from regular mixtures. The multi-faceted applications of the partly-quenched systems to a kaleidoscope of technological and biological processes make the understanding of these systems important and of interest. Present contribution reviews recent developments in theory and simulation of partly-quenched systems containing charges. Specifically, two different models of such systems are discussed: (a) the model in which the nanoporous system (matrix subsystem) formed by charged obstacles is electroneutral, and (b) the model, where the subsystem of obstacles has some net charge. The latter model resembles, for example, the situation in ion exchange resins etc. Various theoretical methods are applied to investigate structural and dynamical peculiarities of such systems. One is the replica Ornstein-Zernike theory, especially adapted for charged systems, and the other is the Monte Carlo computer simulation method. These two approaches are well suited to study thermodynamical parameters, such as the mean activity coefficient of the annealed electrolyte or Donnan's exclusion parameter. Highly relevant issue of dynamics of ions in partly-quenched systems is also addressed. For this purpose, the Brownian dynamic method is used: the self-diffusion coefficients of ions are calculated for various model parameters and discussed in light of the experimental data. These results, together with the thermodynamical data mentioned above, provide additional evidence that properties of the adsorbed fluid substantially differ from those of its bulk counterpart.

Amyloid fibrils, highly ordered protein aggregates, play an important role in the onset of several neurological disorders. Many studies have assessed amyloid fibril formation under specific solution conditions, but they all lack an important phenomena in biological solutions—buffer specific effects. We have focused on the formation of hen egg-white lysozyme (HEWL) fibrils in aqueous solutions of different buffers in both acidic and basic pH range. By means of UV-Vis spectroscopy, fluorescence measurements and CD spectroscopy, we have managed to show that fibrillization of HEWL is affected by buffer identity (glycine, TRIS, phosphate, KCl-HCl, cacodylate, HEPES, acetate), solution pH, sample incubation (agitated vs. static) and added excipients (NaCl and PEG). HEWL only forms amyloid fibrils at pH = 2.0 under agitated conditions in glycine and KCl-HCl buffers of high enough ionic strength. Phosphate buffer on the other hand stabilizes the HEWL molecules. Similar stabilization effect was achieved by addition of PEG12000 molecules to the solution.