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Register a new userDissecting Hydrophobic Hydration and Association
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We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of apolar solutes in water. While local hydrogen bonding in- teractions dominate hydrophobic effects involving small solutes, longer ranged electrostatic and dis- persion interactions are found to be increasingly important in the description of interfacial structure around large solutes. The hydrogen bond network sets the solute length scale at which a crossover in solvation behavior between these small and large length scale regimes is observed. Unbalanced long ranged forces acting on interfacial water molecules are also important in hydrophobic association, illustrated here by analysis of the association of model methane and buckminsterfullerene solutes.
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A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75 % independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse-graining of the twenty kinds of amino acids into just two effective types.
An understanding of density fluctuations in bulk water has made significant contributions to our understanding of the hydration and interactions of idealized, purely repulsive hydrophobic solutes. To similarly inform the hydration of realistic hydrophobic solutes that have dispersive interactions with water, here we characterize water density fluctuations in the presence of attractive fields that correspond to solute-water attractions. We find that when the attractive field acts only in the solute hydration shell, but not in the solute core, it does not significantly alter water density fluctuations in the solute core region. We further find that for a wide range of solute sizes and attraction strengths, the free energetics of turning on the attractive fields in bulk water are accurately captured by linear response theory. Our results also suggest strategies for more efficiently estimating hydration free energies of realistic solutes in bulk water and at interfaces.
Water modeling is a challenging problem. Its anomalies are difficult to reproduce, promoting the proliferation of a large number of computational models, among which researchers select the most appropriate for the property they study. In this chapter, we introduce a coarse-grained model introduced by Franzese and Stanley (FS) that accounts for the many-body interactions of water. We review mean-field calculations and Monte Carlo simulations on water monolayers for a wide range of pressures and temperatures, including extreme conditions. The results show the presence of two dynamic crossovers and explain the origin of diffusion anomalies. Moreover, the model shows that all the different scenarios, proposed in the last decades as alternative explanations of the experimental anomalies of water, can be related by the fine-tuning of the many-body (cooperative) interaction. Once this parameter is set from the experiments, the FS model predicts a phase transition between two liquids with different densities and energies in the supercooled water region, ending in a liquid-liquid critical point. From this critical point stems a liquid-liquid Widom line, i.e., the locus of maxima of the water correlation length, that in the FS model can be directly calculated. The results are consistent with the extrapolations from experiments. Furthermore, they agree with those from atomistic models but make predictions over a much wider thermodynamic region, allowing for a better interpretation of the available experimental data. All these findings provide a coherent picture of the properties of water and confirm the validity of the FS model that has proved to be useful for large-scale simulations of biological systems.
A general strategy is described for finding which amino acid sequences have native states in a desired conformation (inverse design). The approach is used to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional lattice structures. Previous studies employing a sequence-space Monte-Carlo technique resulted in the successful design of one sequence in ten attempts. The present work also entails the exploration of conformations that compete significantly with the target structure for being its ground state. The design procedure is successful in all the ten cases.
We present a statistical field theory to describe large length scale effects induced by solutes in a cold and otherwise placid liquid. The theory divides space into a cubic grid of cells. The side length of each cell is of the order of the bulk correlation length of the bulk liquid. Large length scale states of the cells are specified with an Ising variable. Finer length scale effects are described with a Gaussian field, with mean and variance affected by both the large length scale field and by the constraints imposed by solutes. In the absence of solutes and corresponding constraints, integration over the Gaussian field yields an effective lattice gas Hamiltonian for the large length scale field. In the presence of solutes, the integration adds additional terms to this Hamiltonian. We identify these terms analytically. They can provoke large length scale effects, such as the formation of interfaces and depletion layers. We apply our theory to compute the reversible work to form a bubble in liquid water, as a function of the bubble radius. Comparison with molecular simulation results for the same function indicates that the theory is reasonably accurate. Importantly, simulating the large length scale field involves binary arithmetic only. It thus provides a computationally convenient scheme to incorporate explicit solvent dynamics and structure in simulation studies of large molecular assemblies.
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