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The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the β-hairpin of 2GB1and the α-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm−1. In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 Å radius and extending to at least 10 Å. These variations are of the order of 2−5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the β-hairpin of 2GB1as well as deca-alanine. Within a radius of 3 Å, the perturbation of the solvent structure is very significant with local TPEs that are 10−15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3−5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of liquid silica and beryllium fluoride are performed using the van Beest−Kramer−van Santen and transferable rigid ion model potentials, respectively, in order to compare transport properties. The ionic conductivity (σ), shear viscosity (η) and ionic self-diffusivities (D±) are computed over a fairly wide range of temperatures and densities and deviations from Arrhenius behavior along different isochores is studied. The Stokes−Einstein relation is shown to hold over the entire range of state points, though the effective hydrodynamic radius shows small variations due to thermal fluctuations, compression, and local tetrahedral order. Several alternative tests of the Nernst−Einstein relation are implemented which show that significant network-formation in the anomalous regime leads to a breakdown of this relationship. The relaxation times, τσand τM, associated with the decay of the charge-flux and pressure ACFs respectively, are computed. In the anomalous regime, as the tetrahedral network formation progresses, τMincreases rapidly while τσshows very little variation, indicating a decoupling of charge and momentum transport processes. [ABSTRACT FROM AUTHOR]

The relationship between structural order metrics and the excess entropy is studied using the transferable rigid ion model (TRIM) of beryllium fluoride melt, which is known to display waterlike thermodynamic anomalies. The order map for liquid BeF2, plotted between translational and tetrahedral order metrics, shows a structurally anomalous regime, similar to that seen in water and silica melt, corresponding to a band of state points for which average tetrahedral (qtet) and translational () order are strongly correlated. The tetrahedral order parameter distributions further substantiate the analogous structural properties of BeF2, SiO2, and H2O. A region of excess entropy anomaly can be defined within which the pair correlation contribution to the excess entropy (S2) shows an anomalous rise with isothermal compression. Within this region of anomalous entropy behavior, qtetand S2display a strong negative correlation, indicating the connection between the thermodynamic and the structural anomalies. The existence of this region of excess entropy anomaly must play an important role in determining the existence of diffusional and mobility anomalies, given the excess entropy scaling of transport properties observed in many liquids. [ABSTRACT FROM AUTHOR]