The structure and dynamics of water in ionic solutions at high pressure have been investigated using a combined approach based on extended X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. Modification of the hydration properties of the Zn(2+) ion induced by a pressure increase from ambient condition up to ∼6.4 GPa has been revealed and accurately analyzed. With increasing pressure the first hydration shell of the Zn(2+) ion has been found to retain an octahedral symmetry with a shortening of the Zn-O distance up to 0.09 Å and an increased width associated with thermal motion, as compared to the ambient condition hydration complex. A very interesting picture of the dynamic behavior of the first hydration shell has emerged from the analysis of the simulations: up to 2.5 GPa no exchange events between first and second shell water molecules occurred, while above this pressure value several exchange events take place in the solution following an associative interchange mechanism. This result can be explained by the very high compression and packing of the solvent which force second shell water molecules to enter the Zn(2+) first hydration shell. MD simulations indicate a strong pressure effect also on the structure of the second coordination shell which is compressed and becomes more disordered and less structured with increasing pressure. The water mobility and the ion diffusion coefficient have been found to increase in the high density conditions, as a consequence of the rupture of the hydrogen bond network caused by pressure.

In this paper, by using the perturbed matrix method (PMM) in combination with basic statistical mechanical relations both based on nanosecond time-scale molecular dynamics (MD) simulations, we quantitatively address the thermodynamics of compound 0 (Cpd 0) formation in horseradish peroxidase (HRP) enzyme. Our results, in the same trend of low-temperature experimental data, obtained in cryoenzymology studies indicate that such a reaction can be described essentially as a stepwise spontaneous process: a first step mechanically constrained, strongly exothermic proton transfer from the heme-H2O2 complex to the conserved His42, followed by a solvent-protein relaxation involving a large entropy increase. Critical evaluation of PMM/MD data also reveals the crucial role played by specific residues in the reaction pocket and, more in general, by the conformational fluctuations of the overall environment in physiological conditions.

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Interplay of theory and computation in chemistryexamples from on-water organic catalysis, enzyme catalysis, and single-molecule fluctuations