Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory

Details Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory

2011-08-24

arxiv.org/abs/1108.4876v1

Biology

Quantitative Biology

Biomolecules

16 pages, 5 figures

Scientific paper

Changes in hydration are central to the phenomenon of biomolecular recognition, but it has been difficult to properly frame and answer questions about their precise thermodynamic role. We address this problem by introducing Grid Inhomogeneous Solvation Theory (GIST), which discretizes the equations of Inhomogeneous Solvation Theory on a 3D grid in a volume of interest. Here, the solvent volume is divided into small grid boxes and localized thermodynamic entropies, energies and free energies are defined for each grid box. Thermodynamic solvation quantities are defined in such a manner that summing the quantities over all the grid boxes yields the desired total quantity for the system. This approach smoothly accounts for the thermodynamics of not only highly occupied water sites but also partly occupied and water depleted regions of the solvent, without the need for ad hoc terms drawn from other theories. The GIST method has the further advantage of allowing a rigorous end-states analysis that, for example in the problem of molecular recognition, can account for not only the thermodynamics of displacing water from the surface but also for the thermodynamics of solvent reorganization around the bound complex. As a preliminary application, we present GIST calculations at the 1-body level for the host cucurbit[7]uril, a low molecular weight receptor molecule which represents a tractable model for biomolecular recognition. One of the most striking results is the observation of a toroidal region of water density, at the center of the host's nonpolar cavity, which is significantly disfavored entropically, and hence may contribute to the ability of this small receptor to bind guest molecules with unusually high affinities.

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