Paper Citing NAMD - Abstract
Priya, M. Hamsa; Ashbaugh, H. S.; Paulaitis, M. E.
Cosolvent Preferential Molecular Interactions in Aqueous Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13633-13642, NOV 24 2011
We extend the application of Kirkwood-Buff (KB) solution theory integrals to calculate cosolvent preferential interaction parameters from molecular simulations by deriving from a single simulation trajectory the excess chemical potential of the solute in addition to the solute-solvent molecular distribution functions. The solute excess chemical potential is derived from the potential distribution theorem (PDT) and used to define the local solvent domain around the solute, as distinguished from bulk solution. We show that this KB/PDT characterization of preferential molecular interactions resolves the problem of convergence of the preferential interaction parameter in the bulk solution limit, and as such, gives reliable estimates of preferential interaction parameters for methanol, ethanol, glycerol, and urea in aqueous cosolvent solutions with neopentane or tetramethyl ammonium ion as the solute. Preferential interaction parameters that are also calculated on the basis of cosolvent proximal distributions around the constituent methyl groups of the two solutes with the assumption of group additivity are in good agreement with those obtained by considering the molecular solute as a whole. The results suggest that this approach can be applied to estimate site-specific cosolvent preferential interaction parameters locally on the surface of complex, macromolecular solutes, such as proteins.
