ci7b00410_si_004.xlsx (45.48 kB)
Download fileIncorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model
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posted on 2018-03-21, 00:00 authored by Songling Ma, Sungbo Hwang, Sehan Lee, William E. Acree, Kyoung Tai NoTo
describe the physically realistic solvation free energy surface of
a molecule in a solvent, a generalized version of the solvation free
energy density (G-SFED) calculation method has been developed. In
the G-SFED model, the contribution from the hydrogen bond (HB) between
a solute and a solvent to the solvation free energy was calculated
as the product of the acidity of the donor and the basicity of the
acceptor of an HB pair. The acidity and basicity parameters of a solute
were derived using the summation of acidities and basicities of the
respective acidic and basic functional groups of the solute, and that
of the solvent was experimentally determined. Although the contribution
of HBs to the solvation free energy could be evenly distributed to
grid points on the surface of a molecule, the G-SFED model was still
inadequate to describe the angle dependency of the HB of a solute
with a polarizable continuum solvent. To overcome this shortcoming
of the G-SFED model, the contribution of HBs was formulated using
the geometric parameters of the grid points described in the HB coordinate
system of the solute. We propose an HB angle dependency incorporated
into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent
acidity and basicity densities are defined and parametrized with experimental
data. The G-SFED-HB model was then applied to calculate the solvation
free energies of organic molecules in water, various alcohols and
ethers, and the log P values of diverse organic molecules,
including peptides and a protein. Both the G-SFED model and the G-SFED-HB
model reproduced the experimental solvation free energies with similar
accuracy, whereas the distributions of the SFED on the molecular surface
calculated by the G-SFED and G-SFED-HB models were quite different,
especially for molecules having HB donors or acceptors. Since the
angle dependency of HBs was included in the G-SFED-HB model, the SFED
distribution of the G-SFED-HB model is well described as compared
to that of the G-SFED model.