Computing Activation Energies of Flexible Biomolecules in Generalized Born Continuum Solvent Environments
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Authors
Kemple, Andrew S.
Issue Date
2004
Type
Thesis
Language
en_US
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Abstract
This paper examines the activation energies of a flexible molecule in polar
and nonpolar solvent environments. These solvation effects were studied
using the generalized Born model of solvation developed for CHARMM by
Dominy and Brooks (B. N. Dominy and C. L. Brooks, III J. Phys. Chern. B
103(1999), pp. 3765-3773). This model is based on a parametrization obtained
from a test set of small, rigid molecules and molecular fragments. We
describe in this paper how we optimized the parameters for use throughout
the entire conformational range of a flexible test molecule. High-dielectric
solvent were found to agree with continuous electrostatic environment modeled
by the Poisson-Boltzmann equation to very high precision. Low-dielectric
solvents were also effectively modeled though, for reasons we address in this
paper, with lower precision agreement to Poisson-Boltzmann models.
Description
v, 34 p.
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