Computing Activation Energies of Flexible Biomolecules in Generalized Born Continuum Solvent Environments
Kemple, Andrew S.
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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.