Implicit solvation based on generalized Born theory in different dielectric environments.
In this paper we are investigating the effect of the dielectric environment on atomic Born radii used in generalized Born (GB) methods. Motivated by the Kirkwood expression for the reaction field of a single off-center charge in a spherical cavity, we are proposing extended formalisms for the calculation of Born radii as a function of external and internal dielectric constants. We demonstrate that reaction field energies calculated from environmentally dependent Born radii lead to much improved agreement with Poisson-Boltzmann solutions for low dielectric external environments, such as biological membranes or organic solvent, compared to previous methods where the calculation of Born radii does not depend on the environment. We also examine how this new approach can be applied for the calculation of transfer free energies from vacuum to a given external dielectric for a system with an internal dielectric larger than one. This has not been possible with standard GB theory but is relevant when scoring minimized or average structures with implicit solvent.
Department of Molecular Biology, TPC6, The Scripps Research Institute, La Jolla, California 92037, USA.
Michael
M
Feig
Wonpil
W
Im
Charles L
CL
Brooks
D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D017097:Electric Impedance; D004563:Electrochemistry / Q000379:methods*; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity
D001704:Biopolymers; D012997:Solvents