This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity ...This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity will contain the solute and some explicit solvent molecules,and an intermediate buffer layer and an exterior layer contain the bulk solvent.A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer.The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion.Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions.Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects.In particular,the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent.Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.展开更多
基金The authors would like to thank the financial support provided by the National Institutes of Health(Grant No.1R01GM083600-02)Z.Xu is also partially supported by the Charlotte Research Institute through a Duke Postdoctoral FellowshipW.Cai and Z.Xu are also partially supported by the Department of Energy(Grant No.DEFG0205ER25678).
文摘This paper introduces a three dielectric layer hybrid solvation model for treating electrostatic interactions of biomolecules in solvents using the PoissonBoltzmann equation.In this model,an interior spherical cavity will contain the solute and some explicit solvent molecules,and an intermediate buffer layer and an exterior layer contain the bulk solvent.A special dielectric permittivity profile is used to achieve a continuous dielectric transition from the interior cavity to the exterior layer.The selection of this special profile using a harmonic interpolation allows an analytical solution of the model by generalizing the classical Kirkwood series expansion.Discrete image charges are used to speed up calculations for the electrostatic potential within the interior and buffer layer regions.Semi-analytical and least squares methods are used to construct an accurate discrete image approximation for the reaction field due to solvent with or without salt effects.In particular,the image charges obtained by the least squares method provide accurate approximations to the reaction field independent of the ionic concentration of the solvent.Numerical results are presented to validate the accuracy and effectiveness of the image charge methods.
