Local dielectric constants and Poisson–Boltzmann calculations of DNA counterion distributions

Abstract

Recent work by the authors on the calculation of local solvent dielectric constants around polyelectrolytes using the Poisson–Boltzmann approach is analyzed in terms of the effect on surface potentials and counterion concentrations. Polyelectrolyte surface geometry, local electric fields, and counterion distributions contribute to the self-consistent prediction of local solvent dielectric constants. For an all-atom cell model of DNA with added monovalent salt varying from 0 to 0.5M, the Poisson–Boltzmann-determined electrostatic potential increases (negatively) by 50–100% upon the inclusion of local dielectric constants. This, in turn, implies that hydronium ion concentrations in the major and minor grooves increase by about 0.65 and 0.35 pH units, respectively. While counterion concentrations in the major groove change only slightly, those in the minor groove increase by 60–90%. It is also noted that while the local dielectric constant in the major groove monotonically increases away from the surface toward the bulk value of water the dielectric constant in the minor groove has a minimum about 2 Å from the surface due primarily to the local electric field. Certain other properties, such as ionic and dipole first passage times, are affected little by local dielectric constants (less than about 3%). © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 1087–1093, 1997