A novel method for fast and accurate evaluation of the generalized Born radii in macromolecular solvation electrostatics calculations is proposed, based on the solvent accessibility of the first two solvation layers around an atom. The reverse generalized Born radii calculated by the method have correlation coefficient of 98.7% and RMSD of 0.031 A(-1) with the values obtained using a precise bu...

The stepwise solvation-equilibrium model of Stokes and Robinson isused for a description of departures from ideality in ionic solutions. It is shown howto construct a thermodynamically consistent model including solvation effects. Sim-ple expressions are derived for the mean ion solvation number. The model is appliedto strong electrolyte solutions (pure water+salt and mixed aque...

In an implicit-solvent description of the solvation of charged molecules (solutes), the electrostatic free energy is a functional of concentrations of ions in the solvent. The charge density is determined by such concentrations together with the point charges of the solute atoms, and the electrostatic potential is determined by the Poisson equation with a variable dielectric coefficient. Such a...

the hydration of biomolecules is vitally important in molecular biology, so in this paper thesolvation energy and radial distribution function of dna bases have been calculated by themonte carlo simulation.the geometries of isolated adenine, guanine, cytosine, and thyminehave been optimized using 6-31+g(d,p) basis function sets. these geometries then will be used inthe monte carlo calculation o...

Background: Recent studies have proposed various sources for the origin of cooperativity in simpliied protein folding models. Important contributions to cooperativity that have been discussed include backbone hydrogen bonding, side-chain packing, and hydrophobic interactions. Related work has also focused on what interactions are responsible for making the free energy of the native structure a ...

Internet Electron. J. Mol. Des. 2003, 1, 000–000 Abstract In order to separate the effect of substituents into two parts, referring to the interaction of the reacting molecules and the solvation, the δ∆G, δ∆H and δ∆S reaction constants were defined and determined from the dependence of ∆G, ∆H and ∆S activation parameters on the σ substituent constants, by analogy with the Hammett equation. The ...

The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a fact...

A Gaussian solvent-exclusion model for the solvation free energy is developed. It is based on theoretical considerations and parametrized with experimental data. When combined with the CHARMM 19 polar hydrogen energy function, it provides an effective energy function (EEF1) for proteins in solution. The solvation model assumes that the solvation free energy of a protein molecule is a sum of gro...

This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive ...