Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction e...

Statistical thermodynamics provides a powerful theoretical framework for analyzing, understanding and predicting the conformational properties of biomolecules. The central quantity is the potential of mean force or effective energy as a function of conformation, which consists of the intramolecular energy and the solvation free energy. The intramolecular energy can be reasonably described by mo...

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 ...

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of speci...