An empirical continuum solvation model, solvation free energy density (SFED), has been developed to calculate solvation free energies of a molecule in the most frequently used solvents. A generalized version of the SFED model, generalized-SFED (G-SFED), is proposed here to calculate molecular solvation free energies in virtually any solvent. G-SFED provides an accurate and fast generalized fram...

The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations ...

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from ...

Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate so...

Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other meth...

Does aqueous solvent discriminate among peptide conformers? To address this question, we computed the solvation free energy of a blocked, 12-residue polyalanyl-peptide in explicit water and analyzed its solvent structure. The peptide was modeled in each of 4 conformers: alpha-helix, antiparallel beta-strand, parallel beta-strand, and polyproline II helix (P(II)). Monte Carlo simulations in the ...