the acidity constants (pka) of thirty four (34) ;-substituted carboxylic acids in aqueous solution havebeen calculated using conductor-like polarizable continuum (c-pcm) solvation model. the gasphaseenergies at the density functional theory (dft-mpw1pw91) and solvation energies athartree fock (hf) are combined to estimate the pka values which are very close to the experimentalvalues where, and ...

Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding af...

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more ...

A multiscale coarse-grained approach able to handle efficiently the solvation of microscopic solutes in extended chemical environment is described. That approach is able to compute readily and efficiently very long-range solute/solvent electrostatic microscopic interactions, up to the 1-μm scale, by considering a reduced amount of computational resources. All the required parameters are assigne...

The empirically calculated parameter LogP(o/w), the log(10) of the coefficient for solvent partitioning between 1-octanol and water, has been used to provide the key data for a unique non-covalent interaction force field called HINT (Hydropathic INTeractions). This experimentally-derived force field encodes entropic as well as enthalpic information and also includes some representation of solva...

Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors. Here, we propose a new solvation free energy function through the improvement of the solvent-contact model, and test its applicability in estimating the solvation free energies o...

Grand canonical Monte Carlo simulations are used to investigate the structure of frozen phases in a confined soft sphere (Lennard-Jones) fluid for a bulk state point lying close to the liquid-solid freezing line. The study reveals that the pore fluid not only freezes in the pore, but solid-solid transformations occur in the two, and three-layered structures that form as the pore height is varie...

Protective osmolytes are chemical compounds that shift the protein folding/unfolding equilibrium toward the folded state under osmotic stresses. The most widely considered protection mechanism assumes that osmolytes are depleted from the protein's first solvation shell, leading to entropic stabilization of the folded state. However, recent theoretical and experimental studies suggest that prote...