In an implicit-solvent description of molecular solvation, the electrostatic free energy is given through the electrostatic potential. This potential solves a boundary-value problem of the Poisson-Boltzmann equation in which the dielectric coefficient changes across the solute-solvent interface-the dielectric boundary. The dielectric boundary force acting on such a boundary is the negative firs...

The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree-Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconf...

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...

Two types of imidazolium-based ionic liquid (IL), 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([C(4)mim][NTF(2)]) and 1-butyl-3-methylimidazolium tetrafluoroborate ([C(4)mim][BF(4)]), confined between silica surfaces were investigated by surface force apparatus (SFA)-based resonance shear measurements together with surface force measurements. The surface force profiles in the...

Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to ...

Molecular dynamics simulations on DNA and RNA that include solvent are now being performed under realistic environmental conditions of water activity and salt. Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations. New studies of sequence effects, axis bending, solvation and conformational transitions have appeared.

A nonperturbative theory is presented which allows us to calculate the solvation free energy of polarizable ions near water-vapor and water-oil interfaces. The theory predicts that larger halogen anions are adsorbed at the interface, while the alkali metal cations are repelled from it. The density profiles calculated theoretically are similar to those obtained using molecular dynamics simulatio...

The aim of this communication was to expand the results of numerical analyses performed by Sun et al. on their experimental solubility of fenofibrate in aqueous mixtures of ethanol and acetone at 298.15 K, in terms of the evaluation of the preferential solvation of this compound by the organic solvents and water in the saturated mixtures based on the inverse Kirkwood-Buff integrals (IKBI). ...

The fluctuating charge (FQ) force field, a polarizable potential model in which point charges on atomic sites fluctuate in response to the environment, is applied to the aqueous solvation of acetamide and transand cisN-methylacetamide (NMA). Two parameters are assigned to each kind of atom, corresponding to an electronegativity and a hardness. The FQ model accurately reproduces both the gas-pha...

Protein structure prediction, fold recognition, homology modeling and design rely mainly on statistical effective energy functions. Although the theoretical foundation of such functions is not clear, their usefulness has been demonstrated in many applications. Molecular mechanics force fields, particularly when augmented by implicit solvation models, provide physical effective energy functions ...