The linear pentapeptide, Ala-Tyr-cis-Pro-Tyr-Asp-NMA (AYPYD) is known to have a significant population of type VI turn conformers in aqueous solvent. We have carried out theoretical studies of the conformational energetics of this peptide using a potential of mean force (PMF) consisting of the AMBER/OPLS empirical potential energy function, a macroscopic electrostatic model of polar solvation, ...

A nonlocal continuum theory of solvation is applied using an oscillating dielectric function with spatial dispersion. It is found that a convergent solution cannot be calculated using a model of a fixed solute cavity inside the solvent continuum. This is attributed to the fact that the dielectric oscillations appear as a result of coupling between polarization and density fluctuations, contradi...

We analyze de ciencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of biomolecules with charged groups. The procedure is only a few percents wrong for molecular con gurations of arbitrary sizes, provides explicit values for the...

Thermochemical cycles that involve pKa, gas-phase acidities, aqueous solvation free energies of neutral species, and gas-phase clustering free energies have been used with the cluster pair approximation to determine the absolute aqueous solvation free energy of the proton. The best value obtained in this work is in good agreement with the value reported by Tissandier et al. (Tissandier, M. D.; ...

The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of c...

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...

A dielectric continuum theory for the solvation of a polar molecule in a polar, polarizable solvent is tested using computer simulations of formaldehyde in water. Many classes of experiments, for example those which measure solvent-shifted vertical transition energies or electron transfer rates, require an explicit consideration of the solvent electronic polarization. Due to the computational c...

Equilibrium in the electronic subsystem across the solution-metal interface is considered to connect the standard electrode potential to the statistics of localized electronic states in solution. We argue that a correct derivation of the Nernst equation for the electrode potential requires a careful separation of the relevant time scales. An equation for the standard metal potential is derived ...

Molecular docking is an important tool for the discovery of new biologically active molecules given that the receptor structure is known. An excellent environment for the development of new methods and improvement of the current methods is being provided by the rapid growth in the number of proteins with known structure. The evaluation of the solvation energies outstands among the challenges fo...

Octanol-to-water solvation free energies of acetyl amino amides (Ac-X-amides) [Fauchère, J.L., & Pliska, V. (1983) Eur. J. Med. Chem. --Chim. Ther. 18,369] form the basis for computational comparisons of protein stabilities by means of the atomic solvation parameter formalism of Eisenberg and McLachlan [(1986) Nature 319, 199]. In order to explore this approach for more complex systems, we have...