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...

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...

A Gaussian solvent-exclusion model for the solvation free energy is developed. It is based on theoretical considerations and parametrized with experimental data. When combined with the CHARMM 19 polar hydrogen energy function, it provides an effective energy function (EEF1) for proteins in solution. The solvation model assumes that the solvation free energy of a protein molecule is a sum of gro...

Z. Naturforsch. 54 b, 193-199 (1999); received September 23, 1998 Solvation Structure, EXAFS, ab initio Molecular Orbital Method, Copper(I) Ion The structure parameters around the Cu(I) ion in pyridine (PY), 4-methylpyridine (4MPY), 2-methylpyridine (2MPY), 2,6-dimethylpyridine (26DMPY), and acetonitrile (AN) were de­ termined by the extended X-ray absorption fine structure (EXAFS) method. The ...

The effects of cosolvents on the solubility and hydration of small nonpolar solutes in solution has been investigated using a combination of molecular dynamics simulation and Widom particle insertion calculations. Results were obtained for helium, neon, argon, and methane solutes in solutions of sodium chloride, ammonium sulfate, calcium chloride, ammonium acetate, tetramethylammonium chloride,...