.......................................................................................................................................... 3 Introduction ..................................................................................................................................... 4 Protein Structure ............................................................................................

A coherent framework is presented for determining the free energy change accompanying ligand binding to protein receptors. The most important new feature of the method is the contribution of the flexibility of the free ligand, and hence its conformational change on binding, to the free energy. Flexibility introduces two additional terms in the free energy difference: the internal energy differe...

Molecular dynamics simulations of electron and ion transfer reactions near a smooth surface are presented, analyzing the effect of the geometrical constraint of the surface and the interfacial electric field on the relevant solvation properties of both a monovalent negative ion and a neutral atom. The simulations show that, from the solvation point of view, ion adsorption is an uphill process d...

The total free energy of a molecule includes the classical molecular mechanical energy (which is understood as the free energy in vacuum) and the solvation energy which is caused by the change of the environment of the molecule (solute) from vacuum to solvent. The solvation energy is important to the study of the inter-molecular interactions. In this paper we develop a fast surface-based genera...

in this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (r), alpha helix (α) and beta sheet (b) were investigated theoretically. these structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. computational methods at the hf, b3lyp, x3lyp and m05-2x levels in the ga...

A density functional theory (DFT) protocol for the calculation of redox potentials of copper complexes is developed based on 13 model copper complexes. The redox potentials are calculated in terms of Gibbs free energy change of the redox reaction at the theory level of CAM-B3LYP/6-31+G(d,p)/SMD, with the overall Gibbs free energy change being partitioned into the Gibbs free energy change of the...

Solvation of small and large clusters are studied by simulation, considering a range of solvent-solute attractive energy strengths. Over a wide range of conditions, both for solvation in the Lennard-Jones liquid and in the SPC model of water, it is shown that the mean solvent density varies linearly with changes in solvent-solute adhesion or attractive energy strength. This behavior is understo...

We present a Ginzburg-Landau theory of solvation of ions in polar binary mixtures. The solvation free energy arising from the ion-dipole interaction can strongly depend on the composition and the ion species. Most crucial in phase separation is then the difference in the solvation free energy between the two phases, which is the origin of the Galvani potential difference known in electrochemist...

Proton solvation and proton mobility are both subjects of great interest in chemistry and biology. Here we have studied the hydration shells of H3O+ at temperatures ranging from 260 to 340 K using the multistate empirical valence-bond methodology (MS-EVB2). We have calculated the radial distribution functions for the protonium and its solvation shells. Furthermore, we have determined the Gibbs ...