The CBS-QB3 method was used to calculate the gas-phase free energy difference between 20 phenols and their respective anions, and the CPCM continuum solvation method was applied to calculate the free energy differences of solvation for the phenols and their anions. The CPCM solvation calculations were performed on both gas-phase and solvent-phase optimized structures. Absolute pK(a) calculation...

The binding energy distribution analysis method (BEDAM) for the computation of receptor-ligand standard binding free energies with implicit solvation is presented. The method is based on a well-established statistical mechanics theory of molecular association. It is shown that, in the context of implicit solvation, the theory is homologous to the test particle method of solvation thermodynamics...

The molecular dynamics (MD) simulation method is used to assess structural details for humanprion protein (hereafter PrPN) and its Asp178 Asn mutant (hereafter PrPm) which causes fatalfamilial insomnia disease. The results reveal that the flexibility and instability increase in PrPmcould be related to specific amino acids exposed to the solvent. Solvation free energy of PrPm is 20kjmot1nni2 mor...

In this report, the validity and divergence of the activation energy barrier crossing model for the bound to free type water transition at the interface of the AOT/lecithin mixed reverse micelle (RM) has been investigated for the first time in a wide range of temperatures by time-resolved solvation of fluorophores. Here, picosecond-resolved solvation dynamics of two fluorescent probes, ANS (1-a...

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero lev...

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...