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...

Molecular dynamicdfree energy perturbation simulations of several small amides [acetamide (ACT), N-methylacetamide (NMA), and N,N-dimethylacetamide] and amines [NH3, NH2CH3, NH(CH3)2, and N(CH3)3] in aqueous solution were performed to study the effects on solvation free energies arising from N-methylation. Using pairwise additive potentials, a uniform pattern of solvation effects was always obt...

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 ...

Protein solvation is the key determinant for isothermal, concentration-dependent effects on protein equilibria, such as folding. The required solvation information can be extracted from experimental thermodynamic data using Kirkwood-Buff theory. Here we derive and discuss general properties of proteins and osmolytes that are pertinent to their biochemical behavior. We find that hydration depend...

Recently, a two-step biodiesel production process which uses short-chain alcohols at supercritical conditions has been proposed. In addition, literature reports suggest that the COSMO-SAC thermodynamic model is a suitable alternative for the prediction of VLE for supercritical methanol/methyl esters mixtures. Thus, in this work a simulation study of the two-step supercritical method for the pro...

On 15 September 1849, the Scottish judge and author Henry Cockburn wrote the following in his journal: ‘This day, which was pleased to fair, was given to Pluscarden, nine miles off, and reached by a coach filled inside and out, and two saddle horses. We loitered about the ruin for some hours, and had a turf refection, and a good deal of calotyping, conducted by my friend Cosmo Innes, the Sherif...

Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models whic...

Molecular dynamics simulations are used to study solvation and solvation dynamics of a classic charge in a series of ethers of increasing molecular weights, CH3~CH2OCH2!nH with n51, 2, and 4. Equilibrium structures of the solvated species, ion mobility, linear response solvation functions, and nonequilibrium solvation are studied and compared with the corresponding results for a simple ~Stockma...

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...