Thermodynamic Studies on Amino Acid Solvation in some Aqueous Alcohols

Present paper discusses the behaviour of transfer free energy of some amino acids from water to aqueous solution of Ethanol, 2‐PrOH ad t‐BuOH at different compositions. Dissection of transfer free energy into cavity term, interaction term and electrical term reveals that cavity forming free energy of transfer ΔG_t⁰ (Cav.) plays an important role in dictating actual interaction of amino acids in these mixed solvents. Cavity forming free energy of transfer has been estimated by using Scaled Particle Theory (SPT).     

A supermolecule study of the effect of hydration on the conformational behaviour of leucine-enkephalin

Summary A theoretical conformational study was performed on leu-enkephalin in its zwitterionic form, both in vacuo and in the presence of a number, n, of up to 13 water molecules saturating its first hydration shell. The intramolecular energy of enkephalin as well as the intermolecular enkephalin-water and water-water interaction energies were computed with the SIBFA procedure (Sum of Interactions Between Fragments Ab initio computed), which uses additive ab initio multipole systematics and analytical formulas grounded on ab initio SCF computations. Energy minimizations were performed with a polyvalent minimizer, Merlin, with which three distinct derivative and three distinct nonderivative minimizers can be activated in a sequential fashion.Eight different candidate conformations of enkephalin were used as starting points. These conformations are either those found in distinct X-ray structures, or those proposed on the basis of theoretical computations by other authors. In the absence of hydration, they converged towards distinct folded energy-minima, the best four ones being separated by an energy gap of 8.7 kcal/mol. In marked contrast, with up to n=13, the energetical separation between the six best conformers narrowed down to 4 kcal/mol. They can be characterized by: (a) either a direct or a water-mediated ammonium-carboxylate interaction; b) either a close proximity (as in morphine) or a large separation between the aromatic rings of Tyr and Phe (intercenter separations of 4.5 Å and 10.5 Å, respectively), with each of the four mutual combinations of (a) and (b) being represented.     

离子水化模型和水化能的计算

本文根据静电理论和晶体场理论将金属离子的水化分为水合和水溶剂化两个过程,水化能主要决定于这两个过程的能量变化,并由此推得水化能的计算公式。计算结果与实验值基本相符,从而证明这一模型是合理的。     

Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions

A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree–Fock/6–31G* level. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 548–573, 1998     

An empirical potential function for the interaction between univalent ions in water

A hydration-shell model has been developed for calculating the interaction energy between ions in water. The hydration shell around each ion contains a few tightly bound water molecules and a larger number of less tightly bound molecules. The energies of their interaction with the ion and the size of the hydration shell have been derived from published experimental data for ion-water clusters in the gas phase. An expression derived for the interaction energy of two univalent ions in water incorporates the following effects: a Lennard-Jones 6–12 interaction, a Coulomb interaction between the charges, the polarization of the hydration shells by a neighboring ion, and an energy term for the removal of water from the hydration shells when the hydration shells of two ions overlap. The effective dielectric constant at small ion-ion distances is the only adjustable parameter. Computed interaction energies for aqueous solutions of twelve alkali halides match experimental values, derived from conductimetric measurements, with an average error of ±14%.