A fractional charge model for empirical calculations of peptide-water interactions.
The properties of an empirical model of interaction between a water molecule and polar groups of peptides or small peptides are explored. The H2O molecule is represented by a four-point charges distribution. In electron donor groups, a point charge is located on the axis of the lone pairs orbitals in order to introduce some directionality in hydrogen bonds. The effective potential is approximated by the sum of the coulombic interactions between point charges distribution and of a 6--12 atom-atom potential. The coefficients of this last potential are first adjusted by simulating the geometry of the water dimer. Equilibrium configurations of associated polar molecules and H2O predicted by the model are found to be in good agreement with those resulting from more sophisticated ab initio SCF calculations. Interactions between H2O and the side-chains of the cyclic dipeptide C(L-Thr-L-His) are then calculated. It is shown that internal bridging by water is an essential effect of the solvent. The experimental position of the H2O molecule is reproduced, stability of which depends also on intermolecular interactions.
D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008968:Molecular Conformation; D010455:Peptides; D014867:Water
D010455:Peptides; D014867:Water