Parameterization hydrogen bonding

Most of the data for these parameterization studies came from ah initio calculations although other sources were also used, in particular, to validate the resulting force field. Thus a set of small model molecules with different conformations of the R—N—C—N—R moiety was calculated at various levels of theory and the results used to derive torsional parameters, hydrogen bond parameters and conformationally dependent correction terms for natural bond lengths and angles, as described below ... 

One of the most important developments in the theory of water is the invention of a realistic effective intermolecular pair potential. Although others had made similar suggestions earlier 59>, it is Stillinger and co-workers 60> who have shown, with the aid of molecular dynamics calculations 3>, how satisfactory such a potential can be. The availability of a water-water potential drastically reduces the scope for parameterization in model based theories, and permits investigation of such concepts as "broken hydrogen bond. We shall frequently have occasion to call upon its properties in the following discussion. 

Carbohydrates have been included in the wide range of molecules used in the parameterization of MM2 and of MM3. Alcohol and ether parameters have usually been determined from simple alcohols and ethers themselves. However, carbohydrates contain some unusual features in the acetal linkages, and in the many vicinal hydrogen-bonded hydroxyl groups. The "anomeric effect", first discovered by Edward (15) and popularized by Lemieux (16.), is best known in carbohydrates, although, of course, it occurs in other classes of compounds as well. One apparent result of this effect is that an axial alkoxy substituent is often more stable than the corresponding equatorial substituent when attached at the Cl position of a tetrahydropyranyl ring. This effect can be... 

Representative examples are provided in Table 5-19. Only a single (intermolecular) distance is examined for each system, underlying the fact that the experimental structure data are incomplete. The usual quantum chemical models have been surveyed. Comparisons with molecular mechanics models have not been included even though force fields such as MMFF have been explicitly parameterized to reproduce known hydrogen-bond distances. 

Here Vij denotes the distance between atoms i and j and g(i) the type of the amino acid i. The Leonard-Jones parameters Vij,Rij for potential depths and equilibrium distance) depend on the type of the atom pair and were adjusted to satisfy constraints derived from as a set of 138 proteins of the PDB database [18, 17, 19]. The non-trivial electrostatic interactions in proteins are represented via group-specific dielectric constants ig(i),g(j) depending on the amino-acid to which atom i belongs). The partial charges qi and the dielectric constants were derived in a potential-of-mean-force approach [20]. Interactions with the solvent were first fit in a minimal solvent accessible surface model [21] parameterized by free energies per unit area (7j to reproduce the enthalpies of solvation of the Gly-X-Gly family of peptides [22]. Ai corresponds to the area of atom i that is in contact with a ficticious solvent. Hydrogen bonds are described via dipole-dipole interactions included in the electrostatic terms... 

---