computer modeling in molecular biology.pdf

6 Theory of Transport in Zon Channels 141bony1 and water oxygens is possible at the expense of breaking hydrogen bonds.Thus, in the present system the relative strengths of the strong ion-carbonyl and ionwaterinteractions must be preserved and well balanced with respect to the relativelyweaker but complex water-water, water-peptide and peptide-peptide hydrogen bondinteractions.6.3.1.1 Ab Initio CalculationsThere is no unique method to construct the potential energy function [56, 60-641.The approach chosen in the present study relies primarily on experimental data, supplementedby high level ab initio calculations with small model systems when thenecessary information is not available [65]. Since no experimental estimate of the interactionof Na' with the carbonyl group of the peptide backbone is available atthe present time, it is necessary to rely on ab initio calculations on small modelsystems to supplement this important information. The N-methylacetamidemolecule (NMA) was chosen to model the peptide backbone amide plane groups.The interaction of Naf with water, for which a fair amount of experimental gasphase as well as bulk liquid information is available, was calculated to test the accuracyof the approach. The results of the ab initio calculations involving Na' ion,water and the NMA molecule are given in Table 6-1. It is observed that the calculatedinteraction between Na+ and water is in very good agreement with the experimentalgas phase data [66]. This indicates that the approach to calculate the Na+ NMA interactionis valid and can be used to develop the empirical energy function. For comparison,results on hydrogen bonding interactions involving water and NMA are alsogiven in Table 6-1 [67].6.3.1.2 Functional Form and ParametrizationIt is desirable to keep the empirical potential function as simple as possible forreasons of computational efficiency. The functional form of the empirical force fieldthat was adopted is similar to others used in molecular dynamics of biologicalmacromolecules [56] ; in addition to internal energy functions (bond, angles anddihedrals), the non-bonded interactions are represented as a sum of radially symmetricpair decomposable site-site functions including Coulomb partial charges electrostatic,core repulsion, van der Waals dispersion and induced polarization,'%owbonded = c Eelec Ecore + EvdW Epol - (6-13)pairs