Non-additivity in cation—peptide interactions. A molecular dynamics and ab initio study of Na + in the gramicidin channel

Abstract

The importance of non-additive energy contributions in cation—peptide interactions is investigated, in the context of Na + binding to the gramicidin channel, using molecular dynamics simulations and ab initio calculations. SCF supermolecule calculations are performed for an ensemble of Na + and N-methylacetamide complexes constructed from configurations generated by a molecular dynamics trajectory of the full channel system to represent the gramicidin binding site. A main result is that the ab initio estimates of the excess many-body interactions due to the cation are very well correlated with second-order induction energy obtained from a simple approximation based on atomic polarizabilities.