A molecular dynamics study of the conformation of the alanine dipeptide in aqueous solution using a quantum mechanical potential

Abstract

Molecular dynamics simulations of the aqueous solution of alanine dipeptide have been carried out for seven configurations characteristic of important regions of the Ramachandran plot. A hybrid quantum mechanical-molecular mechanical potential was used that describes the solute using the AM1 Hamiltonian and the solvent using the TIP3P model. The importance of differential solute polarization and the preferential stabilization of the extended structures αL, αR and β have been identified. The results are compared with experiment and with the predictions of the ab initio polarizable continuum model of solvation.