Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results

Abstract

Various empirical potentials (AMBER 3.0, AMBER 4.1, CHARMM 23, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, PM3, MNDO/M) were tested to reproduce the ab initio MP2 stabilization energies of DNA H-bonded base pairs (26 different base pairs). The best performance of an empirical potential is exhibited by AMBER 4.1 and of semi-empirical quantum chemical methods by MNDO/M.