An ab initio QM/MM study of the conformational stability of complexes formed by netropsin and DNA. The importance of van der Waals interactions and hydrogen bonding

The conformational stability of three different conformations of netropsin with DNA have been studied by ab initio QM/MM calculations and the interactions between the netropsin conformers and DNA have been inspected in detail. The importance of hydrogen bonding and van der Waals contacts to the netropsin-DNA complex stability was investigated with calculations in explicit solvent. Several aspects of the netropsin binding characteristics are discussed in terms of structural and energetic differences among the modeled complexes. It was found that van der Waals interactions are at least as important as hydrogen bonding in determining the conformational stability of the resulting complexes.