Molecular orbital calculations of metal ion interaction with nucleic acid bases. I. Binding of Cu(II) with adenine, guanine, uracil, and cytosine

Abstract

AbstractThe reaction of the transition metal ion Cu(II) with nucleic acid bases—adenine, guanine, uracil, and cytosine—has been investigated by conformation energy calculations (CEC) and molecular orbital (MO) methods. Various binding sites, e.g., N7–C6NH2, N7–C6O, N3‐N9, and N1 in purines and N3 and O8 in pyramidines, have been considered. It was found that the energy minima for different binding sites had different values. In addition to the energy minima in the nucleic acid base plane, we have observed out‐of‐plane energy minima, differing in energy by a few kcal/mol in most of the cases. The MO calculations were performed on the most favorable planar positions obtained. It was found that the presence of Cu(II) alters the charge distribution pattern of practically all the atoms of nucleic acid bases. Its main effect is to withdraw electrons from the negatively charged nitrogens and positively charged carbons. The oxygen charge did not alter significantly. The results are compared with the experimental electron spin resonance and x‐ray diffraction studies and their biological significance is discussed.