The influence of the hydrated metal cations binding to adenine-N7 or adenine-N3 on the hydrogen bonding in adenine-thymine base pair: A comparative study

The changes of the hydrogen bonds formed between adenine-thymine Watson-Crick (AT WC) base pair caused by the hydrated metal cation binding on the adenine-N3 of AT WC or the adenine-N7 of AT WC base pair are investigated by the electron density topological analysis and NBO analysis at B3LYP/6-31++G(d,p) level of theory. In comparison with those in the isolated AT base pair, the changes of the hydrogen bonds in AT when presenting the cations at A-N3 position are different from those when presenting the cations at A-N7 position, mainly due to the electron density transfer and the formation of an additional hydrogen bond in complex MZ+AT(N3). The hydrogen bonding energies were calculated at the B3LYP/6-31++G(d,p) and MP2/6-31++G(d,p)//B3LYP/6-31++G(d,p) theory levels, respectively. The results obviously indicate that the hydrogen bonds in the metal-AT(N3) complexes are more stable than those in the complexes metal-AT(N7). At the same time, we also found that the changes of the hydrogen bonds in the complexes Mg2+AT(N3) and Zn2+AT(N3) are quite similar to those in the complex formed by PtCl2(NH3)2 binding to the G-N7 position of guanine-cytosine Watson-Crick. So the N3 position of adenine in minor groove of DNA might have more chance to be a target for platinum-based drug attack than the N7 position of adenine in major groove.