The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs

The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO2) increase the total binding energy (Delta E) of X-G-C derivatives and the electron donating (ED) substituent (CH3) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH3 in the 1 position and F in the 5 position, which in both cases the Delta E value decreases negligibly small. With minor exceptions (X=8-CH3, 8-F, and 9-NO2), both ED and EW substituents increase slightly the Delta E values of X-A-T derivatives. The individual HB energies (a dagger E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO2 substituted derivative in each case.