Substituent effects of R (R=CH3, CH3O, F and NO2) on the A:T and C:G base pairs: a theoretical study

The substituent effect on geometries, energies, frequencies and charge distributions of the various DNA base pair derivatives was evaluated using density functional theory at B3LYP/6-31G* level. The results indicate that the fluorine-substituted cytosine has great influence over the stabilization energy of the various C:G derivatives while the nitro-substituted thymine affects the stabilization energies most deeply among all the A:T derivatives. The N–H stretching vibrational frequency is red shifted and the shift is almost linear correlated with the N–H bond length elongation. There is no direct relationship between the charge distribution and the stabilization energy.