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 fluorinesubstituted cytosine has great influence over the stabilization energy of the various C∶G derivatives while the nitrosubstituted 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.