The electronic spectra and the H-bonding pattern of the sulfur and selenium substituted guanines

The density functional theory (DFT) with B3LYP, M05-2x, and M06-2x functionals, along with the 6-311+G(d, p) basis set, were used in the study of the UV absorption spectra and the H-bonding pairing patterns of the sulfur and selenium substituted guanines. The time-dependent DFT calculations reveal that the red-shifts of the transition energies predicted for guanine for the first gas-phase observable transition amount to 55 nm for S6mG and 86 nm for Se6mG, respectively. These changes in the transition energies are qualitatively comparable to the experimental data for substituted guanines in DNA. The density deformation map reveals that both sulfur and selenium atoms exhibit lesser conjugated with the purine ring, which leads to the small transition energies in S6mG and Se6mG. The decrease in binding energy (3 kcal/mol) of Se6mGmC as compared to that of mGmC is well related to the observation of the melting temperature difference ΔT(m) ~3.9 °C for the Se-DNA versus DNA. The molecular recognition (mGmC pairing) pattern is found to be changed significantly due to the replacement of O6 by S or Se. The substantial base-base plane twisting revealed in this study suggests that the base stacking in the DNA might be interrupted. This study shows that the red-shifts of the transition energies predicted by the M05-2x and M06-2x functionals are close to those revealed by the B3LYP calculations. As M05-2x and M06-2x offer better descriptions for the dispersion interactions, they provide efficient approaches to investigate the influences of the base-stacking on the transition energies.