Structural, electronic and photophysical properties of analogous RNA nucleosides: a theoretical study

We use first-principles density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to investigate the structural, energetic and bonding aspects, and optical properties of two analogues of RNA nucleosides. The results are compared against the findings obtained for the natural and both modified nucleosides, as well as available experimental data. We find that the modified nucleosides form the hydrogen bonded (H-bonded) Watson-Crick (WC) base pairing with a similar H-bonding energy to that obtained for the natural nucleosides. These modified nucleosides can also form WC base pairing with their natural complementary nucleosides. We also focus on the optical absorption properties of these modified nucleosides and their WC H-bonded base pairs in gas phase as well as in implicit water solvent. Our simulated results show that the low energy peaks in the absorption spectra mainly arise because of the pi-pi* electronic transition for both the modified nucleosides. The calculated absorption and emission spectra in the presence of solvent follow the same trend as that found experimentally. Our results demonstrate that the modified nucleosides show significantly different electronic and optical properties, although the basic structural and bonding aspects remain the same. They also give microscopic details of the experimentally observed photophysical properties of the modified nucleosides.