Theoretical study on conformational preferences of ribose in 2-thiouridine—the role of the 2′OHgroup

Abstract

Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3′-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2′ towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2′H2′ stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2′OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3′-endo conformation of ribose.