An ab initio study of a nucleoside: Uridine

Abstract

Ab initio SCF molecular orbital computations have been performed for a nucleoside, uridine, in a specific conformational arrangement (3'-endo conformation of the ribose, gg orientation of the extracyclic CH2OH group, and anti orientation of the base with respect to the sugar) and the results compared with some of those pertaining to the isolated component fragments, uracil and 3'-endo ribose. While the modifications of the atomic charges or of the energies of the molecular orbitals upon the formation of the nucleoside are small, the perturbations produced in some portions of the corresponding electrostatic molecular potential are more profound and more significant. Those occurring in the vicinity of the CO4 carbonyl group account for the probable increase in the proton affinity of uridine with respect to uracil. Those relevant to the O1′ oxygen indicate that the proton affinity of this atom in the free ribose is appreciably shielded in the nucleoside. The oxygens O2′ and O3′ represent non-negligible sites of attraction for positive ions in the free ribose and in the nucleoside.