Theoretical study of the influence of ribose on the proton transfer phenomenon of nucleic acid bases

The first comprehensive theoretical study of ribose's effects on the behavior of proton transfer of nucleic acid base is presented. The specific hydrogen bonding of the ribose hydroxyls plays a very important role in the stabilization of the structure of ribonucleoside. Nine stable uridine conformations have been reported. The intermolecular proton transfer of the isolated, monohydrated uridine complexes in three different regions were extensively explored on the basis of density functional theory at the B3LYP/6-31+G∗ level. With the introduction of the ribose, not only the structural parameters of the nucleic acid bases changed, but also the energy barriers of the proton transfer process changed. Furthermore, changes of the electron distributions of the molecular orbital of the nucleic acid bases were also analyzed by NBO analysis. Consideration of the ribose's influence represents a much more real situation in the RNA.