Ground-state properties of nucleic acid constituents studied by density functional calculations.: 3.: Role of sugar puckering and base orientation on the energetics and geometry of 2′-deoxyribonucleosides and ribonucleosides

In the present paper, we have analyzed the conformational energy and geometrical parameters of the isolated 2'-deoxyribonucleosides and ribonucleosides. Geometry optimization of these nucleic acid constituents has been undertaken by means of density functional theory with the Becke-Lee-Yang-Parr exchange and correlation functional and split valence basis sets, 6-31G(()*()), including nonstandard polarization functions on carbon, nitrogen, and oxygen atoms. For each nucleoside, three major conformers, i.e., C2'-endo/anti, C3'-endo/anti, and C3'-endo/syn, have been taken into consideration, where C3'-endo and C2'-endo refer to the north (N)-type and south (S)-type sugar puckering, respectively, and anti and syn designate the orientation of the base with respect to the sugar. In both families (2'-deoxyribonucleosides and ribonucleosides) the anti orientation of the base stabilized by an intramolecular C-H ... O hydrogen bond formed between the base and the O5' atom of the sugar moiety corresponds to the lowest energy states. In the 2'-deoxyribonucleosides including uracil, guanine, and adenine bases the lowest energy conformer is C2'-endo/anti, whereas in 2'-deoxycytidine the most stable conformer is C3'-endo/anti. In ribonucleosides, the C3'-endo/anti and C2'-endo/anti conformers nearly have the same energy, except in cytidine, where the most stable conformer is C3'-endo/anti. Therefore, a general discussion has been devoted to the exceptional cases of 2'-deoxycytidine and cytidine compared to the other nucleosides. The present calculated results have also been compared with those recently reported at the MP2 level by other authors on the 2'-deoxyribonucleosides or smaller model compounds on one hand, and with the experimental results based on a statistical survey of nucleoside crystal structures on the other hand.