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.
The theoretical analysis of the energy of the conformers of 2@-deoxyribonucleosides presents some subtle but signiÐcant di †erences depending on the nature of the base linked to the sugar. In particular, 2@-deoxycytidine behaves uniquely. Among the structural parameters invoked to explain this phenomenon, one of the most intriguing is the CÈHÉ É ÉO intramolecular hydrogen bond in which the donor atom is H6 (H8) in the pyrimidine (purine) base and the acceptor atom is O5@ of the sugar. In the present work, the network of intramolecular weak bonds is thoroughly investigated for every 2@-deoxynucleoside in both the North (C3@endo/anti) and South (C2@-endo/anti) conformations. In this respect, we use BaderÏs atoms in molecules (AIM) theory to perform a topological study of the electronic density, emphasizing the weak bonding in the nucleosides. Criteria for hydrogen bonding are comprehensively reviewed for each hydrogen bond revealed, and the concept of "" improper ÏÏ hydrogen bonding is addressed. The AIM analysis thus allows us to gain insight into the intrinsic reasons for the strange conformational behaviour of 2@-deoxycytidine.
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