Determination of the complete correlation between the sugar ring puckers and 5'-exocyclic group rotamers in conformationally-flexible nucleic acid components from NMR study.

Inspection of stereochemical models suggests a possible correlation between the proportion (Yg-/Yt) of the g- and t rotamers and the S pucker populations irrespective of the anti-syn conformational composition of the base. Interpretation of the NMR vicinal coupling constants in terms of conformational populations shows a decline of Yg-/Yt with XS approaching zero, consistent with high unfavorability of the Ng- conformational combination in solution, a result supported by a X-ray crystallographic data survey. Hence, the underlying assumption introduced into the present study is that the g- rotamer and the N pucker do not coexist together in solution. Therefore, the limiting value of Yg-/Yt corresponding to the S pucker could be determined for each compound individually. Finally, populations and relative free energies of all conformational combinations of Ng+, Nt, Sg+, St and Sg- (except Ng- which is not important) have been estimated. Results of the present study suggest several interesting regularities concerning the syn-anti effect on populations and energies of the conformational combinations in ribo- and deoxyribo-nucleosides. (a) In the anti-type nucleosides, the Ng+ conformation is about 2 kJ/mol more stable than Nt, but in the syn-type, the Ng+ and Nt have comparable energy. (b) No important changes are observed in the Ng+ population comparing the anti-type and syn-type of ribo- and deoxyribo-nucleosides separately. (c) The Nt is considerable stabilized and simultaneously the Sg+ is strongly destabilized in the syn-type nucleosides relative to the anti-type. (d) Irrespective of the syn-anti composition the St is always more stable (1-2 kJ/mol) than the Sg- conformational combination.