Conformations of cyclic 2,3-nucleotides and 2,3-Cyclic-5-diphosphates. Interrelation between the phase angle of pseudorotation of the sugar and the torsions about the glycosyl C(1)-N and the backbone C(4)-C(5) bonds

Semiempirical potential energy calculations have been carried out for cyclic 2′,3′-nucleotides and their 5′-phosphorylated derivatives, which are the intermediates in the hydrolysis of RNA. Calculations have been performed for both purine and pyrimidine bases for the observed O(1′)-endo, O(1′)-exo and the unpuckered planar sugar ring conformations. It is found that the mode of sugar pucker largely determines the preferred conformations of these molecules. For cyclic 2′,3′-nucleotides themselves, the O(1′)-endo sugars show a preference for the syn glycosyl conformation while the O(1′)-exo sugars exclusively favor the anti conformation regardless of whether the base is a purine or pyrimidine. For the unpuckered planar sugar, the syn conformation is favored for purines and anti for pyrimidines. Both the gauche (+) (60°) and trans (180°) conformations about the C(4′)? C(5′) bond are favored for O(1′)-endo sugars, while the gauche (?) (300°) and trans (180°) are favored for O(1′)-exo sugars. On the contrary, the 5′-phosphorylated cyclic 2′,3′-nucleotides of both purines and pyrimidines show a preference for the anti-gauche (+) conformational combination about the glycosyl and C(4′)? C(5′) bonds for the O(1′)-endo sugars and the anti-trans combination for the O(1′)-exo sugars. The correlation between the phase angle of the sugar ring and the favored torsions about the glycosyl and the backbone C(4′)? C(5′) bonds as one traverses along the pseudorotational pathway of the sugar ring is examined.