Properties of dianionic oxyphosphorane intermediates: Implication to the reaction profile for base-catalyzed RNA hydrolysis

From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis (which also represents the base-catalyzed methanolysis of ethylene phosphate monoanion in reverse), a pentacoordinate dianionic intermediate 2a (Storer et al. J. Am. Chem. Soc. 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. However, the intermediate, which has a well depth on the order of k(B)T, is unlikely to be kinetically significant. The endocyclic P-O(2') bond is found to be much weaker than the exocyclic P-O(5') bond. In agreement with this finding, calculations on 2a at the 6-31+G* level abolishes TS1 and the pentacoordinate intermediate, leaving only TS2 as the sole transition state. Thus, for all the cases examined, the rate-limiting transition-state structure is TS2 which has an extended P-O(5') breaking bond. These results and the mode of cleavage of a simpler compound 3b are in accord with stereoelectronic predictions (see text for the definition). Moreover, solvation appears to stabilize the pentacoordinate intermediate. In the gas phase, the simplest oxyphosphorane 3b has the least tendency to form a pentacoordinate intermediate. However, 3b does form a pentacoordinate intermediate when it is solvated with six water molecules. These results support the hypothesis that phosphoryl-transfer reactions take place via pentacoordinate intermediates not only in acidic but also in basic media.