Molecular orbital calculations on the conformation of nucleic acids and their constituents. IV. Conformations about the exocyclic C(4′)-C(5′) bond

Abstract

Quantum-mechanical computations carried out by the PCILO (perturbative configuration interaction using localized orbitals) method predict that the gg conformation of the exocyclic C(4′)-C(5′) bond should be the most stable one in purine and pyrimidine nucleosides and nucleotides, irrespective of the puckering of the sugar, at least as long as these puckerings belong to the most frequent C(3′)-endo, C(2′)-endo and C(3′)-exo categories. This prediction is in agreement with recent results of NMR studies in solution and with a large body of X-ray crystallographic results, to the extent that the cases in which the compounds exist in the crystal in the gt or tg forms may reasonably be attributed to the effect of environmental forces. The results also provide evidence for a number of fine details of the situation. A particularly significant result concerns the demonstration of an analogy between the behavior of the C(3′)-endo pyrimidine nucleosides and C(2′)-endo purine nucleosides on the one hand (strong preference for the gg conformers in both types) and between the C(2′)-endo pyrimidine nucleosides and C(3′)-endo purine nucleosides on the other (weak preference for the gg conformers in both types). The precision of the PCILO results is much greater than that of empirical or EHT (Extended Hückel theory) computations.