Determination of glycosidic bond conformations of pyrimidine nucleosides and nucleotides using vicinal carbon–proton coupling constants

Abstract

Measurements have been made of 3J(C-6,H-1′) and 3J(C-2,H-1′) magnitudes of pyrimidine nucleosides and nucleotides in solution by natural abundance, 13C n.m.r. spectroscopy and the results have been interpreted in terms of the glycosidic bond conformations of the nucleic acid derivatives. Based on X-ray crystal structure results a four-state conformational model for the glycosidic bond is introduced consisting of an equilibrium between two syn and two anti conformations; each syn or anti conformation is symmetrically related to the C-1′–H-1′ bond direction and appropriate syn and anti conformations are symmetrically related by 180°. It is shown that a quantitative estimate of the glycosidic bond conformation may be determined from the sum of observed coupling constants [i.e., ΣJ=J(C-6,H-1′)+J(C-2,H-1′)] and that the equilibrium composition of syn and anti conformers may be determined from the difference in observed coupling constants, i.e., ΔJ=J(C-6,H-1′)–J(C-2,H-1′). Results for uridine and cytidine derivatives are discussed.