Assignment and conformational properties of the exocyclic 5′-hydroxy-methyl group of nucleosides by nuclear magnetic resonance spectroscopy

Abstract

The assignment of the methylene protons of the exocyclic group of nucleosides has been confirmed by comparison of the H(5′) chemical shifts of corresponding 2′- and 3′-nucleotides and by direct observation of hydrogen bonding between the 5′-hydroxy- and 2-keto-groups of N(3)-methyl-2′,3′-O-isopropylideneuridine in CDCl3 and CCl4 solutions. The assignment of the methylene protons permits calculation of the relative populations of the three C(4′)–C(5′) bond rotamers. The results are consistent with crystal structure analyses of β-nucleosides, i.e. gg > gt > tg. An analysis of the contributions to vicinal proton spin coupling constants and chemical shifts of the exocyclic hydroxymethyl group together with the correct signal assignment confirms the approximate correlation between the sum of proton spin coupling constants and the chemical shift differences between the methylene protons of pyrimidine nucleosides. The method is extended to purine nucleosides.