Characterization of a γ-radiation-induced decomposition product of thymidine. Crystal and molecular structure of the (−)cis(5R,6S) thymidine glycol

Abstract

X-ray crystallography was used to determine the structure of (−)cis(5R,6S)-5,6-dihydroxy-5,6-dihydrothymidine, a γ-radiation induced product of thymidine. The crystals belong to the orthorhombic space group P212121 and have cell dimensions a = 8.420(1) Å, b = 10.422(1) Å, and 13.552(1) Å. The half-chair pucker of the 5,6-saturated pyrimidine ring is similar to that observed for the isolated base with the cis configuration, and is described by the Cremer–Pople parameters Q = 0.48 Å, θ = 62°, and [Formula: see text]. The conformation about the N-glycosyl bond is anti; the χ angle (−111.6(5)°) lies at one extreme of the range previously seen for nucleosides (−180 to −115°). The pucker 2T1 of the sugar (P = 151.2°; τm = 36.5°) contrasts with the O4′-endo type of pucker seen in 5,6-dihydrothymidine (0T4) and (5S)-5-hydroxy-5,6-dihydrothymidine (0T1). The conformation about the C4′—C5′ bond is gauche+. The solid state structure is similar to that determined in aqueous solution by 1H nmr.