Conformation of methyl 3,6-dideoxy-α-D-arabino-hexopyranoside, the immunodominant sugar of Salmonella serogroup D1: crystal structure, 1H nmr analysis, and semi-empirical calculations

Abstract

Methyl 3,6-dideoxy-α-D-arabino-hexopyranoside (methyl tyveloside) crystallizes in the orthorhombic space group P212121 and the cell dimensions are a = 7.478(1), b = 7.933(1), c = 14.064(1) Å. X-ray intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.038. The pyranose ring exists as an almost perfect 4C1 chair and the conformation adopted by the glycosidic methyl group is in agreement with the requirements of the exo-anomeric effect. Both acetal oxygen atoms act as hydrogen-bond acceptors, and the [Formula: see text] bond distances are in agreement with this feature. The 1H nmr spectrum shows that the conformation of the pyranose ring in aqueous solution is indistinguishable from that in the crystal. The minimum energy conformation of a pentasaccharide fragment of a Salmonella O-antigen, calculated with tyvelose coordinates obtained by bond modification, is in good agreement with the conformation which was calculated with tyvelose coordinates obtained from the X-ray analysis.