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

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.