Crystal structures of four thioglycosides involving carbamimidothioate groups

Abstract

The compounds 2′,3′,4′,6′-tetra-O-acetyl-β-D-glucopyranosyl N′-cyano-N-phenylcarbamimidothioate (C22H25N3O9S, 5a), 2′,3′,4′,6′-tetra-O-acetyl-β-D-galactopyranosyl N′-cyano-N-phenylcarbamimidothioate, (C22H25N3O9S, 5b), 2′,3′,4′,6′-tetra-O-acetyl-β-D-galactopyranosyl N′-cyano-N-methylcarbamimidothioate (C17H23N3O9S, 5c), and 2′,3′,4′,6′-tetra-O-acetyl-β-D-galactopyranosyl N′-cyano-N-p-tolylcarbamimidothioate (C23H27N3O9S, 5d) all crystallize in P212121 with Z = 4. For all four structures, the configuration across the central (formal) C=N(CN) double bond of the carbamimidothioate group is Z. The torsion angles C5—O1—C1—S (standard sugar numbering) are all close to 180°, confirming the β position of the substituent. Compound 5b involves an intramolecular hydrogen bond N—H...O1; in 5c this contact is the weaker branch of a three-centre interaction, whereas in 5a and 5d the H...O distances are much longer and do not represent significant interactions. The C—N bond lengths at the central carbon atom of the carbamimidothioate group are almost equal. All C—O—C=O torsion angles of the acetyl groups correspond to a synperiplanar geometry, but otherwise all four molecules display a high degree of conformational flexibility, with many widely differing torsion angles for equivalent groups. In the crystal packing, 5a, 5c and 5d form layer structures involving the classical hydrogen bond N—H...Ncyano and a variety of ‘weak’ hydrogen bonds C—H...O or C—H...S. The packing of 5b is almost featureless and involves a large number of borderline ‘weak’ hydrogen bonds. In an appendix, a potted history of wavelength preferences for structure determination is presented and it is recommended that, even for small organic crystals in non-centrosymmetric space groups, the use of Mo radiation should be considered.

Keywords

• crystal structure
• glucose
• galactose
• carbamimidothioate
• hydrogen bonds