Crystal structures of four thio­glycosides involving carbamimido­thio­ate groups

The structures of the four thio­glycosides, all Z-configured across the C=N(CN) moiety, differ in many important torsion angles. The C—N bond lengths at the central carbon atom of the carbamimido­thio­ate group are almost equal. Three of the four structures form layers by hydrogen bonding.

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⋯N_cyano 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.