Crystal structures of four thio-glycosides involving carbamimido-thio-ate groups.

ABSTRACT: The compounds 2',3',4',6'-tetra-O-acetyl-β-d-gluco-pyranosyl N'-cyano-N-phenyl-carbamimido-thio-ate (C₂₂H₂₅N₃O₉S, 5a), 2',3',4',6'-tetra-O-acetyl-β-d-galacto-pyranosyl N'-cyano-N-phenyl-carbamimido-thio-ate, (C₂₂H₂₅N₃O₉S, 5b), 2',3',4',6'-tetra-O-acetyl-β-d-galacto-pyranosyl N'-cyano-N-methyl-carbamimido-thio-ate (C₁₇H₂₃N₃O₉S, 5c), and 2',3',4',6'-tetra-O-acetyl-β-d-galacto-pyranosyl N'-cyano-N-p-tolyl-carbamimido-thio-ate (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 carbamimido-thio-ate 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 intra-molecular hydrogen bond N-H⋯O1; in 5c this contact is the weaker branch of a three-centre inter-action, whereas in 5a and 5d the H⋯O distances are much longer and do not represent significant inter-actions. The C-N bond lengths at the central carbon atom of the carbamimido-thio-ate group are almost equal. All C-O-C=O torsion angles of the acetyl groups correspond to a synperiplanar geometry, but otherwise all four mol-ecules 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.

SUBMITTER: Abu-Zaied MA 

PROVIDER: S-EPMC11299743 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature