Crystal structure of methyl α-l-rhamnopyranosyl-(1→2)-α-l-rhamnopyranoside monohydrate

The title compound crystallizes with four unique disaccharide molecules and four water molecules in the asymmetric unit. In the crystal, the disaccharide and water molecules form layers parallel to the bc plane via hydrophilic interactions.


Chemical context
The title disaccharide compound is a structural model for part of bacterial O-antigen polysaccharides from Shigella flexneri (Kubler-Kielb et al., 2007) and Escherichia coli (Marie et al., 1998). In the title compound, inter-residue hydrogen bonding is not possible, which thus gives the opportunity to study conformational preferences at the glycosidic linkage devoid of the hydrogen bonds. Furthermore, the major conformation in water differs from that in dimethyl sulfoxide as determined by NMR spectroscopy and molecular dynamics simulations (Pendrill et al., 2016). These conformations can be compared to the present crystal structure obtained from a water:ethanol (1:1) mixed solution.

Structural commentary
The asymmetric unit of the title compound contains four independent disaccharides of closely similar conformation, shown in Figs. 1-3, where the hexopyranose rings have the 1 C 4 chair conformation. In the disaccharide molecule, there are three major degrees of freedom with the glycosidic torsion angles of ' H , H and ' H (C7), which are defined, respectively, by H1A-C1A-O2B-C2B, C1A-O2B-C2B-H2B and The four independent disaccharide molecules, 1-4, in the asymmetric unit together with four adjacent water molecules.

Figure 1
The structure of one of the title disaccharide molecules, disaccharide 1, showing the atom-labelling scheme. The third character of the atom label denotes the rhamnose residue A or B in each disaccharide and the fourth character indicates each independent disaccharide entity. Displacement ellipsoids are drawn at the 50% probability level.
optimization of the title structure has been performed with plane waves and pseudo potentials using NWChem (Valiev et al., 2010). The major differences between the optimized and observed structures are that the O-H distances are slightly longer in the optimized structure than the experimental values and some geometrical details, e.g. torsion angles of hydroxyl groups. The hydrogen-bonding scheme obtained from the DFT-optimized structure was similar, with minor differences between the experimental structure and the DFT-optimized version.

Database survey
A search for related compounds in the CSD (2019 release; Groom et al., 2016) gave only one hit with the rhamnose dimer as fragment, XEBQAY (Eriksson & Widmalm, 2012), with a good fit to the three-dimensional arrangement of the disaccharide element. A search using only the monomer skeleton without hydroxyl H atoms produced 178 hits, but most of these were not relevant for comparison with the title molecule.

Synthesis and crystallization
The title compound was synthesized according to the published procedures (Norberg et al., 1986), where the rhamnosyl residues have the L absolute configuration. Colourless prismatic single crystals were obtained by slow evaporation from a water:ethanol (1:1) mixture solution at ambient temperature.

Refinement
Crystal data, data collection and structural refinement details are summarized in Table 2. Diffraction data from three separate crystals of the approximately same size were merged using the BASF instruction available in the SHELXL program. Although each single crystal showed considerable disorder, the three crystals together provided a complete data set at the expense of a rather high internal R value. Weak ISOR restraints were applied for all non-H atoms. H atoms in the disaccharide molecules were added geometrically (C-H = 1.00 or 0.98 Å and O-H = 0.84 Å ) and treated as riding with U iso (H) = 1.2-1.5U eq (C,O). The O-H bond and HÁ Á ÁH distances in the water molecules were restrained to 0.85 (1) and 1.34 (1) Å , respectively. The orientation of each water molecule was adjusted and restrained with additional DFIX commands using parameters derived from a solid state DFT optimization of the crystal structure.   Data collection: APEX3 (Bruker, 2017); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg, 1999) and Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009), enCIFer (Allen et al., 2004) and publCIF (Westrip, 2010).

Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.