Methyl 4-O-benzyl-α-l-rhamnopyranoside

In the title compound, C14H20O5, an intermediate in the synthesis of oligosaccharides, the glycosidic [H—C—O—C(H3)] torsion angle ϕH is 52.3° and the exo-cyclic [H—C—O—C(H2)] torsion angle θH is −11.7°. The hexapyranose ring has a chair conformation. In the crystal, molecules are linked by O—H⋯O hydrogen bonds, forming chains propagating along [010]. Enclosed within the chains are R 3 3(12) ring motifs involving three molecules. The chains are linked via C—H⋯π interactions, forming a three-dimensional network.


Comment
Bacteria contain many different sugar residues (Herget et al., 2008) in contrast to man where only a dozen monosaccharides are utilized in the formation of polysaccharides, glycoproteins and glycolipids [see Varki et al. (1999)].
In lipopolysaccharides L-rhamnose (6-deoxy-L-mannose) is often present as a sugar component, ranging from one residue per repeating unit, for example, as the terminal residue in the biosynthesized and polymerized oligosaccharide; consequently, it forms the side-chain residue in the O-antigen (Olsson et al., 2005), which often has 10 -25 repeating units. Alternatively, L-rhamnose can make up the O-antigen polysaccharide per se, as a homopolymer (Ansaruzzaman et al., 1996).
The title compound, Fig. 1, has been used in the synthesis of a rhamnosyl-containing trisaccharide (Eklund et al., 2005), the crystal structure of which was recently determined (Eriksson & Widmalm, 2012). The title monosaccharide is the methyl glycoside of α-L-rhamnopyranose and carries a benzyl protecting group at O4 in an ether linkage; the remaining two hydroxyl groups are unprotected and available for further synthetic modifications.
In the crystal, molecules are linked via O-H···O hydrogen bonds, involving both hydroxyl groups, forming chains along the a axis (Table 1 and Fig. 2). They enclose 12-membered R 3 3 (12) ring motifs. There are also C-H ··· π interactions present, between the C7 methyl group and the centroid of the (C41-C46) benzyl ring (Table 1), that link the chains forming a three-dimensional network.
The conformation of the exo-cyclic torsion angle (H4-C4-O4-C40) was analyzed by NMR measurements (see details in the archived CIF) of the long-range heteronuclear coupling constant between nuclei H4 and C40 using a J-HMBC experiment, which resulted in 3 J CH = 6.25 Hz. Interpretation of this coupling constant using the Karplus-type relationship 3 J C,H = 7.6 cos 2 θ -1.7 cosθ + 1.6 (Anderson & Ijeh, 1994) leads to |θ H | = 26° when interpreted as a single conformation, i.e., quite similar to the structure determined in the solid state. The corresponding torsion angle in the crystal structure of 4-O-Benzyl-2,3-O-isopropylidene-α-L-rhamnopyranose was 36.8° (Eriksson et al., 1999).

Experimental
The synthesis of the title compound was performed according to a published procedure (Haines, 1969), where the rhamnosyl residue has the L absolute configuration. The title monosaccharide was crystallized at ambient temperature by slow evaporation from chloroform yielding colourless prismatic crystals. Spectroscopic data and details of the NMR measurements are given in the archived CIF.

Refinement
The OH and C-bound atoms were positioned geometrically and allowed to ride on their parent atoms: O-H = 0.82 Å, C-H = 0.98, 0.96 and 0.92 Å, for CH, CH 3 , and CH(aromatic) H atoms, respectively, with U iso (H) = 1.2U eq (C) and = 1.5U eq (O).
In the final cycles of refinement, in the absence of significant anomalous scattering effects, Friedel pairs were merged and Δf " set to zero. The absolute configuration was set by the a priori knowledge of the absolute configuration of the starting reagent.

Figure 1
The molecular structure of the title molecule with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The long-range heteronuclear NMR coupling constant was measured beteen nuclei H4 (blue) and C40 (graphite).   Table 1 for details). NMR experiments were performed on a Bruker Avance III spectrometer operating at a 1 H frequency of 700 MHz. The title compound was dissolved in chloroform-d and 1 H and 13 C resonances were referenced to internal TMS (δ = 0.0) and the solvent resonance (δ = 77.16), respectively. Resonance assignments were performed using standard experiments for oligosaccharides (Widmalm, G. (2007). NMR spectroscopy of carbohydrates and conformational analysis in solution. Comprehensive glycoscience, J. P. Kamerling,Ed.,Elsevier,Oxford,Vol. 2,  Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 )
x y z U iso */U eq C1