Methyl α-l-rhamnosyl-(1→2)[α-l-rhamnosyl-(1→3)]-α-l-rhamnoside penta­hydrate: synchrotron study

Lars Eriksson; Göran Widmalm

doi:10.1107/S1600536812027390

. 2012 Jun 27;68(Pt 7):o2221–o2222. doi: 10.1107/S1600536812027390

Methyl α-l-rhamnosyl-(1→2)[α-l-rhamnosyl-(1→3)]-α-l-rhamnoside pentahydrate: synchrotron study

Lars Eriksson ^a,^*, Göran Widmalm ^b

PMCID: PMC3394015 PMID: 22798880

Abstract

The title hydrate, C₁₉H₃₄O₁₃·5H₂O, contains a vicinally disubstituted trisaccharide in which the two terminal rhamnosyl sugar groups are positioned adjacent to each other. The conformation of the trisaccharide is described by the glycosidic torsion angles ϕ2 = 48 (1)°, ψ2 = −29 (1)°, ϕ3 = 44 (1)° and ψ3 = 4 (1)°, whereas the ψ2 torsion angle represents a conformation from the major state in solution, the ψ3 torsion angle conformation may have been caught near a potential energy saddle-point when compared to its solution structure, in which at least two but probably three conformational states are populated. Extensive intermolecular O—H⋯O hydrogen bonding is present in the crystal and a water-containing channel is formed along the b-axis direction.

Related literature

For a description of l-rhamnose as part of polysaccharides, see: Marie et al. (1998 ▶); Perry & MacLean (2000 ▶). For a description of the conformational dynamics of the title trisaccharide, see: Eklund et al. (2005 ▶); Jonsson et al. (2011 ▶). For a description of the puckering analysis of the residues, see: Cremer & Pople (1975 ▶). For further background to l-rhamnose, see: Ansaruzzaman et al. (1996 ▶); Varki et al. (1999) ▶; Kulber-Kielb et al. (2007 ▶); Lindberg (1998 ▶); Säwén et al. (2010 ▶).

Experimental

Crystal data

C₁₉H₃₄O₁₃·5H₂O
M _r = 560.54
Monoclinic,
a = 19.345 (3) Å
b = 6.4870 (13) Å
c = 21.145 (3) Å
β = 97.617 (14)°
V = 2630.0 (8) Å³
Z = 4
Synchrotron radiation
λ = 0.8970 Å
μ = 0.22 mm⁻¹
T = 100 K
0.20 × 0.05 × 0.01 mm

Data collection

Bruker SMART 1K CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2002 ▶) T _min = 0.97, T _max = 0.99
17172 measured reflections
2906 independent reflections
2655 reflections with I > 2σ(I)
R _int = 0.046

Refinement

R[F ² > 2σ(F ²)] = 0.033
wR(F ²) = 0.087
S = 1.07
2906 reflections
376 parameters
16 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.56 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Data collection: SMART (Bruker, 1997 ▶); cell refinement: SAINT (Bruker, 1997 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 1999 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812027390/hb6841sup1.cif

e-68-o2221-sup1.cif^{(27.5KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812027390/hb6841Isup2.hkl

e-68-o2221-Isup2.hkl^{(142.7KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
OW1—H101⋯O33ⁱ	0.88 (3)	1.85 (3)	2.726 (2)	176 (2)
OW1—H102⋯OW3ⁱⁱ	0.88 (3)	1.95 (3)	2.802 (2)	162 (2)
OW1—H102⋯O32ⁱⁱⁱ	0.88 (3)	2.55 (3)	2.976 (2)	110 (2)
OW2—H201⋯O12^iv	0.88 (3)	2.03 (3)	2.875 (2)	163 (2)
OW2—H202⋯O35ⁱⁱ	0.87 (3)	2.08 (3)	2.877 (2)	153 (2)
OW3—H301⋯OW5	0.88 (3)	2.04 (3)	2.845 (2)	151 (2)
OW3—H302⋯O13^v	0.88 (3)	1.96 (3)	2.836 (2)	176 (2)
OW4—H401⋯OW3	0.88 (3)	1.97 (3)	2.840 (2)	168 (2)
OW4—H402⋯OW1	0.88 (3)	1.92 (3)	2.771 (2)	160 (2)
OW5—H501⋯O33^vi	0.87 (3)	2.07 (3)	2.918 (2)	168 (2)
OW5—H502⋯OW5^vii	0.87 (3)	2.50 (3)	3.333 (2)	159 (2)
O12—H12A⋯O32ⁱⁱⁱ	0.84	2.01	2.767 (2)	149
O13—H13A⋯O15ⁱⁱ	0.84	2.10	2.858 (2)	149
O14—H14A⋯O24ⁱⁱⁱ	0.84	1.95	2.733 (2)	157
O24—H24A⋯OW2	0.84	1.88	2.722 (2)	176
O32—H32A⋯OW5^viii	0.84	2.13	2.864 (2)	146
O33—H33A⋯O34ⁱ	0.84	1.91	2.684 (2)	152
O34—H34A⋯OW4	0.84	1.86	2.687 (2)	168

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) ; (vi) ; (vii) ; (viii) .

Acknowledgments

This work was supported by a grant from the Swedish Research Council (VR).

supplementary crystallographic information

Comment

In carbohydrate structures from humans the number of different monosaccharides is quite limited; typically seven different sugars are present in glycoproteins and glycolipids (Varki et al., 1999). Constituents of polysaccharides in man add a few more monosaccharides to the repertoire. In bacteria, however, more than 100 different monosaccharide components have been found (Lindberg, 1998). One of them, L-rhamnose (6-deoxy-L-mannose) is present as a major constituent of the O-antigen polysaccharides from Shigella flexneri (Kulber-Kielb et al., 2007) and is the sole monosaccharide in the repeating unit of an O-antigen from a Klebsiella pneumoniae strain (Ansaruzzaman et al., 1996). L-rhamnose is also found a the branch point sugar in some polysaccharides, e.g., from Escherichia coli O139 (Marie et al., 1998) and Yersinia enterocolitica serotype O:28 (Perry & MacLean, 2000).

In the title compound (I) the three sugar components are all L-rhamnose residues having the α-anomeric configuration. The O-methyl residue (a) is vicinally disubstituted at O2 (residue b) and O3 (residue c) which leads to spatial proximity of also the two latter rhamnosyl groups. The major degrees of freedom in trisaccharide (I) are present at the (1 → 2)- and (1 → 3)-linkages, i.e., between residues b and a as well as between residues c and a, respectively. The torsion angles are given by φ2 = 48°, ψ2 = -29°, φ3 = 44° and ψ3 = 4°. In a recent NMR and molecular dynamics (MD) simulation study of (I) in water solution <φ> ≈ 40°, when the exo-anomeric conformation was populated, but non-exo conformations with φ < 0° were also significantly populated (Eklund et al., 2005). The dynamics of the ψ torsion angles were found to be highly correlated with both ψ2 and ψ3 being either > 0° or < 0°. The conformation of the X-ray structure (Figure 1) is reminiscent of the conformational states found from the MD simulation and the values of the glycosidic torsion angles are observed to correspond to conformational regions that are highly populated, albeit the ψ torsion angles in the solid state structure deviate somewhat from the pattern observed from the molecular simulations with water as a solvent.

In studies of the conformational dynamics of the title trisaccharide trans-glycosidic heteronuclear carbon-proton coupling constants were measured (Eklund et al., 2005; Jonsson et al., 2011) which, when interpreted by Karplus-type relationships (Säwén et al., 2010), can yield information on conformation via torsion angles at the glycosidic linkages. Calculation of the three-bond coupling constants based on the torsion angles in the crystal structure of the trisaccharide showed that for the φ torsion angles and the ψ torsion angle at the α-(1 → 2)-linkage the differences to the experimental data were not larger than ca 0.5 Hz, indicating that for these torsions the conformation in the solid state is similar to that populated to a large extent in solution. However, for the ψ torsion angle at the α-(1 → 3)-linkage the corresponding difference was larger, ca 1 Hz, suggesting that in the crystal structure the latter torsion describes a conformation that is less populated in water solution. The crystal structure conformation is still, however, one in a low potential energy region, since conformational exchange occurs for both of the ψ torsion angles between states for which ψ takes either positive or negative values according to the molecular dynamics simulation (Eklund et al., 2005).

The calculated Cremer & Pople (1975) parameters for the three different rings are: ring O15 → C15 [Q=0.570 (2) Å, θ=177.9 (2) ° and φ=20 (9) °], ring O25 → C25 [Q=0.580 (2) Å, θ=171.4 (2) ° and φ=72.5 (14) °] and for the ring O35 → C35 [Q=0.582 (2) Å, θ=177.1 (2) ° and φ=131 (5) °].

Extensive water-water hydrogen bonding was observed (Table 1) between the title compound and water molecules leading to a water channel in the b-direction (Fig. 2 and Fig. 3). The title compound showed hydrogen bonds to water and to other adjacent (symmetry related) trisaccharides, but no intra-molecular hydrogen bonds were found.

Experimental

The synthesis of (I) was described by Eklund et al. (2005) in which all three rhamnosyl residues have the L absolute configuration. The trisaccharide was crystallized at ambient temperature by slow evaporation from a mixture of water and ethanol (1:1). The crystal was mounted in a capillary tube and diffraction data were collected at 100 K on beamline I711 at the Swedish synchrotron radiation facility, MAXLAB, Lund.