Redetermination of methyl 3,4-O-isopropyl­idene-β-D-fucopyran­oside monohydrate

Hoong-Kun Fun; Samuel Robinson Jebas; Sankappa Rai; Prakash Shetty; Arun M Isloor

doi:10.1107/S1600536809012689

. 2009 Apr 8;65(Pt 5):o1002–o1003. doi: 10.1107/S1600536809012689

Redetermination of methyl 3,4-O-isopropylidene-β-D-fucopyranoside monohydrate

Hoong-Kun Fun ^a,^*,^‡, Samuel Robinson Jebas ^a,^§, Sankappa Rai ^b, Prakash Shetty ^c, Arun M Isloor ^d

PMCID: PMC2977692 PMID: 21583828

Abstract

In the title compound, C₁₀H₁₈O₅·H₂O, the fucopyranoside ring adopts a chair conformation. The crystal packing is stabilized by intermolecular O—H⋯O and C—H⋯O hydrogen bonds together with intramolecular O⋯O [2.2936 (8) Å] and intermolecular O⋯O [2.7140 (8)–2.829 (3) Å] short contacts. The molecules are linked together to form an infinite chain along the a axis. This structure has been solved previously but with no R-values [Spiers (1931). Z. Kristallogr. Kristallgeom. Kristallphys. Kristallchem. 78, 101].

Related literature

D-fucose (6-deoxy-D-galactose) is an effective gratuitous inducer of the galactose operon in Escherichia coli, see: Musso et al. (1963 ▶). 6-Deoxyhexose and its derivatives are important components of lipopolysaccharides, see: Bilge et al. (1996 ▶); Villeneuve et al. (2000 ▶); Wu & Mackenzie (1987 ▶); Caroff, Bundle & Perry (1984 ▶); Caroff, Bundle, Perry, Cherwonogrodzky & Dunch (1984 ▶). For a previous structure determination of the title compound, see: Spiers (1931 ▶). For bond-length data, see: Allen et al. (1987 ▶). For ring puckering analysis, see: Cremer & Pople (1975 ▶). For the stability of the temperature controller, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C₁₀H₁₈O₅·H₂O
M _r = 236.26
Orthorhombic,
a = 8.5824 (1) Å
b = 9.2834 (1) Å
c = 14.6711 (2) Å
V = 1168.90 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 100 K
0.50 × 0.27 × 0.27 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T _min = 0.947, T _max = 0.971
64045 measured reflections
3449 independent reflections
3337 reflections with I > 2σ(I)
R _int = 0.032

Refinement

R[F ² > 2σ(F ²)] = 0.026
wR(F ²) = 0.073
S = 1.13
3449 reflections
161 parameters
4 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.27 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809012689/is2405sup1.cif

e-65-o1002-sup1.cif^{(18.6KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809012689/is2405Isup2.hkl

e-65-o1002-Isup2.hkl^{(165.7KB, 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
O4—H1O4⋯O1Wⁱ	0.821 (9)	1.909 (9)	2.7140 (8)	166.4 (16)
O1W—H1W1⋯O4ⁱⁱ	0.834 (8)	1.921 (8)	2.7534 (8)	175.6 (14)
O1W—H2W1⋯O5ⁱⁱⁱ	0.838 (8)	2.113 (11)	2.8294 (8)	143.3 (15)
C9—H9C⋯O3^iv	0.96	2.51	3.4306 (9)	162

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

HKF and SRJ thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. SRJ thanks Universiti Sains Malaysia for a post–doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. AMI is grateful to the Head of the Department of Chemistry and the Director, NITK, Surathkal, India, for providing research facilities. SR thanks Dr Gautam Das, Syngene International Ltd, Bangalore, India, for allocation of research resources.

supplementary crystallographic information

Comment

Buttin has demonstrated that D-fucose (6-deoxy-D-galactose) is an effective gratuitous inducer of the galactose operon in Escherichia coli (Musso et al., 1963). 6-Deoxyhexose and its derivatives are important components of lipopolysaccharides in, amongst others, Vibrio cholerae O1 (Bilge et al., 1996), Brucella spc., Citrobacter freundii F90 (Villeneuve et al., 2000), Salmonella enterica O30, and Escherichia coli O157 (Wu & Mackenzie, 1987). Further investigation revealed that D-fucose derivatives are important component of a repeating pentasaccharide unit in O-chains of the LPS of Yersiniaenterocolitica (Caroff, Bundle & Perry, 1984) and Brucella abortus (Caroff, Bundle, Perry, Cherwonogrodzky & Dunch, 1984). These findings established a molecular basis for extensive serological cross-reactivity between the various antigenic LPSs. These observations prompted us to synthesize the title compound, (I). Herein we report the synthesis and the redetermination of the crystal structure of the title compound.

The title compund has been determined previously (Spiers. 1931), but no R-values were given. The asymmetric unit of (I) (Fig.1) comprises of one molecule of methyl 3,4-O-isopropylidene -β-D–fucopyranoside and a water molecule. The isopropylidene-fucopyranoside ring is non-planar with the maximum deviation from planarity of 0.6532 (6) Å for the atom C5. The fucopyranoside ring adopts the chair conformation with the puckering parameters Q = 0.5344 (6), θ = 20.15 (7)° and φ = 22.3 (2)° (Cremer & Pople, 1975). The bond lengths (Allen et al., 1987) and bond angles show normal values.

The crystal packing is stabilized by O—H···O and C—H···O hydrogen bonds to form infinite one dimensional chain along the [100] direction (Fig. 2). Short contacts of O···O = 2.2936 (8) Å; O···Oⁱ = 2.7140 (8) Å; O···Oⁱⁱ = 2.7535 (8) Å & O···Oⁱⁱⁱ = 2.8293 (8) Å [symmetry codes: (i) x,1 + y,z; (ii) -1/2 + x,3/2 - y,-z & (iii) x,1 + y,z] are observed.

Experimental

The title compound was obtained by stirring a solution of 1,2,3,4 di-O-isopropylidene -α-D-fucopyranoside (0.5 g, 2.1 mmol) in dry methanol (5 ml). To this was added 3M solution of HCl in methanol (5 ml) at 0°C under nitrogen atmosphere. Further the reaction mixture was stirred at ambient temperature for 12 h. The reaction mixture was neutralized with solid sodium bicarbonate (1 g), concentrated, and residue was purified by flash column chromatography using 5% methanol in chloroform as eluent to get compound as foam-like solid which was taken in dry dimethylformamide (5 ml) and to this was added PTSA (Para Toluene Sulphonic Acid) (0.015 g, 2.0 mmol) and 2,2-dimethoxypropane (1.13 g,10 mmol). The mixture was further stirred at ambient temperature for 12 more hours. TLC (30% EtOAc/hexane,Rf-0.5) shows complete conversion of the starting materials. Reaction mixture was neutralized with triethylamine (2 ml) and concentrated under vacuum, residue was purified by column chromatography using 25% ethylacetate in pet ether to get a colourless liquid and the title compound as a white solid, which was recrystalized using hot acetone (yield 0.40 g, 85%; m.p. 328–330 K).