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Acta Cryst. (2009). E65, o1002-o1003    [ doi:10.1107/S1600536809012689 ]

Redetermination of methyl 3,4-O-isopropylidene-[beta]-D-fucopyranoside monohydrate

H.-K. Fun, S. R. Jebas, S. Rai, P. Shetty and A. M. Isloor

Abstract top

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].

Comment top

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 Yersinia enterocolitica (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.

Related literature top

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 stability of the temperature controller, see: Cosier & Glazer (1986).

Experimental top

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).

Refinement top

H atoms were positioned geometrically [C–H = 0.96–0.98 Å] and refined using a riding model, with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(methyl C). A rotating–group model was used for the methyl groups. The O-bound hydrogen atoms were located in a difference Fourier map and allowed to refine freely. Restraints were applied to fix the distance of O4—H = 0.82 (2) Å, O1W—H = 0.84 (2) Å and H1W1—H2W1 = 1.37 (4) Å. 2694 Friedel pairs were merged before final refinement as there is no large anomalous dispersion to determine the absolute configuration.

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom numbering scheme.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed approximately along the c axis, showing an extended molecular chain along the a axis. Dashed lines indicate the hydrogen bondings.
(I) top
Crystal data top
C10H18O5·H2OF(000) = 512
Mr = 236.26Dx = 1.343 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 9413 reflections
a = 8.5824 (1) Åθ = 2.8–41.6°
b = 9.2834 (1) ŵ = 0.11 mm−1
c = 14.6711 (2) ÅT = 100 K
V = 1168.90 (2) Å3Block, colourless
Z = 40.50 × 0.27 × 0.27 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		3449 independent reflections
Radiation source: fine-focus sealed tube3337 reflections with I > 2σ(I)
graphiteRint = 0.032
φ and ω scansθmax = 37.5°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		h = −14→14
Tmin = 0.947, Tmax = 0.971k = −15→15
64045 measured reflectionsl = −25→25
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.026Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.073H atoms treated by a mixture of independent and constrained refinement
S = 1.13 w = 1/[σ2(Fo2) + (0.0439P)2 + 0.0731P]
where P = (Fo2 + 2Fc2)/3
3449 reflections(Δ/σ)max = 0.001
161 parametersΔρmax = 0.31 e Å−3
4 restraintsΔρmin = −0.27 e Å−3
Crystal data top
C10H18O5·H2OV = 1168.90 (2) Å3
Mr = 236.26Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 8.5824 (1) ŵ = 0.11 mm−1
b = 9.2834 (1) ÅT = 100 K
c = 14.6711 (2) Å0.50 × 0.27 × 0.27 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		3449 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		3337 reflections with I > 2σ(I)
Tmin = 0.947, Tmax = 0.971Rint = 0.032
64045 measured reflectionsθmax = 37.5°
Refinement top
R[F2 > 2σ(F2)] = 0.026H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.073Δρmax = 0.31 e Å−3
S = 1.13Δρmin = −0.27 e Å−3
3449 reflectionsAbsolute structure: ?
161 parametersFlack parameter: ?
4 restraintsRogers parameter: ?
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat [Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107] operating at 100.0 (1) K.

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

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 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 (Å2) top
xyzUiso*/Ueq
O10.43844 (6)0.76639 (5)0.05482 (3)0.01206 (8)
O20.46299 (6)0.72835 (6)−0.14722 (3)0.01333 (9)
O30.37807 (7)0.95475 (6)−0.18528 (3)0.01399 (9)
O40.34767 (7)1.13634 (6)−0.01512 (4)0.01634 (10)
O50.48979 (6)0.97492 (6)0.13084 (3)0.01364 (9)
C10.38958 (8)0.91139 (7)0.06752 (4)0.01172 (10)
H1A0.28180.91450.08950.014*
C20.33053 (8)0.68941 (7)−0.00168 (4)0.01206 (10)
H2A0.22680.69640.02590.014*
C30.32312 (8)0.75401 (7)−0.09665 (4)0.01172 (10)
H3A0.23420.7132−0.12960.014*
C40.46232 (8)0.83123 (7)−0.21980 (4)0.01328 (10)
C50.31314 (7)0.91860 (7)−0.09849 (4)0.01160 (10)
H5A0.20380.9487−0.09610.014*
C60.40456 (8)0.99275 (7)−0.02236 (4)0.01164 (10)
H6A0.51480.9961−0.03960.014*
C70.37798 (10)0.77431 (9)−0.30350 (5)0.01941 (13)
H7A0.27380.7469−0.28710.029*
H7B0.43260.6920−0.32690.029*
H7C0.37420.8481−0.34930.029*
C80.62911 (9)0.87289 (9)−0.24007 (5)0.01995 (13)
H8A0.67950.9026−0.18480.030*
H8B0.63050.9508−0.28310.030*
H8C0.68330.7917−0.26530.030*
C90.46504 (9)0.92419 (8)0.22239 (4)0.01716 (12)
H9A0.53300.97490.26330.026*
H9B0.48700.82290.22530.026*
H9C0.35870.94090.23960.026*
C100.37923 (9)0.53235 (7)−0.00202 (5)0.01627 (11)
H10A0.37470.49500.05890.024*
H10B0.48380.5243−0.02470.024*
H10C0.31010.4784−0.04050.024*
O1W0.57299 (7)0.26179 (6)0.08757 (4)0.01852 (10)
H1O40.4072 (16)1.1865 (15)0.0151 (9)0.032 (4)*
H1W10.6579 (13)0.2881 (14)0.0656 (9)0.030 (4)*
H2W10.5836 (19)0.1840 (12)0.1158 (10)0.041 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.01237 (19)0.01127 (17)0.01255 (18)0.00025 (15)−0.00175 (15)0.00011 (15)
O20.01453 (19)0.01320 (18)0.01227 (18)0.00295 (16)0.00272 (15)0.00221 (15)
O30.0180 (2)0.01283 (19)0.01116 (18)0.00330 (17)0.00186 (16)0.00176 (15)
O40.0190 (2)0.01123 (18)0.0188 (2)0.00316 (17)−0.00409 (18)−0.00123 (17)
O50.0155 (2)0.0152 (2)0.01031 (18)−0.00255 (16)−0.00114 (15)−0.00001 (15)
C10.0116 (2)0.0122 (2)0.0114 (2)0.00024 (19)−0.00052 (18)−0.00035 (18)
C20.0118 (2)0.0122 (2)0.0122 (2)−0.00124 (18)−0.00016 (19)0.00084 (18)
C30.0112 (2)0.0126 (2)0.0114 (2)−0.00007 (18)−0.00006 (18)0.00028 (19)
C40.0146 (2)0.0138 (2)0.0114 (2)0.0020 (2)0.00107 (19)0.00140 (19)
C50.0111 (2)0.0127 (2)0.0110 (2)0.00160 (18)−0.00033 (18)0.00072 (18)
C60.0119 (2)0.0111 (2)0.0119 (2)0.00140 (17)−0.00036 (18)0.00060 (18)
C70.0262 (3)0.0196 (3)0.0124 (2)0.0016 (3)−0.0019 (2)−0.0015 (2)
C80.0159 (3)0.0246 (3)0.0193 (3)0.0013 (2)0.0040 (2)0.0059 (3)
C90.0185 (3)0.0222 (3)0.0107 (2)−0.0003 (2)0.0004 (2)0.0003 (2)
C100.0199 (3)0.0121 (2)0.0169 (3)−0.0007 (2)−0.0002 (2)0.0010 (2)
O1W0.0186 (2)0.0147 (2)0.0223 (2)−0.00180 (18)−0.00014 (19)0.00053 (19)
Geometric parameters (Å, °) top
O1—C11.4222 (8)C4—C71.5202 (10)
O1—C21.4336 (8)C5—C61.5287 (9)
O2—C41.4304 (8)C5—H5A0.9800
O2—C31.4311 (8)C6—H6A0.9800
O3—C51.4299 (8)C7—H7A0.9600
O3—C41.4472 (8)C7—H7B0.9600
O4—C61.4236 (8)C7—H7C0.9600
O4—H1O40.821 (9)C8—H8A0.9600
O5—C11.3966 (8)C8—H8B0.9600
O5—C91.4389 (8)C8—H8C0.9600
C1—C61.5251 (9)C9—H9A0.9600
C1—H1A0.9800C9—H9B0.9600
C2—C101.5168 (10)C9—H9C0.9600
C2—C31.5183 (9)C10—H10A0.9600
C2—H2A0.9800C10—H10B0.9600
C3—C51.5306 (9)C10—H10C0.9600
C3—H3A0.9800O1W—H1W10.834 (8)
C4—C81.5123 (10)O1W—H2W10.838 (8)
C1—O1—C2110.92 (5)C6—C5—H5A109.7
C4—O2—C3105.75 (5)C3—C5—H5A109.7
C5—O3—C4108.68 (5)O4—C6—C1111.74 (5)
C6—O4—H1O4111.0 (12)O4—C6—C5107.46 (5)
C1—O5—C9113.06 (5)C1—C6—C5111.43 (5)
O5—C1—O1107.78 (5)O4—C6—H6A108.7
O5—C1—C6108.30 (5)C1—C6—H6A108.7
O1—C1—C6109.30 (5)C5—C6—H6A108.7
O5—C1—H1A110.5C4—C7—H7A109.5
O1—C1—H1A110.5C4—C7—H7B109.5
C6—C1—H1A110.5H7A—C7—H7B109.5
O1—C2—C10107.64 (5)C4—C7—H7C109.5
O1—C2—C3111.14 (5)H7A—C7—H7C109.5
C10—C2—C3112.84 (6)H7B—C7—H7C109.5
O1—C2—H2A108.4C4—C8—H8A109.5
C10—C2—H2A108.4C4—C8—H8B109.5
C3—C2—H2A108.4H8A—C8—H8B109.5
O2—C3—C2112.02 (5)C4—C8—H8C109.5
O2—C3—C5101.77 (5)H8A—C8—H8C109.5
C2—C3—C5114.38 (5)H8B—C8—H8C109.5
O2—C3—H3A109.5O5—C9—H9A109.5
C2—C3—H3A109.5O5—C9—H9B109.5
C5—C3—H3A109.5H9A—C9—H9B109.5
O2—C4—O3105.70 (5)O5—C9—H9C109.5
O2—C4—C8108.26 (6)H9A—C9—H9C109.5
O3—C4—C8109.83 (6)H9B—C9—H9C109.5
O2—C4—C7111.79 (6)C2—C10—H10A109.5
O3—C4—C7108.67 (6)C2—C10—H10B109.5
C8—C4—C7112.38 (6)H10A—C10—H10B109.5
O3—C5—C6110.18 (5)C2—C10—H10C109.5
O3—C5—C3103.19 (5)H10A—C10—H10C109.5
C6—C5—C3114.08 (5)H10B—C10—H10C109.5
O3—C5—H5A109.7H1W1—O1W—H2W1110.4 (12)
C9—O5—C1—O1−72.50 (7)C5—O3—C4—C8−123.77 (6)
C9—O5—C1—C6169.36 (6)C5—O3—C4—C7112.93 (6)
C2—O1—C1—O5173.54 (5)C4—O3—C5—C6106.03 (6)
C2—O1—C1—C6−68.96 (6)C4—O3—C5—C3−16.15 (7)
C1—O1—C2—C10−172.91 (5)O2—C3—C5—O333.37 (6)
C1—O1—C2—C363.06 (7)C2—C3—C5—O3154.36 (5)
C4—O2—C3—C2−161.33 (5)O2—C3—C5—C6−86.15 (6)
C4—O2—C3—C5−38.71 (6)C2—C3—C5—C634.84 (8)
O1—C2—C3—O270.09 (7)O5—C1—C6—O4−66.61 (7)
C10—C2—C3—O2−50.94 (7)O1—C1—C6—O4176.22 (5)
O1—C2—C3—C5−45.05 (8)O5—C1—C6—C5173.15 (5)
C10—C2—C3—C5−166.08 (6)O1—C1—C6—C555.99 (7)
C3—O2—C4—O329.57 (7)O3—C5—C6—O482.09 (6)
C3—O2—C4—C8147.20 (6)C3—C5—C6—O4−162.42 (5)
C3—O2—C4—C7−88.49 (7)O3—C5—C6—C1−155.19 (5)
C5—O3—C4—O2−7.19 (7)C3—C5—C6—C1−39.69 (8)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O4—H1O4···O1Wi0.82 (1)1.91 (1)2.7140 (8)166 (2)
O1W—H1W1···O4ii0.83 (1)1.92 (1)2.7534 (8)176 (1)
O1W—H2W1···O5iii0.84 (1)2.11 (1)2.8294 (8)143 (2)
C9—H9C···O3iv0.962.513.4306 (9)162
Symmetry codes: (i) x, y+1, z; (ii) x+1/2, −y+3/2, −z; (iii) x, y−1, z; (iv) −x+1/2, −y+2, z+1/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O4—H1O4···O1Wi0.82 (1)1.91 (1)2.7140 (8)166 (2)
O1W—H1W1···O4ii0.83 (1)1.92 (1)2.7534 (8)176 (1)
O1W—H2W1···O5iii0.84 (1)2.11 (1)2.8294 (8)143 (2)
C9—H9C···O3iv0.962.513.4306 (9)162
Symmetry codes: (i) x, y+1, z; (ii) x+1/2, −y+3/2, −z; (iii) x, y−1, z; (iv) −x+1/2, −y+2, z+1/2.
Acknowledgements top

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 HOD 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.

references
References top

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