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Acta Crystallogr Sect E Struct Rep Online. 2009 March 1; 65(Pt 3): o570.
Published online 2009 February 21. doi:  10.1107/S1600536809005777
PMCID: PMC2968580

2-De­oxy-2,3-O-isopropyl­idene-2,4-di-C-methyl-β-l-arabinose

Abstract

X-ray crystallography unequivocally confirmed the stereochemistry of the C atom at position 2 in the carbon scaffold of the title mol­ecule, C10H18O4. The pyran­ose ring exists in a chair conformation with the methyl group on the C atom in the 2 position in an equatorial configuration. The absolute stereochemistry was determined from the starting material. The crystal structure consists of O—H(...)O hydrogen-bonded chains of mol­ecules running parallel to the b axis.

Related literature

For de­oxy sugars see: Becker & Lowe (2003 [triangle]); Yoshihara et al. (2008 [triangle]); Gullapalli et al. (2007 [triangle]). For a related structure see: Booth et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o570-scheme1.jpg

Experimental

Crystal data

  • C10H18O4
  • M r = 202.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o570-efi1.jpg
  • a = 6.0641 (3) Å
  • b = 13.4016 (7) Å
  • c = 6.8287 (3) Å
  • β = 102.596 (2)°
  • V = 541.60 (5) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 150 K
  • 0.50 × 0.20 × 0.20 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 [triangle]) T min = 0.89, T max = 0.98
  • 5025 measured reflections
  • 1266 independent reflections
  • 1183 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 0.073
  • S = 0.98
  • 1266 reflections
  • 127 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 0.16 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: COLLECT (Nonius, 2001 [triangle]).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 [triangle]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 [triangle]); molecular graphics: CAMERON (Watkin et al., 1996 [triangle]); software used to prepare material for publication: CRYSTALS.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809005777/lh2774sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809005777/lh2774Isup2.hkl

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

Acknowledgments

We would like to thank the Chemical Crystallography Department and ALT at Oxford University for use of the difractometers.

supplementary crystallographic information

Comment

Deoxy sugars play an important role in the natural world; 2-deoxy ribose forms the sugar backbone of DNA whilst L-fucose, 6-deoxy-L-galactose, is involved in a wide range of mammalian glycan mediated responses (Becker and Lowe, 2003). Whilst the synthesis and biological evaluation of deoxy sugars is relatively common (Yoshihara et al., 2008; Gullapalli et al., 2007), examples of doubly branched analogues are to our knowledge, unknown.

Herein we report the structure of the novel deoxy aldose 3, generated by a short synthetic sequence from di-branched lactone 1 (Booth et al. 2007) (Fig. 1). Hydrogenation of the alkene functionality in 2 could give either epimer at position C-2 of lactone 3 or a mixture of both products. The reaction proved to be extremely stereospecific, generating only one product. Direct crystallization of lactone 3 generated poor quality crystals, however, after reduction to the lactol, crystallization was facile and X-ray crystallography showed the product to be the arabino compound 4 rather than the ribo compound 5. The absolute stereochemistry was determined from the use of 2-C-methyl-D-ribono-1,4-lactone as starting material.

The pyranose ring adopts a chair conformation with methyl group at position 2 (atom C10 in the crystallogrphic labelling scheme) in the equatorial position (Fig. 2). The crystal structure exists O—H···O hydrogen-bonded chains of molecules lying parallel to the b-axis (Fig. 3). Only classical hydrogen bonding has been considered. There are no unusual crystal packing features.

Experimental

The title compound was recrystallized from dichloromethane by slow evaporation: m.p. 349–352 K; [α]D25 -49.6 (c,0.15 in CHCl3).

Refinement

In the absence of significant anomalous scattering, Friedel pairs were merged and the absolute configuration was assigned from the starting material.

The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98, O—H = 0.82 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

Figures

Fig. 1.
Synthetic Scheme
Fig. 2.
The molecular structure showing the crystallographic labelling scheme. Displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
Fig. 3.
Packing diagram for the title compound projected along the a-axis. Hydrogen bonds are indicated by dotted lines.

Crystal data

C10H18O4F(000) = 220
Mr = 202.25Dx = 1.240 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 1185 reflections
a = 6.0641 (3) Åθ = 5–27°
b = 13.4016 (7) ŵ = 0.10 mm1
c = 6.8287 (3) ÅT = 150 K
β = 102.596 (2)°Plate, colourless
V = 541.60 (5) Å30.50 × 0.20 × 0.20 mm
Z = 2

Data collection

Nonius KappaCCD diffractometer1183 reflections with I > 2σ(I)
graphiteRint = 0.036
ω scansθmax = 27.5°, θmin = 5.5°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)h = −7→7
Tmin = 0.89, Tmax = 0.98k = −13→17
5025 measured reflectionsl = −8→8
1266 independent reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.073 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.03P)2 + 0.12P], where P = [max(Fo2,0) + 2Fc2]/3
S = 0.98(Δ/σ)max = 0.0001
1266 reflectionsΔρmax = 0.16 e Å3
127 parametersΔρmin = −0.16 e Å3
1 restraint

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
O10.3944 (2)0.39582 (13)0.04435 (17)0.0245
C20.4077 (3)0.39975 (17)0.2596 (2)0.0228
O30.3257 (2)0.30533 (13)0.30874 (17)0.0224
C40.1684 (3)0.27174 (16)0.1342 (2)0.0195
C50.2816 (3)0.30472 (16)−0.0350 (2)0.0213
C60.1137 (3)0.32628 (18)−0.2291 (3)0.0299
C70.4647 (3)0.23026 (16)−0.0612 (3)0.0275
O80.3798 (2)0.13095 (14)−0.0775 (2)0.0287
C90.3274 (3)0.10066 (16)0.1088 (3)0.0255
C100.1251 (3)0.15996 (16)0.1439 (3)0.0220
C110.0585 (3)0.13084 (17)0.3391 (3)0.0294
O120.2706 (2)0.00005 (14)0.0917 (2)0.0322
C130.2595 (3)0.48536 (17)0.3003 (3)0.0298
C140.6502 (3)0.41048 (18)0.3718 (3)0.0312
H410.02400.30810.11850.0230*
H630.03580.2638−0.28030.0479*
H620.19380.3530−0.32500.0474*
H610.00280.3745−0.20370.0467*
H710.51480.2448−0.18370.0319*
H720.59170.23770.05800.0331*
H910.46390.10910.22070.0329*
H1010.00170.14480.02950.0264*
H1110.00820.06130.33320.0474*
H1120.18910.14100.45200.0465*
H113−0.06620.17300.36090.0474*
H1320.26470.48760.44580.0489*
H1310.32140.54810.26110.0489*
H1330.10410.47590.22470.0491*
H1420.65520.41650.51540.0457*
H1430.71100.47110.32120.0458*
H1410.73620.35150.34600.0456*
H1210.3746−0.03190.05150.0539*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0310 (7)0.0222 (6)0.0214 (6)−0.0072 (5)0.0082 (5)−0.0002 (5)
C20.0259 (8)0.0224 (9)0.0208 (7)−0.0045 (7)0.0066 (6)−0.0005 (7)
O30.0270 (6)0.0202 (7)0.0199 (6)−0.0045 (5)0.0047 (5)−0.0001 (5)
C40.0190 (8)0.0193 (9)0.0205 (8)−0.0003 (6)0.0050 (6)−0.0018 (6)
C50.0233 (8)0.0199 (9)0.0215 (8)−0.0012 (7)0.0069 (6)−0.0017 (7)
C60.0358 (10)0.0297 (11)0.0223 (9)0.0016 (8)0.0025 (7)0.0005 (8)
C70.0276 (9)0.0248 (10)0.0340 (10)0.0003 (8)0.0153 (8)0.0019 (8)
O80.0363 (7)0.0218 (7)0.0333 (7)0.0021 (6)0.0190 (6)0.0004 (6)
C90.0284 (9)0.0196 (9)0.0312 (9)0.0013 (7)0.0124 (7)0.0023 (7)
C100.0212 (8)0.0201 (9)0.0257 (9)−0.0015 (6)0.0074 (6)−0.0011 (7)
C110.0344 (10)0.0236 (9)0.0349 (10)0.0002 (8)0.0176 (8)0.0011 (8)
O120.0366 (7)0.0200 (7)0.0450 (8)0.0021 (6)0.0198 (6)−0.0011 (6)
C130.0327 (10)0.0243 (10)0.0354 (10)−0.0004 (8)0.0141 (8)−0.0007 (8)
C140.0276 (9)0.0324 (11)0.0313 (9)−0.0037 (8)0.0013 (7)−0.0021 (9)

Geometric parameters (Å, °)

O1—C21.4553 (19)O8—C91.436 (2)
O1—C51.446 (2)C9—C101.524 (2)
C2—O31.426 (2)C9—O121.390 (2)
C2—C131.520 (3)C9—H911.003
C2—C141.510 (2)C10—C111.525 (2)
O3—C41.427 (2)C10—H1010.978
C4—C51.533 (2)C11—H1110.979
C4—C101.525 (2)C11—H1120.987
C4—H410.987C11—H1130.981
C5—C61.513 (2)O12—H1210.855
C5—C71.532 (2)C13—H1320.988
C6—H630.986C13—H1310.982
C6—H620.965C13—H1330.979
C6—H610.975C14—H1420.978
C7—O81.423 (2)C14—H1430.986
C7—H710.970C14—H1410.984
C7—H720.996
C2—O1—C5109.06 (12)C7—O8—C9109.94 (14)
O1—C2—O3105.09 (13)O8—C9—C10109.46 (14)
O1—C2—C13107.90 (14)O8—C9—O12107.37 (15)
O3—C2—C13112.10 (14)C10—C9—O12109.02 (14)
O1—C2—C14110.45 (13)O8—C9—H91109.8
O3—C2—C14108.43 (15)C10—C9—H91112.3
C13—C2—C14112.62 (16)O12—C9—H91108.7
C2—O3—C4106.69 (12)C4—C10—C9110.70 (13)
O3—C4—C5102.17 (13)C4—C10—C11111.73 (15)
O3—C4—C10111.32 (14)C9—C10—C11112.32 (15)
C5—C4—C10115.19 (14)C4—C10—H101106.2
O3—C4—H41110.5C9—C10—H101105.6
C5—C4—H41108.0C11—C10—H101110.0
C10—C4—H41109.4C10—C11—H111110.3
C4—C5—O1102.36 (13)C10—C11—H112109.1
C4—C5—C6112.89 (15)H111—C11—H112110.6
O1—C5—C6109.89 (15)C10—C11—H113110.2
C4—C5—C7110.82 (15)H111—C11—H113108.2
O1—C5—C7107.33 (13)H112—C11—H113108.4
C6—C5—C7112.89 (15)C9—O12—H121109.0
C5—C6—H63109.1C2—C13—H132108.4
C5—C6—H62108.8C2—C13—H131108.7
H63—C6—H62110.3H132—C13—H131108.6
C5—C6—H61109.2C2—C13—H133110.2
H63—C6—H61109.3H132—C13—H133110.5
H62—C6—H61110.1H131—C13—H133110.4
C5—C7—O8111.05 (14)C2—C14—H142109.3
C5—C7—H71109.9C2—C14—H143107.3
O8—C7—H71107.2H142—C14—H143110.6
C5—C7—H72106.9C2—C14—H141109.1
O8—C7—H72111.1H142—C14—H141110.1
H71—C7—H72110.7H143—C14—H141110.3

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C6—H61···O12i0.972.593.562 (3)173
O12—H121···O1ii0.861.932.786 (3)179

Symmetry codes: (i) −x, y+1/2, −z; (ii) −x+1, y−1/2, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2774).

References

  • Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst.27, 435.
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  • Booth, K. V., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2007). Acta Cryst. E63, o1128–o1130.
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  • Watkin, D. J., Prout, C. K. & &Pearce, L. J. (1996). CAMERON Chemical Crystallography Laboratory, Oxford, England.
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