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Acta Cryst. (2009). E65, o570    [ doi:10.1107/S1600536809005777 ]

2-Deoxy-2,3-O-isopropylidene-2,4-di-C-methyl-[beta]-L-arabinose

K. V. Booth, S. F. Jenkinson, G. W. J. Fleet and D. J. Watkin

Abstract top

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.

Comment top

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.

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] Fig. 1. Synthetic Scheme
[Figure 2] 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.
[Figure 3] Fig. 3. Packing diagram for the title compound projected along the a-axis. Hydrogen bonds are indicated by dotted lines.
2-Deoxy-2,3-O-isopropylidene-2,4-di-C-methyl-β-L-arabinose top
Crystal data top
C10H18O4F(000) = 220
Mr = 202.25Dx = 1.240 Mg m−3
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 mm−1
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 top
Nonius KappaCCD
diffractometer		1183 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 top
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 Å−3
127 parametersΔρmin = −0.16 e Å−3
1 restraint
Crystal data top
C10H18O4V = 541.60 (5) Å3
Mr = 202.25Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.0641 (3) ŵ = 0.10 mm−1
b = 13.4016 (7) ÅT = 150 K
c = 6.8287 (3) Å0.50 × 0.20 × 0.20 mm
β = 102.596 (2)°
Data collection top
Nonius KappaCCD
diffractometer		1266 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)		1183 reflections with I > 2σ(I)
Tmin = 0.89, Tmax = 0.98Rint = 0.036
5025 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.073Δρmax = 0.16 e Å−3
S = 0.98Δρmin = −0.16 e Å−3
1266 reflectionsAbsolute structure: ?
127 parametersFlack parameter: ?
1 restraintRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
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) top
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, °) top
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, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O12—H121···O1i0.861.932.786 (3)179
Symmetry codes: (i) −x+1, y−1/2, −z.
Acknowledgements top

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

references
References top

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Nonius (2001). COLLECT Nonius BV, Delft, The Netherlands.

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