organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

aDepartment of Organic Chemistry, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England, and bDepartment of Chemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England
*Correspondence e-mail: victoria.booth@chem.ox.ac.uk

(Received 9 February 2009; accepted 18 February 2009; online 21 February 2009)

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[Becker, D. J. & Lowe, B. J. (2003). Glycobiology, 13, 41R-53R.]); Yoshihara et al. (2008[Yoshihara, A., Haraguchi, S., Gullapalli, P., Rao, D., Morimoto, K., Takata, G., Jones, N., Jenkinson, S. F., Wormald, M. R., Dwek, R. A., Fleet, G. W. J. & Izumori, K. (2008). Tetrahedron Asymmetry, 19, 739-745..]); Gullapalli et al. (2007[Gullapalli, P., Shiji, T., Rao, D., Yoshihara, A., Morimoto, K., Takata, G., Fleet, G. W. J. & Izumori, K. (2007). Tetrahedron Asymmetry, 18, 1995-2000.]). For a related structure see: Booth et al. (2007[Booth, K. V., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2007). Acta Cryst. E63, o1128-o1130.]).

[Scheme 1]

Experimental

Crystal data
  • C10H18O4

  • Mr = 202.25

  • Monoclinic, P 21

  • 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[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.89, Tmax = 0.98

  • 5025 measured reflections

  • 1266 independent reflections

  • 1183 reflections with I > 2σ(I)

  • Rint = 0.036

Refinement
  • R[F2 > 2σ(F2)] = 0.030

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O12—H121⋯O1i 0.86 1.93 2.786 (3) 179
Symmetry code: (i) [-x+1, y-{\script{1\over 2}}, -z].

Data collection: COLLECT (Nonius, 2001[Nonius (2001). COLLECT Nonius BV, Delft, The Netherlands.]).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & &Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.]); software used to prepare material for publication: CRYSTALS.

Supporting information


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 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 top
Nonius KappaCCD
diffractometer
1183 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.036
ω scansθmax = 27.5°, θmin = 5.5°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 77
Tmin = 0.89, Tmax = 0.98k = 1317
5025 measured reflectionsl = 88
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 = 0.000076
1266 reflectionsΔρmax = 0.16 e Å3
127 parametersΔρmin = 0.16 e Å3
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 mm1
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 reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0301 restraint
wR(F2) = 0.073H-atom parameters constrained
S = 0.98Δρmax = 0.16 e Å3
1266 reflectionsΔρmin = 0.16 e Å3
127 parameters
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*
H630.03580.26380.28030.0479*
H620.19380.35300.32500.0474*
H610.00280.37450.20370.0467*
H710.51480.24480.18370.0319*
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*
H1130.06620.17300.36090.0474*
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*
H1210.37460.03190.05150.0539*
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, º) 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, º) 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, y1/2, z.

Experimental details

Crystal data
Chemical formulaC10H18O4
Mr202.25
Crystal system, space groupMonoclinic, P21
Temperature (K)150
a, b, c (Å)6.0641 (3), 13.4016 (7), 6.8287 (3)
β (°) 102.596 (2)
V3)541.60 (5)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.50 × 0.20 × 0.20
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.89, 0.98
No. of measured, independent and
observed [I > 2σ(I)] reflections
5025, 1266, 1183
Rint0.036
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.073, 0.98
No. of reflections1266
No. of parameters127
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.16, 0.16

Computer programs: COLLECT (Nonius, 2001)., DENZO/SCALEPACK (Otwinowski & Minor, 1997), DENZO/SCALEPACK (Otwinowski & Minor, 1997, SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996), CRYSTALS (Betteridge et al., 2003.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O12—H121···O1i0.861.932.786 (3)179
Symmetry code: (i) x+1, y1/2, z.
 

Acknowledgements

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

References

First citationAltomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.  CrossRef Web of Science IUCr Journals Google Scholar
First citationBecker, D. J. & Lowe, B. J. (2003). Glycobiology, 13, 41R–53R.  Web of Science CrossRef PubMed CAS Google Scholar
First citationBetteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.  Web of Science CrossRef IUCr Journals Google Scholar
First citationBooth, K. V., Watkin, D. J., Jenkinson, S. F. & Fleet, G. W. J. (2007). Acta Cryst. E63, o1128–o1130.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationGullapalli, P., Shiji, T., Rao, D., Yoshihara, A., Morimoto, K., Takata, G., Fleet, G. W. J. & Izumori, K. (2007). Tetrahedron Asymmetry, 18, 1995–2000.  Web of Science CrossRef CAS Google Scholar
First citationNonius (2001). COLLECT Nonius BV, Delft, The Netherlands.  Google Scholar
First citationOtwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.  Google Scholar
First citationWatkin, D. J., Prout, C. K. & &Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.  Google Scholar
First citationYoshihara, A., Haraguchi, S., Gullapalli, P., Rao, D., Morimoto, K., Takata, G., Jones, N., Jenkinson, S. F., Wormald, M. R., Dwek, R. A., Fleet, G. W. J. & Izumori, K. (2008). Tetrahedron Asymmetry, 19, 739–745..  Web of Science CrossRef CAS Google Scholar

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