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organic compounds
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
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 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); Yoshihara et al. (2008
); Gullapalli et al. (2007
). For a related structure see: Booth et al. (2007
).
Experimental
Crystal data
|
Refinement
|
|
Data collection: COLLECT (Nonius, 2001).; cell DENZO/SCALEPACK (Otwinowski & Minor, 1997
); data reduction: DENZO/SCALEPACK; 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.
Supporting information
10.1107/S1600536809005777/lh2774sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809005777/lh2774Isup2.hkl
The title compound was recrystallized from dichloromethane by slow evaporation: m.p. 349–352 K; [α]D25 -49.6 (c,0.15 in CHCl3).
In the absence of significant
Friedel pairs were merged and the 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.
Data collection: COLLECT (Nonius, 2001).; cell
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.C10H18O4 | F(000) = 220 |
Mr = 202.25 | Dx = 1.240 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 1185 reflections |
a = 6.0641 (3) Å | θ = 5–27° |
b = 13.4016 (7) Å | µ = 0.10 mm−1 |
c = 6.8287 (3) Å | T = 150 K |
β = 102.596 (2)° | Plate, colourless |
V = 541.60 (5) Å3 | 0.50 × 0.20 × 0.20 mm |
Z = 2 |
Nonius KappaCCD diffractometer | 1183 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.036 |
ω scans | θmax = 27.5°, θmin = 5.5° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −7→7 |
Tmin = 0.89, Tmax = 0.98 | k = −13→17 |
5025 measured reflections | l = −8→8 |
1266 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.030 | H-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 reflections | Δρmax = 0.16 e Å−3 |
127 parameters | Δρmin = −0.16 e Å−3 |
1 restraint |
C10H18O4 | V = 541.60 (5) Å3 |
Mr = 202.25 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.0641 (3) Å | µ = 0.10 mm−1 |
b = 13.4016 (7) Å | T = 150 K |
c = 6.8287 (3) Å | 0.50 × 0.20 × 0.20 mm |
β = 102.596 (2)° |
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 = 0.98 | Rint = 0.036 |
5025 measured reflections |
R[F2 > 2σ(F2)] = 0.030 | 1 restraint |
wR(F2) = 0.073 | H-atom parameters constrained |
S = 0.98 | Δρmax = 0.16 e Å−3 |
1266 reflections | Δρmin = −0.16 e Å−3 |
127 parameters |
x | y | z | Uiso*/Ueq | ||
O1 | 0.3944 (2) | 0.39582 (13) | 0.04435 (17) | 0.0245 | |
C2 | 0.4077 (3) | 0.39975 (17) | 0.2596 (2) | 0.0228 | |
O3 | 0.3257 (2) | 0.30533 (13) | 0.30874 (17) | 0.0224 | |
C4 | 0.1684 (3) | 0.27174 (16) | 0.1342 (2) | 0.0195 | |
C5 | 0.2816 (3) | 0.30472 (16) | −0.0350 (2) | 0.0213 | |
C6 | 0.1137 (3) | 0.32628 (18) | −0.2291 (3) | 0.0299 | |
C7 | 0.4647 (3) | 0.23026 (16) | −0.0612 (3) | 0.0275 | |
O8 | 0.3798 (2) | 0.13095 (14) | −0.0775 (2) | 0.0287 | |
C9 | 0.3274 (3) | 0.10066 (16) | 0.1088 (3) | 0.0255 | |
C10 | 0.1251 (3) | 0.15996 (16) | 0.1439 (3) | 0.0220 | |
C11 | 0.0585 (3) | 0.13084 (17) | 0.3391 (3) | 0.0294 | |
O12 | 0.2706 (2) | 0.00005 (14) | 0.0917 (2) | 0.0322 | |
C13 | 0.2595 (3) | 0.48536 (17) | 0.3003 (3) | 0.0298 | |
C14 | 0.6502 (3) | 0.41048 (18) | 0.3718 (3) | 0.0312 | |
H41 | 0.0240 | 0.3081 | 0.1185 | 0.0230* | |
H63 | 0.0358 | 0.2638 | −0.2803 | 0.0479* | |
H62 | 0.1938 | 0.3530 | −0.3250 | 0.0474* | |
H61 | 0.0028 | 0.3745 | −0.2037 | 0.0467* | |
H71 | 0.5148 | 0.2448 | −0.1837 | 0.0319* | |
H72 | 0.5917 | 0.2377 | 0.0580 | 0.0331* | |
H91 | 0.4639 | 0.1091 | 0.2207 | 0.0329* | |
H101 | 0.0017 | 0.1448 | 0.0295 | 0.0264* | |
H111 | 0.0082 | 0.0613 | 0.3332 | 0.0474* | |
H112 | 0.1891 | 0.1410 | 0.4520 | 0.0465* | |
H113 | −0.0662 | 0.1730 | 0.3609 | 0.0474* | |
H132 | 0.2647 | 0.4876 | 0.4458 | 0.0489* | |
H131 | 0.3214 | 0.5481 | 0.2611 | 0.0489* | |
H133 | 0.1041 | 0.4759 | 0.2247 | 0.0491* | |
H142 | 0.6552 | 0.4165 | 0.5154 | 0.0457* | |
H143 | 0.7110 | 0.4711 | 0.3212 | 0.0458* | |
H141 | 0.7362 | 0.3515 | 0.3460 | 0.0456* | |
H121 | 0.3746 | −0.0319 | 0.0515 | 0.0539* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0310 (7) | 0.0222 (6) | 0.0214 (6) | −0.0072 (5) | 0.0082 (5) | −0.0002 (5) |
C2 | 0.0259 (8) | 0.0224 (9) | 0.0208 (7) | −0.0045 (7) | 0.0066 (6) | −0.0005 (7) |
O3 | 0.0270 (6) | 0.0202 (7) | 0.0199 (6) | −0.0045 (5) | 0.0047 (5) | −0.0001 (5) |
C4 | 0.0190 (8) | 0.0193 (9) | 0.0205 (8) | −0.0003 (6) | 0.0050 (6) | −0.0018 (6) |
C5 | 0.0233 (8) | 0.0199 (9) | 0.0215 (8) | −0.0012 (7) | 0.0069 (6) | −0.0017 (7) |
C6 | 0.0358 (10) | 0.0297 (11) | 0.0223 (9) | 0.0016 (8) | 0.0025 (7) | 0.0005 (8) |
C7 | 0.0276 (9) | 0.0248 (10) | 0.0340 (10) | 0.0003 (8) | 0.0153 (8) | 0.0019 (8) |
O8 | 0.0363 (7) | 0.0218 (7) | 0.0333 (7) | 0.0021 (6) | 0.0190 (6) | 0.0004 (6) |
C9 | 0.0284 (9) | 0.0196 (9) | 0.0312 (9) | 0.0013 (7) | 0.0124 (7) | 0.0023 (7) |
C10 | 0.0212 (8) | 0.0201 (9) | 0.0257 (9) | −0.0015 (6) | 0.0074 (6) | −0.0011 (7) |
C11 | 0.0344 (10) | 0.0236 (9) | 0.0349 (10) | 0.0002 (8) | 0.0176 (8) | 0.0011 (8) |
O12 | 0.0366 (7) | 0.0200 (7) | 0.0450 (8) | 0.0021 (6) | 0.0198 (6) | −0.0011 (6) |
C13 | 0.0327 (10) | 0.0243 (10) | 0.0354 (10) | −0.0004 (8) | 0.0141 (8) | −0.0007 (8) |
C14 | 0.0276 (9) | 0.0324 (11) | 0.0313 (9) | −0.0037 (8) | 0.0013 (7) | −0.0021 (9) |
O1—C2 | 1.4553 (19) | O8—C9 | 1.436 (2) |
O1—C5 | 1.446 (2) | C9—C10 | 1.524 (2) |
C2—O3 | 1.426 (2) | C9—O12 | 1.390 (2) |
C2—C13 | 1.520 (3) | C9—H91 | 1.003 |
C2—C14 | 1.510 (2) | C10—C11 | 1.525 (2) |
O3—C4 | 1.427 (2) | C10—H101 | 0.978 |
C4—C5 | 1.533 (2) | C11—H111 | 0.979 |
C4—C10 | 1.525 (2) | C11—H112 | 0.987 |
C4—H41 | 0.987 | C11—H113 | 0.981 |
C5—C6 | 1.513 (2) | O12—H121 | 0.855 |
C5—C7 | 1.532 (2) | C13—H132 | 0.988 |
C6—H63 | 0.986 | C13—H131 | 0.982 |
C6—H62 | 0.965 | C13—H133 | 0.979 |
C6—H61 | 0.975 | C14—H142 | 0.978 |
C7—O8 | 1.423 (2) | C14—H143 | 0.986 |
C7—H71 | 0.970 | C14—H141 | 0.984 |
C7—H72 | 0.996 | ||
C2—O1—C5 | 109.06 (12) | C7—O8—C9 | 109.94 (14) |
O1—C2—O3 | 105.09 (13) | O8—C9—C10 | 109.46 (14) |
O1—C2—C13 | 107.90 (14) | O8—C9—O12 | 107.37 (15) |
O3—C2—C13 | 112.10 (14) | C10—C9—O12 | 109.02 (14) |
O1—C2—C14 | 110.45 (13) | O8—C9—H91 | 109.8 |
O3—C2—C14 | 108.43 (15) | C10—C9—H91 | 112.3 |
C13—C2—C14 | 112.62 (16) | O12—C9—H91 | 108.7 |
C2—O3—C4 | 106.69 (12) | C4—C10—C9 | 110.70 (13) |
O3—C4—C5 | 102.17 (13) | C4—C10—C11 | 111.73 (15) |
O3—C4—C10 | 111.32 (14) | C9—C10—C11 | 112.32 (15) |
C5—C4—C10 | 115.19 (14) | C4—C10—H101 | 106.2 |
O3—C4—H41 | 110.5 | C9—C10—H101 | 105.6 |
C5—C4—H41 | 108.0 | C11—C10—H101 | 110.0 |
C10—C4—H41 | 109.4 | C10—C11—H111 | 110.3 |
C4—C5—O1 | 102.36 (13) | C10—C11—H112 | 109.1 |
C4—C5—C6 | 112.89 (15) | H111—C11—H112 | 110.6 |
O1—C5—C6 | 109.89 (15) | C10—C11—H113 | 110.2 |
C4—C5—C7 | 110.82 (15) | H111—C11—H113 | 108.2 |
O1—C5—C7 | 107.33 (13) | H112—C11—H113 | 108.4 |
C6—C5—C7 | 112.89 (15) | C9—O12—H121 | 109.0 |
C5—C6—H63 | 109.1 | C2—C13—H132 | 108.4 |
C5—C6—H62 | 108.8 | C2—C13—H131 | 108.7 |
H63—C6—H62 | 110.3 | H132—C13—H131 | 108.6 |
C5—C6—H61 | 109.2 | C2—C13—H133 | 110.2 |
H63—C6—H61 | 109.3 | H132—C13—H133 | 110.5 |
H62—C6—H61 | 110.1 | H131—C13—H133 | 110.4 |
C5—C7—O8 | 111.05 (14) | C2—C14—H142 | 109.3 |
C5—C7—H71 | 109.9 | C2—C14—H143 | 107.3 |
O8—C7—H71 | 107.2 | H142—C14—H143 | 110.6 |
C5—C7—H72 | 106.9 | C2—C14—H141 | 109.1 |
O8—C7—H72 | 111.1 | H142—C14—H141 | 110.1 |
H71—C7—H72 | 110.7 | H143—C14—H141 | 110.3 |
D—H···A | D—H | H···A | D···A | D—H···A |
C6—H61···O12i | 0.97 | 2.59 | 3.562 (3) | 173 |
O12—H121···O1ii | 0.86 | 1.93 | 2.786 (3) | 179 |
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x+1, y−1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C10H18O4 |
Mr | 202.25 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 150 |
a, b, c (Å) | 6.0641 (3), 13.4016 (7), 6.8287 (3) |
β (°) | 102.596 (2) |
V (Å3) | 541.60 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.50 × 0.20 × 0.20 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.89, 0.98 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5025, 1266, 1183 |
Rint | 0.036 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.073, 0.98 |
No. of reflections | 1266 |
No. of parameters | 127 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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.
D—H···A | D—H | H···A | D···A | D—H···A |
O12—H121···O1i | 0.86 | 1.93 | 2.786 (3) | 179 |
Symmetry code: (i) −x+1, y−1/2, −z. |
Acknowledgements
We would like to thank the Chemical Crystallography Department and ALT at Oxford University for use of the difractometers.
References
Altomare, 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
Becker, D. J. & Lowe, B. J. (2003). Glycobiology, 13, 41R–53R. Web of Science CrossRef PubMed CAS Google Scholar
Betteridge, 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
Booth, 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
Gullapalli, 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
Nonius (2001). COLLECT Nonius BV, Delft, The Netherlands. Google Scholar
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. Google Scholar
Watkin, D. J., Prout, C. K. & &Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England. Google Scholar
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.. Web of Science CrossRef CAS Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.