PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): o3107.
Published online 2010 November 10. doi:  10.1107/S160053681004482X
PMCID: PMC3011534

1,2,3-Tri-O-acetyl-5-de­oxy-d-ribofuran­ose

Abstract

The title compound, C11H16O7, was obtained from the breakage reaction of the glycosidic bond of 5′-de­oxy-2′,3′-diacetyl­inosine. The ribofuran­ose ring has a C2-exo, C3-endo twist configuration. No alteration of the relative configuration compared with d-(−)-ribose is observed.

Related literature

For possible catalytic mechanisms at the anomeric carbon centre in the cleavage of glycosidic linkages, see: Vocadlo et al. (2001 [triangle]). For the synthesis of the title compound from d-ribose, see: Sairam et al. (2003 [triangle]). For a 5-de­oxy-ribofuran­oid active as an anti­tumour drug, see: Shimma et al. (2000 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o3107-scheme1.jpg

Experimental

Crystal data

  • C11H16O7
  • M r = 260.24
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o3107-efi1.jpg
  • a = 7.592 (2) Å
  • b = 8.505 (2) Å
  • c = 20.445 (2) Å
  • V = 1320.1 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 298 K
  • 0.48 × 0.45 × 0.32 mm

Data collection

  • Siemens SMART 1000 CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.949, T max = 0.966
  • 5470 measured reflections
  • 1368 independent reflections
  • 848 reflections with I > 2σ(I)
  • R int = 0.036

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.133
  • S = 1.04
  • 1368 reflections
  • 168 parameters
  • H-atom parameters constrained
  • Δρmax = 0.18 e Å−3
  • Δρmin = −0.13 e Å−3

Data collection: SMART (Siemens, 1996 [triangle]); cell refinement: SAINT (Siemens, 1996 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681004482X/si2303sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681004482X/si2303Isup2.hkl

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

Acknowledgments

This work was supported by the National Natural Science Foundation of China (grant No. 20802003) and the Scientific Research Fund of Anhui Provincial Education Department (grant No. KJ2008B171)

supplementary crystallographic information

Comment

During the last decades there has been considerable interest in the chemical synthesis of the nucleoside analogues for their biological evaluation of the anti-tumor activity (Sairam et al., 2003). 1,2,3-O-Triacetyl-5-deoxy-D-ribofuranose, as one of the important intermediates, was used to synthesize some anti-cancer drugs such as Doxifluridine, Capecitabine (Shimma et al., 2000), and so on. There were different synthetic routes available in literature for the synthesis of this intermediate. We obtained this compound from inosine as starting material in a linear synthetic route. Possible formation mechanisms of the title compound are shown in Fig. 1. To know the relative stereochemistry of the anomeric position in the ribose, it is therefore necessary to gain the well defined structure of the 1,2,3-O-triacetyl-5-deoxy-D-ribofuranose by X-diffraction method (Fig. 2).

We observed that the ribofuranose ring has a C2-exo, C3-endo twist configuration and the anomeric carbons are always β configuration in the crystal packing. We suppose that the mechanism of the breakage reaction of the glycosidic bond is similar to that of the glycoside hydrolase (Vocadlo et al., 2001). Firstly, the nucleophilic group of the cation resin attacks the anomeric centre of the 5'-deoxy-2',3'-diacetyl-inosine, resulting in the formation of a glycosyl intermediate. Then a nucleophilic acetic anhydride as a base acts the glycosyl intermediate by acetolysis, giving the title product. In another way, the product obtained with sulfuric acid as catalyst is a α/β anomeric mixture and the yield is much lower. This difference may be because the intermediate produced using strong acid is a carbocation and the furan ring may be decomposed to some byproducts.

Experimental

The title compound was prepared from the reaction of the breakage of the glycosidic bond of 5'-Deoxy-2',3'-diacetyl-inosine, which was gained from inosine by halogenation, hydrogenization and acetylation in turn. 5'-Deoxy-2',3'-diacetyl-inosine (6.72 g, 20 mmol) and cation-exchange resin (6 g) were added to a solution of acetic anhydride/acetic acid (60 ml, 9: 1), was heated to 358 K and reacted under stirring for 8 h. The reacting mixture was filtered and the filtrate was concentrated in vacuo. The residue was resolved in ethyl acetate, then the precipitate was filtered and the filtrate was washed by the saturated solution of NaHCO3. The organic layer was dried with anhydrous Na2SO4, filtered, and concentrated in vacuo. The residue was recrystallized from methanol/water. The purified title compound was subsequently dissolved in methanol and added water to the solution until it turned cloudy. Upon standing at room temperature, a colorless block appeared and was separated from the solvent by decantation.

Refinement

All H atoms were positioned geometrically and refined using a riding model, with C—H distances of 0.98 Å (methyl), with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(C-methyl).

In the absence of significant anomalous scattering effects, Friedel pairs were averaged.

Figures

Fig. 1.
Possible formation mechanisms of the title compound.
Fig. 2.
ORTEP drawing of the title compound with atomic numbering scheme and thermal ellipsoids at 30% probability level.

Crystal data

C11H16O7Dx = 1.309 Mg m3
Mr = 260.24Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 1390 reflections
a = 7.592 (2) Åθ = 2.6–21.6°
b = 8.505 (2) ŵ = 0.11 mm1
c = 20.445 (2) ÅT = 298 K
V = 1320.1 (5) Å3Prism, colourless
Z = 40.48 × 0.45 × 0.32 mm
F(000) = 552

Data collection

Siemens SMART 1000 CCD area-detector diffractometer1368 independent reflections
Radiation source: fine-focus sealed tube848 reflections with I > 2σ(I)
graphiteRint = 0.036
[var phi] and ω scansθmax = 25.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −9→8
Tmin = 0.949, Tmax = 0.966k = −10→9
5470 measured reflectionsl = −24→11

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041H-atom parameters constrained
wR(F2) = 0.133w = 1/[σ2(Fo2) + (0.0609P)2 + 0.2525P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
1368 reflectionsΔρmax = 0.18 e Å3
168 parametersΔρmin = −0.13 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.022 (4)

Special details

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

xyzUiso*/Ueq
O10.1176 (4)0.2987 (4)0.07061 (14)0.0875 (10)
O20.2931 (4)0.3413 (4)0.16197 (14)0.0848 (10)
O30.4083 (8)0.5348 (6)0.1051 (2)0.162 (2)
O40.2959 (4)−0.0158 (4)0.07017 (13)0.0873 (11)
O50.5372 (5)−0.0822 (5)0.1230 (2)0.1261 (16)
O6−0.0276 (4)−0.0744 (3)0.12588 (12)0.0711 (9)
O70.0619 (5)−0.1341 (4)0.22641 (13)0.0952 (12)
C10.2710 (6)0.2524 (6)0.1032 (2)0.0750 (13)
H10.37420.26330.07480.090*
C20.2469 (6)0.0844 (6)0.12401 (18)0.0695 (12)
H20.31040.05910.16440.083*
C30.0506 (6)0.0772 (5)0.13214 (17)0.0628 (11)
H30.01920.12140.17480.075*
C4−0.0187 (6)0.1839 (5)0.07907 (19)0.0678 (11)
H4−0.03170.12350.03850.081*
C5−0.1893 (6)0.2655 (5)0.0940 (2)0.0917 (16)
H5A−0.17620.32740.13300.138*
H5B−0.28020.18860.10050.138*
H5C−0.22060.33270.05810.138*
C60.3685 (7)0.4813 (7)0.1569 (3)0.0917 (15)
C70.3865 (8)0.5618 (7)0.2211 (3)0.1153 (19)
H7A0.46130.50070.24920.173*
H7B0.27250.57260.24090.173*
H7C0.43740.66390.21460.173*
C80.4508 (7)−0.0888 (6)0.0750 (2)0.0784 (13)
C90.4968 (8)−0.1728 (7)0.0142 (2)0.111 (2)
H9A0.5860−0.1152−0.00880.166*
H9B0.3940−0.1822−0.01280.166*
H9C0.5403−0.27570.02480.166*
C10−0.0159 (6)−0.1698 (5)0.1781 (2)0.0681 (11)
C11−0.1095 (8)−0.3204 (6)0.1666 (2)0.0968 (16)
H11A−0.0379−0.38770.13990.145*
H11B−0.2191−0.30010.14480.145*
H11C−0.1320−0.37090.20780.145*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.090 (2)0.087 (2)0.086 (2)−0.018 (2)−0.0159 (18)0.0309 (18)
O20.095 (2)0.089 (2)0.0703 (19)−0.023 (2)−0.0001 (17)0.0068 (19)
O30.232 (6)0.137 (4)0.116 (3)−0.093 (4)0.011 (4)0.022 (3)
O40.087 (2)0.115 (3)0.0599 (17)0.025 (2)−0.0058 (16)−0.0044 (18)
O50.099 (3)0.135 (4)0.145 (3)0.029 (3)−0.043 (3)−0.031 (3)
O60.098 (2)0.0548 (17)0.0604 (16)−0.0068 (19)−0.0069 (15)0.0085 (14)
O70.148 (3)0.079 (2)0.0585 (17)−0.009 (2)−0.0165 (19)0.0096 (16)
C10.070 (3)0.095 (4)0.060 (2)−0.010 (3)0.000 (2)0.004 (2)
C20.073 (3)0.088 (3)0.048 (2)0.006 (3)−0.006 (2)0.001 (2)
C30.077 (3)0.062 (3)0.050 (2)0.001 (3)−0.0017 (19)0.010 (2)
C40.077 (3)0.064 (2)0.062 (2)−0.008 (3)−0.012 (2)0.010 (2)
C50.081 (3)0.074 (3)0.120 (4)0.003 (3)−0.013 (3)0.016 (3)
C60.100 (4)0.086 (4)0.089 (4)−0.024 (3)−0.009 (3)0.015 (3)
C70.132 (5)0.101 (4)0.112 (4)−0.019 (4)−0.028 (4)−0.003 (4)
C80.073 (3)0.076 (3)0.086 (3)−0.002 (3)0.005 (3)0.007 (3)
C90.118 (4)0.113 (4)0.102 (4)0.007 (4)0.030 (3)0.008 (4)
C100.086 (3)0.062 (3)0.057 (2)0.009 (3)0.006 (2)0.011 (2)
C110.135 (4)0.067 (3)0.088 (3)−0.015 (3)−0.014 (3)0.018 (3)

Geometric parameters (Å, °)

O1—C11.399 (5)C4—C51.501 (6)
O1—C41.433 (5)C4—H40.9800
O2—C61.325 (6)C5—H5A0.9600
O2—C11.429 (5)C5—H5B0.9600
O3—C61.192 (6)C5—H5C0.9600
O4—C81.333 (6)C6—C71.485 (7)
O4—C21.441 (5)C7—H7A0.9600
O5—C81.183 (6)C7—H7B0.9600
O6—C101.344 (4)C7—H7C0.9600
O6—C31.425 (5)C8—C91.475 (6)
O7—C101.190 (5)C9—H9A0.9600
C1—C21.502 (6)C9—H9B0.9600
C1—H10.9800C9—H9C0.9600
C2—C31.500 (6)C10—C111.484 (6)
C2—H20.9800C11—H11A0.9600
C3—C41.509 (5)C11—H11B0.9600
C3—H30.9800C11—H11C0.9600
C1—O1—C4110.6 (3)C4—C5—H5C109.5
C6—O2—C1117.4 (4)H5A—C5—H5C109.5
C8—O4—C2116.5 (3)H5B—C5—H5C109.5
C10—O6—C3116.6 (3)O3—C6—O2121.4 (5)
O1—C1—O2110.4 (4)O3—C6—C7125.8 (5)
O1—C1—C2107.5 (4)O2—C6—C7112.7 (5)
O2—C1—C2106.3 (3)C6—C7—H7A109.5
O1—C1—H1110.8C6—C7—H7B109.5
O2—C1—H1110.8H7A—C7—H7B109.5
C2—C1—H1110.8C6—C7—H7C109.5
O4—C2—C1108.4 (3)H7A—C7—H7C109.5
O4—C2—C3108.5 (4)H7B—C7—H7C109.5
C1—C2—C3101.0 (4)O5—C8—O4121.9 (5)
O4—C2—H2112.7O5—C8—C9126.3 (5)
C1—C2—H2112.7O4—C8—C9111.8 (5)
C3—C2—H2112.7C8—C9—H9A109.5
O6—C3—C2116.1 (4)C8—C9—H9B109.5
O6—C3—C4109.5 (3)H9A—C9—H9B109.5
C2—C3—C4104.0 (3)C8—C9—H9C109.5
O6—C3—H3109.0H9A—C9—H9C109.5
C2—C3—H3109.0H9B—C9—H9C109.5
C4—C3—H3109.0O7—C10—O6122.6 (4)
O1—C4—C5109.4 (4)O7—C10—C11126.1 (4)
O1—C4—C3104.1 (3)O6—C10—C11111.4 (4)
C5—C4—C3115.6 (4)C10—C11—H11A109.5
O1—C4—H4109.1C10—C11—H11B109.5
C5—C4—H4109.1H11A—C11—H11B109.5
C3—C4—H4109.1C10—C11—H11C109.5
C4—C5—H5A109.5H11A—C11—H11C109.5
C4—C5—H5B109.5H11B—C11—H11C109.5
H5A—C5—H5B109.5

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SI2303).

References

  • Sairam, P., Puranik, R., Rao, B. S., Swamy, P. V. & Chandra, S. (2003). Carbohydr. Res.338, 303–306. [PubMed]
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Shimma, N., Umeda, I., Arasaki, M., Murasaki, C., Masubuchi, K., Kohchi, Y., Miwa, M., Ura, M., Sawada, N., Tahara, H., Kuruma, I., Horii, I. & Ishitsuka, H. (2000). Bioorg. Med. Chem.8, 1697–1706. [PubMed]
  • Siemens (1996). SMART and SAINT Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.
  • Vocadlo, D. J., Davies, G. J., Laine, R. & Withers, S. G. (2001). Nature (London), 412, 835–838. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography