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

Tang, W.-J.; Lin, Z.-C.; Tang, M.-F.; Li, J.

doi:10.1107/S160053681004482X

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 66| Part 12| December 2010| Page o3107

https://doi.org/10.1107/S160053681004482X

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

Wen-Jian Tang,^a Zhi-Cai Lin,^a Min-Fang Tang ^a and Jun Li ^a ^*

^aSchool of Pharmacy, Anhui Medical University, Hefei 230032, People's Republic of China
^*Correspondence e-mail: ahmupharm@126.com

(Received 18 October 2010; accepted 2 November 2010; online 10 November 2010)

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 ). For the synthesis of the title compound from D-ribose, see: Sairam et al. (2003 ). For a 5-deoxy-ribofuranoid active as an antitumour drug, see: Shimma et al. (2000 ).

Experimental

Crystal data

C₁₁H₁₆O₇
M_r = 260.24
Orthorhombic, P 2₁ 2₁ 2₁
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 ) 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[F² > 2σ(F²)] = 0.041
wR(F²) = 0.133
S = 1.04
1368 reflections
168 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.13 e Å⁻³

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

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053681004482X/si2303Isup2.hkl

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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.

Structure description top

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

Computing details top

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

Figures top

	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.

1,2,3-Tri-O-acetyl-5-deoxy-D-ribofuranose top

Crystal data top

C₁₁H₁₆O₇	D_x = 1.309 Mg m⁻³
M_r = 260.24	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 1390 reflections
a = 7.592 (2) Å	θ = 2.6–21.6°
b = 8.505 (2) Å	µ = 0.11 mm⁻¹
c = 20.445 (2) Å	T = 298 K
V = 1320.1 (5) Å³	Prism, colourless
Z = 4	0.48 × 0.45 × 0.32 mm
F(000) = 552

Data collection top

Siemens SMART 1000 CCD area-detector diffractometer	1368 independent reflections
Radiation source: fine-focus sealed tube	848 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.036
φ and ω scans	θ_max = 25.0°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −9→8
T_min = 0.949, T_max = 0.966	k = −10→9
5470 measured reflections	l = −24→11

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.041	H-atom parameters constrained
wR(F²) = 0.133	w = 1/[σ²(F_o²) + (0.0609P)² + 0.2525P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
1368 reflections	Δρ_max = 0.18 e Å⁻³
168 parameters	Δρ_min = −0.13 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.022 (4)

Crystal data top

C₁₁H₁₆O₇	V = 1320.1 (5) Å³
M_r = 260.24	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 7.592 (2) Å	µ = 0.11 mm⁻¹
b = 8.505 (2) Å	T = 298 K
c = 20.445 (2) Å	0.48 × 0.45 × 0.32 mm

Data collection top

Siemens SMART 1000 CCD area-detector diffractometer	1368 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	848 reflections with I > 2σ(I)
T_min = 0.949, T_max = 0.966	R_int = 0.036
5470 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	0 restraints
wR(F²) = 0.133	H-atom parameters constrained
S = 1.04	Δρ_max = 0.18 e Å⁻³
1368 reflections	Δρ_min = −0.13 e Å⁻³
168 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.1176 (4)	0.2987 (4)	0.07061 (14)	0.0875 (10)
O2	0.2931 (4)	0.3413 (4)	0.16197 (14)	0.0848 (10)
O3	0.4083 (8)	0.5348 (6)	0.1051 (2)	0.162 (2)
O4	0.2959 (4)	−0.0158 (4)	0.07017 (13)	0.0873 (11)
O5	0.5372 (5)	−0.0822 (5)	0.1230 (2)	0.1261 (16)
O6	−0.0276 (4)	−0.0744 (3)	0.12588 (12)	0.0711 (9)
O7	0.0619 (5)	−0.1341 (4)	0.22641 (13)	0.0952 (12)
C1	0.2710 (6)	0.2524 (6)	0.1032 (2)	0.0750 (13)
H1	0.3742	0.2633	0.0748	0.090*
C2	0.2469 (6)	0.0844 (6)	0.12401 (18)	0.0695 (12)
H2	0.3104	0.0591	0.1644	0.083*
C3	0.0506 (6)	0.0772 (5)	0.13214 (17)	0.0628 (11)
H3	0.0192	0.1214	0.1748	0.075*
C4	−0.0187 (6)	0.1839 (5)	0.07907 (19)	0.0678 (11)
H4	−0.0317	0.1235	0.0385	0.081*
C5	−0.1893 (6)	0.2655 (5)	0.0940 (2)	0.0917 (16)
H5A	−0.1762	0.3274	0.1330	0.138*
H5B	−0.2802	0.1886	0.1005	0.138*
H5C	−0.2206	0.3327	0.0581	0.138*
C6	0.3685 (7)	0.4813 (7)	0.1569 (3)	0.0917 (15)
C7	0.3865 (8)	0.5618 (7)	0.2211 (3)	0.1153 (19)
H7A	0.4613	0.5007	0.2492	0.173*
H7B	0.2725	0.5726	0.2409	0.173*
H7C	0.4374	0.6639	0.2146	0.173*
C8	0.4508 (7)	−0.0888 (6)	0.0750 (2)	0.0784 (13)
C9	0.4968 (8)	−0.1728 (7)	0.0142 (2)	0.111 (2)
H9A	0.5860	−0.1152	−0.0088	0.166*
H9B	0.3940	−0.1822	−0.0128	0.166*
H9C	0.5403	−0.2757	0.0248	0.166*
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	−0.3877	0.1399	0.145*
H11B	−0.2191	−0.3001	0.1448	0.145*
H11C	−0.1320	−0.3709	0.2078	0.145*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.090 (2)	0.087 (2)	0.086 (2)	−0.018 (2)	−0.0159 (18)	0.0309 (18)
O2	0.095 (2)	0.089 (2)	0.0703 (19)	−0.023 (2)	−0.0001 (17)	0.0068 (19)
O3	0.232 (6)	0.137 (4)	0.116 (3)	−0.093 (4)	0.011 (4)	0.022 (3)
O4	0.087 (2)	0.115 (3)	0.0599 (17)	0.025 (2)	−0.0058 (16)	−0.0044 (18)
O5	0.099 (3)	0.135 (4)	0.145 (3)	0.029 (3)	−0.043 (3)	−0.031 (3)
O6	0.098 (2)	0.0548 (17)	0.0604 (16)	−0.0068 (19)	−0.0069 (15)	0.0085 (14)
O7	0.148 (3)	0.079 (2)	0.0585 (17)	−0.009 (2)	−0.0165 (19)	0.0096 (16)
C1	0.070 (3)	0.095 (4)	0.060 (2)	−0.010 (3)	0.000 (2)	0.004 (2)
C2	0.073 (3)	0.088 (3)	0.048 (2)	0.006 (3)	−0.006 (2)	0.001 (2)
C3	0.077 (3)	0.062 (3)	0.050 (2)	0.001 (3)	−0.0017 (19)	0.010 (2)
C4	0.077 (3)	0.064 (2)	0.062 (2)	−0.008 (3)	−0.012 (2)	0.010 (2)
C5	0.081 (3)	0.074 (3)	0.120 (4)	0.003 (3)	−0.013 (3)	0.016 (3)
C6	0.100 (4)	0.086 (4)	0.089 (4)	−0.024 (3)	−0.009 (3)	0.015 (3)
C7	0.132 (5)	0.101 (4)	0.112 (4)	−0.019 (4)	−0.028 (4)	−0.003 (4)
C8	0.073 (3)	0.076 (3)	0.086 (3)	−0.002 (3)	0.005 (3)	0.007 (3)
C9	0.118 (4)	0.113 (4)	0.102 (4)	0.007 (4)	0.030 (3)	0.008 (4)
C10	0.086 (3)	0.062 (3)	0.057 (2)	0.009 (3)	0.006 (2)	0.011 (2)
C11	0.135 (4)	0.067 (3)	0.088 (3)	−0.015 (3)	−0.014 (3)	0.018 (3)

Geometric parameters (Å, º) top

O1—C1	1.399 (5)	C4—C5	1.501 (6)
O1—C4	1.433 (5)	C4—H4	0.9800
O2—C6	1.325 (6)	C5—H5A	0.9600
O2—C1	1.429 (5)	C5—H5B	0.9600
O3—C6	1.192 (6)	C5—H5C	0.9600
O4—C8	1.333 (6)	C6—C7	1.485 (7)
O4—C2	1.441 (5)	C7—H7A	0.9600
O5—C8	1.183 (6)	C7—H7B	0.9600
O6—C10	1.344 (4)	C7—H7C	0.9600
O6—C3	1.425 (5)	C8—C9	1.475 (6)
O7—C10	1.190 (5)	C9—H9A	0.9600
C1—C2	1.502 (6)	C9—H9B	0.9600
C1—H1	0.9800	C9—H9C	0.9600
C2—C3	1.500 (6)	C10—C11	1.484 (6)
C2—H2	0.9800	C11—H11A	0.9600
C3—C4	1.509 (5)	C11—H11B	0.9600
C3—H3	0.9800	C11—H11C	0.9600

C1—O1—C4	110.6 (3)	C4—C5—H5C	109.5
C6—O2—C1	117.4 (4)	H5A—C5—H5C	109.5
C8—O4—C2	116.5 (3)	H5B—C5—H5C	109.5
C10—O6—C3	116.6 (3)	O3—C6—O2	121.4 (5)
O1—C1—O2	110.4 (4)	O3—C6—C7	125.8 (5)
O1—C1—C2	107.5 (4)	O2—C6—C7	112.7 (5)
O2—C1—C2	106.3 (3)	C6—C7—H7A	109.5
O1—C1—H1	110.8	C6—C7—H7B	109.5
O2—C1—H1	110.8	H7A—C7—H7B	109.5
C2—C1—H1	110.8	C6—C7—H7C	109.5
O4—C2—C1	108.4 (3)	H7A—C7—H7C	109.5
O4—C2—C3	108.5 (4)	H7B—C7—H7C	109.5
C1—C2—C3	101.0 (4)	O5—C8—O4	121.9 (5)
O4—C2—H2	112.7	O5—C8—C9	126.3 (5)
C1—C2—H2	112.7	O4—C8—C9	111.8 (5)
C3—C2—H2	112.7	C8—C9—H9A	109.5
O6—C3—C2	116.1 (4)	C8—C9—H9B	109.5
O6—C3—C4	109.5 (3)	H9A—C9—H9B	109.5
C2—C3—C4	104.0 (3)	C8—C9—H9C	109.5
O6—C3—H3	109.0	H9A—C9—H9C	109.5
C2—C3—H3	109.0	H9B—C9—H9C	109.5
C4—C3—H3	109.0	O7—C10—O6	122.6 (4)
O1—C4—C5	109.4 (4)	O7—C10—C11	126.1 (4)
O1—C4—C3	104.1 (3)	O6—C10—C11	111.4 (4)
C5—C4—C3	115.6 (4)	C10—C11—H11A	109.5
O1—C4—H4	109.1	C10—C11—H11B	109.5
C5—C4—H4	109.1	H11A—C11—H11B	109.5
C3—C4—H4	109.1	C10—C11—H11C	109.5
C4—C5—H5A	109.5	H11A—C11—H11C	109.5
C4—C5—H5B	109.5	H11B—C11—H11C	109.5
H5A—C5—H5B	109.5

Experimental details

Crystal data
Chemical formula	C₁₁H₁₆O₇
M_r	260.24
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	298
a, b, c (Å)	7.592 (2), 8.505 (2), 20.445 (2)
V (Å³)	1320.1 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.48 × 0.45 × 0.32

Data collection
Diffractometer	Siemens SMART 1000 CCD area-detector
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.949, 0.966
No. of measured, independent and observed [I > 2σ(I)] reflections	5470, 1368, 848
R_int	0.036
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.133, 1.04
No. of reflections	1368
No. of parameters	168
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.13

Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Acknowledgements

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)

References

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