1-(2-Bromo-2-de­oxy-β-d-xylofuranos­yl)uracil

Zhong-Gao Zhou; Shun-Guo Fu; Wu-Leng Lai; Chun-Feng Wang

doi:10.1107/S1600536810051081

. 2010 Dec 11;67(Pt 1):o111. doi: 10.1107/S1600536810051081

1-(2-Bromo-2-deoxy-β-d-xylofuranosyl)uracil

Zhong-Gao Zhou ^a,^*, Shun-Guo Fu ^b, Wu-Leng Lai ^a, Chun-Feng Wang ^a

PMCID: PMC3050214 PMID: 21522623

Abstract

In the title compound, C₉H₁₁BrN₂O₅, the ribofuranose ring has a C2-exo, C3-endo twist configuration and is attached to the uracil unit via a β-N₁-glycosidic bond. The crystal structure is stabilized by two intermolecular O—H⋯O interactions and one intermolecular N—H⋯O interaction.

Related literature

For the synthesis of the title compound and its analogues, see: Shakya et al. (2010 ▶). For a related structure, see: Suck et al. (1972 ▶). For the use of the title compound as a pharmaceutical intermediate, see: Haraguchi et al. (1993 ▶); Kittaka et al. (1992 ▶); Pozharskii et al. (1997) ▶; Sairam et al. (2003 ▶). For the biological activity of nucleoside derivatives, see: Johar et al. (2005 ▶).

Experimental

Crystal data

C₉H₁₁BrN₂O₅
M _r = 307.11
Orthorhombic,
a = 4.8444 (3) Å
b = 12.7237 (10) Å
c = 17.4388 (13) Å
V = 1074.90 (13) Å³
Z = 4
Mo Kα radiation
μ = 3.84 mm⁻¹
T = 296 K
0.30 × 0.20 × 0.06 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T _min = 0.583, T _max = 0.746
6683 measured reflections
2091 independent reflections
1956 reflections with I > 2σ(I)
R _int = 0.023

Refinement

R[F ² > 2σ(F ²)] = 0.021
wR(F ²) = 0.048
S = 1.02
2091 reflections
155 parameters
H-atom parameters constrained
Δρ_max = 0.20 e Å⁻³
Δρ_min = −0.34 e Å⁻³
Absolute structure: Flack (1983 ▶), 834 Friedel pairs
Flack parameter: 0.016 (9)

Data collection: SMART (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); 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 ▶) and DIAMOND (Brandenburg, 1999 ▶); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810051081/hg2764sup1.cif

e-67-0o111-sup1.cif^{(15.7KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810051081/hg2764Isup2.hkl

e-67-0o111-Isup2.hkl^{(102.9KB, hkl)}

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2B⋯O4ⁱ	0.82	2.03	2.841 (2)	169
N2—H2C⋯O3ⁱⁱ	0.86	2.17	2.983 (2)	158
O3—H3B⋯O5ⁱⁱⁱ	0.82	1.96	2.769 (2)	167

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) .

Acknowledgments

This work was supported by the NNSF of China (grant 20861001) and the Key Laboratory of Jiangxi University for Functional Materials Chemistry.

supplementary crystallographic information

Comment

In the last few decades, there has been dramatic progress in the synthesis of the nucleoside analogues for their biological evaluation of the anticancer activity (Johar et al., 2005; Shakya et al., 2010; Suck et al., 1972). The title compound (I) can be used as important pharmaceutical intermediates (Haraguchi et al., 1993; Kittaka et al., 1992; Pozharskii et al., 1997; Sairam et al., 2003). The synthetic procedure is described below. To know the relative stereochemistry of the anomeric position in the ribofuranose ring, it is necessary to gain the well defined structure of (I) by X-diffraction method. The molecular structure of the title compound is shown in Fig. 1. From the single-crystal structure 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. The crystal structure of (I) is stabilized by two intermolecular O—H···O interactions and one intermolecular N—H···O interaction (Table 1, Fig. 2).

Experimental

All reagents and solvents were used as obtained commercially without further purification. NMR spectra was recorded on Bruker AV 400 MHz NMR spectrometers at ambient temperature. The title compound was prepared according to the reported procedure (Shakya et al., 2010). Detritylation of 1-(3-Bromo-3-deoxy-5-O-trityl-β-D-arabinofuranosyl)uracil using 80% aqueous acetic acid (v/v) at 90 °C for 30 min, then cooled to room temperature, after the solvent were distilled off a white solid of the title compound was obtained in about 70% yield. 1H NMR (400 MHz, DMSO-d6): δ 3.65–3.77 (m, 2H, H-5'), 4.26–4.39 (m, 3H, H-2', H-3', H-4'), 4.89 (t, J = 4.88 Hz, 1H, 5'-OH), 5.64 (dd, J = 8.54 and 1.83 Hz, 1H, H-5), 6.04 (d, J = 3.05 Hz, 1H, H-1'), 6.09 (d, J = 1.83 Hz, 1H, 3'-OH), 7.72 (d, J = 7.93 Hz, 1H, H-6), 11.39 (s, 1H, NH). In a sample vial, colorless block-shaped single crystals were grown from DMSO and water (v/v = 1:1) at room temperature.