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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 1| January 2011| Page o111
https://doi.org/10.1107/S1600536810051081

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

Zhong-Gao Zhou,a* Shun-Guo Fu,b Wu-Leng Laia and Chun-Feng Wanga

aCollege of Chemistry and Life Science, Gannan Normal University, Ganzhou 341000, People's Republic of China, and bSchool of Chemical and Environmental Sciences, Henan Normal University, Xinxiang 453007, People's Republic of China
*Correspondence e-mail: zhgzhou@foxmail.com

(Received 29 November 2010; accepted 6 December 2010; online 11 December 2010)

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[Shakya, N., Srivastav, N. C., Desroches, N., Agrawal, B., Kunimoto, D. Y. & Kumar, R. (2010). J. Med. Chem. 53, 4130-4140.]). For a related structure, see: Suck et al. (1972[Suck, D., Saenger, W. & Hobbs, J. (1972). Biochim. Biophys. Acta, 259, 157-163.]). For the use of the title compound as a pharmaceutical inter­mediate, see: Haraguchi et al. (1993[Haraguchi, K., Itoh, Y., Tanaka, H., Yamaguchi, K. & Miyasaka, T. (1993). Tetrahedron Lett. 33, 6913-6916.]); Kittaka et al. (1992[Kittaka, A., Tanaka, H., Miyasaka, T. & Yamaguchi, K. (1992). Nucleosides Nucleotides, 11, 37-47.]); Pozharskii et al. (1997)[Pozharskii, A. F., Soldatenkov, A. T. & Katritzky, A. R. (1997). Heterocycles in Life and Society. New York: John Wiley and Sons.]; Sairam et al. (2003[Sairam, P., Puranik, R., Rao, B. S., Swamy, P. V. & Chandra, S. (2003). Carbohydr. Res. 338, 303-306.]). For the biological activity of nucleoside derivatives, see: Johar et al. (2005[Johar, M., Manning, T., Kunimoto, D. Y. & Kumar, R. (2005). Bioorg. Med. Chem. 13, 6663-6671.]).

[Scheme 1]

Experimental

Crystal data

  • C9H11BrN2O5

  • Mr = 307.11

  • Orthorhombic, P 21 21 21

  • 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[Bruker (2008). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.583, Tmax = 0.746

  • 6683 measured reflections

  • 2091 independent reflections

  • 1956 reflections with I > 2σ(I)

  • Rint = 0.023
Refinement

  • R[F2 > 2σ(F2)] = 0.021

  • wR(F2) = 0.048

  • S = 1.02

  • 2091 reflections

  • 155 parameters

  • H-atom parameters constrained

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.34 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 834 Friedel pairs

  • Flack parameter: 0.016 (9)

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
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [-x+{\script{3\over 2}}, -y, z+{\script{1\over 2}}]; (iii) [-x+{\script{1\over 2}}, -y, z-{\script{1\over 2}}].

Data collection: SMART (Bruker, 2008[Bruker (2008). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and DIAMOND (Brandenburg, 1999[Brandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXTL.

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810051081/hg2764Isup2.hkl

checkCIF report


Comment top

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).

Related literature top

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 top

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.

Refinement top

The N-bound and the C-bound H atoms were positioned geometrically and refined using a riding model: N—H = 0.86 Å and C—H = 0.93–0.98 Å, with Uiso(H) = 1.2Uiso(N,C); while the O-bound H atoms were placed in idealized positions and constrained to ride on their parent atoms: O—H = 0.82 Å, with Uiso(H) = 1.5 times Uiso(O).

Structure description top

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).

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).

Computing details top

Data collection: SMART (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL97 (Sheldrick, 2008) and DIAMOND (Brandenburg, 1999); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. The three-dimensional structure of the title compound formed by intermolecular hydrogen bonds viewed down the a axis. The intermolecular hydrogen bonds are shown as dashed lines.
1-(2-Bromo-2-deoxy-β-D-xylofuranosyl)uracil top
Crystal data top
C9H11BrN2O5F(000) = 616
Mr = 307.11Dx = 1.898 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3827 reflections
a = 4.8444 (3) Åθ = 2.3–26.6°
b = 12.7237 (10) ŵ = 3.84 mm−1
c = 17.4388 (13) ÅT = 296 K
V = 1074.90 (13) Å3Block, colourless
Z = 40.30 × 0.20 × 0.06 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		2091 independent reflections
Radiation source: fine-focus sealed tube1956 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
phi and ω scansθmax = 26.0°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		h = −5→5
Tmin = 0.583, Tmax = 0.746k = −12→15
6683 measured reflectionsl = −17→21
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.048 w = 1/[σ2(Fo2) + (0.0196P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max = 0.001
2091 reflectionsΔρmax = 0.20 e Å−3
155 parametersΔρmin = −0.34 e Å−3
0 restraintsAbsolute structure: Flack (1983), 834 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.016 (9)
Crystal data top
C9H11BrN2O5V = 1074.90 (13) Å3
Mr = 307.11Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 4.8444 (3) ŵ = 3.84 mm−1
b = 12.7237 (10) ÅT = 296 K
c = 17.4388 (13) Å0.30 × 0.20 × 0.06 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		2091 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		1956 reflections with I > 2σ(I)
Tmin = 0.583, Tmax = 0.746Rint = 0.023
6683 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.048Δρmax = 0.20 e Å−3
S = 1.02Δρmin = −0.34 e Å−3
2091 reflectionsAbsolute structure: Flack (1983), 834 Friedel pairs
155 parametersAbsolute structure parameter: 0.016 (9)
0 restraints
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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
xyzUiso*/Ueq
Br10.27277 (5)−0.100786 (17)0.715735 (13)0.03335 (9)
N10.5109 (4)0.10657 (15)0.81851 (10)0.0218 (4)
N20.4796 (4)0.08084 (15)0.94956 (10)0.0263 (5)
H2C0.53950.05050.99040.032*
C10.3861 (5)0.04049 (18)0.68858 (12)0.0225 (5)
H1A0.22760.08780.69370.027*
C20.6127 (5)0.07596 (18)0.74317 (13)0.0234 (5)
H2A0.75210.02060.74840.028*
C30.6883 (5)0.15620 (18)0.62383 (11)0.0262 (5)
H3A0.86880.14690.59940.031*
C40.5166 (5)0.0564 (2)0.61047 (12)0.0258 (6)
H4A0.37620.06750.57080.031*
C50.5620 (5)0.2564 (2)0.59440 (14)0.0354 (6)
H5A0.67040.31600.61150.042*
H5B0.56160.25600.53880.042*
C60.6060 (5)0.05312 (19)0.88240 (13)0.0241 (5)
C70.2656 (5)0.15228 (17)0.95953 (11)0.0257 (5)
C80.1829 (5)0.20597 (17)0.89049 (12)0.0244 (5)
H8A0.04600.25710.89210.029*
C90.3045 (5)0.18165 (17)0.82441 (12)0.0243 (5)
H9A0.24860.21660.78020.029*
O10.7292 (4)0.16509 (12)0.70608 (7)0.0290 (4)
O20.2882 (4)0.26569 (14)0.62192 (11)0.0494 (5)
H2B0.24480.32790.62360.074*
O30.7002 (4)−0.02551 (13)0.58996 (8)0.0339 (4)
H3B0.6137−0.07300.56920.051*
O40.7873 (4)−0.01293 (12)0.88008 (8)0.0332 (4)
O50.1654 (4)0.16566 (13)1.02337 (8)0.0351 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.03955 (14)0.02863 (14)0.03187 (14)−0.00614 (13)0.00305 (12)−0.00212 (10)
N10.0252 (9)0.0242 (11)0.0162 (9)0.0052 (10)−0.0018 (8)−0.0013 (9)
N20.0350 (11)0.0281 (12)0.0157 (10)0.0027 (10)−0.0039 (9)0.0051 (9)
C10.0248 (12)0.0197 (12)0.0229 (12)0.0001 (10)0.0001 (9)−0.0030 (10)
C20.0210 (11)0.0240 (13)0.0252 (12)−0.0011 (10)0.0022 (10)−0.0032 (10)
C30.0255 (13)0.0352 (14)0.0178 (11)−0.0011 (12)0.0034 (10)−0.0009 (10)
C40.0246 (12)0.0309 (14)0.0218 (12)0.0025 (12)−0.0003 (10)−0.0023 (11)
C50.0363 (15)0.0342 (15)0.0357 (15)−0.0072 (13)−0.0011 (12)0.0064 (13)
C60.0268 (13)0.0207 (13)0.0247 (13)−0.0053 (12)−0.0044 (10)0.0017 (11)
C70.0277 (13)0.0260 (12)0.0235 (11)−0.0059 (12)−0.0005 (12)−0.0015 (9)
C80.0265 (13)0.0241 (12)0.0225 (12)0.0026 (11)−0.0018 (10)−0.0030 (10)
C90.0251 (13)0.0232 (12)0.0245 (12)−0.0002 (11)−0.0046 (10)0.0008 (10)
O10.0332 (9)0.0331 (9)0.0208 (7)−0.0096 (9)0.0003 (9)0.0002 (6)
O20.0309 (11)0.0294 (9)0.0879 (14)−0.0012 (10)0.0003 (11)0.0049 (9)
O30.0382 (10)0.0327 (9)0.0309 (9)0.0040 (9)0.0079 (8)−0.0120 (7)
O40.0367 (10)0.0306 (9)0.0323 (9)0.0106 (10)−0.0057 (9)0.0008 (7)
O50.0433 (11)0.0416 (11)0.0203 (8)0.0005 (9)0.0073 (8)0.0001 (8)
Geometric parameters (Å, º) top
Br1—C11.938 (2)C3—H3A0.9800
N1—C61.384 (3)C4—O31.416 (3)
N1—C91.387 (3)C4—H4A0.9800
N1—C21.456 (3)C5—O21.416 (3)
N2—C61.368 (3)C5—H5A0.9700
N2—C71.390 (3)C5—H5B0.9700
N2—H2C0.8600C6—O41.216 (3)
C1—C41.515 (3)C7—O51.226 (2)
C1—C21.522 (3)C7—C81.441 (3)
C1—H1A0.9800C8—C91.331 (3)
C2—O11.422 (3)C8—H8A0.9300
C2—H2A0.9800C9—H9A0.9300
C3—O11.452 (2)O2—H2B0.8200
C3—C51.504 (4)O3—H3B0.8200
C3—C41.536 (3)
C6—N1—C9121.24 (18)C1—C4—C3101.55 (17)
C6—N1—C2118.83 (18)O3—C4—H4A111.3
C9—N1—C2119.68 (17)C1—C4—H4A111.3
C6—N2—C7127.57 (18)C3—C4—H4A111.3
C6—N2—H2C116.2O2—C5—C3109.7 (2)
C7—N2—H2C116.2O2—C5—H5A109.7
C4—C1—C2102.81 (19)C3—C5—H5A109.7
C4—C1—Br1117.50 (16)O2—C5—H5B109.7
C2—C1—Br1109.06 (15)C3—C5—H5B109.7
C4—C1—H1A109.0H5A—C5—H5B108.2
C2—C1—H1A109.0O4—C6—N2122.0 (2)
Br1—C1—H1A109.0O4—C6—N1123.6 (2)
O1—C2—N1109.36 (18)N2—C6—N1114.4 (2)
O1—C2—C1103.78 (18)O5—C7—N2119.96 (19)
N1—C2—C1113.54 (18)O5—C7—C8125.7 (2)
O1—C2—H2A110.0N2—C7—C8114.38 (18)
N1—C2—H2A110.0C9—C8—C7119.4 (2)
C1—C2—H2A110.0C9—C8—H8A120.3
O1—C3—C5109.06 (19)C7—C8—H8A120.3
O1—C3—C4106.75 (17)C8—C9—N1122.9 (2)
C5—C3—C4115.4 (2)C8—C9—H9A118.5
O1—C3—H3A108.5N1—C9—H9A118.5
C5—C3—H3A108.5C2—O1—C3109.45 (16)
C4—C3—H3A108.5C5—O2—H2B109.5
O3—C4—C1112.99 (19)C4—O3—H3B109.5
O3—C4—C3107.85 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2B···O4i0.822.032.841 (2)169
N2—H2C···O3ii0.862.172.983 (2)158
O3—H3B···O5iii0.821.962.769 (2)167
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) −x+3/2, −y, z+1/2; (iii) −x+1/2, −y, z−1/2.

Experimental details

Crystal data
Chemical formulaC9H11BrN2O5
Mr307.11
Crystal system, space groupOrthorhombic, P212121
Temperature (K)296
a, b, c (Å)4.8444 (3), 12.7237 (10), 17.4388 (13)
V (Å3)1074.90 (13)
Z4
Radiation typeMo Kα
µ (mm−1)3.84
Crystal size (mm)0.30 × 0.20 × 0.06
Data collection
DiffractometerBruker SMART CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2008)
Tmin, Tmax0.583, 0.746
No. of measured, independent and
observed [I > 2σ(I)] reflections		6683, 2091, 1956
Rint0.023
(sin θ/λ)max (Å−1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.048, 1.02
No. of reflections2091
No. of parameters155
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.20, −0.34
Absolute structureFlack (1983), 834 Friedel pairs
Absolute structure parameter0.016 (9)

Computer programs: SMART (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL97 (Sheldrick, 2008) and DIAMOND (Brandenburg, 1999), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2B···O4i0.822.032.841 (2)169
N2—H2C···O3ii0.862.172.983 (2)158
O3—H3B···O5iii0.821.962.769 (2)167
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) −x+3/2, −y, z+1/2; (iii) −x+1/2, −y, z−1/2.
 

Acknowledgements

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

References

First citationBrandenburg, K. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
 First citationBruker (2008). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationHaraguchi, K., Itoh, Y., Tanaka, H., Yamaguchi, K. & Miyasaka, T. (1993). Tetrahedron Lett. 33, 6913–6916.  CSD CrossRef Web of Science Google Scholar
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ISSN: 2056-9890
Volume 67| Part 1| January 2011| Page o111
https://doi.org/10.1107/S1600536810051081
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