1-(2-Bromo-2-de-oxy-β-d-xylofuranos-yl)uracil.

In the title compound, C(9)H(11)BrN(2)O(5), the ribofuran-ose ring has a C2-exo, C3-endo twist configuration and is attached to the uracil unit via a β-N(1)-glycosidic bond. The crystal structure is stabilized by two inter-molecular O-H⋯O inter-actions and one inter-molecular N-H⋯O inter-action.

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 = 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

Δρmax = 0.20 e Å−3

Δρmin = −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.

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

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

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

C9H11BrN2O5	F(000) = 616
Mr = 307.11	Dx = 1.898 Mg m−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 3827 reflections
a = 4.8444 (3) Å	θ = 2.3–26.6°
b = 12.7237 (10) Å	µ = 3.84 mm−1
c = 17.4388 (13) Å	T = 296 K
V = 1074.90 (13) Å3	Block, colourless
Z = 4	0.30 × 0.20 × 0.06 mm

Bruker SMART CCD area-detector diffractometer	2091 independent reflections
Radiation source: fine-focus sealed tube	1956 reflections with I > 2σ(I)
graphite	Rint = 0.023
phi and ω scans	θmax = 26.0°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −5→5
Tmin = 0.583, Tmax = 0.746	k = −12→15
6683 measured reflections	l = −17→21

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)] = 0.021	H-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 reflections	Δρmax = 0.20 e Å−3
155 parameters	Δρmin = −0.34 e Å−3
0 restraints	Absolute structure: Flack (1983), 834 Friedel pairs
Primary atom site location: structure-invariant direct methods	Flack parameter: 0.016 (9)

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.

	x	y	z	Uiso*/Ueq
Br1	0.27277 (5)	−0.100786 (17)	0.715735 (13)	0.03335 (9)
N1	0.5109 (4)	0.10657 (15)	0.81851 (10)	0.0218 (4)
N2	0.4796 (4)	0.08084 (15)	0.94956 (10)	0.0263 (5)
H2C	0.5395	0.0505	0.9904	0.032*
C1	0.3861 (5)	0.04049 (18)	0.68858 (12)	0.0225 (5)
H1A	0.2276	0.0878	0.6937	0.027*
C2	0.6127 (5)	0.07596 (18)	0.74317 (13)	0.0234 (5)
H2A	0.7521	0.0206	0.7484	0.028*
C3	0.6883 (5)	0.15620 (18)	0.62383 (11)	0.0262 (5)
H3A	0.8688	0.1469	0.5994	0.031*
C4	0.5166 (5)	0.0564 (2)	0.61047 (12)	0.0258 (6)
H4A	0.3762	0.0675	0.5708	0.031*
C5	0.5620 (5)	0.2564 (2)	0.59440 (14)	0.0354 (6)
H5A	0.6704	0.3160	0.6115	0.042*
H5B	0.5616	0.2560	0.5388	0.042*
C6	0.6060 (5)	0.05312 (19)	0.88240 (13)	0.0241 (5)
C7	0.2656 (5)	0.15228 (17)	0.95953 (11)	0.0257 (5)
C8	0.1829 (5)	0.20597 (17)	0.89049 (12)	0.0244 (5)
H8A	0.0460	0.2571	0.8921	0.029*
C9	0.3045 (5)	0.18165 (17)	0.82441 (12)	0.0243 (5)
H9A	0.2486	0.2166	0.7802	0.029*
O1	0.7292 (4)	0.16509 (12)	0.70608 (7)	0.0290 (4)
O2	0.2882 (4)	0.26569 (14)	0.62192 (11)	0.0494 (5)
H2B	0.2448	0.3279	0.6236	0.074*
O3	0.7002 (4)	−0.02551 (13)	0.58996 (8)	0.0339 (4)
H3B	0.6137	−0.0730	0.5692	0.051*
O4	0.7873 (4)	−0.01293 (12)	0.88008 (8)	0.0332 (4)
O5	0.1654 (4)	0.16566 (13)	1.02337 (8)	0.0351 (4)

	U11	U22	U33	U12	U13	U23
Br1	0.03955 (14)	0.02863 (14)	0.03187 (14)	−0.00614 (13)	0.00305 (12)	−0.00212 (10)
N1	0.0252 (9)	0.0242 (11)	0.0162 (9)	0.0052 (10)	−0.0018 (8)	−0.0013 (9)
N2	0.0350 (11)	0.0281 (12)	0.0157 (10)	0.0027 (10)	−0.0039 (9)	0.0051 (9)
C1	0.0248 (12)	0.0197 (12)	0.0229 (12)	0.0001 (10)	0.0001 (9)	−0.0030 (10)
C2	0.0210 (11)	0.0240 (13)	0.0252 (12)	−0.0011 (10)	0.0022 (10)	−0.0032 (10)
C3	0.0255 (13)	0.0352 (14)	0.0178 (11)	−0.0011 (12)	0.0034 (10)	−0.0009 (10)
C4	0.0246 (12)	0.0309 (14)	0.0218 (12)	0.0025 (12)	−0.0003 (10)	−0.0023 (11)
C5	0.0363 (15)	0.0342 (15)	0.0357 (15)	−0.0072 (13)	−0.0011 (12)	0.0064 (13)
C6	0.0268 (13)	0.0207 (13)	0.0247 (13)	−0.0053 (12)	−0.0044 (10)	0.0017 (11)
C7	0.0277 (13)	0.0260 (12)	0.0235 (11)	−0.0059 (12)	−0.0005 (12)	−0.0015 (9)
C8	0.0265 (13)	0.0241 (12)	0.0225 (12)	0.0026 (11)	−0.0018 (10)	−0.0030 (10)
C9	0.0251 (13)	0.0232 (12)	0.0245 (12)	−0.0002 (11)	−0.0046 (10)	0.0008 (10)
O1	0.0332 (9)	0.0331 (9)	0.0208 (7)	−0.0096 (9)	0.0003 (9)	0.0002 (6)
O2	0.0309 (11)	0.0294 (9)	0.0879 (14)	−0.0012 (10)	0.0003 (11)	0.0049 (9)
O3	0.0382 (10)	0.0327 (9)	0.0309 (9)	0.0040 (9)	0.0079 (8)	−0.0120 (7)
O4	0.0367 (10)	0.0306 (9)	0.0323 (9)	0.0106 (10)	−0.0057 (9)	0.0008 (7)
O5	0.0433 (11)	0.0416 (11)	0.0203 (8)	0.0005 (9)	0.0073 (8)	0.0001 (8)

Br1—C1	1.938 (2)	C3—H3A	0.9800
N1—C6	1.384 (3)	C4—O3	1.416 (3)
N1—C9	1.387 (3)	C4—H4A	0.9800
N1—C2	1.456 (3)	C5—O2	1.416 (3)
N2—C6	1.368 (3)	C5—H5A	0.9700
N2—C7	1.390 (3)	C5—H5B	0.9700
N2—H2C	0.8600	C6—O4	1.216 (3)
C1—C4	1.515 (3)	C7—O5	1.226 (2)
C1—C2	1.522 (3)	C7—C8	1.441 (3)
C1—H1A	0.9800	C8—C9	1.331 (3)
C2—O1	1.422 (3)	C8—H8A	0.9300
C2—H2A	0.9800	C9—H9A	0.9300
C3—O1	1.452 (2)	O2—H2B	0.8200
C3—C5	1.504 (4)	O3—H3B	0.8200
C3—C4	1.536 (3)
C6—N1—C9	121.24 (18)	C1—C4—C3	101.55 (17)
C6—N1—C2	118.83 (18)	O3—C4—H4A	111.3
C9—N1—C2	119.68 (17)	C1—C4—H4A	111.3
C6—N2—C7	127.57 (18)	C3—C4—H4A	111.3
C6—N2—H2C	116.2	O2—C5—C3	109.7 (2)
C7—N2—H2C	116.2	O2—C5—H5A	109.7
C4—C1—C2	102.81 (19)	C3—C5—H5A	109.7
C4—C1—Br1	117.50 (16)	O2—C5—H5B	109.7
C2—C1—Br1	109.06 (15)	C3—C5—H5B	109.7
C4—C1—H1A	109.0	H5A—C5—H5B	108.2
C2—C1—H1A	109.0	O4—C6—N2	122.0 (2)
Br1—C1—H1A	109.0	O4—C6—N1	123.6 (2)
O1—C2—N1	109.36 (18)	N2—C6—N1	114.4 (2)
O1—C2—C1	103.78 (18)	O5—C7—N2	119.96 (19)
N1—C2—C1	113.54 (18)	O5—C7—C8	125.7 (2)
O1—C2—H2A	110.0	N2—C7—C8	114.38 (18)
N1—C2—H2A	110.0	C9—C8—C7	119.4 (2)
C1—C2—H2A	110.0	C9—C8—H8A	120.3
O1—C3—C5	109.06 (19)	C7—C8—H8A	120.3
O1—C3—C4	106.75 (17)	C8—C9—N1	122.9 (2)
C5—C3—C4	115.4 (2)	C8—C9—H9A	118.5
O1—C3—H3A	108.5	N1—C9—H9A	118.5
C5—C3—H3A	108.5	C2—O1—C3	109.45 (16)
C4—C3—H3A	108.5	C5—O2—H2B	109.5
O3—C4—C1	112.99 (19)	C4—O3—H3B	109.5
O3—C4—C3	107.85 (18)

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

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) ; (ii) ; (iii) .