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The absolute configuration of the title compound, C9H11BrN2O5, has been determined. The crystal structure is stabilized by a network of hydrogen bonds in which atoms from both the uracil and deoxy­ribose moieties of the mol­ecule participate. The stability of the structure is also affected by several short contacts that are formed by O atoms in the carbonyl groups. The original crystal structure determination [Iball, Morgan & Wilson (1966). Proc. R. Soc. London Ser. A, 295, 320-333] was carried out at room temperature and was refined from data measured by photographic methods. The present crystal structure is of significantly higher precision.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807046077/lh2504sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807046077/lh2504Isup2.hkl
Contains datablock I

CCDC reference: 663835

Key indicators

  • Single-crystal X-ray study
  • T = 118 K
  • Mean [sigma](C-C) = 0.002 Å
  • R factor = 0.021
  • wR factor = 0.055
  • Data-to-parameter ratio = 33.3

checkCIF/PLATON results

No syntax errors found



Alert level B PLAT432_ALERT_2_B Short Inter X...Y Contact O2 .. C2 .. 2.79 Ang.
Alert level C PLAT153_ALERT_1_C The su's on the Cell Axes are Equal (x 100000) 100 Ang. PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 = 3 PLAT431_ALERT_2_C Short Inter HL..A Contact Br1 .. Br1 .. 3.55 Ang. PLAT431_ALERT_2_C Short Inter HL..A Contact Br1 .. Br1 .. 3.55 Ang. PLAT432_ALERT_2_C Short Inter X...Y Contact O2 .. C2' .. 2.98 Ang. PLAT432_ALERT_2_C Short Inter X...Y Contact O4 .. C3' .. 3.01 Ang. PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 1
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 36.30 From the CIF: _reflns_number_total 5127 Count of symmetry unique reflns 2799 Completeness (_total/calc) 183.17% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 2328 Fraction of Friedel pairs measured 0.832 Are heavy atom types Z>Si present yes PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1' = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3' = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4' = . R PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 7 ALERT level C = Check and explain 5 ALERT level G = General alerts; check 4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 5 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

5-Bromo-2'-deoxyuridine (BDU, I), together with its iodine analogue, are useful in treating the viral disease herpes simplex (HSV) without causing any damage to the host (Kaufman et al., 1962; Kaufman, 1962). BDU and other thymidine analogues have found application not only in the treatment of HSV, but also other viruses like varicella zoster virus (VZV), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) (Zhivkova & Stankova, 2000). Moreover, BDU is used as a molecular tracer in measuring and indicating the presence of HIV-1 and SIV viruses (Tamarit et al., 2000; De Boer et al., 2003). Therefore determination of the absolute configuration of BDU is important for better understanding of the molecular interactions responsible for the antiviral activity. The structural data may also help in the design of other antiviral compounds.

The room temperature structure has been previously reported (Iball et al., 1966). The structure reported here was determined at 118 K and its absolute configuration was elucidated. The title compound crystallizes in the P21 space group with one molecule in the asymmetric unit (Fig. 1). The packing in the crystal structure (Fig. 2) is very similar to the one observed in an analogous compound with chlorine substituted for bromine (Young & Morris, 1973). The iodine analogue crystallized in the triclinic system (Camerman & Trotter, 1965). The crystal lattice of the title compound is densely packed and stabilized by several hydrogen bonds (Table 1, Fig. 2), which results in a rigid structure and diffraction to high resolution. Moreover the crystal is stabilized by multiple short contacts, such as between atoms O1 and C2.

Related literature top

For related literature, see: Camerman & Trotter (1965); De Boer et al. (2003); Iball et al. (1966); Kaufman (1962); Kaufman et al. (1962); Tamarit et al. (2000); Young & Morris (1973); Zhivkova & Stankova (2000).

Experimental top

(+)-5-Bromo-2'-deoxyuridine (97%) was purchased from Aldrich. The crystal of used for X-ray diffraction study, was obtained by slow evaporation of an ethanol solution of the title compound.

Refinement top

All hydrogen atoms were placed in ideal positions and were allowed to refine using the riding model with an isotropic displacement parameter 1.2 times that of the adjacent non-hydrogen atom. The distances were set up as SHELXL (Sheldrick, 1997) default values.

Structure description top

5-Bromo-2'-deoxyuridine (BDU, I), together with its iodine analogue, are useful in treating the viral disease herpes simplex (HSV) without causing any damage to the host (Kaufman et al., 1962; Kaufman, 1962). BDU and other thymidine analogues have found application not only in the treatment of HSV, but also other viruses like varicella zoster virus (VZV), cytomegalovirus (CMV) and Epstein-Barr virus (EBV) (Zhivkova & Stankova, 2000). Moreover, BDU is used as a molecular tracer in measuring and indicating the presence of HIV-1 and SIV viruses (Tamarit et al., 2000; De Boer et al., 2003). Therefore determination of the absolute configuration of BDU is important for better understanding of the molecular interactions responsible for the antiviral activity. The structural data may also help in the design of other antiviral compounds.

The room temperature structure has been previously reported (Iball et al., 1966). The structure reported here was determined at 118 K and its absolute configuration was elucidated. The title compound crystallizes in the P21 space group with one molecule in the asymmetric unit (Fig. 1). The packing in the crystal structure (Fig. 2) is very similar to the one observed in an analogous compound with chlorine substituted for bromine (Young & Morris, 1973). The iodine analogue crystallized in the triclinic system (Camerman & Trotter, 1965). The crystal lattice of the title compound is densely packed and stabilized by several hydrogen bonds (Table 1, Fig. 2), which results in a rigid structure and diffraction to high resolution. Moreover the crystal is stabilized by multiple short contacts, such as between atoms O1 and C2.

For related literature, see: Camerman & Trotter (1965); De Boer et al. (2003); Iball et al. (1966); Kaufman (1962); Kaufman et al. (1962); Tamarit et al. (2000); Young & Morris (1973); Zhivkova & Stankova (2000).

Computing details top

Data collection: HKL-2000 (Otwinowski & Minor, 1997); cell refinement: HKL-2000 (Otwinowski & Minor, 1997); data reduction: HKL-2000 (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990) and HKL-3000SM (Minor et al., 2006); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997) and HKL-3000SM (Minor et al., 2006); molecular graphics: HKL-3000SM (Minor et al., 2006), Mercury (Macrae et al., 2006), ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: HKL-3000SM (Minor et al., 2006).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level and hydrogen atoms are drawn as spheres of an arbitrary radius.
[Figure 2] Fig. 2. The molecular packing shown along the [010] axis. Hydrogen bonds are marked in green.
(+)-5-bromo-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]- pyrimidine-2,4-dione top
Crystal data top
C9H11BrN2O5F(000) = 308
Mr = 307.10Dx = 1.922 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71074 Å
Hall symbol: P 2ybCell parameters from 50017 reflections
a = 9.159 (1) Åθ = 3.4–36.3°
b = 5.067 (1) ŵ = 3.89 mm1
c = 12.041 (1) ÅT = 118 K
β = 108.27 (2)°Block, colourless
V = 530.64 (13) Å30.48 × 0.36 × 0.28 mm
Z = 2
Data collection top
Rigaku R-AXIS RAPID
diffractometer
5127 independent reflections
Radiation source: fine-focus sealed tube5084 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.040
Detector resolution: 10 pixels mm-1θmax = 36.3°, θmin = 3.4°
ω scans with χ offseth = 1515
Absorption correction: multi-scan
(Otwinowski et al., 2003)
k = 88
Tmin = 0.20, Tmax = 0.34l = 2019
50017 measured reflections
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) = 0.055 w = 1/[σ2(Fo2) + (0.0319P)2 + 0.2794P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.001
5127 reflectionsΔρmax = 0.49 e Å3
154 parametersΔρmin = 0.71 e Å3
1 restraintAbsolute structure: Flack (1983), 2325 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.003 (4)
Crystal data top
C9H11BrN2O5V = 530.64 (13) Å3
Mr = 307.10Z = 2
Monoclinic, P21Mo Kα radiation
a = 9.159 (1) ŵ = 3.89 mm1
b = 5.067 (1) ÅT = 118 K
c = 12.041 (1) Å0.48 × 0.36 × 0.28 mm
β = 108.27 (2)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
5127 independent reflections
Absorption correction: multi-scan
(Otwinowski et al., 2003)
5084 reflections with I > 2σ(I)
Tmin = 0.20, Tmax = 0.34Rint = 0.040
50017 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.055Δρmax = 0.49 e Å3
S = 1.04Δρmin = 0.71 e Å3
5127 reflectionsAbsolute structure: Flack (1983), 2325 Friedel pairs
154 parametersAbsolute structure parameter: 0.003 (4)
1 restraint
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
Br10.473749 (11)1.16469 (3)0.095388 (8)0.01312 (3)
N30.66121 (10)0.6900 (3)0.37944 (8)0.01119 (16)
H30.75080.66430.42910.013*
N10.40144 (11)0.5755 (2)0.30904 (9)0.00981 (14)
O1'0.17705 (10)0.3420 (2)0.21144 (8)0.01273 (15)
C3'0.02368 (12)0.4037 (2)0.33875 (10)0.01077 (16)
H3'0.07020.50450.33150.013*
O3'0.04776 (10)0.2022 (2)0.42633 (8)0.01338 (17)
H3"0.02550.10030.40870.016*
C1'0.27203 (12)0.4251 (2)0.32355 (9)0.00976 (16)
H1'0.31100.27010.37250.012*
C4'0.02472 (12)0.2945 (2)0.21923 (10)0.00998 (16)
H4'0.00460.10420.21590.012*
C40.65106 (13)0.8828 (3)0.29697 (10)0.01201 (17)
C60.38024 (12)0.7642 (2)0.22349 (10)0.01052 (16)
H60.28250.79000.17080.013*
C20.54369 (12)0.5328 (2)0.39153 (10)0.01011 (16)
O20.56615 (11)0.3696 (2)0.46919 (9)0.01548 (16)
C50.49829 (13)0.9133 (2)0.21428 (9)0.01099 (16)
O5'0.06987 (12)0.3682 (2)0.00909 (8)0.01670 (16)
H5"'0.07720.20830.00170.025*
C2'0.16485 (13)0.5801 (2)0.37371 (10)0.01131 (16)
H2'0.20690.59780.45800.014*
H2"0.14260.75380.33860.014*
O40.76514 (12)1.0107 (2)0.29704 (10)0.01909 (19)
C5'0.09319 (14)0.4298 (3)0.11780 (10)0.01425 (19)
H5'0.19550.37450.11540.017*
H5"0.08620.61930.12970.017*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.01537 (4)0.01416 (4)0.01014 (4)0.00113 (5)0.00447 (3)0.00256 (4)
N30.0069 (3)0.0154 (5)0.0102 (3)0.0010 (3)0.0012 (2)0.0013 (3)
N10.0067 (3)0.0133 (3)0.0089 (3)0.0016 (3)0.0017 (3)0.0012 (3)
O1'0.0078 (3)0.0210 (4)0.0096 (3)0.0029 (3)0.0031 (2)0.0052 (3)
C3'0.0083 (4)0.0142 (4)0.0097 (4)0.0010 (3)0.0027 (3)0.0003 (3)
O3'0.0108 (3)0.0184 (5)0.0097 (3)0.0048 (3)0.0015 (2)0.0028 (3)
C1'0.0077 (4)0.0125 (4)0.0089 (4)0.0020 (3)0.0023 (3)0.0005 (3)
C4'0.0075 (3)0.0128 (4)0.0086 (4)0.0021 (3)0.0010 (3)0.0008 (3)
C40.0100 (4)0.0158 (5)0.0098 (4)0.0025 (3)0.0025 (3)0.0007 (3)
C60.0085 (4)0.0136 (4)0.0087 (4)0.0004 (3)0.0017 (3)0.0011 (3)
C20.0074 (4)0.0131 (4)0.0096 (4)0.0001 (3)0.0023 (3)0.0005 (3)
O20.0103 (3)0.0180 (4)0.0162 (4)0.0006 (3)0.0014 (3)0.0075 (3)
C50.0101 (4)0.0136 (4)0.0084 (4)0.0004 (3)0.0017 (3)0.0014 (3)
O5'0.0193 (4)0.0206 (4)0.0089 (3)0.0012 (3)0.0027 (3)0.0009 (3)
C2'0.0105 (4)0.0129 (4)0.0111 (4)0.0020 (3)0.0042 (3)0.0026 (3)
O40.0116 (4)0.0262 (5)0.0175 (4)0.0077 (3)0.0016 (3)0.0059 (4)
C5'0.0117 (4)0.0199 (5)0.0099 (4)0.0021 (4)0.0016 (3)0.0011 (4)
Geometric parameters (Å, º) top
Br1—C51.8765 (11)C1'—H1'0.9800
N3—C41.3752 (17)C4'—C5'1.5169 (17)
N3—C21.3830 (15)C4'—H4'0.9800
N3—H30.8600C4—O41.2293 (14)
N1—C61.3742 (15)C4—C51.4490 (16)
N1—C21.3855 (14)C6—C51.3515 (16)
N1—C1'1.4647 (14)C6—H60.9300
O1'—C1'1.4213 (14)C2—O21.2163 (15)
O1'—C4'1.4476 (14)O5'—C5'1.4252 (16)
C3'—O3'1.4345 (15)O5'—H5"'0.8200
C3'—C2'1.5188 (16)C2'—H2'0.9700
C3'—C4'1.5448 (16)C2'—H2"0.9700
C3'—H3'0.9800C5'—H5'0.9700
O3'—H3"0.8200C5'—H5"0.9700
C1'—C2'1.5221 (16)
C4—N3—C2127.34 (9)O4—C4—N3120.59 (11)
C4—N3—H3116.3O4—C4—C5125.57 (12)
C2—N3—H3116.3N3—C4—C5113.83 (10)
C6—N1—C2121.76 (10)C5—C6—N1121.45 (10)
C6—N1—C1'121.46 (9)C5—C6—H6119.3
C2—N1—C1'116.58 (10)N1—C6—H6119.3
C1'—O1'—C4'107.65 (8)O2—C2—N3121.51 (10)
O3'—C3'—C2'107.09 (9)O2—C2—N1123.49 (11)
O3'—C3'—C4'112.66 (10)N3—C2—N1115.00 (10)
C2'—C3'—C4'102.46 (9)C6—C5—C4120.61 (10)
O3'—C3'—H3'111.4C6—C5—Br1122.30 (8)
C2'—C3'—H3'111.4C4—C5—Br1117.10 (8)
C4'—C3'—H3'111.4C5'—O5'—H5"'109.5
C3'—O3'—H3"109.5C3'—C2'—C1'100.68 (9)
O1'—C1'—N1108.55 (9)C3'—C2'—H2'111.6
O1'—C1'—C2'104.53 (9)C1'—C2'—H2'111.6
N1—C1'—C2'115.19 (10)C3'—C2'—H2"111.6
O1'—C1'—H1'109.5C1'—C2'—H2"111.6
N1—C1'—H1'109.5H2'—C2'—H2"109.4
C2'—C1'—H1'109.5O5'—C5'—C4'111.51 (10)
O1'—C4'—C5'109.27 (9)O5'—C5'—H5'109.3
O1'—C4'—C3'106.75 (8)C4'—C5'—H5'109.3
C5'—C4'—C3'112.17 (10)O5'—C5'—H5"109.3
O1'—C4'—H4'109.5C4'—C5'—H5"109.3
C5'—C4'—H4'109.5H5'—C5'—H5"108.0
C3'—C4'—H4'109.5
C4'—O1'—C1'—N1156.77 (9)C4—N3—C2—N11.11 (18)
C4'—O1'—C1'—C2'33.36 (12)C6—N1—C2—O2179.12 (12)
C6—N1—C1'—O1'44.95 (14)C1'—N1—C2—O24.17 (18)
C2—N1—C1'—O1'140.08 (11)C6—N1—C2—N31.13 (17)
C6—N1—C1'—C2'71.81 (14)C1'—N1—C2—N3176.09 (10)
C2—N1—C1'—C2'103.16 (12)N1—C6—C5—C41.67 (18)
C1'—O1'—C4'—C5'131.84 (10)N1—C6—C5—Br1177.99 (9)
C1'—O1'—C4'—C3'10.32 (12)O4—C4—C5—C6178.98 (13)
O3'—C3'—C4'—O1'98.19 (10)N3—C4—C5—C61.47 (17)
C2'—C3'—C4'—O1'16.54 (12)O4—C4—C5—Br11.34 (18)
O3'—C3'—C4'—C5'142.16 (10)N3—C4—C5—Br1178.21 (9)
C2'—C3'—C4'—C5'103.11 (11)O3'—C3'—C2'—C1'83.90 (10)
C2—N3—C4—O4179.17 (13)C4'—C3'—C2'—C1'34.83 (11)
C2—N3—C4—C51.25 (18)O1'—C1'—C2'—C3'42.75 (11)
C2—N1—C6—C51.51 (18)N1—C1'—C2'—C3'161.76 (9)
C1'—N1—C6—C5176.22 (11)O1'—C4'—C5'—O5'49.61 (13)
C4—N3—C2—O2179.14 (13)C3'—C4'—C5'—O5'167.79 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O3i0.862.112.944 (1)163
O3—H3"···O4ii0.822.022.745 (1)148
O5—H5"···O5iii0.822.212.877 (1)139
Symmetry codes: (i) x+1, y+1/2, z+1; (ii) x1, y1, z; (iii) x, y1/2, z.

Experimental details

Crystal data
Chemical formulaC9H11BrN2O5
Mr307.10
Crystal system, space groupMonoclinic, P21
Temperature (K)118
a, b, c (Å)9.159 (1), 5.067 (1), 12.041 (1)
β (°) 108.27 (2)
V3)530.64 (13)
Z2
Radiation typeMo Kα
µ (mm1)3.89
Crystal size (mm)0.48 × 0.36 × 0.28
Data collection
DiffractometerRigaku R-AXIS RAPID
Absorption correctionMulti-scan
(Otwinowski et al., 2003)
Tmin, Tmax0.20, 0.34
No. of measured, independent and
observed [I > 2σ(I)] reflections
50017, 5127, 5084
Rint0.040
(sin θ/λ)max1)0.833
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.055, 1.04
No. of reflections5127
No. of parameters154
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.49, 0.71
Absolute structureFlack (1983), 2325 Friedel pairs
Absolute structure parameter0.003 (4)

Computer programs: HKL-2000 (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 1990) and HKL-3000SM (Minor et al., 2006), SHELXL97 (Sheldrick, 1997) and HKL-3000SM (Minor et al., 2006), HKL-3000SM (Minor et al., 2006), Mercury (Macrae et al., 2006), ORTEPIII (Burnett & Johnson, 1996) and ORTEP-3 (Farrugia, 1997).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O3'i0.862.112.944 (1)162.9
O3'—H3"···O4ii0.822.022.745 (1)147.5
O5'—H5"'···O5'iii0.822.212.877 (1)139.3
Symmetry codes: (i) x+1, y+1/2, z+1; (ii) x1, y1, z; (iii) x, y1/2, z.
 

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