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

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ISSN: 2056-9890

3-Benzoyl-5-chloro­uracil

aIndustrial Research Limited, PO Box 31-310, Lower Hutt, New Zealand
*Correspondence e-mail: g.gainsford@irl.cri.nz

(Received 4 January 2009; accepted 11 January 2009; online 17 January 2009)

The dihedral angle between the planes of two aromatic rings in the title compound [systematic name: 3-benzoyl-5-chloro-pyrimidine-2,4(1H,3H)-dione], C11H7ClN2O3, is 86.79 (6)°. Centrosymmetric dimers formed by N—H⋯O hydrogen bonds are linked through C—H⋯O inter­actions, forming a two-dimensional network parallel to (10[\overline{1}]).

Related literature

For a related structure, see: Parvez et al. (2007[Parvez, M., Phillips, S. E. & Sutherland, T. C. (2007). Acta Cryst. E63, o733-o734.]). For graph-set notation, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]). For the synthesis, see: Birck et al. (2009[Birck, M. T., Clinch, K., Gainsford, G. J., Schramm, V. L. & Tyler, P. C. (2009). Helv. Chim. Acta. Submitted.]).

[Scheme 1]

Experimental

Crystal data
  • C11H7ClN2O3

  • Mr = 250.64

  • Monoclinic, C 2/c

  • a = 21.9357 (9) Å

  • b = 5.4020 (2) Å

  • c = 19.9642 (9) Å

  • β = 113.169 (2)°

  • V = 2174.89 (16) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.35 mm−1

  • T = 133 (2) K

  • 0.34 × 0.21 × 0.03 mm

Data collection
  • Bruker APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Blessing, 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]; Bruker, 2006[Bruker (2006). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.810, Tmax = 0.990

  • 24616 measured reflections

  • 2899 independent reflections

  • 2189 reflections with I > 2σ(I)

  • Rint = 0.047

Refinement
  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 0.110

  • S = 1.07

  • 2899 reflections

  • 162 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.37 e Å−3

  • Δρmin = −0.42 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N⋯O14i 0.86 (3) 1.91 (3) 2.770 (2) 173 (3)
C9—H9⋯O15ii 0.95 2.46 3.182 (3) 133
C10—H10⋯O15iii 0.95 2.57 3.447 (3) 153
Symmetry codes: (i) [-x+{\script{3\over 2}}, -y+{\script{5\over 2}}, -z+1]; (ii) x, y+1, z; (iii) [-x+1, y+1, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2006[Bruker (2006). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2006[Bruker (2006). APEX2, SAINT and SADABS. 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: ORTEP in WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]) and Mercury (Bruno et al., 2002[Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389-397.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]).

Supporting information


Comment top

The title compound, (I), was prepared for incorporation into potential thymidine phosphorylase inhibitors (Birck et al., 2009). Its molecular structure is shown in Fig.1, labelled in the same way as the closely related 5-methyl adduct, 3-benzoylthymine (II) (Parvez et al., 2007). The dihedral angle between the aromatic rings in (I) is 86.79 (10)° compared with 83.82 (6)° in (II). The N3–C7–C8–C9 torsion angle of the ring-linkage is -6.9 (2)° in (I) and -11.8 (2)° in (II). Bond distances are normal.

The crystal packing is dominated by centrosymmetric N1—H1N···O14 hydrogen bonded dimers (common graph-set R22(8), Bernstein et al., 1995) linked by weaker C–H···O interactions (Table 1). These two types of packing interactions are also found in (II), though not reported, as is illustrated in the comparison Fig 2. The replacement of the methyl group in (II) by chlorine in (I) has not enhanced the packing interactions: neither group/atom play a significant role.

Related literature top

For a related structure, see: Parvez et al. (2007). For graph-set notation, see: Bernstein et al. (1995). For the synthesis, see: Birck et al. (2009).

Experimental top

Synthetic details are given in Birck et al. (2009).

Refinement top

Atoms H1N and H6 were located in a difference map and refined freely. All other H atoms were restrained using riding models (C-H = 0.95 Å), with Uiso values constrained to 1.2 times that of the Ueq of their parent atom.

Computing details top

Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP in WinGX (Farrugia, 1999) and Mercury (Bruno et al., 2002); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are shown at the 30% probability level.
[Figure 2] Fig. 2. Comparison of similar hydrogen bond interactions (dotted lines) in (I) & (II) (MERCURY; Bruno et al., 2002). Only the hydrogen atoms involved are included. Nitrogen and Oxygen atoms are shown as balls. Colours: Nitrogen, blue (light gray); Oxygen, red (black); Carbon, (gray); Hydrogen, dark blue. Coordinates of (II) are labelled as in deposited data (SEVQUG) and additional molecules shown in purple for clarity. Symmetry Codes: (i) 3/2 - x, 5/2 - y, 1 - z (ii) x, y + 1, z (iii) 3/2 - x, 3/2 - y, 1 - z (iv) 2 - x, 1 - y, -z (v) 1/2 + x, 1/2 - y, -z (vi) 3/2 - x, 1/2 + y, z
3-Benzoyl-5-chloro-pyrimidine-2,4(1H,3H)-dione top
Crystal data top
C11H7ClN2O3F(000) = 1024
Mr = 250.64Dx = 1.531 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 6298 reflections
a = 21.9357 (9) Åθ = 2.2–28.7°
b = 5.4020 (2) ŵ = 0.35 mm1
c = 19.9642 (9) ÅT = 133 K
β = 113.169 (2)°Plate, colourless
V = 2174.89 (16) Å30.34 × 0.21 × 0.03 mm
Z = 8
Data collection top
Bruker–Nonius APEXII CCD area-detector
diffractometer
2899 independent reflections
Radiation source: fine-focus sealed tube2189 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.047
Detector resolution: 8.333 pixels mm-1θmax = 29.0°, θmin = 3.5°
ϕ and ω scansh = 2929
Absorption correction: multi-scan
(SADABS; Blessing, 1995; Bruker, 2006)
k = 77
Tmin = 0.810, Tmax = 0.990l = 2727
24616 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110H atoms treated by a mixture of independent and constrained refinement
S = 1.07 w = 1/[σ2(Fo2) + (0.0468P)2 + 2.9413P]
where P = (Fo2 + 2Fc2)/3
2899 reflections(Δ/σ)max = 0.001
162 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = 0.42 e Å3
Crystal data top
C11H7ClN2O3V = 2174.89 (16) Å3
Mr = 250.64Z = 8
Monoclinic, C2/cMo Kα radiation
a = 21.9357 (9) ŵ = 0.35 mm1
b = 5.4020 (2) ÅT = 133 K
c = 19.9642 (9) Å0.34 × 0.21 × 0.03 mm
β = 113.169 (2)°
Data collection top
Bruker–Nonius APEXII CCD area-detector
diffractometer
2899 independent reflections
Absorption correction: multi-scan
(SADABS; Blessing, 1995; Bruker, 2006)
2189 reflections with I > 2σ(I)
Tmin = 0.810, Tmax = 0.990Rint = 0.047
24616 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.110H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.37 e Å3
2899 reflectionsΔρmin = 0.42 e Å3
162 parameters
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. An extinction parameter was refined. 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
Cl160.72366 (2)0.47956 (9)0.28923 (3)0.03151 (14)
O140.68050 (6)1.0941 (2)0.50072 (7)0.0230 (3)
O150.61273 (7)0.4522 (3)0.34170 (8)0.0316 (3)
O170.60738 (6)0.5865 (3)0.49746 (7)0.0259 (3)
N10.73929 (7)1.0080 (3)0.43155 (8)0.0196 (3)
H1N0.7670 (11)1.123 (5)0.4545 (12)0.034 (6)*
N30.64590 (6)0.7803 (3)0.41885 (8)0.0185 (3)
C20.68836 (8)0.9710 (3)0.45337 (9)0.0178 (3)
C40.65184 (8)0.6191 (3)0.36658 (10)0.0212 (4)
C50.70867 (8)0.6748 (3)0.34898 (10)0.0206 (3)
C60.74965 (8)0.8616 (3)0.38121 (10)0.0204 (3)
H60.7865 (11)0.905 (4)0.3704 (11)0.025 (5)*
C70.59307 (8)0.7215 (3)0.44632 (10)0.0189 (3)
C80.52873 (8)0.8413 (3)0.40703 (10)0.0204 (4)
C90.51969 (9)1.0174 (4)0.35368 (11)0.0280 (4)
H90.55541.06040.34030.034*
C100.45871 (10)1.1310 (4)0.31977 (12)0.0367 (5)
H100.45241.25240.28320.044*
C110.40709 (10)1.0666 (5)0.33943 (13)0.0398 (5)
H110.36501.14260.31560.048*
C120.41587 (10)0.8944 (5)0.39288 (14)0.0458 (6)
H120.38000.85270.40610.055*
C130.47664 (10)0.7816 (4)0.42752 (13)0.0375 (5)
H130.48300.66400.46510.045*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl160.0351 (3)0.0321 (3)0.0358 (3)0.0100 (2)0.0230 (2)0.0132 (2)
O140.0189 (6)0.0250 (6)0.0294 (7)0.0055 (5)0.0141 (5)0.0060 (5)
O150.0311 (7)0.0315 (8)0.0372 (8)0.0164 (6)0.0186 (6)0.0120 (6)
O170.0181 (6)0.0285 (7)0.0323 (7)0.0009 (5)0.0112 (5)0.0095 (6)
N10.0141 (6)0.0217 (7)0.0250 (8)0.0068 (6)0.0098 (6)0.0051 (6)
N30.0131 (6)0.0190 (7)0.0249 (8)0.0042 (5)0.0091 (6)0.0012 (6)
C20.0122 (7)0.0185 (8)0.0225 (8)0.0023 (6)0.0065 (6)0.0010 (6)
C40.0189 (8)0.0226 (8)0.0230 (9)0.0047 (7)0.0091 (7)0.0011 (7)
C50.0193 (8)0.0212 (8)0.0239 (9)0.0016 (6)0.0112 (7)0.0022 (7)
C60.0157 (7)0.0232 (8)0.0236 (9)0.0014 (7)0.0092 (7)0.0001 (7)
C70.0138 (7)0.0194 (8)0.0257 (9)0.0047 (6)0.0099 (7)0.0015 (7)
C80.0143 (7)0.0212 (8)0.0259 (9)0.0010 (6)0.0079 (7)0.0027 (7)
C90.0210 (8)0.0324 (10)0.0341 (10)0.0011 (8)0.0145 (8)0.0095 (8)
C100.0299 (10)0.0415 (12)0.0403 (13)0.0105 (9)0.0156 (9)0.0181 (10)
C110.0218 (9)0.0514 (14)0.0462 (13)0.0136 (9)0.0136 (9)0.0153 (11)
C120.0188 (9)0.0631 (16)0.0621 (16)0.0099 (10)0.0229 (10)0.0265 (13)
C130.0210 (9)0.0467 (13)0.0504 (13)0.0052 (9)0.0202 (9)0.0245 (10)
Geometric parameters (Å, º) top
Cl16—C51.7179 (18)C7—C81.468 (2)
O14—C21.222 (2)C8—C91.383 (3)
O15—C41.209 (2)C8—C131.394 (2)
O17—C71.192 (2)C9—C101.382 (3)
N1—C21.364 (2)C9—H90.95
N1—C61.366 (2)C10—C111.381 (3)
N1—H1N0.87 (3)C10—H100.95
N3—C21.378 (2)C11—C121.371 (3)
N3—C41.404 (2)C11—H110.95
N3—C71.498 (2)C12—C131.379 (3)
C4—C51.453 (2)C12—H120.95
C5—C61.336 (2)C13—H130.95
C6—H60.94 (2)
C2—N1—C6122.97 (15)C8—C7—N3115.49 (14)
C2—N1—H1N115.5 (15)C9—C8—C13119.96 (17)
C6—N1—H1N121.3 (15)C9—C8—C7122.09 (15)
C2—N3—C4126.39 (14)C13—C8—C7117.87 (16)
C2—N3—C7116.31 (14)C10—C9—C8120.02 (17)
C4—N3—C7116.87 (13)C10—C9—H9120.0
O14—C2—N1123.34 (15)C8—C9—H9120.0
O14—C2—N3121.36 (14)C11—C10—C9119.52 (19)
N1—C2—N3115.29 (15)C11—C10—H10120.2
O15—C4—N3120.65 (15)C9—C10—H10120.2
O15—C4—C5126.35 (17)C12—C11—C10120.82 (19)
N3—C4—C5113.00 (15)C12—C11—H11119.6
C6—C5—C4121.21 (16)C10—C11—H11119.6
C6—C5—Cl16121.45 (13)C11—C12—C13120.15 (19)
C4—C5—Cl16117.23 (13)C11—C12—H12119.9
C5—C6—N1121.09 (16)C13—C12—H12119.9
C5—C6—H6123.4 (13)C12—C13—C8119.51 (19)
N1—C6—H6115.4 (13)C12—C13—H13120.2
O17—C7—C8126.97 (15)C8—C13—H13120.2
O17—C7—N3117.53 (15)
C6—N1—C2—O14176.60 (17)C2—N3—C7—O1784.6 (2)
C6—N1—C2—N32.5 (2)C4—N3—C7—O1788.4 (2)
C4—N3—C2—O14176.59 (17)C2—N3—C7—C894.63 (18)
C7—N3—C2—O144.3 (2)C4—N3—C7—C892.32 (19)
C4—N3—C2—N12.6 (2)O17—C7—C8—C9172.27 (19)
C7—N3—C2—N1174.86 (14)N3—C7—C8—C96.9 (3)
C2—N3—C4—O15177.38 (17)O17—C7—C8—C134.6 (3)
C7—N3—C4—O155.1 (3)N3—C7—C8—C13176.25 (18)
C2—N3—C4—C51.5 (2)C13—C8—C9—C101.2 (3)
C7—N3—C4—C5173.75 (15)C7—C8—C9—C10177.94 (19)
O15—C4—C5—C6178.47 (19)C8—C9—C10—C110.2 (4)
N3—C4—C5—C60.3 (3)C9—C10—C11—C121.0 (4)
O15—C4—C5—Cl162.2 (3)C10—C11—C12—C130.4 (4)
N3—C4—C5—Cl16176.58 (12)C11—C12—C13—C80.9 (4)
C4—C5—C6—N10.4 (3)C9—C8—C13—C121.7 (4)
Cl16—C5—C6—N1176.52 (14)C7—C8—C13—C12178.6 (2)
C2—N1—C6—C51.6 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O14i0.86 (3)1.91 (3)2.770 (2)173 (3)
C9—H9···O15ii0.952.463.182 (3)133
C10—H10···O15iii0.952.573.447 (3)153
Symmetry codes: (i) x+3/2, y+5/2, z+1; (ii) x, y+1, z; (iii) x+1, y+1, z+1/2.

Experimental details

Crystal data
Chemical formulaC11H7ClN2O3
Mr250.64
Crystal system, space groupMonoclinic, C2/c
Temperature (K)133
a, b, c (Å)21.9357 (9), 5.4020 (2), 19.9642 (9)
β (°) 113.169 (2)
V3)2174.89 (16)
Z8
Radiation typeMo Kα
µ (mm1)0.35
Crystal size (mm)0.34 × 0.21 × 0.03
Data collection
DiffractometerBruker–Nonius APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Blessing, 1995; Bruker, 2006)
Tmin, Tmax0.810, 0.990
No. of measured, independent and
observed [I > 2σ(I)] reflections
24616, 2899, 2189
Rint0.047
(sin θ/λ)max1)0.682
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.110, 1.07
No. of reflections2899
No. of parameters162
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.37, 0.42

Computer programs: APEX2 (Bruker, 2006), SAINT (Bruker, 2006), SHELXS97 (Sheldrick, 2008), ORTEP in WinGX (Farrugia, 1999) and Mercury (Bruno et al., 2002), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O14i0.86 (3)1.91 (3)2.770 (2)173 (3)
C9—H9···O15ii0.952.463.182 (3)133
C10—H10···O15iii0.952.573.447 (3)153
Symmetry codes: (i) x+3/2, y+5/2, z+1; (ii) x, y+1, z; (iii) x+1, y+1, z+1/2.
 

Acknowledgements

We thank Dr J. Wikaira and Dr C. Fitchett of the University of Canterbury, New Zealand, for their assistance with the data collection.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBirck, M. T., Clinch, K., Gainsford, G. J., Schramm, V. L. & Tyler, P. C. (2009). Helv. Chim. Acta. Submitted.  Google Scholar
First citationBlessing, R. H. (1995). Acta Cryst. A51, 33–38.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationBruker (2006). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389–397.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
First citationParvez, M., Phillips, S. E. & Sutherland, T. C. (2007). Acta Cryst. E63, o733–o734.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2003). J. Appl. Cryst. 36, 7–13.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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