Acta Cryst. (2009). E65, o342 [ doi:10.1107/S1600536809001287 ]
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-HO interactions, forming a two-dimensional network parallel to (10
).
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.
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).
![[Figure 1]](./ci2757fig1thm.gif)
| Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are shown at the 30% probability level. |
![[Figure 2]](./ci2757fig2thm.gif)
| 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 |
| C11H7ClN2O3 | F(000) = 1024 |
| Mr = 250.64 | Dx = 1.531 Mg m−3 |
| Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
| Hall symbol: -C 2yc | Cell parameters from 6298 reflections |
| a = 21.9357 (9) Å | θ = 2.2–28.7° |
| b = 5.4020 (2) Å | µ = 0.35 mm−1 |
| c = 19.9642 (9) Å | T = 133 K |
| β = 113.169 (2)° | Plate, colourless |
| V = 2174.89 (16) Å3 | 0.34 × 0.21 × 0.03 mm |
| Z = 8 |
| Bruker–Nonius APEXII CCD area-detector diffractometer | 2899 independent reflections |
| Radiation source: fine-focus sealed tube | 2189 reflections with I > 2σ(I) |
| graphite | Rint = 0.047 |
| Detector resolution: 8.333 pixels mm-1 | θmax = 29.0°, θmin = 3.5° |
| φ and ω scans | h = −29→29 |
| Absorption correction: multi-scan (SADABS; Blessing, 1995; Bruker, 2006) | k = −7→7 |
| Tmin = 0.810, Tmax = 0.990 | l = −27→27 |
| 24616 measured reflections |
| Refinement on F2 | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
| wR(F2) = 0.110 | H 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 parameters | Δρmax = 0.37 e Å−3 |
| 0 restraints | Δρmin = −0.42 e Å−3 |
| C11H7ClN2O3 | V = 2174.89 (16) Å3 |
| Mr = 250.64 | Z = 8 |
| Monoclinic, C2/c | Mo Kα radiation |
| a = 21.9357 (9) Å | µ = 0.35 mm−1 |
| b = 5.4020 (2) Å | T = 133 K |
| c = 19.9642 (9) Å | 0.34 × 0.21 × 0.03 mm |
| β = 113.169 (2)° |
| 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 = 0.990 | Rint = 0.047 |
| 24616 measured reflections | θmax = 29.0° |
| R[F2 > 2σ(F2)] = 0.041 | H atoms treated by a mixture of independent and constrained refinement |
| wR(F2) = 0.110 | Δρmax = 0.37 e Å−3 |
| S = 1.07 | Δρmin = −0.42 e Å−3 |
| 2899 reflections | Absolute structure: ? |
| 162 parameters | Flack parameter: ? |
| 0 restraints | Rogers parameter: ? |
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. |
| x | y | z | Uiso*/Ueq | ||
| Cl16 | 0.72366 (2) | 0.47956 (9) | 0.28923 (3) | 0.03151 (14) | |
| O14 | 0.68050 (6) | 1.0941 (2) | 0.50072 (7) | 0.0230 (3) | |
| O15 | 0.61273 (7) | 0.4522 (3) | 0.34170 (8) | 0.0316 (3) | |
| O17 | 0.60738 (6) | 0.5865 (3) | 0.49746 (7) | 0.0259 (3) | |
| N1 | 0.73929 (7) | 1.0080 (3) | 0.43155 (8) | 0.0196 (3) | |
| H1N | 0.7670 (11) | 1.123 (5) | 0.4545 (12) | 0.034 (6)* | |
| N3 | 0.64590 (6) | 0.7803 (3) | 0.41885 (8) | 0.0185 (3) | |
| C2 | 0.68836 (8) | 0.9710 (3) | 0.45337 (9) | 0.0178 (3) | |
| C4 | 0.65184 (8) | 0.6191 (3) | 0.36658 (10) | 0.0212 (4) | |
| C5 | 0.70867 (8) | 0.6748 (3) | 0.34898 (10) | 0.0206 (3) | |
| C6 | 0.74965 (8) | 0.8616 (3) | 0.38121 (10) | 0.0204 (3) | |
| H6 | 0.7865 (11) | 0.905 (4) | 0.3704 (11) | 0.025 (5)* | |
| C7 | 0.59307 (8) | 0.7215 (3) | 0.44632 (10) | 0.0189 (3) | |
| C8 | 0.52873 (8) | 0.8413 (3) | 0.40703 (10) | 0.0204 (4) | |
| C9 | 0.51969 (9) | 1.0174 (4) | 0.35368 (11) | 0.0280 (4) | |
| H9 | 0.5554 | 1.0604 | 0.3403 | 0.034* | |
| C10 | 0.45871 (10) | 1.1310 (4) | 0.31977 (12) | 0.0367 (5) | |
| H10 | 0.4524 | 1.2524 | 0.2832 | 0.044* | |
| C11 | 0.40709 (10) | 1.0666 (5) | 0.33943 (13) | 0.0398 (5) | |
| H11 | 0.3650 | 1.1426 | 0.3156 | 0.048* | |
| C12 | 0.41587 (10) | 0.8944 (5) | 0.39288 (14) | 0.0458 (6) | |
| H12 | 0.3800 | 0.8527 | 0.4061 | 0.055* | |
| C13 | 0.47664 (10) | 0.7816 (4) | 0.42752 (13) | 0.0375 (5) | |
| H13 | 0.4830 | 0.6640 | 0.4651 | 0.045* |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cl16 | 0.0351 (3) | 0.0321 (3) | 0.0358 (3) | −0.0100 (2) | 0.0230 (2) | −0.0132 (2) |
| O14 | 0.0189 (6) | 0.0250 (6) | 0.0294 (7) | −0.0055 (5) | 0.0141 (5) | −0.0060 (5) |
| O15 | 0.0311 (7) | 0.0315 (8) | 0.0372 (8) | −0.0164 (6) | 0.0186 (6) | −0.0120 (6) |
| O17 | 0.0181 (6) | 0.0285 (7) | 0.0323 (7) | 0.0009 (5) | 0.0112 (5) | 0.0095 (6) |
| N1 | 0.0141 (6) | 0.0217 (7) | 0.0250 (8) | −0.0068 (6) | 0.0098 (6) | −0.0051 (6) |
| N3 | 0.0131 (6) | 0.0190 (7) | 0.0249 (8) | −0.0042 (5) | 0.0091 (6) | −0.0012 (6) |
| C2 | 0.0122 (7) | 0.0185 (8) | 0.0225 (8) | −0.0023 (6) | 0.0065 (6) | 0.0010 (6) |
| C4 | 0.0189 (8) | 0.0226 (8) | 0.0230 (9) | −0.0047 (7) | 0.0091 (7) | −0.0011 (7) |
| C5 | 0.0193 (8) | 0.0212 (8) | 0.0239 (9) | −0.0016 (6) | 0.0112 (7) | −0.0022 (7) |
| C6 | 0.0157 (7) | 0.0232 (8) | 0.0236 (9) | −0.0014 (7) | 0.0092 (7) | −0.0001 (7) |
| C7 | 0.0138 (7) | 0.0194 (8) | 0.0257 (9) | −0.0047 (6) | 0.0099 (7) | −0.0015 (7) |
| C8 | 0.0143 (7) | 0.0212 (8) | 0.0259 (9) | −0.0010 (6) | 0.0079 (7) | 0.0027 (7) |
| C9 | 0.0210 (8) | 0.0324 (10) | 0.0341 (10) | 0.0011 (8) | 0.0145 (8) | 0.0095 (8) |
| C10 | 0.0299 (10) | 0.0415 (12) | 0.0403 (13) | 0.0105 (9) | 0.0156 (9) | 0.0181 (10) |
| C11 | 0.0218 (9) | 0.0514 (14) | 0.0462 (13) | 0.0136 (9) | 0.0136 (9) | 0.0153 (11) |
| C12 | 0.0188 (9) | 0.0631 (16) | 0.0621 (16) | 0.0099 (10) | 0.0229 (10) | 0.0265 (13) |
| C13 | 0.0210 (9) | 0.0467 (13) | 0.0504 (13) | 0.0052 (9) | 0.0202 (9) | 0.0245 (10) |
| Cl16—C5 | 1.7179 (18) | C7—C8 | 1.468 (2) |
| O14—C2 | 1.222 (2) | C8—C9 | 1.383 (3) |
| O15—C4 | 1.209 (2) | C8—C13 | 1.394 (2) |
| O17—C7 | 1.192 (2) | C9—C10 | 1.382 (3) |
| N1—C2 | 1.364 (2) | C9—H9 | 0.95 |
| N1—C6 | 1.366 (2) | C10—C11 | 1.381 (3) |
| N1—H1N | 0.87 (3) | C10—H10 | 0.95 |
| N3—C2 | 1.378 (2) | C11—C12 | 1.371 (3) |
| N3—C4 | 1.404 (2) | C11—H11 | 0.95 |
| N3—C7 | 1.498 (2) | C12—C13 | 1.379 (3) |
| C4—C5 | 1.453 (2) | C12—H12 | 0.95 |
| C5—C6 | 1.336 (2) | C13—H13 | 0.95 |
| C6—H6 | 0.94 (2) | ||
| C2—N1—C6 | 122.97 (15) | C8—C7—N3 | 115.49 (14) |
| C2—N1—H1N | 115.5 (15) | C9—C8—C13 | 119.96 (17) |
| C6—N1—H1N | 121.3 (15) | C9—C8—C7 | 122.09 (15) |
| C2—N3—C4 | 126.39 (14) | C13—C8—C7 | 117.87 (16) |
| C2—N3—C7 | 116.31 (14) | C10—C9—C8 | 120.02 (17) |
| C4—N3—C7 | 116.87 (13) | C10—C9—H9 | 120.0 |
| O14—C2—N1 | 123.34 (15) | C8—C9—H9 | 120.0 |
| O14—C2—N3 | 121.36 (14) | C11—C10—C9 | 119.52 (19) |
| N1—C2—N3 | 115.29 (15) | C11—C10—H10 | 120.2 |
| O15—C4—N3 | 120.65 (15) | C9—C10—H10 | 120.2 |
| O15—C4—C5 | 126.35 (17) | C12—C11—C10 | 120.82 (19) |
| N3—C4—C5 | 113.00 (15) | C12—C11—H11 | 119.6 |
| C6—C5—C4 | 121.21 (16) | C10—C11—H11 | 119.6 |
| C6—C5—Cl16 | 121.45 (13) | C11—C12—C13 | 120.15 (19) |
| C4—C5—Cl16 | 117.23 (13) | C11—C12—H12 | 119.9 |
| C5—C6—N1 | 121.09 (16) | C13—C12—H12 | 119.9 |
| C5—C6—H6 | 123.4 (13) | C12—C13—C8 | 119.51 (19) |
| N1—C6—H6 | 115.4 (13) | C12—C13—H13 | 120.2 |
| O17—C7—C8 | 126.97 (15) | C8—C13—H13 | 120.2 |
| O17—C7—N3 | 117.53 (15) | ||
| C6—N1—C2—O14 | 176.60 (17) | C2—N3—C7—O17 | −84.6 (2) |
| C6—N1—C2—N3 | −2.5 (2) | C4—N3—C7—O17 | 88.4 (2) |
| C4—N3—C2—O14 | −176.59 (17) | C2—N3—C7—C8 | 94.63 (18) |
| C7—N3—C2—O14 | −4.3 (2) | C4—N3—C7—C8 | −92.32 (19) |
| C4—N3—C2—N1 | 2.6 (2) | O17—C7—C8—C9 | 172.27 (19) |
| C7—N3—C2—N1 | 174.86 (14) | N3—C7—C8—C9 | −6.9 (3) |
| C2—N3—C4—O15 | 177.38 (17) | O17—C7—C8—C13 | −4.6 (3) |
| C7—N3—C4—O15 | 5.1 (3) | N3—C7—C8—C13 | 176.25 (18) |
| C2—N3—C4—C5 | −1.5 (2) | C13—C8—C9—C10 | −1.2 (3) |
| C7—N3—C4—C5 | −173.75 (15) | C7—C8—C9—C10 | −177.94 (19) |
| O15—C4—C5—C6 | −178.47 (19) | C8—C9—C10—C11 | −0.2 (4) |
| N3—C4—C5—C6 | 0.3 (3) | C9—C10—C11—C12 | 1.0 (4) |
| O15—C4—C5—Cl16 | −2.2 (3) | C10—C11—C12—C13 | −0.4 (4) |
| N3—C4—C5—Cl16 | 176.58 (12) | C11—C12—C13—C8 | −0.9 (4) |
| C4—C5—C6—N1 | −0.4 (3) | C9—C8—C13—C12 | 1.7 (4) |
| Cl16—C5—C6—N1 | −176.52 (14) | C7—C8—C13—C12 | 178.6 (2) |
| C2—N1—C6—C5 | 1.6 (3) |
| D—H···A | D—H | H···A | D···A | 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+3/2, −y+5/2, −z+1; (ii) x, y+1, z; (iii) −x+1, y+1, −z+1/2. |
| D—H···A | D—H | H···A | D···A | 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+3/2, −y+5/2, −z+1; (ii) x, y+1, z; (iii) −x+1, y+1, −z+1/2. |
We thank Dr J. Wikaira and Dr C. Fitchett of the University of Canterbury, New Zealand, for their assistance with the data collection.
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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.