organic compounds
Methyl 4-[(5-chloropyrimidin-2-yl)carbamoyl]benzoate
aDepartment of Chemistry, Chung-Yuan Christian University, Chung-Li, Taiwan
*Correspondence e-mail: jdchen@cycu.edu.tw
Molecules of the title compound, C13H10ClN3O3, form centrosymmetric dimers via intermolecular N—H⋯N hydrogen bonds generating an R22(8) motif. The dimers are further connected through an O⋯Cl—C halogen bond [O⋯Cl = 3.233 (1) Å and O⋯Cl—C = 167.33 (1)°] into a chain along [110]. The secondary amide group adopts a cis conformation. Weak C—H⋯N hydrogen bonds among the methyl benzoate and pyrimidyl rings are also observed in the crystal structure.
Related literature
For silver complexes of the title compound, see: Wu et al. (2011). For the conformation of the amide group in similar compounds, see: Forbes et al. (2001); Oertli et al. (1992).
Experimental
Crystal data
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Refinement
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Data collection: XSCANS (Siemens, 1995); cell XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536811025268/gk2391sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811025268/gk2391Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536811025268/gk2391Isup3.cml
The title compound was prepared according to a published procedure (Wu et al., 2011). Block crystals suitable for X-ray crystallography were obtained by slow evaporation of the solvent from a solution of the title compound in methanol.
H atoms bound to C and N atoms were placed in idealized positions and constrained to ride on their parent atoms, with C—H = 0.93 - 0.96Å and N—H = 0.86 Å, and with Uiso(H) = 1.2 or 1.5 Ueq(C/N).
Data collection: XSCANS (Siemens, 1995); cell
XSCANS (Siemens, 1995); data reduction: SHELXTL (Sheldrick, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C13H10ClN3O3 | Z = 2 |
Mr = 291.69 | F(000) = 300 |
Triclinic, P1 | Dx = 1.560 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.9068 (8) Å | Cell parameters from 28 reflections |
b = 7.3378 (9) Å | θ = 4.7–13.3° |
c = 15.816 (4) Å | µ = 0.32 mm−1 |
α = 78.259 (14)° | T = 295 K |
β = 82.030 (13)° | Block, colourless |
γ = 67.986 (10)° | 0.5 × 0.4 × 0.3 mm |
V = 620.78 (19) Å3 |
Siemens P4 diffractometer | 1715 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.026 |
Graphite monochromator | θmax = 25.0°, θmin = 2.6° |
ω scans | h = −1→7 |
Absorption correction: ψ scan (XSCANS; Siemens, 1995) | k = −8→8 |
Tmin = 0.888, Tmax = 0.918 | l = −18→18 |
2811 measured reflections | 3 standard reflections every 97 reflections |
2140 independent reflections | intensity decay: none |
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.098 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0507P)2 + 0.1938P] where P = (Fo2 + 2Fc2)/3 |
2140 reflections | (Δ/σ)max < 0.001 |
182 parameters | Δρmax = 0.17 e Å−3 |
0 restraints | Δρmin = −0.21 e Å−3 |
C13H10ClN3O3 | γ = 67.986 (10)° |
Mr = 291.69 | V = 620.78 (19) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.9068 (8) Å | Mo Kα radiation |
b = 7.3378 (9) Å | µ = 0.32 mm−1 |
c = 15.816 (4) Å | T = 295 K |
α = 78.259 (14)° | 0.5 × 0.4 × 0.3 mm |
β = 82.030 (13)° |
Siemens P4 diffractometer | 1715 reflections with I > 2σ(I) |
Absorption correction: ψ scan (XSCANS; Siemens, 1995) | Rint = 0.026 |
Tmin = 0.888, Tmax = 0.918 | 3 standard reflections every 97 reflections |
2811 measured reflections | intensity decay: none |
2140 independent reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.098 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.17 e Å−3 |
2140 reflections | Δρmin = −0.21 e Å−3 |
182 parameters |
Experimental. 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. |
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 | ||
Cl | 0.10131 (12) | 0.38338 (9) | 0.11742 (4) | 0.0550 (2) | |
C1 | 0.3775 (4) | 0.5274 (3) | 0.18741 (12) | 0.0397 (5) | |
H1A | 0.3782 | 0.4287 | 0.2349 | 0.048* | |
C2 | 0.2528 (4) | 0.5446 (3) | 0.11729 (12) | 0.0367 (5) | |
C3 | 0.2556 (4) | 0.6923 (3) | 0.04841 (13) | 0.0431 (5) | |
H3A | 0.1746 | 0.7055 | −0.0001 | 0.052* | |
C4 | 0.4859 (4) | 0.7890 (3) | 0.12062 (11) | 0.0325 (4) | |
C5 | 0.7163 (4) | 0.9541 (3) | 0.18183 (12) | 0.0347 (4) | |
C6 | 0.6516 (4) | 0.8916 (3) | 0.27530 (11) | 0.0318 (4) | |
C7 | 0.8388 (4) | 0.8014 (3) | 0.33151 (12) | 0.0359 (5) | |
H7A | 1.0007 | 0.7763 | 0.3104 | 0.043* | |
C8 | 0.7837 (4) | 0.7492 (3) | 0.41870 (12) | 0.0363 (5) | |
H8A | 0.9091 | 0.6881 | 0.4562 | 0.044* | |
C9 | 0.5424 (4) | 0.7875 (3) | 0.45062 (11) | 0.0311 (4) | |
C10 | 0.3554 (4) | 0.8838 (3) | 0.39472 (12) | 0.0347 (4) | |
H10A | 0.1930 | 0.9141 | 0.4162 | 0.042* | |
C11 | 0.4102 (4) | 0.9345 (3) | 0.30739 (12) | 0.0354 (5) | |
H11A | 0.2848 | 0.9976 | 0.2701 | 0.043* | |
C12 | 0.4893 (4) | 0.7203 (3) | 0.54431 (12) | 0.0331 (4) | |
C13 | 0.1836 (4) | 0.6842 (3) | 0.65241 (12) | 0.0411 (5) | |
H13A | 0.0194 | 0.6854 | 0.6568 | 0.062* | |
H13B | 0.1925 | 0.7730 | 0.6878 | 0.062* | |
H13C | 0.2932 | 0.5516 | 0.6718 | 0.062* | |
N1 | 0.4973 (3) | 0.6482 (3) | 0.18929 (10) | 0.0408 (4) | |
N2 | 0.3709 (3) | 0.8174 (3) | 0.04906 (10) | 0.0393 (4) | |
N3 | 0.6073 (3) | 0.9194 (2) | 0.11818 (10) | 0.0378 (4) | |
H3B | 0.6161 | 0.9910 | 0.0684 | 0.045* | |
O1 | 0.8550 (3) | 1.0460 (3) | 0.16089 (9) | 0.0527 (4) | |
O2 | 0.6419 (3) | 0.6464 (3) | 0.59689 (9) | 0.0512 (4) | |
O3 | 0.2527 (3) | 0.7486 (2) | 0.56330 (8) | 0.0406 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl | 0.0698 (4) | 0.0616 (4) | 0.0504 (3) | −0.0436 (3) | −0.0186 (3) | 0.0026 (3) |
C1 | 0.0561 (14) | 0.0391 (11) | 0.0274 (10) | −0.0232 (10) | −0.0099 (9) | 0.0038 (8) |
C2 | 0.0417 (12) | 0.0423 (11) | 0.0315 (10) | −0.0212 (10) | −0.0039 (9) | −0.0052 (8) |
C3 | 0.0539 (13) | 0.0585 (13) | 0.0267 (10) | −0.0312 (11) | −0.0121 (9) | −0.0006 (9) |
C4 | 0.0379 (11) | 0.0393 (10) | 0.0220 (9) | −0.0168 (9) | −0.0034 (8) | −0.0017 (7) |
C5 | 0.0418 (11) | 0.0381 (11) | 0.0285 (10) | −0.0203 (9) | −0.0041 (8) | −0.0023 (8) |
C6 | 0.0418 (11) | 0.0350 (10) | 0.0255 (9) | −0.0210 (9) | −0.0059 (8) | −0.0036 (8) |
C7 | 0.0319 (11) | 0.0478 (12) | 0.0332 (10) | −0.0200 (9) | −0.0044 (8) | −0.0057 (8) |
C8 | 0.0382 (11) | 0.0443 (12) | 0.0299 (10) | −0.0183 (9) | −0.0122 (8) | −0.0003 (8) |
C9 | 0.0369 (11) | 0.0347 (10) | 0.0264 (9) | −0.0172 (9) | −0.0080 (8) | −0.0031 (7) |
C10 | 0.0333 (11) | 0.0424 (11) | 0.0292 (10) | −0.0150 (9) | −0.0048 (8) | −0.0028 (8) |
C11 | 0.0375 (12) | 0.0425 (11) | 0.0265 (10) | −0.0149 (9) | −0.0104 (8) | 0.0007 (8) |
C12 | 0.0392 (12) | 0.0347 (10) | 0.0287 (10) | −0.0165 (9) | −0.0085 (9) | −0.0024 (8) |
C13 | 0.0477 (13) | 0.0498 (12) | 0.0272 (10) | −0.0225 (10) | −0.0024 (9) | 0.0007 (9) |
N1 | 0.0575 (11) | 0.0432 (10) | 0.0283 (9) | −0.0268 (9) | −0.0143 (8) | 0.0047 (7) |
N2 | 0.0504 (11) | 0.0522 (11) | 0.0224 (8) | −0.0285 (9) | −0.0084 (7) | 0.0016 (7) |
N3 | 0.0519 (11) | 0.0469 (10) | 0.0217 (8) | −0.0287 (9) | −0.0091 (7) | 0.0045 (7) |
O1 | 0.0702 (11) | 0.0736 (11) | 0.0343 (8) | −0.0522 (10) | −0.0029 (7) | −0.0013 (7) |
O2 | 0.0452 (9) | 0.0793 (11) | 0.0298 (8) | −0.0269 (8) | −0.0155 (7) | 0.0074 (7) |
O3 | 0.0394 (8) | 0.0553 (9) | 0.0254 (7) | −0.0196 (7) | −0.0060 (6) | 0.0043 (6) |
Cl—C2 | 1.730 (2) | C7—H7A | 0.9300 |
C1—N1 | 1.332 (3) | C8—C9 | 1.387 (3) |
C1—C2 | 1.374 (3) | C8—H8A | 0.9300 |
C1—H1A | 0.9300 | C9—C10 | 1.390 (3) |
C2—C3 | 1.375 (3) | C9—C12 | 1.492 (3) |
C3—N2 | 1.334 (3) | C10—C11 | 1.382 (3) |
C3—H3A | 0.9300 | C10—H10A | 0.9300 |
C4—N1 | 1.328 (2) | C11—H11A | 0.9300 |
C4—N2 | 1.341 (2) | C12—O2 | 1.206 (2) |
C4—N3 | 1.387 (2) | C12—O3 | 1.334 (2) |
C5—O1 | 1.217 (2) | C13—O3 | 1.446 (2) |
C5—N3 | 1.378 (3) | C13—H13A | 0.9600 |
C5—C6 | 1.497 (3) | C13—H13B | 0.9600 |
C6—C11 | 1.385 (3) | C13—H13C | 0.9600 |
C6—C7 | 1.391 (3) | N3—H3B | 0.8600 |
C7—C8 | 1.381 (3) | ||
N1—C1—C2 | 121.82 (17) | C8—C9—C10 | 119.59 (17) |
N1—C1—H1A | 119.1 | C8—C9—C12 | 119.08 (17) |
C2—C1—H1A | 119.1 | C10—C9—C12 | 121.31 (17) |
C1—C2—C3 | 117.43 (19) | C11—C10—C9 | 120.16 (18) |
C1—C2—Cl | 120.22 (15) | C11—C10—H10A | 119.9 |
C3—C2—Cl | 122.34 (16) | C9—C10—H10A | 119.9 |
N2—C3—C2 | 122.04 (18) | C10—C11—C6 | 120.13 (18) |
N2—C3—H3A | 119.0 | C10—C11—H11A | 119.9 |
C2—C3—H3A | 119.0 | C6—C11—H11A | 119.9 |
N1—C4—N2 | 126.16 (18) | O2—C12—O3 | 123.57 (18) |
N1—C4—N3 | 119.57 (16) | O2—C12—C9 | 124.38 (19) |
N2—C4—N3 | 114.23 (16) | O3—C12—C9 | 112.05 (16) |
O1—C5—N3 | 118.93 (17) | O3—C13—H13A | 109.5 |
O1—C5—C6 | 120.70 (17) | O3—C13—H13B | 109.5 |
N3—C5—C6 | 120.25 (17) | H13A—C13—H13B | 109.5 |
C11—C6—C7 | 119.85 (17) | O3—C13—H13C | 109.5 |
C11—C6—C5 | 121.36 (17) | H13A—C13—H13C | 109.5 |
C7—C6—C5 | 118.62 (18) | H13B—C13—H13C | 109.5 |
C8—C7—C6 | 119.92 (19) | C4—N1—C1 | 116.57 (16) |
C8—C7—H7A | 120.0 | C3—N2—C4 | 115.95 (16) |
C6—C7—H7A | 120.0 | C5—N3—C4 | 131.10 (16) |
C7—C8—C9 | 120.30 (18) | C5—N3—H3B | 114.4 |
C7—C8—H8A | 119.9 | C4—N3—H3B | 114.4 |
C9—C8—H8A | 119.9 | C12—O3—C13 | 116.21 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3B···N2i | 0.86 | 2.10 | 2.959 (2) | 176 |
C13—H13C···N1ii | 0.96 | 2.57 | 3.339 (2) | 138 |
Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C13H10ClN3O3 |
Mr | 291.69 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 295 |
a, b, c (Å) | 5.9068 (8), 7.3378 (9), 15.816 (4) |
α, β, γ (°) | 78.259 (14), 82.030 (13), 67.986 (10) |
V (Å3) | 620.78 (19) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.32 |
Crystal size (mm) | 0.5 × 0.4 × 0.3 |
Data collection | |
Diffractometer | Siemens P4 diffractometer |
Absorption correction | ψ scan (XSCANS; Siemens, 1995) |
Tmin, Tmax | 0.888, 0.918 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2811, 2140, 1715 |
Rint | 0.026 |
(sin θ/λ)max (Å−1) | 0.594 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.098, 1.02 |
No. of reflections | 2140 |
No. of parameters | 182 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.17, −0.21 |
Computer programs: XSCANS (Siemens, 1995), SHELXTL (Sheldrick, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3B···N2i | 0.86 | 2.10 | 2.959 (2) | 176 |
C13—H13C···N1ii | 0.96 | 2.57 | 3.339 (2) | 138 |
Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+1, −y+1, −z+1. |
Acknowledgements
We are grateful to the National Science Council of the Republic of China for support.
References
Forbes, C. C., Beatty, A. M. & Smith, B. D. (2001). Org. Lett. 3, 3595–3598. Web of Science CSD CrossRef PubMed CAS Google Scholar
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Siemens (1995). XSCANS. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA. Google Scholar
Wu, C.-J., Sie, M.-J., Hsiao, H.-L. & Chen, J.-D. (2011). CrystEngComm, 13, 4121–4130. Web of Science CSD CrossRef CAS Google Scholar
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The silver(I) complex containg methyl 4-(5-chloropyrimidin-2-ylcarbamoyl)benzoate ligand has been reported, which shows a two-dimensional network (Wu et al., 2011). Within this project the crystal structure of the title compound was determined (Fig. 1). In its crystal structure intermolecular N—H···N hydrogen bonds are found (Table 1) and the molecules are also interlinked through C—Cl···O interactions [3.233 (1) Å and 167.33 (1)°]. Weak C—H···N hydrogen bonds among the methyl benzoate and pyrimidyl rings are also observed in the solid state (Fig. 2). In the crystal structure the amide group of the title compound adopts the cis conformation, which is in marked contrast to the trans conformation found in the Ag complex (Wu et al., 2011).