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

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ISSN: 2056-9890

Methyl 4-[N-(5-bromo­pyrimidin-2-yl)carbamo­yl]benzoate

aDepartment of Chemistry, Chung-Yuan Christian University, Chung-Li 320, Taiwan
*Correspondence e-mail: jdchen@cycu.edu.tw

(Received 7 June 2012; accepted 14 July 2012; online 18 July 2012)

In the title compound, C13H10BrN3O3, the pyrimidine and benzene rings are twisted with an inter­planar angle of 58.4 (1)°. The secondary amide group adopts a cis conformation with an H—N—C—O torsion angle of 14.8 (1)°. In the crystal, mol­ecules are connected into inversion dimers via pairs of N—H⋯N hydrogen bonds, generating an R22(8) motif. The dimers are further connected through a C—Br⋯O inter­action [3.136 (1) Å and 169.31 (1)°] into a chain along [110]. Weak C—H⋯N hydrogen bonds between the methyl benzoate groups and pyrimidine rings are also observed in the crystal structure.

Related literature

For methyl-4-(5-bromo­pyrimidin-2-ylcarbamo­yl)benzoate and its metal complexes, see: Wu et al. (2011[Wu, C.-J., Sie, M.-J., Hsiao, H.-L. & Chen, J.-D. (2011). CrystEngComm, 13, 4121-4130.]). For the conformation of related amides, see Forbes et al. (2001[Forbes, C. C., Beatty, A. M. & Smith, B. D. (2001). Org. Lett. 3, 3595-3598.]); Oertli et al. (1992[Oertli, G., Meyer, W. R., Suter, U. W., Joho, F. B., Gramlich, V. & Petter, W. (1992). Helv. Chim. Acta, 75, 184-189.]); Lu et al. (2011a[Lu, C.-H., Wu, C.-J., Yeh, C.-W. & Chen, J.-D. (2011a). Acta Cryst. E67, o1872.],b[Lu, C.-H., Wu, C.-J., Yeh, C.-W., Hu, H.-L. & Chen, J.-D. (2011b). Acta Cryst. E67, o1858.]). For C—Br⋯O inter­actions, see: Rowland & Taylor (1996[Rowland, R. S. & Taylor, R. (1996). J. Phys. Chem. 100, 7384-7391.]).

[Scheme 1]

Experimental

Crystal data
  • C13H10BrN3O3

  • Mr = 336.15

  • Triclinic, [P \overline 1]

  • a = 5.9398 (6) Å

  • b = 7.4137 (7) Å

  • c = 15.897 (2) Å

  • α = 77.846 (9)°

  • β = 81.613 (7)°

  • γ = 68.185 (9)°

  • V = 633.58 (12) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 3.26 mm−1

  • T = 295 K

  • 0.4 × 0.3 × 0.2 mm

Data collection
  • Siemens P4 diffractometer

  • Absorption correction: ψ scan (XSCANS; Siemens, 1995[Siemens (1995). XSCANS. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.]) Tmin = 0.953, Tmax = 0.984

  • 2880 measured reflections

  • 2192 independent reflections

  • 1841 reflections with I > 2σ(I)

  • Rint = 0.027

  • 3 standard reflections every 97 reflections intensity decay: none

Refinement
  • R[F2 > 2σ(F2)] = 0.034

  • wR(F2) = 0.076

  • S = 1.05

  • 2192 reflections

  • 186 parameters

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

  • Δρmax = 0.30 e Å−3

  • Δρmin = −0.41 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3A⋯N1i 0.84 (4) 2.14 (1) 2.98 (1) 175 (1)
C13—H13B⋯N2ii 0.96 2.58 3.37 (1) 139
Symmetry codes: (i) -x+1, -y, -z+1; (ii) -x+1, -y+1, -z.

Data collection: XSCANS (Siemens, 1995[Siemens (1995). XSCANS. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.]); cell refinement: XSCANS; data reduction: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); 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: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Several silver(I) complexes containg Methyl-4-(5-halopyrimidin-2-ylcarbamoyl)benzoate ligands have been reported, which show two-dimensional structures (Wu, et al., 2011). Within this project the crystal structure of the title compound was determined (Fig.1). The pyrimidyl and phenyl rings are not coplanar but twisted with an interplanar angle of 58.4 (1)°. Several C—O lengths are found in the title compound for amide [C5—O1 = 1.220 (4) Å] and methyl benzoate groups [C12—O3 = 1.200 (4), C12—O2 = 1.335 (4) and C13—O2 = 1.448 (4) Å], and the C—N—C angles in pyrimidyl group [C1—N1—C2 = 116.1 (3) and C1—N2—C4 = 116.5 (3)°] is smaller than that in amide group [C1—N3—C5 = 131.2 (3)°]. In its crystal structure intermolecular N—H···N hydrogen bonds are found (Tab. 1) and the molecules are also interlinked through C—Br···O van der Waals interactions [3.136 (1) Å and 169.31 (1) °] (Rowland et al., 1996). The weak C—H···N hydrogen bonds among the methyl benzoate and pyrimidyl rings are also found in the solid state (Fig. 2). In the crystal structure of the title compound the amide group adopts cis conformation with the H3A—N3—C5—O1 torsion angle of 14.8 (1) °, which is same as the chloro one (Lu, et al., 2011a). This conformation is different from that in the Ag complex, which is trans (Wu, et al., 2011; Lu, et al., 2011b).

Related literature top

For methyl-4-(5-bromopyrimidin-2-ylcarbamoyl)benzoate and its metal complexes, see: Wu et al. (2011). For the conformation of related amides, see Forbes et al. (2001); Oertli et al. (1992); Lu et al. (2011a,b). For C—Br···O

interactions, see: Rowland & Taylor (1996).

Experimental top

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 evaporization of the solvent from a solution of the title compound in methanol.

Refinement top

H atoms bound to C atoms were placed in idealized positions and constrained to ride on their parent atoms, with C—H = 0.93 - 0.96 Å, and with Uiso(H) = 1.2 or 1.5 Ueq(C). The amine hydrogen atom (H3A) that is involved in the N—H···N hydrogen bond was freely refined.

Computing details top

Data collection: XSCANS (Siemens, 1995); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. Crystal structure of the title compound with atom labeling and displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. Partial packing diagram showing C—H···N and N—H···N hydrogen bonds and C—Br···O interactions among the molecule, with atom labeling. Symmetric code: (i) 1 - x, -y, 1 - z; (ii) 1 - x, 1 - y, -z; (iii) -1 + x, -1 + y, z.
Methyl 4-[N-(5-bromopyrimidin-2-yl)carbamoyl]benzoate top
Crystal data top
C13H10BrN3O3Z = 2
Mr = 336.15F(000) = 336
Triclinic, P1Dx = 1.762 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.9398 (6) ÅCell parameters from 26 reflections
b = 7.4137 (7) Åθ = 4.9–13.5°
c = 15.897 (2) ŵ = 3.26 mm1
α = 77.846 (9)°T = 295 K
β = 81.613 (7)°Block, colourless
γ = 68.185 (9)°0.4 × 0.3 × 0.2 mm
V = 633.58 (12) Å3
Data collection top
Siemens P4
diffractometer
1841 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.027
Graphite monochromatorθmax = 25.0°, θmin = 2.6°
ω scansh = 61
Absorption correction: ψ scan
(XSCANS; Siemens, 1995)
k = 88
Tmin = 0.953, Tmax = 0.984l = 1818
2880 measured reflections3 standard reflections every 97 reflections
2192 independent reflections intensity decay: none
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)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.076H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0258P)2 + 0.579P]
where P = (Fo2 + 2Fc2)/3
2192 reflections(Δ/σ)max < 0.001
186 parametersΔρmax = 0.30 e Å3
0 restraintsΔρmin = 0.41 e Å3
Crystal data top
C13H10BrN3O3γ = 68.185 (9)°
Mr = 336.15V = 633.58 (12) Å3
Triclinic, P1Z = 2
a = 5.9398 (6) ÅMo Kα radiation
b = 7.4137 (7) ŵ = 3.26 mm1
c = 15.897 (2) ÅT = 295 K
α = 77.846 (9)°0.4 × 0.3 × 0.2 mm
β = 81.613 (7)°
Data collection top
Siemens P4
diffractometer
1841 reflections with I > 2σ(I)
Absorption correction: ψ scan
(XSCANS; Siemens, 1995)
Rint = 0.027
Tmin = 0.953, Tmax = 0.9843 standard reflections every 97 reflections
2880 measured reflections intensity decay: none
2192 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0340 restraints
wR(F2) = 0.076H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.30 e Å3
2192 reflectionsΔρmin = 0.41 e Å3
186 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. 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
Br0.90598 (7)0.62807 (6)0.37876 (2)0.04607 (14)
C10.5123 (6)0.2085 (4)0.37807 (18)0.0302 (7)
C20.7390 (6)0.3054 (5)0.4494 (2)0.0401 (8)
H2A0.81840.29260.49780.048*
C30.7438 (6)0.4513 (5)0.3806 (2)0.0341 (7)
C40.6228 (6)0.4664 (5)0.3101 (2)0.0373 (8)
H4A0.62410.56310.26220.045*
C50.2842 (6)0.0432 (5)0.3186 (2)0.0346 (7)
C60.3460 (6)0.1063 (4)0.22515 (19)0.0307 (7)
C70.5876 (6)0.0638 (5)0.1926 (2)0.0354 (7)
H7A0.71200.00040.22950.043*
C80.6427 (6)0.1155 (5)0.1058 (2)0.0345 (7)
H8A0.80400.08610.08400.041*
C90.4556 (6)0.2120 (4)0.05051 (18)0.0298 (7)
C100.2152 (6)0.2496 (5)0.0825 (2)0.0360 (8)
H10A0.09070.31070.04550.043*
C110.1611 (6)0.1958 (5)0.1703 (2)0.0358 (7)
H11A0.00030.22020.19180.043*
C120.5083 (6)0.2803 (5)0.0433 (2)0.0329 (7)
C130.8156 (7)0.3160 (5)0.1514 (2)0.0426 (8)
H13A0.97810.31680.15540.064*
H13B0.70630.44640.17130.064*
H13C0.81000.22710.18640.064*
N10.6247 (5)0.1816 (4)0.44924 (16)0.0370 (6)
N20.5040 (5)0.3454 (4)0.30896 (16)0.0384 (7)
N30.3906 (5)0.0797 (4)0.38148 (17)0.0342 (6)
O10.1470 (5)0.0495 (4)0.34026 (15)0.0528 (7)
O20.7440 (4)0.2520 (3)0.06249 (13)0.0405 (6)
O30.3578 (5)0.3532 (4)0.09519 (15)0.0528 (7)
H3A0.383 (7)0.012 (6)0.431 (3)0.048 (11)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br0.0571 (2)0.0489 (2)0.0434 (2)0.03436 (18)0.01250 (16)0.00359 (15)
C10.0366 (18)0.0300 (16)0.0243 (16)0.0142 (14)0.0003 (13)0.0018 (12)
C20.048 (2)0.052 (2)0.0272 (17)0.0276 (18)0.0105 (15)0.0027 (15)
C30.0395 (18)0.0342 (17)0.0308 (17)0.0177 (15)0.0031 (14)0.0009 (13)
C40.051 (2)0.0373 (18)0.0284 (17)0.0243 (17)0.0072 (15)0.0032 (14)
C50.0408 (19)0.0347 (17)0.0309 (17)0.0198 (16)0.0003 (14)0.0014 (14)
C60.0410 (19)0.0309 (16)0.0271 (16)0.0214 (14)0.0034 (14)0.0029 (13)
C70.0390 (19)0.0389 (18)0.0291 (17)0.0163 (15)0.0089 (14)0.0020 (14)
C80.0333 (18)0.0404 (18)0.0318 (17)0.0164 (15)0.0023 (14)0.0042 (14)
C90.0382 (18)0.0309 (16)0.0241 (15)0.0169 (14)0.0059 (13)0.0015 (12)
C100.0368 (19)0.0447 (19)0.0307 (17)0.0196 (16)0.0090 (14)0.0013 (14)
C110.0332 (18)0.0456 (19)0.0337 (17)0.0206 (15)0.0035 (14)0.0042 (14)
C120.0383 (19)0.0331 (17)0.0310 (17)0.0171 (15)0.0070 (15)0.0018 (13)
C130.050 (2)0.052 (2)0.0258 (17)0.0240 (18)0.0018 (15)0.0047 (15)
N10.0472 (17)0.0451 (16)0.0244 (13)0.0269 (14)0.0052 (12)0.0033 (12)
N20.0566 (18)0.0393 (15)0.0264 (14)0.0267 (14)0.0134 (13)0.0049 (12)
N30.0481 (17)0.0404 (16)0.0215 (13)0.0281 (14)0.0050 (12)0.0037 (12)
O10.0677 (17)0.0703 (18)0.0384 (14)0.0513 (15)0.0006 (12)0.0005 (12)
O20.0412 (14)0.0524 (14)0.0252 (11)0.0196 (11)0.0037 (10)0.0059 (10)
O30.0464 (15)0.0795 (19)0.0324 (13)0.0284 (14)0.0129 (12)0.0089 (12)
Geometric parameters (Å, º) top
Br—C31.887 (3)C7—H7A0.9300
C1—N21.322 (4)C8—C91.395 (4)
C1—N11.339 (4)C8—H8A0.9300
C1—N31.385 (4)C9—C101.388 (4)
C2—N11.329 (4)C9—C121.498 (4)
C2—C31.372 (4)C10—C111.392 (4)
C2—H2A0.9300C10—H10A0.9300
C3—C41.382 (4)C11—H11A0.9300
C4—N21.336 (4)C12—O31.200 (4)
C4—H4A0.9300C12—O21.335 (4)
C5—O11.220 (4)C13—O21.448 (4)
C5—N31.377 (4)C13—H13A0.9600
C5—C61.495 (4)C13—H13B0.9600
C6—C111.379 (4)C13—H13C0.9600
C6—C71.394 (5)N3—H3A0.84 (4)
C7—C81.377 (4)
N2—C1—N1126.4 (3)C10—C9—C8120.0 (3)
N2—C1—N3119.5 (3)C10—C9—C12118.8 (3)
N1—C1—N3114.2 (3)C8—C9—C12121.2 (3)
N1—C2—C3122.2 (3)C9—C10—C11119.8 (3)
N1—C2—H2A118.9C9—C10—H10A120.1
C3—C2—H2A118.9C11—C10—H10A120.1
C2—C3—C4117.3 (3)C6—C11—C10120.0 (3)
C2—C3—Br123.2 (2)C6—C11—H11A120.0
C4—C3—Br119.6 (2)C10—C11—H11A120.0
N2—C4—C3121.5 (3)O3—C12—O2123.8 (3)
N2—C4—H4A119.2O3—C12—C9124.5 (3)
C3—C4—H4A119.2O2—C12—C9111.7 (3)
O1—C5—N3118.9 (3)O2—C13—H13A109.5
O1—C5—C6120.4 (3)O2—C13—H13B109.5
N3—C5—C6120.6 (3)H13A—C13—H13B109.5
C11—C6—C7120.1 (3)O2—C13—H13C109.5
C11—C6—C5119.0 (3)H13A—C13—H13C109.5
C7—C6—C5120.7 (3)H13B—C13—H13C109.5
C8—C7—C6120.2 (3)C2—N1—C1116.1 (3)
C8—C7—H7A119.9C1—N2—C4116.5 (3)
C6—C7—H7A119.9C5—N3—C1131.2 (3)
C7—C8—C9119.8 (3)C5—N3—H3A115 (3)
C7—C8—H8A120.1C1—N3—H3A113 (3)
C9—C8—H8A120.1C12—O2—C13116.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N1i0.84 (4)2.14 (1)2.98 (1)175 (1)
C13—H13B···N2ii0.962.583.37 (1)139
Symmetry codes: (i) x+1, y, z+1; (ii) x+1, y+1, z.

Experimental details

Crystal data
Chemical formulaC13H10BrN3O3
Mr336.15
Crystal system, space groupTriclinic, P1
Temperature (K)295
a, b, c (Å)5.9398 (6), 7.4137 (7), 15.897 (2)
α, β, γ (°)77.846 (9), 81.613 (7), 68.185 (9)
V3)633.58 (12)
Z2
Radiation typeMo Kα
µ (mm1)3.26
Crystal size (mm)0.4 × 0.3 × 0.2
Data collection
DiffractometerSiemens P4
diffractometer
Absorption correctionψ scan
(XSCANS; Siemens, 1995)
Tmin, Tmax0.953, 0.984
No. of measured, independent and
observed [I > 2σ(I)] reflections
2880, 2192, 1841
Rint0.027
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.076, 1.05
No. of reflections2192
No. of parameters186
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.30, 0.41

Computer programs: XSCANS (Siemens, 1995), SHELXTL (Sheldrick, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N1i0.84 (4)2.14 (1)2.98 (1)175 (1)
C13—H13B···N2ii0.962.583.37 (1)139
Symmetry codes: (i) x+1, y, z+1; (ii) x+1, y+1, z.
 

Acknowledgements

We are grateful to the National Science Council of the Republic of China for support.

References

First citationForbes, C. C., Beatty, A. M. & Smith, B. D. (2001). Org. Lett. 3, 3595–3598.  Web of Science CSD CrossRef PubMed CAS
First citationLu, C.-H., Wu, C.-J., Yeh, C.-W. & Chen, J.-D. (2011a). Acta Cryst. E67, o1872.  Web of Science CSD CrossRef IUCr Journals
First citationLu, C.-H., Wu, C.-J., Yeh, C.-W., Hu, H.-L. & Chen, J.-D. (2011b). Acta Cryst. E67, o1858.  Web of Science CSD CrossRef IUCr Journals
First citationOertli, G., Meyer, W. R., Suter, U. W., Joho, F. B., Gramlich, V. & Petter, W. (1992). Helv. Chim. Acta, 75, 184–189.  CSD CrossRef CAS Web of Science
First citationRowland, R. S. & Taylor, R. (1996). J. Phys. Chem. 100, 7384–7391.  CSD CrossRef CAS Web of Science
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSiemens (1995). XSCANS. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.
First citationWu, C.-J., Sie, M.-J., Hsiao, H.-L. & Chen, J.-D. (2011). CrystEngComm, 13, 4121–4130.  Web of Science CSD CrossRef CAS

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