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

Hu, H.-L.; Wu, C.-J.; Yeh, C.-W.; Chen, J.-D.

doi:10.1107/S1600536812032102

organic compounds

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Volume 68| Part 8| August 2012| Page o2497

https://doi.org/10.1107/S1600536812032102

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

Hui-Ling Hu,^a Chia-Jun Wu,^a Chun-Wei Yeh ^a and Jhy-Der Chen ^a ^*

^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 ). 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

Crystal data

C₁₃H₁₀BrN₃O₃
M_r = 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 ) T_min = 0.953, T_max = 0.984
2880 measured reflections
2192 independent reflections
1841 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.30 e Å⁻³
Δρ_min = −0.41 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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); cell refinement: XSCANS; 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; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536812032102/gw2122sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812032102/gw2122Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812032102/gw2122Isup3.cml

checkCIF report

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.

Structure description 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).

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

	Fig. 1. Crystal structure of the title compound with atom labeling and displacement ellipsoids drawn at the 30% probability level.
	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

C₁₃H₁₀BrN₃O₃	Z = 2
M_r = 336.15	F(000) = 336
Triclinic, P1	D_x = 1.762 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.9398 (6) Å	Cell parameters from 26 reflections
b = 7.4137 (7) Å	θ = 4.9–13.5°
c = 15.897 (2) Å	µ = 3.26 mm⁻¹
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 tube	R_int = 0.027
Graphite monochromator	θ_max = 25.0°, θ_min = 2.6°
ω scans	h = −6→1
Absorption correction: ψ scan (XSCANS; Siemens, 1995)	k = −8→8
T_min = 0.953, T_max = 0.984	l = −18→18
2880 measured reflections	3 standard reflections every 97 reflections
2192 independent reflections	intensity decay: none

Refinement top

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.076	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0258P)² + 0.579P] where P = (F_o² + 2F_c²)/3
2192 reflections	(Δ/σ)_max < 0.001
186 parameters	Δρ_max = 0.30 e Å⁻³
0 restraints	Δρ_min = −0.41 e Å⁻³

Crystal data top

C₁₃H₁₀BrN₃O₃	γ = 68.185 (9)°
M_r = 336.15	V = 633.58 (12) Å³
Triclinic, P1	Z = 2
a = 5.9398 (6) Å	Mo Kα radiation
b = 7.4137 (7) Å	µ = 3.26 mm⁻¹
c = 15.897 (2) Å	T = 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)	R_int = 0.027
T_min = 0.953, T_max = 0.984	3 standard reflections every 97 reflections
2880 measured reflections	intensity decay: none
2192 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.034	0 restraints
wR(F²) = 0.076	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.30 e Å⁻³
2192 reflections	Δρ_min = −0.41 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Br	0.90598 (7)	0.62807 (6)	0.37876 (2)	0.04607 (14)
C1	0.5123 (6)	0.2085 (4)	0.37807 (18)	0.0302 (7)
C2	0.7390 (6)	0.3054 (5)	0.4494 (2)	0.0401 (8)
H2A	0.8184	0.2926	0.4978	0.048*
C3	0.7438 (6)	0.4513 (5)	0.3806 (2)	0.0341 (7)
C4	0.6228 (6)	0.4664 (5)	0.3101 (2)	0.0373 (8)
H4A	0.6241	0.5631	0.2622	0.045*
C5	0.2842 (6)	0.0432 (5)	0.3186 (2)	0.0346 (7)
C6	0.3460 (6)	0.1063 (4)	0.22515 (19)	0.0307 (7)
C7	0.5876 (6)	0.0638 (5)	0.1926 (2)	0.0354 (7)
H7A	0.7120	0.0004	0.2295	0.043*
C8	0.6427 (6)	0.1155 (5)	0.1058 (2)	0.0345 (7)
H8A	0.8040	0.0861	0.0840	0.041*
C9	0.4556 (6)	0.2120 (4)	0.05051 (18)	0.0298 (7)
C10	0.2152 (6)	0.2496 (5)	0.0825 (2)	0.0360 (8)
H10A	0.0907	0.3107	0.0455	0.043*
C11	0.1611 (6)	0.1958 (5)	0.1703 (2)	0.0358 (7)
H11A	0.0003	0.2202	0.1918	0.043*
C12	0.5083 (6)	0.2803 (5)	−0.0433 (2)	0.0329 (7)
C13	0.8156 (7)	0.3160 (5)	−0.1514 (2)	0.0426 (8)
H13A	0.9781	0.3168	−0.1554	0.064*
H13B	0.7063	0.4464	−0.1713	0.064*
H13C	0.8100	0.2271	−0.1864	0.064*
N1	0.6247 (5)	0.1816 (4)	0.44924 (16)	0.0370 (6)
N2	0.5040 (5)	0.3454 (4)	0.30896 (16)	0.0384 (7)
N3	0.3906 (5)	0.0797 (4)	0.38148 (17)	0.0342 (6)
O1	0.1470 (5)	−0.0495 (4)	0.34026 (15)	0.0528 (7)
O2	0.7440 (4)	0.2520 (3)	−0.06249 (13)	0.0405 (6)
O3	0.3578 (5)	0.3532 (4)	−0.09519 (15)	0.0528 (7)
H3A	0.383 (7)	0.012 (6)	0.431 (3)	0.048 (11)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br	0.0571 (2)	0.0489 (2)	0.0434 (2)	−0.03436 (18)	−0.01250 (16)	0.00359 (15)
C1	0.0366 (18)	0.0300 (16)	0.0243 (16)	−0.0142 (14)	−0.0003 (13)	−0.0018 (12)
C2	0.048 (2)	0.052 (2)	0.0272 (17)	−0.0276 (18)	−0.0105 (15)	0.0027 (15)
C3	0.0395 (18)	0.0342 (17)	0.0308 (17)	−0.0177 (15)	−0.0031 (14)	−0.0009 (13)
C4	0.051 (2)	0.0373 (18)	0.0284 (17)	−0.0243 (17)	−0.0072 (15)	0.0032 (14)
C5	0.0408 (19)	0.0347 (17)	0.0309 (17)	−0.0198 (16)	0.0003 (14)	−0.0014 (14)
C6	0.0410 (19)	0.0309 (16)	0.0271 (16)	−0.0214 (14)	−0.0034 (14)	−0.0029 (13)
C7	0.0390 (19)	0.0389 (18)	0.0291 (17)	−0.0163 (15)	−0.0089 (14)	0.0020 (14)
C8	0.0333 (18)	0.0404 (18)	0.0318 (17)	−0.0164 (15)	−0.0023 (14)	−0.0042 (14)
C9	0.0382 (18)	0.0309 (16)	0.0241 (15)	−0.0169 (14)	−0.0059 (13)	−0.0015 (12)
C10	0.0368 (19)	0.0447 (19)	0.0307 (17)	−0.0196 (16)	−0.0090 (14)	−0.0013 (14)
C11	0.0332 (18)	0.0456 (19)	0.0337 (17)	−0.0206 (15)	−0.0035 (14)	−0.0042 (14)
C12	0.0383 (19)	0.0331 (17)	0.0310 (17)	−0.0171 (15)	−0.0070 (15)	−0.0018 (13)
C13	0.050 (2)	0.052 (2)	0.0258 (17)	−0.0240 (18)	−0.0018 (15)	0.0047 (15)
N1	0.0472 (17)	0.0451 (16)	0.0244 (13)	−0.0269 (14)	−0.0052 (12)	0.0033 (12)
N2	0.0566 (18)	0.0393 (15)	0.0264 (14)	−0.0267 (14)	−0.0134 (13)	0.0049 (12)
N3	0.0481 (17)	0.0404 (16)	0.0215 (13)	−0.0281 (14)	−0.0050 (12)	0.0037 (12)
O1	0.0677 (17)	0.0703 (18)	0.0384 (14)	−0.0513 (15)	0.0006 (12)	−0.0005 (12)
O2	0.0412 (14)	0.0524 (14)	0.0252 (11)	−0.0196 (11)	−0.0037 (10)	0.0059 (10)
O3	0.0464 (15)	0.0795 (19)	0.0324 (13)	−0.0284 (14)	−0.0129 (12)	0.0089 (12)

Geometric parameters (Å, º) top

Br—C3	1.887 (3)	C7—H7A	0.9300
C1—N2	1.322 (4)	C8—C9	1.395 (4)
C1—N1	1.339 (4)	C8—H8A	0.9300
C1—N3	1.385 (4)	C9—C10	1.388 (4)
C2—N1	1.329 (4)	C9—C12	1.498 (4)
C2—C3	1.372 (4)	C10—C11	1.392 (4)
C2—H2A	0.9300	C10—H10A	0.9300
C3—C4	1.382 (4)	C11—H11A	0.9300
C4—N2	1.336 (4)	C12—O3	1.200 (4)
C4—H4A	0.9300	C12—O2	1.335 (4)
C5—O1	1.220 (4)	C13—O2	1.448 (4)
C5—N3	1.377 (4)	C13—H13A	0.9600
C5—C6	1.495 (4)	C13—H13B	0.9600
C6—C11	1.379 (4)	C13—H13C	0.9600
C6—C7	1.394 (5)	N3—H3A	0.84 (4)
C7—C8	1.377 (4)

N2—C1—N1	126.4 (3)	C10—C9—C8	120.0 (3)
N2—C1—N3	119.5 (3)	C10—C9—C12	118.8 (3)
N1—C1—N3	114.2 (3)	C8—C9—C12	121.2 (3)
N1—C2—C3	122.2 (3)	C9—C10—C11	119.8 (3)
N1—C2—H2A	118.9	C9—C10—H10A	120.1
C3—C2—H2A	118.9	C11—C10—H10A	120.1
C2—C3—C4	117.3 (3)	C6—C11—C10	120.0 (3)
C2—C3—Br	123.2 (2)	C6—C11—H11A	120.0
C4—C3—Br	119.6 (2)	C10—C11—H11A	120.0
N2—C4—C3	121.5 (3)	O3—C12—O2	123.8 (3)
N2—C4—H4A	119.2	O3—C12—C9	124.5 (3)
C3—C4—H4A	119.2	O2—C12—C9	111.7 (3)
O1—C5—N3	118.9 (3)	O2—C13—H13A	109.5
O1—C5—C6	120.4 (3)	O2—C13—H13B	109.5
N3—C5—C6	120.6 (3)	H13A—C13—H13B	109.5
C11—C6—C7	120.1 (3)	O2—C13—H13C	109.5
C11—C6—C5	119.0 (3)	H13A—C13—H13C	109.5
C7—C6—C5	120.7 (3)	H13B—C13—H13C	109.5
C8—C7—C6	120.2 (3)	C2—N1—C1	116.1 (3)
C8—C7—H7A	119.9	C1—N2—C4	116.5 (3)
C6—C7—H7A	119.9	C5—N3—C1	131.2 (3)
C7—C8—C9	119.8 (3)	C5—N3—H3A	115 (3)
C7—C8—H8A	120.1	C1—N3—H3A	113 (3)
C9—C8—H8A	120.1	C12—O2—C13	116.6 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Experimental details

Crystal data
Chemical formula	C₁₃H₁₀BrN₃O₃
M_r	336.15
Crystal system, space group	Triclinic, 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)
V (Å³)	633.58 (12)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	3.26
Crystal size (mm)	0.4 × 0.3 × 0.2

Data collection
Diffractometer	Siemens P4
Absorption correction	ψ scan (XSCANS; Siemens, 1995)
T_min, T_max	0.953, 0.984
No. of measured, independent and observed [I > 2σ(I)] reflections	2880, 2192, 1841
R_int	0.027
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.034, 0.076, 1.05
No. of reflections	2192
No. of parameters	186
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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.

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
Lu, C.-H., Wu, C.-J., Yeh, C.-W. & Chen, J.-D. (2011a). Acta Cryst. E67, o1872. Web of Science CSD CrossRef IUCr Journals Google Scholar
Lu, 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 Google Scholar
Oertli, 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 Google Scholar
Rowland, R. S. & Taylor, R. (1996). J. Phys. Chem. 100, 7384–7391. CSD CrossRef CAS Web of Science Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
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