supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers buy article online

Acta Cryst. (2007). E63, o2930    [ doi:10.1107/S1600536807022842 ]

2-(4,6-Dimethoxypyrimidine-2-ylsulfanyl)-N-(3-nitrophenyl)benzamide

B. Mao, J. Lv, J. Wu and Q. Yu

Abstract top

The title compound, C19H16N4O5S, was synthesized by the reaction of 2-(4,6-dimethoxypyrimidine-2-ylsulfanyl)benzoic acid and 3-nitroaniline in the presence of N,N'-dicyclohexylcarbodiimide catalyst in dichloromethane. Intramolecular N-H...N hydrogen bonds are found in the crystal structure.

Comment top

4,6-Dimethoxypyrimidines with a phenoxy substructure at the 2-position exhibit marked herbicidal activity (Nezu et al., 1996; Tamaru et al., 1997; Hudson et al., 2002). The title compound, (I,) has showed herbicidal activity against various grass and broadleaf weeds. The present X-ray crystal structure analysis was undertaken for understanding the relationship between structure and activity.

The bond lengths and angles in the pyrimidine moiety are close to those found in related compounds (Hall et al., 1999; Lin et al., 2001). Particularly, the angle N3—C14—N4 [125.68 (1)°] deviates significantly from the normal value. In the two benzene rings, the angles are close to 120° which are close to Caromatic—Caromatic—C = 120° (Park et al., 2005). There is an N—H..N intramolecular hydrogen bond between the proton on N1 and the pyrimidine nitrogen N3. Weak C—H···O, C—H···S and C—H···π interactions give rise to the formation of a 3-D network.

Related literature top

For related literature, see: Hall et al. (1999); Hudson et al. (2002); Lin et al. (2001); Nezu et al. (1996); Park et al. (2005); Tamaru et al. (1997).

Experimental top

N,N'-dicyclohexylcarbodiimide (1.08 g,0.055 mol) dissolved in 10 ml of dichloromethane was added dropwise over 20 minutes to the vortex of a stirred solution of 2-(4,6-dimethoxypyrimidin-2-ylsulfanyl)benzoic acid (1.60 g,0.0055 mol) and 3-nitrobenzenamine (0.69 g,0.005 mol) in 30 ml dichloromethane at 273 K. Subsequently,the mixture was stirred 6 h more at room temperature and the resulting solution filtered and washed with dichloromethane. A solution of 50 ml of 10% sodium hydroxide was added and stirred 1 h more and extracted twice with dichloromethane. The separated dichloromethane layer, dried with magnesium sulfate, was evaporated in vacuo leaving a crude of white powder. These crystals were dissolved in ethanol and left to slowly evaporate at room temperature. After 5 d, single crystals suitable for X-ray analysis were obtained (m.p. 399–402 K).

Refinement top

All H atoms were placed in calculated positions with C—H = 0.93Å (aromatic) or C—H=0.96Å (methoxy) and N—H = 0.86 Å, and included in the final cycles of refinement in the riding-model approximation,with Uiso(H) = 1.2Ueq of the carrier atoms.

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: CRYSTALS (Watkin et al., 1996); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: CrystalStructure.

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the hydrogen bond N1—H111—N3, with displacement ellipsoids drawn at the 50% probability level.
2-(4,6-Dimethoxypyrimidine-2-ylsulfanyl)-N-(3-nitrophenyl)benzamide top
Crystal data top
C19H16N4O5SF(000) = 856.00
Mr = 412.42Dx = 1.435 Mg m−3
Monoclinic, CcMo Kα radiation, λ = 0.71075 Å
Hall symbol: C -2ycCell parameters from 10239 reflections
a = 18.3554 (9) Åθ = 3.1–27.4°
b = 12.3477 (6) ŵ = 0.21 mm−1
c = 8.4209 (5) ÅT = 298 K
β = 91.0467 (17)°Chunk, colorless
V = 1908.25 (17) Å30.46 × 0.42 × 0.38 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer		3417 reflections with F2 > 2σ(F2)
Detector resolution: 10.00 pixels mm-1Rint = 0.022
ω scansθmax = 27.5°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		h = −21→23
Tmin = 0.904, Tmax = 0.923k = −15→15
8657 measured reflectionsl = −10→10
3670 independent reflections
Refinement top
Refinement on F2 w = 1/[0.0009Fo2 + 1.0000σ(Fo2)]/(4Fo2)
R[F2 > 2σ(F2)] = 0.032(Δ/σ)max < 0.001
wR(F2) = 0.081Δρmax = 0.24 e Å−3
S = 1.02Δρmin = −0.26 e Å−3
3670 reflectionsExtinction correction: Larson (1970)
264 parametersExtinction coefficient: 105 (15)
0 restraintsAbsolute structure: Flack (1983), 1523 Friedel pairs
H-atom parameters constrainedFlack parameter: 0.10 (5)
Crystal data top
C19H16N4O5SV = 1908.25 (17) Å3
Mr = 412.42Z = 4
Monoclinic, CcMo Kα radiation
a = 18.3554 (9) ŵ = 0.21 mm−1
b = 12.3477 (6) ÅT = 298 K
c = 8.4209 (5) Å0.46 × 0.42 × 0.38 mm
β = 91.0467 (17)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer		3670 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		3417 reflections with F2 > 2σ(F2)
Tmin = 0.904, Tmax = 0.923Rint = 0.022
8657 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.081Δρmax = 0.24 e Å−3
S = 1.02Δρmin = −0.26 e Å−3
3670 reflectionsAbsolute structure: Flack (1983), 1523 Friedel pairs
264 parametersFlack parameter: 0.10 (5)
0 restraints
Special details top

Refinement. Refinement using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.38203 (3)0.89646 (3)1.00620 (6)0.03648 (10)
O10.20595 (9)0.69864 (12)0.8983 (2)0.0557 (4)
O20.50881 (17)0.37440 (19)0.5022 (4)0.1185 (10)
O30.52021 (13)0.54516 (18)0.4747 (3)0.1079 (9)
O40.46729 (6)0.83461 (12)0.45837 (14)0.0450 (3)
O50.64111 (8)0.86050 (14)0.86357 (17)0.0523 (4)
N10.31393 (9)0.71447 (12)0.76172 (19)0.0401 (4)
N20.48791 (12)0.46688 (18)0.5254 (2)0.0716 (7)
N30.43379 (8)0.86439 (12)0.71021 (16)0.0323 (3)
N40.51846 (9)0.88144 (12)0.92085 (18)0.0355 (3)
C10.30560 (10)0.94420 (14)0.8979 (2)0.0354 (4)
C20.29690 (11)1.05629 (16)0.8877 (2)0.0471 (5)
C30.23477 (13)1.09949 (17)0.8202 (3)0.0588 (6)
C40.18135 (12)1.0331 (2)0.7665 (3)0.0617 (7)
C50.18849 (12)0.92221 (19)0.7784 (2)0.0528 (5)
C60.25096 (10)0.87629 (13)0.8422 (2)0.0382 (4)
C70.25500 (10)0.75374 (14)0.8420 (2)0.0393 (4)
C80.33403 (10)0.60581 (13)0.7330 (2)0.0387 (4)
C90.29172 (12)0.51721 (16)0.7826 (2)0.0528 (6)
C100.31533 (16)0.41336 (18)0.7446 (3)0.0676 (7)
C110.37916 (14)0.39460 (17)0.6621 (3)0.0619 (7)
C120.41987 (12)0.48333 (16)0.6158 (2)0.0495 (5)
C130.39828 (12)0.58838 (14)0.6484 (2)0.0454 (5)
C140.45121 (9)0.88014 (12)0.8598 (2)0.0299 (3)
C150.48988 (10)0.85016 (13)0.60663 (19)0.0330 (4)
C160.56137 (10)0.84840 (14)0.6536 (2)0.0382 (4)
C170.57184 (10)0.86377 (13)0.8152 (2)0.0357 (4)
C180.52246 (12)0.8213 (2)0.3362 (2)0.0561 (6)
C190.65252 (12)0.8676 (2)1.0318 (2)0.0663 (7)
H20.33331.10190.92690.057*
H30.22951.17420.81140.071*
H40.13921.06250.72100.074*
H50.15070.87780.74290.063*
H90.24920.52780.83900.063*
H100.28750.35440.77560.081*
H110.39410.32450.63860.074*
H130.42600.64680.61470.055*
H160.59940.83790.58380.046*
H1110.34260.76270.72370.048*
H1810.55290.88450.33380.067*
H1820.55180.75890.36030.067*
H1830.49880.81190.23450.067*
H1910.62680.81001.08290.080*
H1920.63480.93601.06910.080*
H1930.70360.86161.05640.080*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0305 (2)0.0476 (2)0.03144 (19)0.0019 (2)0.00422 (12)−0.00328 (18)
O10.0418 (8)0.0508 (7)0.0751 (10)−0.0089 (7)0.0182 (7)0.0001 (6)
O20.112 (2)0.0647 (11)0.181 (2)0.0312 (13)0.0587 (19)−0.0176 (14)
O30.0800 (16)0.0715 (12)0.174 (2)0.0058 (12)0.0649 (16)−0.0083 (13)
O40.0333 (7)0.0721 (8)0.0296 (5)0.0036 (6)0.0002 (5)−0.0037 (5)
O50.0267 (6)0.0909 (10)0.0390 (7)0.0035 (6)−0.0050 (5)−0.0005 (6)
N10.0320 (8)0.0336 (7)0.0547 (9)−0.0044 (6)0.0059 (6)−0.0015 (5)
N20.0611 (14)0.0560 (12)0.0982 (16)0.0114 (10)0.0141 (11)−0.0125 (10)
N30.0250 (7)0.0396 (6)0.0324 (7)−0.0014 (5)0.0012 (5)0.0010 (5)
N40.0283 (7)0.0449 (7)0.0333 (7)0.0014 (6)−0.0004 (5)−0.0003 (5)
C10.0255 (8)0.0412 (8)0.0397 (9)0.0036 (7)0.0071 (6)−0.0028 (6)
C20.0387 (11)0.0394 (9)0.0633 (12)−0.0017 (8)0.0074 (8)−0.0041 (8)
C30.0489 (13)0.0406 (10)0.0871 (17)0.0083 (9)0.0076 (11)0.0062 (10)
C40.0385 (12)0.0606 (12)0.0859 (16)0.0141 (10)−0.0037 (11)0.0098 (11)
C50.0284 (10)0.0566 (10)0.0732 (13)0.0002 (9)−0.0038 (8)0.0000 (9)
C60.0287 (9)0.0410 (8)0.0449 (9)0.0014 (7)0.0041 (7)−0.0006 (7)
C70.0306 (9)0.0431 (8)0.0440 (9)−0.0051 (7)−0.0004 (6)−0.0024 (7)
C80.0365 (10)0.0346 (8)0.0446 (9)−0.0032 (7)−0.0074 (7)−0.0017 (6)
C90.0487 (13)0.0421 (10)0.0677 (13)−0.0087 (9)0.0082 (9)0.0006 (8)
C100.0665 (17)0.0381 (10)0.099 (2)−0.0090 (11)0.0114 (13)0.0031 (10)
C110.0656 (16)0.0355 (9)0.0845 (17)0.0023 (10)−0.0022 (12)−0.0056 (9)
C120.0466 (12)0.0445 (10)0.0572 (11)0.0050 (9)−0.0029 (9)−0.0079 (8)
C130.0419 (11)0.0378 (8)0.0565 (11)−0.0013 (8)−0.0001 (8)−0.0040 (7)
C140.0252 (8)0.0314 (7)0.0332 (7)−0.0005 (6)0.0022 (5)0.0015 (5)
C150.0302 (8)0.0388 (8)0.0299 (8)0.0009 (7)0.0008 (6)0.0032 (6)
C160.0286 (8)0.0517 (9)0.0344 (8)0.0019 (7)0.0048 (6)0.0030 (7)
C170.0244 (8)0.0441 (8)0.0386 (8)0.0006 (7)−0.0011 (6)0.0035 (7)
C180.0487 (12)0.0900 (15)0.0297 (9)0.0020 (11)0.0061 (8)−0.0040 (9)
C190.0338 (12)0.121 (2)0.0436 (11)0.0063 (12)−0.0112 (8)−0.0028 (12)
Geometric parameters (Å, °) top
S1—C11.7608 (18)C8—C131.405 (2)
S1—C141.7973 (17)C9—C101.393 (3)
O1—C71.231 (2)C10—C111.393 (4)
O2—N21.221 (3)C11—C121.386 (3)
O3—N21.216 (3)C12—C131.385 (2)
O4—C151.322 (2)C15—C161.364 (2)
O4—C181.466 (2)C16—C171.384 (2)
O5—C171.329 (2)N1—H1110.860
O5—C191.431 (2)C2—H20.930
N1—C71.374 (2)C3—H30.930
N1—C81.414 (2)C4—H40.930
N2—C121.488 (3)C5—H50.930
N3—C141.308 (2)C9—H90.930
N3—C151.373 (2)C10—H100.930
N4—C141.329 (2)C11—H110.930
N4—C171.353 (2)C13—H130.930
C1—C21.396 (2)C16—H160.930
C1—C61.383 (2)C18—H1810.960
C2—C31.373 (3)C18—H1820.960
C3—C41.350 (3)C18—H1830.960
C4—C51.379 (3)C19—H1910.960
C5—C61.379 (2)C19—H1920.960
C6—C71.515 (2)C19—H1930.960
C8—C91.409 (2)
C1—S1—C14104.39 (8)N3—C15—C16123.14 (15)
C15—O4—C18118.05 (14)C15—C16—C17113.49 (16)
C17—O5—C19115.06 (15)O5—C17—N4120.25 (16)
C7—N1—C8129.00 (15)O5—C17—C16114.34 (16)
O2—N2—O3122.0 (2)N4—C17—C16125.41 (16)
O2—N2—C12118.6 (2)C7—N1—H111115.5
O3—N2—C12119.4 (2)C8—N1—H111115.5
C14—N3—C15117.24 (14)C1—C2—H2119.9
C14—N4—C17114.99 (15)C3—C2—H2119.9
S1—C1—C2116.94 (14)C2—C3—H3120.1
S1—C1—C6122.61 (14)C4—C3—H3120.1
C2—C1—C6119.94 (16)C3—C4—H4119.6
C1—C2—C3120.26 (18)C5—C4—H4119.6
C2—C3—C4119.7 (2)C4—C5—H5119.5
C3—C4—C5120.8 (2)C6—C5—H5119.5
C4—C5—C6120.9 (2)C8—C9—H9120.9
C1—C6—C5118.40 (17)C10—C9—H9120.9
C1—C6—C7124.81 (16)C9—C10—H10118.8
C5—C6—C7116.78 (16)C11—C10—H10118.8
O1—C7—N1125.63 (17)C10—C11—H11120.9
O1—C7—C6121.04 (16)C12—C11—H11120.9
N1—C7—C6113.08 (15)C8—C13—H13120.3
N1—C8—C9122.62 (17)C12—C13—H13120.3
N1—C8—C13117.14 (15)C15—C16—H16123.3
C9—C8—C13120.22 (17)C17—C16—H16123.3
C8—C9—C10118.1 (2)O4—C18—H181109.5
C9—C10—C11122.4 (2)O4—C18—H182109.5
C10—C11—C12118.1 (2)O4—C18—H183109.5
N2—C12—C11119.84 (19)H181—C18—H182109.5
N2—C12—C13118.36 (18)H181—C18—H183109.5
C11—C12—C13121.8 (2)H182—C18—H183109.5
C8—C13—C12119.32 (18)O5—C19—H191109.5
S1—C14—N3120.91 (12)O5—C19—H192109.5
S1—C14—N4113.35 (12)O5—C19—H193109.5
N3—C14—N4125.68 (15)H191—C19—H192109.5
O4—C15—N3113.12 (15)H191—C19—H193109.5
O4—C15—C16123.71 (16)H192—C19—H193109.5
C1—S1—C14—N3−24.72 (16)C2—C1—C6—C5−0.5 (2)
C1—S1—C14—N4157.85 (12)C2—C1—C6—C7178.00 (17)
C14—S1—C1—C2−92.52 (15)C6—C1—C2—C3−1.1 (3)
C14—S1—C1—C695.79 (16)C1—C2—C3—C41.4 (3)
C18—O4—C15—N3178.38 (17)C2—C3—C4—C5−0.2 (3)
C18—O4—C15—C16−3.9 (2)C3—C4—C5—C6−1.4 (3)
C19—O5—C17—N45.0 (2)C4—C5—C6—C11.7 (3)
C19—O5—C17—C16−175.2 (2)C4—C5—C6—C7−176.9 (2)
C7—N1—C8—C92.2 (3)C1—C6—C7—O1128.8 (2)
C7—N1—C8—C13−179.17 (18)C1—C6—C7—N1−56.6 (2)
C8—N1—C7—O1−3.7 (3)C5—C6—C7—O1−52.7 (2)
C8—N1—C7—C6−177.95 (16)C5—C6—C7—N1121.85 (19)
O2—N2—C12—C11−4.4 (3)N1—C8—C9—C10178.3 (2)
O2—N2—C12—C13176.9 (2)N1—C8—C13—C12−179.31 (18)
O3—N2—C12—C11174.3 (2)C9—C8—C13—C12−0.6 (3)
O3—N2—C12—C13−4.4 (3)C13—C8—C9—C10−0.3 (3)
C14—N3—C15—O4179.89 (15)C8—C9—C10—C110.9 (3)
C14—N3—C15—C162.1 (2)C9—C10—C11—C12−0.4 (4)
C15—N3—C14—S1−178.51 (12)C10—C11—C12—N2−179.2 (2)
C15—N3—C14—N4−1.4 (2)C10—C11—C12—C13−0.5 (3)
C14—N4—C17—O5−178.28 (16)N2—C12—C13—C8179.73 (19)
C14—N4—C17—C162.0 (2)C11—C12—C13—C81.1 (3)
C17—N4—C14—S1176.74 (12)O4—C15—C16—C17−178.33 (16)
C17—N4—C14—N3−0.5 (2)N3—C15—C16—C17−0.8 (2)
S1—C1—C2—C3−172.99 (18)C15—C16—C17—O5178.93 (16)
S1—C1—C6—C5170.98 (16)C15—C16—C17—N4−1.4 (2)
S1—C1—C6—C7−10.6 (2)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N(1)—H(111)···N(3)0.8602.0982.914 (2)158.2
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N(1)—H(111)···N(3)0.8602.0982.914 (2)158.2
references
References top

Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565–?.

Flack, H. D. (1983). Acta Cryst. A39, 876–881.

Hall, M. B., Niu, S. & Reibenspies, J. H. (1999). Polyhedron, 18, 1717–1724.

Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.

Hudson, H. R., Wu, J. & Xu, W. L. (2002). Chem Res. Chin. Univ. 18, 481–490.

Lin, C. J., Hwang, W. S. & Chiang, M. Y. (2001). Polyhedron, 20, 3275–3280.

Nezu, Y., Miyazaki, M., Sugiyama, K., Wada, N., Kajiwara, I. & Miyazawa, T. (1996). Pestic. Sci. 47, 115–124.

Park, S. Y., Lee, S. W., Oh, T. J. & Blackwell, J. (2005). Macromolecules, 38, 3713–3718.

Rigaku (1998). PROCESS-AUTO. Version 1.06. Rigaku Corporation, Tokyo, Japan.

Rigaku/MSC (2004). CrystalStructure. Version 3.6.0. Rigaku/MSC, 9009 New Trails Drive, The Woodlands, TX 77381-5209, USA.

Tamaru, M., Masuyama, N., Sato, M., Takabe, F., Inoue, J. & Betteridge, P. W. (1997). Pestic. Sci. 49, 76–84.

Watkin, D. J., Prout, C. K., Carruthers, J. R. & Betteridge, P. W. (1996). CRYSTALS. Issue 10. Chemical Crystallography Laboratory, University of Oxford, England.