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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.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807022842/hg2230sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807022842/hg2230Isup2.hkl
Contains datablock I

CCDC reference: 651458

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](Wave) = 0.000 Å
  • R factor = 0.032
  • wR factor = 0.081
  • Data-to-parameter ratio = 13.9

checkCIF/PLATON results

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Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 27.47 From the CIF: _reflns_number_total 3670 Count of symmetry unique reflns 2187 Completeness (_total/calc) 167.81% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 1483 Fraction of Friedel pairs measured 0.678 Are heavy atom types Z>Si present yes
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 0 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

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.

Structure description 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.

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).

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 m3
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 mm1
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 = 2123
Tmin = 0.904, Tmax = 0.923k = 1515
8657 measured reflectionsl = 1010
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 Å3
S = 1.02Δρmin = 0.26 e Å3
3670 reflectionsExtinction correction: Larson (1970)
264 parametersExtinction coefficient: 105 (15)
0 restraintsAbsolute structure: Flack (1983), 1523 Friedel pairs
H-atom parameters constrainedAbsolute structure 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 mm1
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 reflections
Refinement top
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.081Δρmax = 0.24 e Å3
S = 1.02Δρmin = 0.26 e Å3
3670 reflectionsAbsolute structure: Flack (1983), 1523 Friedel pairs
264 parametersAbsolute structure 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, º) 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—N324.72 (16)C2—C1—C6—C50.5 (2)
C1—S1—C14—N4157.85 (12)C2—C1—C6—C7178.00 (17)
C14—S1—C1—C292.52 (15)C6—C1—C2—C31.1 (3)
C14—S1—C1—C695.79 (16)C1—C2—C3—C41.4 (3)
C18—O4—C15—N3178.38 (17)C2—C3—C4—C50.2 (3)
C18—O4—C15—C163.9 (2)C3—C4—C5—C61.4 (3)
C19—O5—C17—N45.0 (2)C4—C5—C6—C11.7 (3)
C19—O5—C17—C16175.2 (2)C4—C5—C6—C7176.9 (2)
C7—N1—C8—C92.2 (3)C1—C6—C7—O1128.8 (2)
C7—N1—C8—C13179.17 (18)C1—C6—C7—N156.6 (2)
C8—N1—C7—O13.7 (3)C5—C6—C7—O152.7 (2)
C8—N1—C7—C6177.95 (16)C5—C6—C7—N1121.85 (19)
O2—N2—C12—C114.4 (3)N1—C8—C9—C10178.3 (2)
O2—N2—C12—C13176.9 (2)N1—C8—C13—C12179.31 (18)
O3—N2—C12—C11174.3 (2)C9—C8—C13—C120.6 (3)
O3—N2—C12—C134.4 (3)C13—C8—C9—C100.3 (3)
C14—N3—C15—O4179.89 (15)C8—C9—C10—C110.9 (3)
C14—N3—C15—C162.1 (2)C9—C10—C11—C120.4 (4)
C15—N3—C14—S1178.51 (12)C10—C11—C12—N2179.2 (2)
C15—N3—C14—N41.4 (2)C10—C11—C12—C130.5 (3)
C14—N4—C17—O5178.28 (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—C17178.33 (16)
C17—N4—C14—N30.5 (2)N3—C15—C16—C170.8 (2)
S1—C1—C2—C3172.99 (18)C15—C16—C17—O5178.93 (16)
S1—C1—C6—C5170.98 (16)C15—C16—C17—N41.4 (2)
S1—C1—C6—C710.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N(1)—H(111)···N(3)0.862.102.914 (2)158

Experimental details

Crystal data
Chemical formulaC19H16N4O5S
Mr412.42
Crystal system, space groupMonoclinic, Cc
Temperature (K)298
a, b, c (Å)18.3554 (9), 12.3477 (6), 8.4209 (5)
β (°) 91.0467 (17)
V3)1908.25 (17)
Z4
Radiation typeMo Kα
µ (mm1)0.21
Crystal size (mm)0.46 × 0.42 × 0.38
Data collection
DiffractometerRigaku R-AXIS RAPID
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.904, 0.923
No. of measured, independent and
observed [F2 > 2σ(F2)] reflections
8657, 3670, 3417
Rint0.022
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.081, 1.02
No. of reflections3670
No. of parameters264
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.24, 0.26
Absolute structureFlack (1983), 1523 Friedel pairs
Absolute structure parameter0.10 (5)

Computer programs: PROCESS-AUTO (Rigaku, 1998), PROCESS-AUTO, CrystalStructure (Rigaku/MSC, 2004), SIR97 (Altomare et al., 1999), CRYSTALS (Watkin et al., 1996), ORTEP-3 for Windows (Farrugia, 1997), CrystalStructure.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N(1)—H(111)···N(3)0.8602.0982.914 (2)158.2
 

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