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The title compound, C15H13Cl3N4O3S, is one of the thio­urea herbicides with a pyrimidine ring attached to the distal N atom of the bridge of the thio­urea. The crystal structure determination reveals that intra­molecular N—H...O hydrogen bonds form a six-membered and a five-membered ring, which indicates the coordination behavior of this potentially multidentate compound.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805040869/sg6044sup1.cif
Contains datablocks 5, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805040869/sg60445sup2.hkl
Contains datablock 5

CCDC reference: 296648

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.006 Å
  • R factor = 0.052
  • wR factor = 0.139
  • Data-to-parameter ratio = 14.0

checkCIF/PLATON results

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Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 6 PLAT480_ALERT_4_C Long H...A H-Bond Reported H15C .. N2 .. 2.96 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H8C .. O3 .. 2.67 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H8B .. S1 .. 2.89 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H7A .. S1 .. 2.96 Ang.
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 6 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 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 1 ALERT type 3 Indicator that the structure quality may be low 4 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

Thiourea compounds display high biological activities as herbicides with low toxicity and low residue content, and are used extensively as pesticides, fungicides and regulating agents of plant growth in the agrochemical industry (Pu et al., 1994; McCourt et al., 2005). Due to the low toxicity to mammals, birds, fish, amphibians etc., work on thiourea derivatives as herbicides is a subject of intensive research and many novel structural thioureas herbicides have appeared in the literature (Ehrenfreund 1988; Takematsu et al., 1988; Kehne et al., 1991). Although some of the phenoxyl thioureas have been described (Xue et al., 2000), so far, relatively a few reports on crystal structuresemploying thioureas with a pyrimidine ring attached to the distal N atom are available (Xue et al., 2005). We have developed the synthesis of (5) and report here the crystal structure of the title compound. The key feature of this phenoxyl thiourea is that the aromatic ring, 2,4-dichlorophenoxypropionyl group is linked to thiourea bridge by an amido bond and the pyrimidine ring substituted in both meta positions is attached to the distal N atom of thiourea, which might provide an opportunity for the study of cooperative effect between the two types of biologically active molecule.

A single-crystal X-ray structure determination (Fig. 1) shows that the molecular structure of (5) consists of a phenoxypropionyl group and a pyrimidine group in approximately opposite directions around the bridge of thiourea, where both groups are in almost the same plane. The configuration of (5) with S1—C10 = 1.637 (3) Å and an N2—C10—S1 angle of 129.5 (2)° is similar to that of 2-chlorobenzoyl-3-(4-methylphenyl)thiourea with S1—C8 = 1.660 (2) Å and an N1—C8—S1 angle of 126.36 (13)° reported by Li et al. (2000). In comparison with this compound, the C—O and C—N distance of the CONH bond [O2—C9 = 1.225 (3) Å versus O—C10 = 1.220 (2) Å and N1—C9 = 1.364 (4) Å versus N2—C10 = 1.357 (2) Å] are in the expected range (Table 1). There are intramolecular N2—H2B···O2 [2.657 (3) Å, 141°] and N1—H1A···O1 [2.533 (3) Å, 113.8°] hydrogen bonds, forming a six-membered ring and a five-membered ring (Table. 2), which indicates the coordination behavior of these potentially multdentate systems. Zhang, Dago and co-workers (Zhang et al., 1996; Cao et al., 1996; Dago et al., 1989) also observed similar intramolecular hydrogen-bonding patterns in the molecular structure of benzoylthioureas.

Experimental top

2,4-Dichlorophenoxypropionic acid and isothiocyanate derivative were synthesized by using the reported method (Jiang et al., 2000; Wang et al., 2001). The synthetic routes are outlined in the scheme. Reaction of isothiocyanate derivative with 4-chloro-6-methoxyl-2-amino-pyrimidine was successfully carried out using acetonitrile as solvent as follows. To a stirred solution of (3) (0.50 g, 1.81 mmol) in acetonitrile (10 ml) was slowly added a solution of 4-chloro-6-methoxyl-2-amino-pyrimidine (0.29 g, 0.81 mmol) in dry acetonitrile (10 ml) over a period of 30 min at room temperature under nitrogen. The mixture was refluxed and stirred for two hours. After evaporation of most of the solvent, the residue was cooled to room temperature and water (5 ml) was added to quench the reaction. Then the residue was repeatedly extracted with 50 ml of diethyl ether. The combined organic layer was washed with water and brine, and then dried over Na2SO4. After evaporation of the solvent, the residue was crystallized from a solution of DMF/C2H5OH/H2O (1:5:1 v/v/v = 1/5/1) to give (5) as yellow crystals in 53% isolated yield.

Refinement top

H atoms were positioned geometrically (C—H = 0.93–0.98 Å) and refined using the riding-model approximation, with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(C).

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SMART; data reduction: SAINT (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1998); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. The structure of the title compound, showing the atom-numbering scheme and displacement ellipsoids at the ??% probability level. Hydrogen bonds are shown as dashed lines.
[Figure 2] Fig. 2. Perspective view of the molecular packing of the title compound, viewed down the a axis. Hydrogen bonds are shown as dashed lines.
N'-(4-Chloro-6-methoxypyrimidin-2-yl)- N-[2-(2,4-dichlorophenoxy)propionyl]thiourea top
Crystal data top
C15H13Cl3N4O3SZ = 2
Mr = 435.70F(000) = 444
Triclinic, P1Dx = 1.517 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.939 (5) ÅCell parameters from 763 reflections
b = 10.183 (7) Åθ = 5.2–54.0°
c = 12.764 (9) ŵ = 0.61 mm1
α = 105.302 (10)°T = 298 K
β = 105.729 (9)°Plate, yellow
γ = 90.698 (11)°0.15 × 0.15 × 0.05 mm
V = 954.1 (11) Å3
Data collection top
Bruker SMART CCD area-detector
diffractometer
3289 independent reflections
Radiation source: fine-focus sealed tube2056 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
ϕ and ω scansθmax = 25.0°, θmin = 1.7°
Absorption correction: multi-scan
(SADABS; Bruker, 1998)
h = 98
Tmin = 0.914, Tmax = 0.970k = 812
3986 measured reflectionsl = 1513
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)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.139H-atom parameters constrained
S = 0.92 w = 1/[σ2(Fo2) + (0.0803P)2]
where P = (Fo2 + 2Fc2)/3
3289 reflections(Δ/σ)max < 0.001
235 parametersΔρmax = 0.35 e Å3
0 restraintsΔρmin = 0.35 e Å3
Crystal data top
C15H13Cl3N4O3Sγ = 90.698 (11)°
Mr = 435.70V = 954.1 (11) Å3
Triclinic, P1Z = 2
a = 7.939 (5) ÅMo Kα radiation
b = 10.183 (7) ŵ = 0.61 mm1
c = 12.764 (9) ÅT = 298 K
α = 105.302 (10)°0.15 × 0.15 × 0.05 mm
β = 105.729 (9)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
3289 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1998)
2056 reflections with I > 2σ(I)
Tmin = 0.914, Tmax = 0.970Rint = 0.029
3986 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.139H-atom parameters constrained
S = 0.92Δρmax = 0.35 e Å3
3289 reflectionsΔρmin = 0.35 e Å3
235 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
Cl11.0076 (2)0.18363 (13)0.50979 (10)0.1061 (5)
Cl21.25298 (12)0.53913 (12)0.32880 (10)0.0828 (4)
Cl30.54098 (14)0.97877 (14)0.36176 (10)0.0955 (4)
N10.9193 (3)0.6547 (3)0.0613 (2)0.0476 (7)
H1A0.99590.62400.10880.057*
N20.8628 (3)0.7666 (3)0.0768 (2)0.0474 (7)
H2B0.75710.73620.08500.057*
N31.0360 (3)0.9066 (3)0.1330 (2)0.0488 (7)
N40.7243 (3)0.8685 (3)0.2104 (2)0.0529 (7)
O10.8935 (3)0.5490 (2)0.2157 (2)0.0558 (6)
O20.6221 (3)0.6516 (3)0.0110 (2)0.0600 (7)
O31.1951 (3)1.0461 (3)0.1932 (2)0.0659 (7)
S11.20328 (11)0.74398 (10)0.02729 (8)0.0601 (3)
C10.9687 (6)0.2914 (4)0.4211 (3)0.0678 (11)
C21.1087 (6)0.3628 (4)0.4124 (3)0.0669 (11)
H2A1.22250.35410.45300.080*
C31.0785 (5)0.4483 (4)0.3423 (3)0.0540 (9)
C40.9088 (4)0.4616 (3)0.2819 (3)0.0505 (8)
C50.7707 (5)0.3861 (4)0.2920 (3)0.0610 (10)
H5A0.65640.39240.25070.073*
C60.8006 (6)0.3017 (4)0.3624 (3)0.0691 (11)
H6A0.70720.25240.36980.083*
C70.7222 (4)0.5686 (4)0.1499 (3)0.0505 (8)
H7A0.65380.47950.11460.061*
C80.6249 (5)0.6609 (4)0.2211 (3)0.0665 (10)
H8A0.60790.62080.27800.100*
H8B0.51270.67300.17390.100*
H8C0.69180.74810.25690.100*
C90.7492 (4)0.6273 (3)0.0583 (3)0.0468 (8)
C100.9893 (4)0.7245 (3)0.0003 (3)0.0427 (7)
C110.8781 (4)0.8511 (3)0.1438 (3)0.0453 (8)
C120.7373 (5)0.9523 (4)0.2726 (3)0.0565 (9)
C130.8900 (5)1.0161 (4)0.2718 (3)0.0572 (9)
H13A0.89331.07420.31660.069*
C141.0405 (4)0.9872 (3)0.1985 (3)0.0503 (8)
C151.3498 (4)1.0112 (4)0.1189 (4)0.0694 (11)
H15A1.45241.05900.12200.104*
H15B1.35830.91440.14260.104*
H15C1.34131.03680.04260.104*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.1870 (14)0.0792 (8)0.0703 (7)0.0294 (8)0.0423 (8)0.0448 (7)
Cl20.0531 (6)0.1018 (9)0.0993 (8)0.0029 (5)0.0139 (5)0.0459 (7)
Cl30.0698 (7)0.1381 (11)0.0930 (8)0.0085 (7)0.0036 (6)0.0764 (8)
N10.0409 (15)0.0528 (17)0.0526 (17)0.0028 (13)0.0095 (12)0.0243 (14)
N20.0372 (14)0.0583 (17)0.0506 (16)0.0015 (13)0.0092 (12)0.0251 (15)
N30.0489 (16)0.0493 (16)0.0533 (16)0.0052 (13)0.0182 (13)0.0193 (14)
N40.0495 (16)0.0634 (19)0.0504 (16)0.0059 (14)0.0130 (13)0.0246 (15)
O10.0449 (13)0.0635 (15)0.0657 (15)0.0014 (11)0.0082 (11)0.0373 (13)
O20.0418 (12)0.0724 (17)0.0680 (15)0.0032 (11)0.0034 (11)0.0362 (14)
O30.0594 (15)0.0680 (17)0.0831 (18)0.0010 (13)0.0266 (13)0.0361 (15)
S10.0420 (5)0.0743 (7)0.0717 (6)0.0076 (4)0.0162 (4)0.0334 (6)
C10.109 (3)0.053 (2)0.048 (2)0.014 (2)0.027 (2)0.020 (2)
C20.084 (3)0.068 (3)0.047 (2)0.024 (2)0.014 (2)0.018 (2)
C30.060 (2)0.055 (2)0.0468 (19)0.0064 (17)0.0145 (17)0.0140 (18)
C40.059 (2)0.047 (2)0.049 (2)0.0063 (17)0.0166 (17)0.0176 (17)
C50.063 (2)0.062 (2)0.062 (2)0.0057 (19)0.0158 (18)0.027 (2)
C60.097 (3)0.056 (2)0.062 (2)0.007 (2)0.033 (2)0.019 (2)
C70.0412 (18)0.055 (2)0.057 (2)0.0027 (16)0.0074 (16)0.0258 (18)
C80.066 (2)0.076 (3)0.072 (3)0.014 (2)0.028 (2)0.035 (2)
C90.0404 (18)0.0437 (19)0.053 (2)0.0032 (15)0.0062 (15)0.0147 (17)
C100.0451 (18)0.0389 (17)0.0429 (17)0.0023 (14)0.0145 (14)0.0076 (15)
C110.0480 (19)0.0464 (19)0.0424 (18)0.0029 (15)0.0154 (15)0.0114 (16)
C120.059 (2)0.066 (2)0.049 (2)0.0097 (19)0.0147 (17)0.0241 (19)
C130.068 (2)0.059 (2)0.055 (2)0.0076 (19)0.0243 (18)0.0254 (19)
C140.058 (2)0.0449 (19)0.054 (2)0.0037 (17)0.0240 (17)0.0144 (17)
C150.055 (2)0.069 (3)0.091 (3)0.0034 (19)0.023 (2)0.030 (2)
Geometric parameters (Å, º) top
Cl1—C11.748 (4)C1—C21.365 (6)
Cl2—C31.728 (4)C2—C31.384 (5)
Cl3—C121.734 (4)C2—H2A0.9300
N1—C91.364 (4)C3—C41.387 (5)
N1—C101.398 (4)C4—C51.384 (5)
N1—H1A0.8600C5—C61.379 (5)
N2—C101.358 (4)C5—H5A0.9300
N2—C111.390 (4)C6—H6A0.9300
N2—H2B0.8600C7—C81.502 (5)
N3—C141.323 (4)C7—C91.507 (4)
N3—C111.326 (4)C7—H7A0.9800
N4—C111.329 (4)C8—H8A0.9600
N4—C121.330 (4)C8—H8B0.9600
O1—C41.367 (4)C8—H8C0.9600
O1—C71.439 (4)C12—C131.364 (5)
O2—C91.225 (3)C13—C141.392 (5)
O3—C141.337 (4)C13—H13A0.9300
O3—C151.446 (4)C15—H15A0.9600
S1—C101.637 (3)C15—H15B0.9600
C1—C61.362 (6)C15—H15C0.9600
C9—N1—C10130.5 (3)C8—C7—H7A108.9
C9—N1—H1A114.8C9—C7—H7A108.9
C10—N1—H1A114.8C7—C8—H8A109.5
C10—N2—C11129.9 (3)C7—C8—H8B109.5
C10—N2—H2B115.0H8A—C8—H8B109.5
C11—N2—H2B115.0C7—C8—H8C109.5
C14—N3—C11115.6 (3)H8A—C8—H8C109.5
C11—N4—C12113.4 (3)H8B—C8—H8C109.5
C4—O1—C7119.5 (2)O2—C9—N1123.8 (3)
C14—O3—C15116.8 (3)O2—C9—C7120.0 (3)
C6—C1—C2121.8 (4)N1—C9—C7116.2 (3)
C6—C1—Cl1119.4 (3)N2—C10—N1112.5 (3)
C2—C1—Cl1118.8 (3)N2—C10—S1129.5 (2)
C1—C2—C3119.0 (4)N1—C10—S1118.0 (2)
C1—C2—H2A120.5N3—C11—N4128.1 (3)
C3—C2—H2A120.5N3—C11—N2118.8 (3)
C2—C3—C4120.6 (3)N4—C11—N2113.0 (3)
C2—C3—Cl2120.1 (3)N4—C12—C13125.4 (3)
C4—C3—Cl2119.3 (3)N4—C12—Cl3115.6 (3)
O1—C4—C5125.5 (3)C13—C12—Cl3119.0 (3)
O1—C4—C3115.9 (3)C12—C13—C14114.6 (3)
C5—C4—C3118.6 (3)C12—C13—H13A122.7
C6—C5—C4120.7 (4)C14—C13—H13A122.7
C6—C5—H5A119.6N3—C14—O3119.2 (3)
C4—C5—H5A119.6N3—C14—C13122.8 (3)
C1—C6—C5119.2 (4)O3—C14—C13118.0 (3)
C1—C6—H6A120.4O3—C15—H15A109.5
C5—C6—H6A120.4O3—C15—H15B109.5
O1—C7—C8112.1 (3)H15A—C15—H15B109.5
O1—C7—C9106.9 (2)O3—C15—H15C109.5
C8—C7—C9111.0 (3)H15A—C15—H15C109.5
O1—C7—H7A108.9H15B—C15—H15C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C15—H15C···N2i0.962.963.688 (5)134
C8—H8C···O3i0.962.673.435 (5)138
C8—H8B···S1ii0.962.893.837 (4)171
C7—H7A···S1iii0.982.963.545 (4)120
C7—H7A···O2iv0.982.403.281 (4)150
N2—H2B···O20.861.932.657 (3)141
N1—H1A···O10.862.062.533 (3)114
Symmetry codes: (i) x+2, y+2, z; (ii) x1, y, z; (iii) x+2, y+1, z; (iv) x+1, y+1, z.

Experimental details

Crystal data
Chemical formulaC15H13Cl3N4O3S
Mr435.70
Crystal system, space groupTriclinic, P1
Temperature (K)298
a, b, c (Å)7.939 (5), 10.183 (7), 12.764 (9)
α, β, γ (°)105.302 (10), 105.729 (9), 90.698 (11)
V3)954.1 (11)
Z2
Radiation typeMo Kα
µ (mm1)0.61
Crystal size (mm)0.15 × 0.15 × 0.05
Data collection
DiffractometerBruker SMART CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 1998)
Tmin, Tmax0.914, 0.970
No. of measured, independent and
observed [I > 2σ(I)] reflections
3986, 3289, 2056
Rint0.029
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.139, 0.92
No. of reflections3289
No. of parameters235
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.35, 0.35

Computer programs: SMART (Bruker, 1998), SMART, SAINT (Bruker, 1998), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1998), SHELXTL.

Selected geometric parameters (Å, º) top
N1—C91.364 (4)O2—C91.225 (3)
N1—C101.398 (4)S1—C101.637 (3)
N2—C101.358 (4)
C9—N1—C10130.5 (3)N2—C10—N1112.5 (3)
O1—C7—C9106.9 (2)N2—C10—S1129.5 (2)
N1—C9—C7116.2 (3)N1—C10—S1118.0 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C15—H15C···N2i0.962.963.688 (5)134
C8—H8C···O3i0.962.673.435 (5)138
C8—H8B···S1ii0.962.893.837 (4)171
C7—H7A···S1iii0.982.963.545 (4)120
C7—H7A···O2iv0.982.403.281 (4)150
N2—H2B···O20.861.932.657 (3)141
N1—H1A···O10.862.062.533 (3)114
Symmetry codes: (i) x+2, y+2, z; (ii) x1, y, z; (iii) x+2, y+1, z; (iv) x+1, y+1, z.
 

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