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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2307.
Published online 2010 August 18. doi:  10.1107/S1600536810031740
PMCID: PMC3008046

4-(4-Chloro-5-methyl-3-trifluoro­meth­yl-1H-pyrazol-1-yl)-6-(prop-2-ynyl­oxy)pyrimidine

Abstract

The molecule of the title compound, C12H8ClF3N4O, is twisted as indicated by the C—O—C—C torsion angle of 76.9 (3)°. Moreover, the trifluoro­methyl group shows rotational disorder of the F atoms, with site-occupancy factors of 0.653 (6) and 0.347 (6). The dihedral angle between the rings is 1.88 (12) Å.

Related literature

For the applications of pyrazole derivatives, see: Hirai et al. (2002 [triangle]); Krishnaiah et al. (2002 [triangle]); Ohno et al. (2004 [triangle]); Li et al. (2008 [triangle]); Shiga et al. (2003 [triangle]); Vicentini et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2307-scheme1.jpg

Experimental

Crystal data

  • C12H8ClF3N4O
  • M r = 316.67
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2307-efi1.jpg
  • a = 7.8331 (13) Å
  • b = 7.7258 (12) Å
  • c = 21.757 (4) Å
  • β = 99.270 (11)°
  • V = 1299.5 (4) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 3.02 mm−1
  • T = 173 K
  • 0.20 × 0.20 × 0.10 mm

Data collection

  • Rigaku R-AXIS RAPID IP area-detector diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 [triangle]) T min = 0.583, T max = 0.752
  • 8543 measured reflections
  • 2361 independent reflections
  • 2009 reflections with I > 2σ(I)
  • R int = 0.043

Refinement

  • R[F 2 > 2σ(F 2)] = 0.044
  • wR(F 2) = 0.106
  • S = 1.07
  • 2361 reflections
  • 220 parameters
  • 69 restraints
  • H-atom parameters constrained
  • Δρmax = 0.31 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: RAPID-AUTO (Rigaku, 2001 [triangle]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP (Siemens, 1998 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810031740/rn2068sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810031740/rn2068Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the Agricultural Public Sector Research and Special Funds (200803021) and the Major State Basic Reasearch Development Program of China (No. 2006CB101907 and No. 2010CB126106).

supplementary crystallographic information

Comment

There is much agrochemical interest in pyrazole derivatives because of their excellent bioactivity (Krishnaiah et al., 2002; Ohno et al., 2004; Li et al., 2008 Shiga et al., 2003; Vicentini et al., 2007). Numerous herbicides such as pyrazolate, pyrazoxyfen, benzofenap, pyraflufen-ethyl, fluazolate and pyrazosulfuron-ethyl with pyrazole moieties were commercialized (Hirai et al., 2002). Recently, a novel pyrazole derivative (I) with a trifluoromethyl group was synthesized. The trifluoromethyl group shows rotational disorder of the F atoms, with site occupancy factors of 0.653 (6) and 0.347 (6). This molecule is twisted, prop-2-ynyloxy is out of the pyrimidine ring plane, as indicated by the C(8)—O(1)—C(10)—C(11) torsion angle of 76.9 (3)°. The crystal structure of the title compound is shown in Fig. 1.

Experimental

The title compound (0.15 g) was dissolved in the mixed solvent of ethanol and acetone (25 mL) at room temperature. Colorless single crystals of compound (I) were obtained through slow evaporation after two weeks.

Refinement

The trifluoromethyl group shows rotational disorder of the F atoms, with site occupancy factors of 0.653 (6) and 0.347 (6).All the hydrogen atoms were placed at their geometrical position with C—H = 0.93-0.98Å and Uiso(H) = 1.2-1.5Ueq(C).

Figures

Fig. 1.
The structure of the title compound with labeling scheme; displacement ellipsoids are shown at the 30% probability level and atoms F1', F2' and F3' representing the smaller fraction of the disordered trifluoromethyl group have been excluded.

Crystal data

C12H8ClF3N4OF(000) = 640
Mr = 316.67Dx = 1.619 Mg m3
Monoclinic, P21/nCu Kα radiation, λ = 1.54186 Å
a = 7.8331 (13) ÅCell parameters from 564 reflections
b = 7.7258 (12) Åθ = 2.2–68.3°
c = 21.757 (4) ŵ = 3.02 mm1
β = 99.270 (11)°T = 173 K
V = 1299.5 (4) Å3Platelet, colorless
Z = 40.20 × 0.20 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID IP area-detector diffractometer2361 independent reflections
Radiation source: rotating anode2009 reflections with I > 2σ(I)
graphiteRint = 0.043
ω scans at fixed χ = 45°θmax = 68.3°, θmin = 4.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)h = −9→9
Tmin = 0.583, Tmax = 0.752k = −9→6
8543 measured reflectionsl = −26→22

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044H-atom parameters constrained
wR(F2) = 0.106w = 1/[σ2(Fo2) + (0.0399P)2 + 0.8523P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.016
2361 reflectionsΔρmax = 0.31 e Å3
220 parametersΔρmin = −0.22 e Å3
69 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0054 (5)

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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)

xyzUiso*/UeqOcc. (<1)
Cl10.05485 (8)0.66461 (9)0.12912 (3)0.0419 (2)
F10.0581 (14)1.0026 (19)0.2067 (6)0.068 (3)0.65 (3)
F20.1586 (17)1.2382 (8)0.1787 (5)0.066 (2)0.65 (3)
F30.3301 (10)1.040 (2)0.2184 (4)0.080 (3)0.65 (3)
F1'0.038 (2)1.038 (4)0.2018 (12)0.062 (4)0.35 (3)
F2'0.229 (4)1.227 (2)0.1908 (8)0.074 (4)0.35 (3)
F3'0.298 (3)0.977 (3)0.2215 (7)0.076 (4)0.35 (3)
O10.4744 (2)1.4528 (2)−0.08155 (7)0.0328 (4)
N10.2473 (2)1.0968 (3)0.07612 (9)0.0307 (5)
N20.2397 (2)0.9953 (2)0.02454 (9)0.0273 (4)
N30.2814 (3)0.9661 (3)−0.07855 (9)0.0339 (5)
N40.4008 (2)1.1943 (3)−0.13275 (9)0.0300 (5)
C10.1864 (3)0.9977 (3)0.11729 (11)0.0298 (5)
C20.1401 (3)0.8333 (3)0.09272 (11)0.0292 (5)
C30.1757 (3)0.8320 (3)0.03301 (11)0.0280 (5)
C40.1845 (3)1.0661 (4)0.18093 (13)0.0407 (6)
C50.1542 (3)0.6869 (3)−0.01239 (12)0.0369 (6)
H5A0.26300.6681−0.02820.055*
H5B0.06260.7155−0.04710.055*
H5C0.12280.58140.00820.055*
C60.2966 (3)1.0682 (3)−0.02856 (10)0.0261 (5)
C70.3362 (3)1.0361 (3)−0.12775 (12)0.0349 (6)
H7A0.32840.9648−0.16370.042*
C80.4111 (3)1.2901 (3)−0.08172 (11)0.0271 (5)
C90.3614 (3)1.2338 (3)−0.02663 (10)0.0275 (5)
H9A0.37141.30420.00960.033*
C100.5077 (3)1.5223 (3)−0.14053 (11)0.0350 (6)
H10A0.56621.4332−0.16240.042*
H10B0.58611.6231−0.13250.042*
C110.3481 (3)1.5756 (3)−0.18034 (11)0.0355 (6)
C120.2244 (4)1.6239 (4)−0.21331 (13)0.0516 (8)
H120.12401.6632−0.24010.062*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0394 (4)0.0400 (4)0.0474 (4)−0.0066 (3)0.0100 (3)0.0144 (3)
F10.087 (5)0.079 (5)0.049 (3)−0.028 (4)0.042 (4)−0.006 (3)
F20.111 (5)0.046 (2)0.048 (3)0.007 (3)0.035 (3)−0.0082 (17)
F30.055 (2)0.137 (6)0.046 (3)0.014 (3)−0.0046 (18)−0.036 (3)
F1'0.040 (5)0.092 (9)0.058 (6)0.002 (5)0.021 (4)−0.015 (6)
F2'0.128 (9)0.058 (5)0.044 (5)−0.048 (6)0.034 (6)−0.014 (4)
F3'0.089 (7)0.092 (8)0.038 (4)0.028 (5)−0.015 (4)0.006 (5)
O10.0436 (10)0.0302 (9)0.0243 (9)−0.0109 (8)0.0043 (7)0.0016 (7)
N10.0350 (11)0.0304 (11)0.0280 (11)−0.0009 (9)0.0088 (8)−0.0017 (8)
N20.0286 (10)0.0263 (10)0.0275 (10)−0.0011 (8)0.0057 (8)0.0002 (8)
N30.0423 (12)0.0294 (11)0.0307 (11)−0.0047 (9)0.0079 (9)−0.0037 (9)
N40.0310 (10)0.0307 (11)0.0288 (11)−0.0015 (9)0.0064 (8)−0.0027 (8)
C10.0274 (12)0.0326 (13)0.0302 (13)0.0023 (10)0.0070 (9)0.0035 (10)
C20.0239 (11)0.0312 (13)0.0329 (13)−0.0002 (10)0.0058 (9)0.0075 (10)
C30.0220 (11)0.0263 (12)0.0350 (13)0.0006 (9)0.0023 (9)0.0026 (10)
C40.0404 (14)0.0476 (17)0.0370 (15)−0.0060 (13)0.0149 (12)0.0012 (12)
C50.0393 (13)0.0305 (13)0.0405 (15)−0.0069 (11)0.0053 (11)−0.0012 (11)
C60.0237 (11)0.0276 (12)0.0269 (12)0.0016 (9)0.0040 (9)0.0013 (9)
C70.0447 (14)0.0318 (14)0.0292 (13)−0.0044 (11)0.0095 (11)−0.0075 (10)
C80.0243 (11)0.0260 (12)0.0305 (13)−0.0012 (9)0.0032 (9)0.0005 (10)
C90.0320 (12)0.0254 (12)0.0248 (12)−0.0024 (10)0.0035 (9)−0.0017 (9)
C100.0406 (14)0.0362 (14)0.0290 (13)−0.0099 (11)0.0078 (10)0.0053 (11)
C110.0497 (15)0.0310 (14)0.0269 (13)0.0004 (12)0.0093 (11)−0.0015 (10)
C120.0613 (19)0.0503 (18)0.0402 (16)0.0150 (15)−0.0008 (14)−0.0051 (14)

Geometric parameters (Å, °)

Cl1—C21.715 (2)C1—C21.403 (3)
F1—C41.309 (7)C1—C41.484 (4)
F2—C41.344 (6)C2—C31.372 (3)
F3—C41.306 (7)C3—C51.486 (3)
F1'—C41.316 (12)C5—H5A0.9800
F2'—C41.300 (11)C5—H5B0.9800
F3'—C41.339 (10)C5—H5C0.9800
O1—C81.352 (3)C6—C91.374 (3)
O1—C101.452 (3)C7—H7A0.9500
N1—C11.324 (3)C8—C91.389 (3)
N1—N21.362 (3)C9—H9A0.9500
N2—C31.380 (3)C10—C111.461 (3)
N2—C61.420 (3)C10—H10A0.9900
N3—C71.330 (3)C10—H10B0.9900
N3—C61.333 (3)C11—C121.170 (4)
N4—C81.326 (3)C12—H120.9500
N4—C71.334 (3)
C8—O1—C10117.33 (18)F3—C4—C1112.9 (4)
C1—N1—N2104.57 (19)F1—C4—C1112.9 (7)
N1—N2—C3112.62 (19)F1'—C4—C1113.8 (12)
N1—N2—C6117.62 (18)F3'—C4—C1109.1 (8)
C3—N2—C6129.8 (2)F2—C4—C1110.0 (4)
C7—N3—C6114.7 (2)C3—C5—H5A109.5
C8—N4—C7114.6 (2)C3—C5—H5B109.5
N1—C1—C2111.4 (2)H5A—C5—H5B109.5
N1—C1—C4119.0 (2)C3—C5—H5C109.5
C2—C1—C4129.5 (2)H5A—C5—H5C109.5
C3—C2—C1106.7 (2)H5B—C5—H5C109.5
C3—C2—Cl1125.8 (2)N3—C6—C9124.0 (2)
C1—C2—Cl1127.46 (19)N3—C6—N2115.5 (2)
C2—C3—N2104.7 (2)C9—C6—N2120.5 (2)
C2—C3—C5128.1 (2)N3—C7—N4127.9 (2)
N2—C3—C5127.3 (2)N3—C7—H7A116.1
F2'—C4—F381.9 (8)N4—C7—H7A116.1
F2'—C4—F1119.3 (10)N4—C8—O1119.6 (2)
F3—C4—F1108.6 (7)N4—C8—C9124.1 (2)
F2'—C4—F1'109.0 (14)O1—C8—C9116.3 (2)
F3—C4—F1'118.7 (11)C6—C9—C8114.7 (2)
F1—C4—F1'14.2 (15)C6—C9—H9A122.6
F2'—C4—F3'104.4 (9)C8—C9—H9A122.6
F3—C4—F3'24.2 (8)O1—C10—C11111.7 (2)
F1—C4—F3'89.7 (10)O1—C10—H10A109.3
F1'—C4—F3'102.3 (13)C11—C10—H10A109.3
F2'—C4—F225.2 (10)O1—C10—H10B109.3
F3—C4—F2106.6 (5)C11—C10—H10B109.3
F1—C4—F2105.4 (7)H10A—C10—H10B107.9
F1'—C4—F292.4 (11)C12—C11—C10177.0 (3)
F3'—C4—F2127.7 (7)C11—C12—H12180.0
F2'—C4—C1116.8 (7)
C1—N1—N2—C3−0.5 (2)C2—C1—C4—F1'−49.2 (13)
C1—N1—N2—C6179.62 (18)N1—C1—C4—F3'−112.0 (12)
N2—N1—C1—C20.1 (2)C2—C1—C4—F3'64.2 (13)
N2—N1—C1—C4177.0 (2)N1—C1—C4—F232.5 (7)
N1—C1—C2—C30.3 (3)C2—C1—C4—F2−151.3 (7)
C4—C1—C2—C3−176.2 (2)C7—N3—C6—C90.6 (3)
N1—C1—C2—Cl1−179.60 (17)C7—N3—C6—N2−179.65 (19)
C4—C1—C2—Cl13.9 (4)N1—N2—C6—N3−177.90 (19)
C1—C2—C3—N2−0.6 (2)C3—N2—C6—N32.3 (3)
Cl1—C2—C3—N2179.31 (16)N1—N2—C6—C91.8 (3)
C1—C2—C3—C5178.3 (2)C3—N2—C6—C9−178.0 (2)
Cl1—C2—C3—C5−1.8 (4)C6—N3—C7—N4−1.0 (4)
N1—N2—C3—C20.7 (2)C8—N4—C7—N30.4 (4)
C6—N2—C3—C2−179.5 (2)C7—N4—C8—O1−179.9 (2)
N1—N2—C3—C5−178.1 (2)C7—N4—C8—C90.6 (3)
C6—N2—C3—C51.7 (4)C10—O1—C8—N47.7 (3)
N1—C1—C4—F2'6.0 (16)C10—O1—C8—C9−172.72 (19)
C2—C1—C4—F2'−177.7 (16)N3—C6—C9—C80.2 (3)
N1—C1—C4—F3−86.4 (9)N2—C6—C9—C8−179.49 (19)
C2—C1—C4—F389.9 (9)N4—C8—C9—C6−0.9 (3)
N1—C1—C4—F1150.0 (8)O1—C8—C9—C6179.58 (19)
C2—C1—C4—F1−33.8 (8)C8—O1—C10—C1176.9 (3)
N1—C1—C4—F1'134.5 (13)O1—C10—C11—C12149 (6)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RN2068).

References

  • Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
  • Hirai, K., Uchida, A. & Ohno, R. (2002). Herbicide Classes in Development, edited by P. Boger, K. Hirai & K. Wakabyashi, pp. 279–289. Heidelberg: Springer-Verlag.
  • Krishnaiah, A. & Narsaiah, B. (2002). J Fluorine Chem 115, 9–11.
  • Li, H. B., Zhu, Y. Q., Song, X. W., Hu, F. Z., Liu, B., Li, Y. H., Niu, Z. X., Liu, P., Wang, Z. H., Song, H. B., Zou, X. M. & Yang, H. Z. (2008). J Agric Food Chem 56, 9535–9542. [PubMed]
  • Ohno, R., Watanabe, A., Nagaoka, M., Ueda, T., Sakurai, H., Hori, M. & Hirai, K. (2004). J Pestic Sci 29, 15-26.
  • Rigaku (2001). RAPID-AUTO Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Shiga, Y., Okada, I., Ikeda, Y., Takizawa, E. & Fukuchi, T. (2003). J Pestic Sci 28, 313–314.
  • Siemens (1998). XP Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.
  • Vicentini, C. B., Romagnoli, C., Andreotti, E. & Mares, D. (2007). J Agric Food Chem 55, 10331–10338. [PubMed]

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