Home Crystal structure of 4-((2-methyl-6-(trifluoromethyl)pyrimidin-4-yl)oxy)benzoic acid, C13H9F3N2O3
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Crystal structure of 4-((2-methyl-6-(trifluoromethyl)pyrimidin-4-yl)oxy)benzoic acid, C13H9F3N2O3

  • Wen-Neng Wu ORCID logo EMAIL logo , Qiang Fei , Yong-Hui Ge and Xiu-Hai Gan
Published/Copyright: March 25, 2020

Abstract

C13H9F3N2O3, monoclinic, P21/c (no. 14), a = 8.6952(7) Å, b = 19.6715(18) Å, c = 8.0995(8) Å, β = 110.691(3)°, V = 1296.0(2) Å3, Z = 4, Rgt(F) = 0.0558, wRref(F2) = 0.1358, T = 298(2) K.

CCDC no.: 1965889

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Colourless block
Size:0.30 × 0.27 × 0.10 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.14 mm−1
Diffractometer, scan mode:CCD, φ and ω
θmax, completeness:25.0°, >99%
N(hkl)measured, N(hkl)unique, Rint:6503, 2290, 0.066
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 1237
N(param)refined:191
Programs:Bruker [1], SHELX [2]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

AtomxyzUiso*/Ueq
F10.0828(2)0.81901(13)1.3721(3)0.1159(9)
F2−0.0740(2)0.83549(12)1.1076(3)0.1119(8)
F30.0187(2)0.73781(13)1.1919(3)0.1068(8)
N10.4796(3)0.83773(12)1.0814(3)0.0539(6)
N20.3434(3)0.78537(13)1.2559(3)0.0606(7)
O10.8158(2)0.95736(13)0.4385(3)0.0912(8)
H10.89430.97050.41330.137*
O20.9716(3)0.99741(13)0.7010(3)0.0903(8)
O30.3322(2)0.90623(11)0.8472(2)0.0673(6)
C10.8430(4)0.96901(17)0.6009(4)0.0653(9)
C20.7139(3)0.94836(14)0.6706(4)0.0557(8)
C30.7361(3)0.95991(15)0.8464(4)0.0600(8)
H30.83440.97840.92150.072*
C40.6131(3)0.94408(15)0.9102(4)0.0606(8)
H40.62740.95191.02790.073*
C50.4690(3)0.91658(14)0.7975(4)0.0571(8)
C60.4459(3)0.90429(16)0.6236(4)0.0659(9)
H60.34810.88520.54900.079*
C70.5691(3)0.92053(15)0.5612(4)0.0661(9)
H70.55420.91250.44340.079*
C80.3410(3)0.86677(15)0.9872(4)0.0552(8)
C90.4763(3)0.79749(15)1.2135(4)0.0546(8)
C100.2060(3)0.81714(16)1.1579(4)0.0558(8)
C110.1957(3)0.85940(16)1.0215(4)0.0607(8)
H110.09900.88170.95600.073*
C120.6342(3)0.76481(16)1.3207(4)0.0727(9)
H12A0.61900.73911.41460.109*
H12B0.71600.79921.36950.109*
H12C0.66940.73501.24720.109*
C130.0579(4)0.8031(2)1.2070(5)0.0748(10)

Source of material

All solvents were dried by standard methods in advance and distilled before use. 4-Chloro-2-methyl-6-(trifluoromethyl)pyrimidine (0.01 mol), Cs2CO3 (0.02 mol), and ethyl 4-hydroxybenzoate (0.012 mol) were added in a 100 mL three-necked round-bottomed flask. The samples were reacted for 2–3 h at room temperature, and the solvent was removed. Water was added to the residue, the precipitate formed was filtered off and recrystallized from ethanol to yield 70% of methyl 4-((2-methyl-6-(trifluoromethyl)-pyrimidin-4-yl)oxy)benzoate. 1H NMR (DMSO-d6, ppm) δ: 8.06 (d, 2H, J = 9.0 Hz, Ph-H), 6.67 7.58 (s, 1H, pyrimidine-H), 7.42 (d, 2H, J = 9.0 Hz, Ph-H), 3.87 (s, 3H, CH3O), 2.51 (s, 3H, CH3); 13C NMR (DMSO-d6, ppm) δ: 170.05, 169.67, 165.95, 156.71 (q, J = 35.25 Hz), 155.97, 131.60, 127.75, 122.39, 121.78 (q, J = 272.85 Hz), 103.83, 52.69, 25.82; HRMS (ESI): Calcd. for C14H11F3N2O3 [M+H]+: 313.0797; found: 313.0795. Methyl 4-((2-methyl-6-(trifluoromethyl)pyrimidin-4-yl)oxy)benzoate (0.01 mol), THF (10 mL), KOH (0.02 mol), and H2O (5 mL) were added. The samples were reacted for 6 h at room temperature, and the solvent was removed. Water was added to the residue and acidified with concentrated hydrochloric acid to pH 2–3. The precipitate formed was filtered off and recrystallized from ethanol to yield 70% of title compound. Colorless single crystals were grown and obtained in ethanol after 8 h. 1H NMR (DMSO-d6, ppm) δ: 12.56 (s, 1H), 7.80 (d, 2H, J = 8.4 Hz, Ph-H), 7.48 (s, 1H, pyrimidine-H), 6.83 (d, 2H, J = 8.4 Hz, Ph-H), 2.35 (s, 3H, CH3); 13C NMR (DMSO-d6, ppm) δ: 167.63, 162.69, 162.06, 151.96 (q, J = 35.25 Hz), 131.98, 122.09 (q, J = 273.00 Hz), 121.82, 115.56, 111.07, 25.90; HRMS (ESI): Calcd. for C13H9F3N2O3 [M+H]+: 299.0640; found: 299.0638.

Experimental details

The room-temperature structure was refined using full-matrix least-squares as implemented in the SHELXL program [2]. H atoms were constrained to ride on their pivot atoms.

Comment

Pyrimidine compounds and their derivatives have been playing a significant role in the pharmaceutical and pesticide chemistry [3], [4]. In recent years, many pyrimidine compounds have displayed applications as antifungal, antibacterial, insecticidal, herbicidal, and antiviral agents [5], [6], [7], [8], [9], [10]. A series of pyrimidine derivatives have been synthesized, which show novel structure and herbicidal activity [11].

The title structure crystallises in the monoclinic space group P21/c with one molecule in the asymmetric unit. All bond lengths and angles are within normal ranges. The angle subtended by C(5), O(3) and C(8) is 121.5(2)°. The bond lengths of C(1)-O(1) and C(1)-O(2) are 1.272(3) and 1.257(3) Å respectively, in accordance with the single- and double-bond characters of these bonds, respectively. The hydroxy H atom could be located on a difference Fourier map. In the structure of the title compound there are two intermolecular hydrogen bonds, O(1)—H(1)⋯O(2) [D⋯A 2.638(4) Å, DHA = 164.9°] and C(12)—H(12A)⋯N(1) [D⋯A 3.513(4) Å, DHA = 159.9°].

Acknowledgements

We gratefully acknowledge support by China Postdoctoral Science Foundation (NO.: 2017M623070), the National Natural Science Foundation of China (NO.: 31701821), the Guizhou Science and Technology Fund Project (NO.: [2019]1015), Guiyang University Hospital Research Project (NO.: 2017ZD10), The Guizhou province Biological and Pharmaceutical engineering Research Centerand (NO.: QJHKY[2019]051), and the Construction Project of Key Laboratories from the Education Department of Guizhou Province (No.: QJHKY[2018]001).

References

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Received: 2020-01-08
Accepted: 2020-02-29
Published Online: 2020-03-25
Published in Print: 2020-06-25

©2020 Wen-Neng Wu et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 Public License.

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  71. Crystal structure of 8a,8a′′-oxybis(8aH-8,9-dioxa-3a1λ4-aza-8aλ4-borabenzo[fg]tetracene), C34H22B2N2O5
  72. Crystal structure of bromido-triphenyl-(triphenylarsine oxide-κO)tin(IV), C36H30AsBrOSn
  73. Crystal structure of catena-poly[chlorido-(μ2-formato-κ2O:O′)-(1,10-phenathroline-κ2N,N′)copper(II)], C26H18Cl2Cu2N4O4
  74. The crystal structure of poly[(μ10-5-carboxyisophthalato-κ10O)disodium], C9H4Na2O6
  75. The crystal structure of 3,5-difluoroisonicotinic acid, C6H3F2NO2
  76. The crystal structure of ethyl-1-(N-(adamantan-1-yl)-carbamothioyl)piperidine-4-carboxylate, C19H30N2O2S
  77. Crystal structure of 5-methyl-3-phenyl-1-tosyl-1,2,3,4-tetrahydropyridine, C19H21NO2S
  78. Crystal structure of bis((3-chlorosalicylidene)-ethylenediaminato-κ4N,N′,O,O′)nickel (II), C16H12Cl2NiN2O2
  79. Crystal structure of (E)-N′-(2-chloro-6-hydroxybenzylidene)-4-hydroxybenzohydrazide — dihydrofuran-2(3H)-one (1/1), C18H17ClN2O5
  80. Crystal structure of bis((3-bromosalicylidene)-ethylenediaminato-κ4N,N′,O,O′) nickel (II), C16H12Br2NiN2O2
  81. Crystal structure of trimethylsulfoxonium tetrachloridocobaltate(II) [(CH3)3SO]2CoCl4
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