Home Physical Sciences Crystal structure of 4-chloro-2-methyl-6-(4-(trifluoromethoxy)phenyl)pyrimidine, C12H8ClF3N2O
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Crystal structure of 4-chloro-2-methyl-6-(4-(trifluoromethoxy)phenyl)pyrimidine, C12H8ClF3N2O

  • Jean-Luc Bertrand , Cristian O. Salas and Iván Brito EMAIL logo
Published/Copyright: November 16, 2017

Abstract

C12H8ClF3N2O, tetragonal, I4̅ (no. 82), a = 23.280(6) Å, c = 4.7191(15) Å, V = 2557.6(15) Å3, Z = 8, Rgt = 0.0700, wRref(F2) = 0.1933, T = 296(2) K.

CCDC no.: 1474902

The asymmetric unit of the title crystal structure is shown in the figure. Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Block, colorless
Size:0.13 × 0.13 × 0.05 mm
Wavelength:Cu Kα radiation (1.54178 Å)
μ:2.96 mm−1
Diffractometer, scan mode:Bruker D8-Venture IμS, φ and ω-scans
2θmax, completeness:58.9°, >95%
N(hkl)measured, N(hkl)unique, Rint:2940, 1505, 0.070
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 931
N(param)refined:173
Programs:Bruker programs [1], SHELX [2], OLEX2 [3], PLATON [4]
Table 2:

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

AtomxyzUiso*/Ueq
Cl10.58916(11)0.52207(10)0.2176(7)0.1145(12)
O10.6442(4)0.8823(3)0.949(4)0.181(6)
F10.6130(3)0.9653(3)1.030(2)0.166(3)
F20.5887(6)0.9236(4)0.663(3)0.215(5)
F30.5547(4)0.8953(4)1.028(3)0.186(4)
N10.6986(3)0.6179(3)0.815(2)0.094(3)
N20.6733(4)0.5322(3)0.578(2)0.093(3)
C10.7532(4)0.5307(5)0.904(3)0.119(4)
H1B0.78580.52880.77920.179*
H1C0.74080.49250.94960.179*
H1A0.76390.55051.07460.179*
C20.7058(4)0.5622(4)0.762(3)0.096(3)
C30.6554(3)0.6462(4)0.688(3)0.086(3)
C40.6193(4)0.6178(4)0.496(3)0.088(3)
H40.58920.63620.40430.106*
C50.6318(4)0.5604(4)0.453(3)0.089(3)
C60.6498(4)0.7085(4)0.758(3)0.091(3)
C70.6881(4)0.7342(4)0.940(3)0.114(4)
H70.71710.71251.02220.136*
C80.6841(5)0.7915(5)1.000(3)0.120(4)
H80.70940.80851.12750.144*
C90.6423(5)0.8236(4)0.871(4)0.125(5)
C100.6020(5)0.7994(4)0.694(4)0.128(5)
H100.57250.82150.61780.154*
C110.6064(4)0.7413(4)0.634(3)0.111(4)
H110.58030.72420.51030.133*
C120.6041(9)0.9153(7)0.928(5)0.137(5)

Source of material

The title compound suitable was obtained from: 4,6-dichloro-2-methylpyrimidine (100 mg, 0.61 mmol) and (4-(trifluoromethoxy)phenyl)boronic acid (189 mg, 0.92 mmol) in dioxane (2 mL), which were added to a solution of dichlorido-bis(triphenylphosphine)palladium(II) (17 mg, 0.024 mmol) and Cs2CO3 2 M (1 mL, 2 mmol). The mixture was stirred at 80 °C for 30 min. in a microwave reactor. The mixture was cooled to room temperature and extracted with EtOAc, and the organic layer was dried over anhydrous Na2SO4. After filtration, the filtrate was evaporated and purified by chromatography (petroleum ether/EtOAc, 10:1) to give the product as a white solid (71 mg, 40%). Colorless crystals suitable for X-ray analysis were grown in chloroform by slow evaporation of the solvent at room temperature over a period of 24 h.

IR (KBr, cm−1): 1611 (Nsp2-Csp2), 1508 (Csp2-Cl), 1265 (Csp2-O). 1H NMR (CDCl3, 400 MHz) δ 8.08 (d, J = 8.8 Hz, 2H, H-7), 7.49 (s, 1H, H-3), 7.32 (d, J = 8.3 Hz, 2H, H-6), 2.75 (s, 3H, H-12) ppm. 13C NMR (CDCl3, 101 MHz) δ 169.48 (C-1), 164.38 (C-4), 161.92 (C-2), 151.69–151.67 (C-11), 134.33 (C-5), 129.18 (C-7), 124.35–116.64 (C-11), 121.21 (C-6), 114,00 (C-3), 26.08 (C-12) ppm. MS calculated for C12H9ClF3N2O [M + H] 289.04 found 288.80.

Experimental details

H atoms were located in the difference Fourier map, but refined with fixed individual displacement parameters, using a riding model with C—H distances of 0.93 Å (for aromatic rings), 0.96 Å (for CH3 group) with U(H) values of 1.2Ueq(C) for CH in aromatic moiety and 1.5Ueq(C) for CH3.

Discussion

The pyrimidine nucleus, as well as other nitrogenous heterocyclic systems, have been considered in the design of various compounds with diverse biological properties, especially for the development of new anti-tumor agents [5], [6], [7], [8]. Considering this antecedents, several synthetic efforts have been carried out to obtain new 2,4,6-trisubstituted pyrimidine derivatives and later, study their cytotoxic effects in different tumor cell lines. To access a compound such as our here reported, a pivotal step is a carbon-carbon Suzuki coupling, which is obtained from the 4,6-dichloro-2-methylpyrimidine with (4-(trifluoromethoxy)phenyl)boronic acid and dichlorido-bis(triphenylphosphine)palladium(II) as a catalyst.

The dihedral angle formed by the aryl ring with the pyrimidine ring is 3.0(6)°. Bond lengths and angles are all in the expected ranges of a chloro substituated pyrimidine [9]. There are some weak intramolecular C—H⋯N hydrogen-bonding interactions in the crystal structure. The crystal packing is furthermore stabilized by van der Waals interactions.

Acknowledgements

This investigation was supported by FONDECYT (Research Grant) N° 1161816. IB thanks to Fondequip (EQM13–0021).

References

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Received: 2017-7-20
Accepted: 2017-10-16
Published Online: 2017-11-16
Published in Print: 2018-1-26

©2018 Jean-Luc Bertrand et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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