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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 6| June 2010| Page o1448
https://doi.org/10.1107/S1600536810018854

2-Chloro-4-(1H-pyrazol-1-yl)-5-(tri­fluoro­meth­yl)pyrimidine

Kevin D. Bunker,a Curtis Moore,b Cynthia L. Palmer,a Arnold L. Rheingoldb and Alex Yanovskya*

aPfizer Global Research and Development, La Jolla Labs, 10770 Science Center Drive, San Diego, CA 92121, USA, and bDepartment of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
*Correspondence e-mail: alex.yanovsky@pfizer.com

(Received 18 May 2010; accepted 20 May 2010; online 26 May 2010)

The reaction of 2,4-dichloro-5-(trifluoro­meth­yl)pyrimidine with 1H-pyrazole gave two structural isomers in a 1:1 ratio that were separable by chromatography. The title compound, C8H4ClF3N4, was the first product to elute and was characterized in the present study to confirm that substitution by the pyrazolyl group had occurred at position 4. The mol­ecule (with the exception of the F atoms) is essentially planar, with a mean deviation of 0.034 Å from the least-squares plane through all non-H and non-F atoms. The bond angles in the pyrimidine ring show a pronounced alternating pattern with three angles, including those at the two N atoms being narrower, and the remaining three wider than 120°.

Related literature

For the structures of similar pyrazolylpyrimidine derivatives, see: Peresypkina et al. (2005[Peresypkina, E. V., Bushuev, M. B., Virovets, A. V., Krivopalov, V. P., Lavrenova, L. G. & Larionov, S. V. (2005). Acta Cryst. B61, 164-173.]); Liu et al. (2005[Liu, W.-M., Zhu, Y.-Q., Wang, Y.-F., Li, G.-C. & Yang, H.-Z. (2005). Acta Cryst. E61, o1821-o1822.]); Brunet et al. (2007[Brunet, E., Juanes, O., Sedano, R. & Rodriguez-Ubis, J. C. (2007). Tetrahedron Lett. 48, 1091-1094.]). For statistics on endocyclic angular distortions in triazine derivatives similar to those observed in the title compound, see: Allington et al. (2001[Allington, R. D., Attwood, D., Hamerton, I., Hay, J. N. & Howlin, B. J. (2001). Comp. Theor. Polym. Sci. 11, 467-473.]).

[Scheme 1]

Experimental

Crystal data

  • C8H4ClF3N4

  • Mr = 248.60

  • Orthorhombic, P 21 21 21

  • a = 5.5776 (3) Å

  • b = 7.7117 (4) Å

  • c = 21.8335 (12) Å

  • V = 939.12 (9) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 3.90 mm−1

  • T = 100 K

  • 0.40 × 0.21 × 0.10 mm
Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.305, Tmax = 0.697

  • 3416 measured reflections

  • 1402 independent reflections

  • 1273 reflections with I > 2σ(I)

  • Rint = 0.030

  • θmax = 61.9°
Refinement

  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.082

  • S = 1.02

  • 1402 reflections

  • 145 parameters

  • H-atom parameters constrained

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.22 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 503 Friedel pairs

  • Flack parameter: 0.05 (2)

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810018854/ez2213sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810018854/ez2213Isup2.hkl

checkCIF report


Comment top

The reaction of 2,4-dichloro-5-(trifluoromethyl)pyrimidine with 1H-pyrazole gave two structural isomers in a 1:1 ratio that were separable by chromatography. The title compound was the first product to elute and was characterized in the present study to confirm substitution by N-pyrazolyl group to have occurred at position 4 (Fig. 1).

The molecule (with the exception of the F atoms) is essentially planar: the maximum displacement of the N1 atom from the plane, drawn through all non-F and non-H atoms, is equal to 0.076 (4) Å. Other pyrazolylpyrimidine derivatives were also shown to have planar molecules (Peresypkina et al., 2005; Liu et al., 2005; Brunet et al., 2007).

The geometry of the pyrimidine ring is characterized by alternating of bond angle distortions: angles at the N3, N4 and C5 atoms [112.8 (3); 116.1 (3); 115.4 (3)°] are all narrower, whereas the remaining angles in the ring at the C4, C6 and C7 atoms [121.2 (3); 124.7 (3); 129.7 (3)°] are wider than 120°. Such angular distortions were also observed in other pyrimidine structures (see, for instance, the above quoted papers). The study by Allington et al. (2001) contains analysis of some statistics on similar angular distortions in the triazine derivatives.

The dramatic difference between the exocyclic bond angles C4—C5—C8 127.1 (3)° and C6—C5—C8 117.5 (3)° can be attributed to the repulsion of the CF3-group from pyrazolyl substituent (the F1···N1 and F2···N1 distances are 2.720 (3) Å and 2.774 (3) Å respectively).

Related literature top

For the structures of similar pyrazolylpyrimidine derivatives, see: Peresypkina et al. (2005); Liu et al. (2005); Brunet et al. (2007). For statistics on endocyclic angular distortions in triazine derivatives similar to those observed in the title compound, see: Allington et al. (2001).

Experimental top

2-Chloro-4-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine and 4-chloro-2-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine. To a N,N-dimethylacetamide (46.0 ml) solution of pyrazole (726 mg, 10.7 mmol) and potassium carbonate (3.84 g, 27.8 mmol) was added 2,4-dichloro-5-trifluoromethyl-pyrimidine (2.01 g, 1.250 ml, 9.27 mmol) by syringe in one shot at rt. The mixture was stirred overnight and monitored by TLC (20% EtOAc/heptane). After consumption of starting material, the reaction mixture was diluted with water and extracted with EtOAc (3×). The organic layers were combined, dried, and concentrated. The crude residue was subjected to flash chromatography (silica gel, 0-40% EtOAc/heptane), and three major bands eluted. The first major band was isolated to give 460 mg (20%) of 2-chloro-4-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine. The second band was also collected to give 460 mg (20%) of 4-chloro-2-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine. The third band was found to be 2,4-di(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine and was not isolated. X-ray quality crystals of the first product to elute were grown in DCM/heptane upon slow evaporation.

2-chloro-4-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine: 1H NMR (400 MHz, CHLOROFORM-d) δ ppm 6.56 (dd, J=2.77, 1.51 Hz, 1 H) 7.89 (d, J=0.76 Hz, 1 H) 8.59 (dd, J=2.77, 0.76 Hz, 1 H) 8.96 (s, 1 H). 13C NMR (101 MHz, CHLOROFORM-d) δ ppm 109.96 (s, 1 C) 111.39 - 112.97 (m, 1 C) 117.69 - 126.63 (m, 1 C) 130.42 (s, 1 C) 145.57 (s, 1 C) 155.57 (s, 1 C) 160.86 (q, J=7.09 Hz, 1 C) 163.04 (s, 1 C).

4-chloro-2-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine: 1H NMR (400 MHz, CHLOROFORM-d) δ ppm 6.57 (dd, J=2.77, 1.51 Hz, 1 H) 7.90 (d, J=1.01 Hz, 1 H) 8.59 (dd, J=2.77, 0.50 Hz, 1 H) 8.92 (s, 1 H). 13C NMR (101 MHz, CHLOROFORM-d) δ ppm 110.22 (s, 1 C) 121.68 (q, J=272.65 Hz, 1 C) 120.34 (q, J=33.99 Hz, 1 C) 130.23 (s, 1 C) 145.59 (s, 1 C) 156.64 (s, 1 C) 158.07 (q, J=5.14 Hz, 1 C) 161.02 (s, 1 C).

Refinement top

All H atoms were placed in geometrically calculated positions (C—H 0.93 Å) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom.

Structure description top

The reaction of 2,4-dichloro-5-(trifluoromethyl)pyrimidine with 1H-pyrazole gave two structural isomers in a 1:1 ratio that were separable by chromatography. The title compound was the first product to elute and was characterized in the present study to confirm substitution by N-pyrazolyl group to have occurred at position 4 (Fig. 1).

The molecule (with the exception of the F atoms) is essentially planar: the maximum displacement of the N1 atom from the plane, drawn through all non-F and non-H atoms, is equal to 0.076 (4) Å. Other pyrazolylpyrimidine derivatives were also shown to have planar molecules (Peresypkina et al., 2005; Liu et al., 2005; Brunet et al., 2007).

The geometry of the pyrimidine ring is characterized by alternating of bond angle distortions: angles at the N3, N4 and C5 atoms [112.8 (3); 116.1 (3); 115.4 (3)°] are all narrower, whereas the remaining angles in the ring at the C4, C6 and C7 atoms [121.2 (3); 124.7 (3); 129.7 (3)°] are wider than 120°. Such angular distortions were also observed in other pyrimidine structures (see, for instance, the above quoted papers). The study by Allington et al. (2001) contains analysis of some statistics on similar angular distortions in the triazine derivatives.

The dramatic difference between the exocyclic bond angles C4—C5—C8 127.1 (3)° and C6—C5—C8 117.5 (3)° can be attributed to the repulsion of the CF3-group from pyrazolyl substituent (the F1···N1 and F2···N1 distances are 2.720 (3) Å and 2.774 (3) Å respectively).

For the structures of similar pyrazolylpyrimidine derivatives, see: Peresypkina et al. (2005); Liu et al. (2005); Brunet et al. (2007). For statistics on endocyclic angular distortions in triazine derivatives similar to those observed in the title compound, see: Allington et al. (2001).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound, showing 50% probability displacement ellipsoids and atom numbering scheme. H atoms are drawn as circles with arbitrary small radius.
2-Chloro-4-(1H-pyrazol-1-yl)-5-(trifluoromethyl)pyrimidine top
Crystal data top
C8H4ClF3N4F(000) = 496
Mr = 248.60Dx = 1.758 Mg m−3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 2204 reflections
a = 5.5776 (3) Åθ = 4.1–61.5°
b = 7.7117 (4) ŵ = 3.90 mm−1
c = 21.8335 (12) ÅT = 100 K
V = 939.12 (9) Å3Rod, colourless
Z = 40.40 × 0.21 × 0.10 mm
Data collection top
Bruker APEXII CCD
diffractometer		1402 independent reflections
Radiation source: fine-focus sealed tube1273 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
φ and ω scansθmax = 61.9°, θmin = 4.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −6→6
Tmin = 0.305, Tmax = 0.697k = −8→8
3416 measured reflectionsl = −25→24
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.082 w = 1/[σ2(Fo2) + (0.048P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max = 0.001
1402 reflectionsΔρmax = 0.21 e Å−3
145 parametersΔρmin = −0.22 e Å−3
0 restraintsAbsolute structure: Flack (1983), 503 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.05 (2)
Crystal data top
C8H4ClF3N4V = 939.12 (9) Å3
Mr = 248.60Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 5.5776 (3) ŵ = 3.90 mm−1
b = 7.7117 (4) ÅT = 100 K
c = 21.8335 (12) Å0.40 × 0.21 × 0.10 mm
Data collection top
Bruker APEXII CCD
diffractometer		1402 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		1273 reflections with I > 2σ(I)
Tmin = 0.305, Tmax = 0.697Rint = 0.030
3416 measured reflectionsθmax = 61.9°
Refinement top
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.082Δρmax = 0.21 e Å−3
S = 1.02Δρmin = −0.22 e Å−3
1402 reflectionsAbsolute structure: Flack (1983), 503 Friedel pairs
145 parametersAbsolute structure parameter: 0.05 (2)
0 restraints
Special details top

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) top
xyzUiso*/Ueq
Cl10.18059 (15)0.39628 (9)0.50346 (4)0.0390 (2)
F10.7206 (4)1.0219 (2)0.35103 (8)0.0430 (5)
F20.4712 (4)0.9283 (2)0.28305 (8)0.0450 (5)
F30.3535 (5)1.0974 (2)0.35501 (11)0.0629 (7)
N10.8456 (5)0.7028 (3)0.30856 (11)0.0326 (6)
N20.7484 (5)0.5994 (3)0.35248 (10)0.0262 (5)
N30.1542 (5)0.7067 (3)0.45907 (11)0.0308 (6)
N40.4754 (5)0.5271 (3)0.42520 (10)0.0272 (6)
C10.8693 (6)0.4455 (4)0.35742 (13)0.0312 (7)
H1A0.83380.35310.38480.037*
C21.0494 (6)0.4503 (4)0.31581 (13)0.0312 (7)
H2A1.16610.36350.30790.037*
C31.0253 (6)0.6127 (4)0.28693 (13)0.0332 (7)
H3A1.12820.65240.25520.040*
C40.5510 (6)0.6502 (3)0.38708 (12)0.0250 (6)
C50.4336 (6)0.8113 (4)0.38345 (13)0.0283 (6)
C60.2380 (6)0.8301 (3)0.42115 (13)0.0304 (7)
H6A0.15610.93810.42040.037*
C70.2831 (6)0.5640 (3)0.45766 (12)0.0296 (7)
C80.4981 (7)0.9624 (4)0.34258 (14)0.0378 (8)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0460 (5)0.0364 (3)0.0347 (4)−0.0015 (3)0.0081 (4)0.0070 (3)
F10.0604 (15)0.0304 (8)0.0382 (10)−0.0103 (9)0.0101 (10)−0.0007 (7)
F20.0489 (13)0.0564 (12)0.0298 (10)0.0079 (10)−0.0012 (8)0.0164 (8)
F30.0824 (18)0.0377 (10)0.0685 (14)0.0283 (12)0.0320 (13)0.0215 (10)
N10.0390 (16)0.0315 (12)0.0272 (14)0.0008 (12)0.0052 (12)0.0051 (10)
N20.0341 (15)0.0238 (10)0.0208 (11)0.0022 (11)−0.0010 (10)0.0006 (9)
N30.0295 (15)0.0341 (13)0.0288 (14)0.0000 (12)0.0027 (11)−0.0013 (10)
N40.0355 (16)0.0256 (10)0.0205 (12)−0.0014 (11)−0.0022 (11)−0.0010 (9)
C10.043 (2)0.0259 (14)0.0242 (14)0.0034 (13)−0.0011 (14)−0.0004 (11)
C20.0343 (19)0.0304 (14)0.0288 (16)0.0047 (12)−0.0038 (14)−0.0053 (12)
C30.038 (2)0.0353 (15)0.0262 (15)0.0021 (15)0.0067 (13)−0.0006 (13)
C40.0296 (16)0.0269 (13)0.0185 (13)−0.0009 (11)−0.0032 (13)−0.0021 (11)
C50.0361 (18)0.0272 (14)0.0215 (14)0.0029 (12)−0.0055 (14)−0.0006 (12)
C60.0332 (18)0.0269 (13)0.0312 (15)0.0043 (12)−0.0014 (14)−0.0001 (11)
C70.038 (2)0.0311 (15)0.0198 (13)−0.0031 (13)−0.0031 (13)0.0008 (11)
C80.050 (2)0.0337 (15)0.0300 (17)0.0120 (15)0.0064 (15)0.0052 (13)
Geometric parameters (Å, º) top
Cl1—C71.732 (3)N4—C41.331 (4)
F1—C81.336 (4)C1—C21.355 (5)
F2—C81.334 (4)C1—H1A0.9500
F3—C81.345 (4)C2—C31.408 (4)
N1—C31.308 (4)C2—H2A0.9500
N1—N21.360 (3)C3—H3A0.9500
N2—C11.369 (4)C4—C51.406 (4)
N2—C41.392 (4)C5—C61.374 (5)
N3—C71.315 (4)C5—C81.511 (4)
N3—C61.345 (4)C6—H6A0.9500
N4—C71.316 (4)
C3—N1—N2104.4 (2)N2—C4—C5125.9 (3)
N1—N2—C1111.6 (3)C6—C5—C4115.4 (3)
N1—N2—C4122.2 (2)C6—C5—C8117.5 (3)
C1—N2—C4126.2 (2)C4—C5—C8127.1 (3)
C7—N3—C6112.8 (3)N3—C6—C5124.7 (3)
C7—N4—C4116.1 (3)N3—C6—H6A117.6
C2—C1—N2106.8 (3)C5—C6—H6A117.6
C2—C1—H1A126.6N3—C7—N4129.7 (3)
N2—C1—H1A126.6N3—C7—Cl1115.5 (2)
C1—C2—C3104.7 (3)N4—C7—Cl1114.7 (2)
C1—C2—H2A127.6F2—C8—F1107.9 (3)
C3—C2—H2A127.6F2—C8—F3106.4 (3)
N1—C3—C2112.6 (3)F1—C8—F3105.3 (3)
N1—C3—H3A123.7F2—C8—C5113.4 (3)
C2—C3—H3A123.7F1—C8—C5113.9 (3)
N4—C4—N2112.9 (2)F3—C8—C5109.6 (3)
N4—C4—C5121.2 (3)

Experimental details

Crystal data
Chemical formulaC8H4ClF3N4
Mr248.60
Crystal system, space groupOrthorhombic, P212121
Temperature (K)100
a, b, c (Å)5.5776 (3), 7.7117 (4), 21.8335 (12)
V (Å3)939.12 (9)
Z4
Radiation typeCu Kα
µ (mm−1)3.90
Crystal size (mm)0.40 × 0.21 × 0.10
Data collection
DiffractometerBruker APEXII CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.305, 0.697
No. of measured, independent and
observed [I > 2σ(I)] reflections		3416, 1402, 1273
Rint0.030
θmax (°)61.9
(sin θ/λ)max (Å−1)0.572
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.082, 1.02
No. of reflections1402
No. of parameters145
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.21, −0.22
Absolute structureFlack (1983), 503 Friedel pairs
Absolute structure parameter0.05 (2)

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

 

References

First citationAllington, R. D., Attwood, D., Hamerton, I., Hay, J. N. & Howlin, B. J. (2001). Comp. Theor. Polym. Sci. 11, 467–473.  Web of Science CrossRef CAS Google Scholar
 First citationBruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBrunet, E., Juanes, O., Sedano, R. & Rodriguez-Ubis, J. C. (2007). Tetrahedron Lett. 48, 1091–1094.  Web of Science CSD CrossRef CAS Google Scholar
 First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationLiu, W.-M., Zhu, Y.-Q., Wang, Y.-F., Li, G.-C. & Yang, H.-Z. (2005). Acta Cryst. E61, o1821–o1822.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationPeresypkina, E. V., Bushuev, M. B., Virovets, A. V., Krivopalov, V. P., Lavrenova, L. G. & Larionov, S. V. (2005). Acta Cryst. B61, 164–173.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 6| June 2010| Page o1448
https://doi.org/10.1107/S1600536810018854
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