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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 67| Part 3| March 2011| Page o573
doi:10.1107/S1600536811003928

2-Methyl-6-(tri­fluoro­meth­yl)imidazo[1,2-a]pyridine-3-carbo­nitrile

Hoong-Kun Fun,a*‡ Mohd Mustaqim Rosli,a D. J. Madhu Kumar,b D. Jagadeesh Prasadb and G. K. Nagarajab

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, Mangalore University, Mangalore, Karnataka, India
*Correspondence e-mail: hkfun@usm.my

(Received 16 December 2010; accepted 31 January 2011; online 5 February 2011)

In the title compound, C10H6F3N3, the imidazo[1,2-a]pyridine group is essentially planar with a maximum deviation of 0.021 (1) Å. The F atoms in the trifluoro­methyl group and the methyl H atoms are each disordered over two sets of sites with refined site occupancies of 0.68 (1):0.32 (1). In the crystal, mol­ecules are linked into infinite chains through two C—H⋯N inter­actions forming R22(12) and R22(8) hydrogen-bond ring motifs. These chains are stacked along the a axis.

Related literature

For the biological activity of imidazole derivatives, see: Biftu et al. (2006[Biftu, T., Feng, D., Liang, G.-B., Qian, X., Scribner, A., Dennis, R., Lee, S., Liberator, P. A., Brown, C., Gurnett, A., Leavitt, P. S., Thompson, D., Mathew, J., Misura, A., Samaras, S., Tamas, T., Sina, J. F., McNulty, K. A., McKnight, C. G., Schmatz, D. M. & Wyvratt, M. (2006). Bioorg. Med. Chem. Lett. 16, 2479-2483.]); Elhakmoui et al. (1994[Elhakmoui, A., Gueiffier, A., Milhavet, J. C., Blache, Y., Chapat, J. P., Chavignon, O., Teulade, J.-C., Snoeck, R., Andrei, G. & Clercq, E. D. (1994). Bioorg. Med. Chem. Lett. 4, 1937-1940.]); Fisher & Lusi (1972[Fisher, M. H. & Lusi, A. (1972). J. Med. Chem. 15, 982-985.]); Gudmundsson & Johns (2003[Gudmundsson, K. S. & Johns, B. A. (2003). Org. Lett. 5, 1369-1372.], 2007[Gudmundsson, K. S. & Johns, B. A. (2007). Bioorg. Med. Chem. Lett. 17, 2735-2739.]); Kaminski et al. (1989[Kaminski, J. J., Puchalski, C., Solomon, D. M., Rizvi, R. K., Conn, D. J., Elliot, A. J., Lovey, R. G., Guzik, H., Chiu, P. J. S., Long, J. F. & McPhail, A. T. (1989). J. Med. Chem. 32, 1686-1700.]); Rewankar et al. (1975[Rewankar, G. R., Matthews, J. R. & Robins, R. K. (1975). J. Med. Chem. 18, 1253-1255.]); Rupert et al. (2003[Rupert, K. C., Henry, J. R., Dodd, J. H., Wadsworth, S. A., Cavender, D. E., Olini, G. C., Fahmy, B. & Siekierka, J. J. (2003). Bioorg. Med. Chem. Lett. 13, 347-350.]). For graph-set descriptions of hydrogen-bond ring motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data

  • C10H6F3N3

  • Mr = 225.18

  • Monoclinic, P 21 /c

  • a = 5.6871 (3) Å

  • b = 8.5437 (5) Å

  • c = 20.5403 (13) Å

  • β = 96.653 (4)°

  • V = 991.31 (10) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 297 K

  • 0.43 × 0.22 × 0.07 mm
Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.945, Tmax = 0.991

  • 10175 measured reflections

  • 2820 independent reflections

  • 1720 reflections with I > 2σ(I)

  • Rint = 0.029
Refinement

  • R[F2 > 2σ(F2)] = 0.049

  • wR(F2) = 0.130

  • S = 1.03

  • 2820 reflections

  • 176 parameters

  • H-atom parameters constrained

  • Δρmax = 0.13 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C1—H1A⋯N3i 0.93 2.45 3.384 (2) 176
C4—H4A⋯N2ii 0.93 2.53 3.428 (2) 163
Symmetry codes: (i) -x, -y+1, -z+1; (ii) -x+2, -y, -z+1.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811003928/fl2329sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811003928/fl2329Isup2.hkl

checkCIF report


Comment top

The imidazole nucleus is a widely used pharmacophore in medicinal compounds due to its broad spectrum of biological activities. Moreover imidazole derivatives are isosteres of naturally-occurring nucleotides which allow them to interact easily with the biopolymers of the living systems. It has been known that imidazo[1,2-a]pyridine derivatives exhibit diverse biological activities (Gudmundsson & Johns, 2003) and were used as antiviral (Elhakmoui et al., 1994), antiulcer (Kaminski et al., 1989), antibacterial (Rewankar et al., 1975), antifungal (Fisher & Lusi, 1972), antiprotozoal (Biftu et al., 2006), antiherpes (Gudmundsson & Johns, 2007) and anti-inflammatory (Rupert et al., 2003) compounds.

All bond lengths and angles in the compound are within normal range. The imidazo[1,2-a] pyridine group is planar with maximum deviation of -0.021 (1)Å for atom N1 (Fig. 1). The F atoms in the trifluoromethyl group and the methyl H atoms are disordered over two positions with refined site occupancies of 0.68 (1):0.32 (1).

In the crystal structure, the molecules form infinite chains through C1—H1A···N3i and C4—H4A···N2ii (Table 1) interactions. These interactions also form R22(12) and R22(8) hydrogen ring motifs, respectively (Bernstein et al., 1995). The chains are stacked along the a-axis (Fig. 2).

Related literature top

For the biological activity of imidazole derivatives, see: Biftu et al. (2006); Elhakmoui et al. (1994); Fisher & Lusi (1972); Gudmundsson & Johns (2003, 2007); Kaminski et al. (1989); Rewankar et al. (1975); Rupert et al. (2003). For graph-set descriptions of hydrogen-bond ring motifs, see: Bernstein et al. (1995).

Experimental top

A mixture of 5-(trifluoromethyl) pyridin-2-amine (0.01mol) and dimethylacetamide dimethyl acetal (0.03mol) was refluxed for 24 hr at 900 C. The resultant product was recrystallized from ethanol. The product so obtained (0.01mol) was refluxed with bromoacetonitrile (0.01mol) in toluene at 600 C. The product was then removed by evaporation of toluene under reduced pressure and it was isolated by column chromatography using ethyl acetate as an eluent. It was then recrystallized by slow evaporation from ethanol to give crystals suitable for x-ray analysis.

Refinement top

H atoms were placed in calculated positions [C–H = 0.93–0.96 Å] and refined as riding with Uiso(H) = 1.2eq(C) or 1.5Ueq(methyl C). A rotating group model was used for the methyl group. The F atoms in trifluoromethyl group and the H atoms in methyl group are disordered over two position with refined site occupancies of 0.68 (1):0.32 (1).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing 30% probability displacement ellipsoids and the atom-numbering scheme. Open bonds show minor components.
[Figure 2] Fig. 2. The crystal packing of (I) viewed along the a axis showing molecular chains stacked down the a-axis. Dashed lines indicate hydrogen bonds. H atoms not involved in the hydrogen bond interactions have been omitted for clarity. Only major components are shown.
2-Methyl-6-(trifluoromethyl)imidazo[1,2-a]pyridine-3-carbonitrile top
Crystal data top
C10H6F3N3F(000) = 456
Mr = 225.18Dx = 1.509 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2837 reflections
a = 5.6871 (3) Åθ = 2.6–25.3°
b = 8.5437 (5) ŵ = 0.13 mm−1
c = 20.5403 (13) ÅT = 297 K
β = 96.653 (4)°Plate, colourless
V = 991.31 (10) Å30.43 × 0.22 × 0.07 mm
Z = 4
Data collection top
Bruker APEXII DUO CCD area-detector
diffractometer		2820 independent reflections
Radiation source: fine-focus sealed tube1720 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
ϕ and ω scansθmax = 29.8°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		h = −7→7
Tmin = 0.945, Tmax = 0.991k = −11→11
10175 measured reflectionsl = −28→28
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)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0575P)2 + 0.0655P]
where P = (Fo2 + 2Fc2)/3
2820 reflections(Δ/σ)max < 0.001
176 parametersΔρmax = 0.13 e Å−3
0 restraintsΔρmin = −0.22 e Å−3
Crystal data top
C10H6F3N3V = 991.31 (10) Å3
Mr = 225.18Z = 4
Monoclinic, P21/cMo Kα radiation
a = 5.6871 (3) ŵ = 0.13 mm−1
b = 8.5437 (5) ÅT = 297 K
c = 20.5403 (13) Å0.43 × 0.22 × 0.07 mm
β = 96.653 (4)°
Data collection top
Bruker APEXII DUO CCD area-detector
diffractometer		2820 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		1720 reflections with I > 2σ(I)
Tmin = 0.945, Tmax = 0.991Rint = 0.029
10175 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0490 restraints
wR(F2) = 0.130H-atom parameters constrained
S = 1.03Δρmax = 0.13 e Å−3
2820 reflectionsΔρmin = −0.22 e Å−3
176 parameters
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 > 2sigma(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*/UeqOcc. (<1)
C100.2247 (4)0.2282 (2)0.30231 (9)0.0633 (5)
F10.1174 (15)0.0950 (4)0.2794 (3)0.1138 (18)0.675 (13)
F20.3304 (7)0.2905 (11)0.2575 (3)0.134 (2)0.675 (13)
F30.0427 (9)0.3205 (5)0.3079 (2)0.0858 (13)0.675 (13)
F1A0.246 (3)0.1157 (11)0.2609 (4)0.097 (3)0.325 (13)
F2A0.329 (2)0.3390 (12)0.2678 (6)0.131 (4)0.325 (13)
F3A0.0178 (17)0.271 (2)0.3077 (6)0.141 (5)0.325 (13)
N10.46963 (19)0.24647 (12)0.47742 (6)0.0410 (3)
N20.7873 (2)0.15187 (14)0.54049 (6)0.0528 (3)
N30.1553 (2)0.49667 (17)0.57317 (7)0.0660 (4)
C10.3230 (3)0.27046 (16)0.42094 (8)0.0447 (4)
H1A0.18880.33280.42060.054*
C20.3776 (3)0.20129 (17)0.36531 (7)0.0478 (4)
C30.5809 (3)0.10468 (18)0.36599 (8)0.0541 (4)
H3A0.61610.05810.32740.065*
C40.7237 (3)0.07997 (17)0.42235 (8)0.0530 (4)
H4A0.85540.01530.42280.064*
C50.6712 (2)0.15294 (16)0.48021 (8)0.0455 (4)
C60.6634 (3)0.24616 (17)0.57735 (8)0.0486 (4)
C70.4662 (2)0.30593 (16)0.54019 (7)0.0432 (3)
C80.2918 (3)0.40991 (17)0.55779 (7)0.0468 (4)
C90.7402 (3)0.2770 (2)0.64782 (8)0.0654 (5)
H9A0.75330.17970.67130.098*0.675 (13)
H9B0.62560.34250.66540.098*0.675 (13)
H9C0.89100.32870.65230.098*0.675 (13)
H9D0.89040.22780.66030.098*0.325 (13)
H9E0.62500.23530.67380.098*0.325 (13)
H9F0.75470.38780.65490.098*0.325 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C100.0701 (12)0.0666 (11)0.0522 (10)0.0091 (10)0.0024 (9)−0.0014 (8)
F10.131 (3)0.0749 (15)0.117 (3)0.001 (2)−0.065 (3)−0.0194 (17)
F20.085 (2)0.255 (7)0.0643 (18)0.003 (3)0.0218 (15)0.049 (3)
F30.093 (3)0.095 (2)0.0627 (18)0.0467 (16)−0.0183 (18)−0.0041 (12)
F1A0.116 (6)0.093 (4)0.071 (3)0.011 (4)−0.032 (4)−0.018 (3)
F2A0.213 (10)0.090 (5)0.082 (5)−0.027 (4)−0.018 (5)0.050 (3)
F3A0.039 (3)0.302 (15)0.081 (5)0.003 (6)0.002 (3)0.042 (8)
N10.0356 (6)0.0390 (6)0.0485 (7)0.0048 (5)0.0053 (5)0.0016 (5)
N20.0445 (7)0.0524 (7)0.0604 (8)0.0094 (6)0.0009 (6)0.0029 (6)
N30.0590 (8)0.0662 (9)0.0748 (10)0.0127 (7)0.0158 (7)−0.0053 (7)
C10.0389 (7)0.0421 (7)0.0524 (9)0.0057 (6)0.0024 (7)0.0051 (6)
C20.0468 (8)0.0463 (8)0.0498 (9)0.0012 (6)0.0043 (7)0.0004 (6)
C30.0525 (9)0.0530 (9)0.0580 (10)0.0038 (7)0.0117 (8)−0.0084 (7)
C40.0432 (8)0.0486 (8)0.0680 (10)0.0103 (7)0.0096 (8)−0.0042 (7)
C50.0371 (7)0.0400 (7)0.0593 (9)0.0067 (6)0.0046 (7)0.0022 (6)
C60.0451 (8)0.0471 (8)0.0532 (9)0.0008 (6)0.0045 (7)0.0036 (6)
C70.0403 (7)0.0434 (7)0.0462 (8)0.0040 (6)0.0064 (6)0.0027 (6)
C80.0435 (8)0.0466 (8)0.0509 (8)0.0023 (6)0.0078 (7)0.0010 (6)
C90.0651 (11)0.0746 (12)0.0540 (10)0.0025 (9)−0.0037 (9)0.0045 (8)
Geometric parameters (Å, º) top
C10—F3A1.249 (10)C2—C31.420 (2)
C10—F21.273 (4)C3—C41.351 (2)
C10—F1A1.298 (7)C3—H3A0.9300
C10—F31.316 (4)C4—C51.405 (2)
C10—F11.350 (5)C4—H4A0.9300
C10—F2A1.359 (9)C6—C71.379 (2)
C10—C21.491 (2)C6—C91.486 (2)
N1—C11.3635 (19)C7—C81.4095 (19)
N1—C71.3880 (18)C9—H9A0.9600
N1—C51.3931 (17)C9—H9B0.9600
N2—C51.3340 (19)C9—H9C0.9600
N2—C61.3571 (19)C9—H9D0.9600
N3—C81.1442 (17)C9—H9E0.9600
C1—C21.354 (2)C9—H9F0.9600
C1—H1A0.9300
F3A—C10—F1A115.7 (7)C2—C3—H3A119.8
F2—C10—F3104.8 (4)C3—C4—C5119.33 (13)
F2—C10—F1109.4 (4)C3—C4—H4A120.3
F3—C10—F1102.0 (4)C5—C4—H4A120.3
F3A—C10—F2A108.3 (9)N2—C5—N1111.00 (12)
F1A—C10—F2A95.5 (7)N2—C5—C4130.66 (13)
F3A—C10—C2115.4 (6)N1—C5—C4118.32 (14)
F2—C10—C2114.5 (3)N2—C6—C7110.63 (14)
F1A—C10—C2111.4 (4)N2—C6—C9122.40 (14)
F3—C10—C2113.7 (3)C7—C6—C9126.97 (14)
F1—C10—C2111.5 (2)C6—C7—N1106.29 (12)
F2A—C10—C2108.4 (5)C6—C7—C8129.98 (14)
C1—N1—C7131.48 (12)N1—C7—C8123.71 (13)
C1—N1—C5122.71 (12)N3—C8—C7178.02 (17)
C7—N1—C5105.77 (12)C6—C9—H9A109.5
C5—N2—C6106.31 (12)C6—C9—H9B109.5
C2—C1—N1118.37 (13)C6—C9—H9C109.5
C2—C1—H1A120.8C6—C9—H9D109.5
N1—C1—H1A120.8C6—C9—H9E109.5
C1—C2—C3120.76 (15)H9D—C9—H9E109.5
C1—C2—C10119.84 (14)C6—C9—H9F109.5
C3—C2—C10119.40 (14)H9D—C9—H9F109.5
C4—C3—C2120.49 (14)H9E—C9—H9F109.5
C4—C3—H3A119.8
C7—N1—C1—C2176.78 (13)C6—N2—C5—N1−0.64 (16)
C5—N1—C1—C2−0.6 (2)C6—N2—C5—C4177.88 (15)
N1—C1—C2—C30.7 (2)C1—N1—C5—N2178.33 (12)
N1—C1—C2—C10−178.43 (14)C7—N1—C5—N20.40 (16)
F3A—C10—C2—C1−22.2 (11)C1—N1—C5—C4−0.4 (2)
F2—C10—C2—C1120.0 (5)C7—N1—C5—C4−178.32 (13)
F1A—C10—C2—C1−156.7 (8)C3—C4—C5—N2−177.24 (15)
F3—C10—C2—C1−0.4 (4)C3—C4—C5—N11.2 (2)
F1—C10—C2—C1−115.0 (5)C5—N2—C6—C70.64 (17)
F2A—C10—C2—C199.5 (6)C5—N2—C6—C9−178.97 (14)
F3A—C10—C2—C3158.6 (11)N2—C6—C7—N1−0.40 (16)
F2—C10—C2—C3−59.1 (5)C9—C6—C7—N1179.19 (14)
F1A—C10—C2—C324.1 (8)N2—C6—C7—C8−178.74 (14)
F3—C10—C2—C3−179.6 (3)C9—C6—C7—C80.8 (3)
F1—C10—C2—C365.8 (5)C1—N1—C7—C6−177.68 (14)
F2A—C10—C2—C3−79.7 (6)C5—N1—C7—C60.00 (15)
C1—C2—C3—C40.1 (2)C1—N1—C7—C80.8 (2)
C10—C2—C3—C4179.24 (15)C5—N1—C7—C8178.48 (13)
C2—C3—C4—C5−1.0 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···N3i0.932.453.384 (2)176
C4—H4A···N2ii0.932.533.428 (2)163
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+2, −y, −z+1.

Experimental details

Crystal data
Chemical formulaC10H6F3N3
Mr225.18
Crystal system, space groupMonoclinic, P21/c
Temperature (K)297
a, b, c (Å)5.6871 (3), 8.5437 (5), 20.5403 (13)
β (°) 96.653 (4)
V (Å3)991.31 (10)
Z4
Radiation typeMo Kα
µ (mm−1)0.13
Crystal size (mm)0.43 × 0.22 × 0.07
Data collection
DiffractometerBruker APEXII DUO CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.945, 0.991
No. of measured, independent and
observed [I > 2σ(I)] reflections		10175, 2820, 1720
Rint0.029
(sin θ/λ)max (Å−1)0.700
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.049, 0.130, 1.03
No. of reflections2820
No. of parameters176
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.13, −0.22

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···N3i0.932.453.384 (2)176
C4—H4A···N2ii0.932.533.428 (2)163
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+2, −y, −z+1.
 

Footnotes

‡Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

HKF and MMR thank USM for the Research University Grant (No. 1001/PFIZIK/ 811160).

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ISSN: 2056-9890
Volume 67| Part 3| March 2011| Page o573
doi:10.1107/S1600536811003928
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