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

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ISSN: 2056-9890

2-[(1H-Imidazol-1-yl)meth­yl]-1-[4-(tri­fluoro­meth­yl)phen­yl]-1H-indole

aKey Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, People's Republic of China
*Correspondence e-mail: jpliu@ynu.edu.cn

(Received 1 March 2012; accepted 9 March 2012; online 17 March 2012)

In the title compound, C19H14F3N3, the dihedral angles between the mean planes of the indole ring and the 4-CF3-phenyl and imidazole rings are 54.95 (4) and 61.36 (7)°, respectively.

Related literature

For background to indole derivatives and their biological activity, see: Muftuoglua & Mustatab (2010[Muftuoglua, Y. & Mustatab, G. (2010). Bioorg. Med. Chem. Lett. 20, 3050-3064.]); Jiao et al. (2010[Jiao, J., Xiang, H. & Liao, Q. (2010). Curr. Med. Chem. 17, 3476-3487.]). For related structures, see: Borgne et al. (1999[Borgne, M. L., Marchand, P., Delevoye-Seiller, B., Robert, J.-M., Baut, G. L., Hartmann, R. W. & Palzer, M. (1999). Bioorg. Med. Chem. Lett. 9, 333-336.]); Lézé et al. (2006[Lézé, M.-P., Borgne, M. L., Pinson, P., Palusczak, A., Duflos, M., Baut, G. L. & Hartmann, R. W. (2006). Bioorg. Med. Chem. Lett. 16, 1134-1137.]); Marchand et al. (2003[Marchand, P., Borgne, M. L., Palzer, M., Baut, G. L. & Hartmann, R. W. (2003). Bioorg. Med. Chem. Lett. 13, 1553-1555.]).

[Scheme 1]

Experimental

Crystal data
  • C19H14F3N3

  • Mr = 341.33

  • Orthorhombic, P b c a

  • a = 10.3732 (17) Å

  • b = 7.9960 (13) Å

  • c = 37.665 (6) Å

  • V = 3124.0 (9) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 100 K

  • 0.53 × 0.26 × 0.05 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2004[Sheldrick, G. M. (2004). SADBAS. University of Göttingen, Germany.]) Tmin = 0.943, Tmax = 0.994

  • 30000 measured reflections

  • 4505 independent reflections

  • 3217 reflections with I > 2σ(I)

  • Rint = 0.093

Refinement
  • R[F2 > 2σ(F2)] = 0.079

  • wR(F2) = 0.214

  • S = 0.99

  • 4505 reflections

  • 226 parameters

  • H-atom parameters constrained

  • Δρmax = 0.51 e Å−3

  • Δρmin = −0.38 e Å−3

Data collection: APEX2 (Bruker, 1998[Bruker (1998). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1998[Bruker (1998). SMART 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


Comment top

Iodole derivatives are an important class of heterocycles in medicinal chemistry (Borgne et al., 1999; Marchand et al., 2003; Lézé et al., 2006; Jiao et al., 2010; Muftuoglua & Mustatab, 2010). In continuation of our studies on N-aromatization in the indole ring, we present here the the crystal structure of the title compound, C19H14F3N3, (I). With one molecule in the asymmetric unit, the dihedral angles between the mean planes of the indole ring and the 4-CF3-phenyl and imidazole rings are 54.95 (4)° and 61.36 (7)°, respectively (Fig. 1). Bond lengths and angles are in normal ranges.

Related literature top

For background to indole derivatives and their biological activity, see: Muftuoglua & Mustatab (2010); Jiao et al. (2010). For related structures, see: Borgne et al. (1999); Lézé et al. (2006); Marchand et al. (2003).

Experimental top

The title compound, C19H14F3N3, was prepared in one step. (1-(4-(trifluoromethyl)phenyl)-1H-indol-2-yl)methanol (50 mg, 0.17 mmol) and N,N'-carbonyldiimidazole (83 mg, 3 equiv) in dry CH3CN was stirred for 48 h at room temperature. The solvent was evaporated and the residue purified on silica gel to give the title compound,(I). Yield: 53% (33 mg). Recrystallization from absolute ethyl acetate gave colorless and clear single crystals for X-ray diffraction measurement.

Refinement top

H-atoms were placed in calculated positions [C—H = 0.99 Å for aliphatic H, 0.95 Å for aromatic H, Uiso(H)= 1.2Ueq(C)] and were included in the refinement in the riding model approximation.

Computing details top

Data collection: APEX2 (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT (Bruker, 1998); 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. The molecular structure of (I) showing the atomic numbering and 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The crystal packing of (I) viewed along the b axis. H atoms have been removed for clarity.
2-[(1H-Imidazol-1-yl)methyl]-1-[4-(trifluoromethyl)phenyl]-1H- indole top
Crystal data top
C19H14F3N3F(000) = 1408
Mr = 341.33Dx = 1.451 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 5075 reflections
a = 10.3732 (17) Åθ = 2.2–30.1°
b = 7.9960 (13) ŵ = 0.11 mm1
c = 37.665 (6) ÅT = 100 K
V = 3124.0 (9) Å3Laminiplantation, colourless
Z = 80.53 × 0.26 × 0.05 mm
Data collection top
Bruker APEXII CCD
diffractometer
4505 independent reflections
Radiation source: fine-focus sealed tube3217 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.093
Detector resolution: 0.71 pixels mm-1θmax = 30.2°, θmin = 1.1°
ϕ and ω scansh = 1414
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
k = 1111
Tmin = 0.943, Tmax = 0.994l = 5252
30000 measured reflections
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)] = 0.079Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.214H-atom parameters constrained
S = 0.99 w = 1/[σ2(Fo2) + (0.0877P)2 + 8.8995P]
where P = (Fo2 + 2Fc2)/3
4505 reflections(Δ/σ)max = 0.001
226 parametersΔρmax = 0.51 e Å3
0 restraintsΔρmin = 0.38 e Å3
Crystal data top
C19H14F3N3V = 3124.0 (9) Å3
Mr = 341.33Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 10.3732 (17) ŵ = 0.11 mm1
b = 7.9960 (13) ÅT = 100 K
c = 37.665 (6) Å0.53 × 0.26 × 0.05 mm
Data collection top
Bruker APEXII CCD
diffractometer
4505 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)
3217 reflections with I > 2σ(I)
Tmin = 0.943, Tmax = 0.994Rint = 0.093
30000 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0790 restraints
wR(F2) = 0.214H-atom parameters constrained
S = 0.99Δρmax = 0.51 e Å3
4505 reflectionsΔρmin = 0.38 e Å3
226 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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
F10.1652 (2)0.1525 (3)0.97255 (6)0.0444 (6)
F20.1194 (2)0.4118 (3)0.97874 (6)0.0422 (6)
F30.0238 (2)0.2278 (3)1.01033 (5)0.0430 (6)
N10.3126 (2)0.1845 (3)0.86957 (5)0.0130 (4)
N20.0946 (2)0.1498 (3)0.80082 (6)0.0141 (4)
N30.0810 (2)0.2676 (3)0.77776 (7)0.0229 (5)
C10.2961 (3)0.1098 (3)0.83609 (6)0.0133 (5)
C20.4120 (3)0.1060 (3)0.81894 (6)0.0143 (5)
H20.42750.05960.79610.017*
C30.6355 (3)0.2300 (4)0.83646 (7)0.0192 (6)
H30.68020.19960.81540.023*
C40.6967 (3)0.3203 (4)0.86292 (8)0.0228 (6)
H40.78390.35350.85980.027*
C50.6313 (3)0.3638 (4)0.89460 (7)0.0215 (6)
H50.67580.42480.91240.026*
C60.5041 (3)0.3194 (4)0.90018 (7)0.0167 (5)
H60.46040.34840.92150.020*
C70.4424 (2)0.2299 (3)0.87310 (7)0.0147 (5)
C80.5063 (3)0.1844 (3)0.84135 (7)0.0151 (5)
C90.2173 (3)0.2037 (3)0.89657 (7)0.0140 (5)
C100.1007 (2)0.2828 (3)0.88912 (7)0.0144 (5)
H100.08410.32420.86590.017*
C110.0090 (3)0.3010 (4)0.91571 (7)0.0168 (5)
H110.07120.35300.91060.020*
C120.0349 (3)0.2429 (3)0.94987 (7)0.0160 (5)
C130.1510 (3)0.1651 (3)0.95761 (7)0.0170 (5)
H130.16790.12570.98090.020*
C140.2428 (3)0.1450 (3)0.93089 (6)0.0164 (5)
H140.32250.09160.93600.020*
C150.0667 (3)0.2588 (4)0.97782 (7)0.0205 (6)
C160.1706 (3)0.0383 (3)0.82356 (7)0.0152 (5)
H16A0.18840.06610.81030.018*
H16B0.11810.00830.84460.018*
C170.0343 (3)0.1775 (4)0.80402 (7)0.0189 (5)
H170.08490.13640.82310.023*
C180.0239 (3)0.2973 (4)0.75601 (7)0.0202 (6)
H180.02070.35960.73460.024*
C190.1328 (3)0.2251 (3)0.76948 (7)0.0166 (5)
H190.21690.22640.75950.020*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0345 (11)0.0602 (15)0.0383 (12)0.0245 (11)0.0181 (9)0.0139 (11)
F20.0478 (13)0.0346 (11)0.0444 (12)0.0137 (10)0.0285 (10)0.0034 (10)
F30.0367 (11)0.0788 (17)0.0134 (9)0.0105 (11)0.0078 (8)0.0042 (10)
N10.0148 (10)0.0162 (10)0.0081 (9)0.0008 (8)0.0002 (8)0.0005 (8)
N20.0169 (11)0.0151 (10)0.0105 (10)0.0008 (8)0.0006 (8)0.0022 (8)
N30.0195 (12)0.0278 (13)0.0215 (12)0.0005 (10)0.0042 (10)0.0042 (10)
C10.0195 (12)0.0123 (11)0.0082 (10)0.0026 (9)0.0004 (9)0.0018 (9)
C20.0207 (13)0.0143 (11)0.0079 (10)0.0023 (10)0.0011 (9)0.0015 (9)
C30.0161 (13)0.0258 (14)0.0157 (12)0.0045 (11)0.0025 (10)0.0014 (11)
C40.0149 (12)0.0335 (16)0.0202 (13)0.0007 (11)0.0004 (10)0.0006 (12)
C50.0167 (13)0.0314 (15)0.0165 (13)0.0001 (11)0.0042 (10)0.0047 (11)
C60.0173 (12)0.0213 (13)0.0114 (11)0.0022 (10)0.0001 (9)0.0021 (10)
C70.0145 (11)0.0171 (12)0.0123 (11)0.0021 (9)0.0007 (9)0.0008 (9)
C80.0172 (12)0.0177 (12)0.0104 (11)0.0040 (10)0.0001 (9)0.0002 (9)
C90.0186 (12)0.0132 (11)0.0102 (11)0.0002 (9)0.0027 (9)0.0011 (9)
C100.0177 (12)0.0170 (12)0.0085 (11)0.0010 (10)0.0009 (9)0.0014 (9)
C110.0163 (12)0.0216 (13)0.0125 (12)0.0004 (10)0.0007 (9)0.0006 (10)
C120.0188 (12)0.0188 (12)0.0104 (11)0.0032 (10)0.0021 (10)0.0014 (9)
C130.0236 (13)0.0197 (13)0.0076 (11)0.0016 (10)0.0014 (10)0.0015 (9)
C140.0190 (12)0.0196 (13)0.0106 (11)0.0023 (10)0.0005 (10)0.0009 (10)
C150.0214 (13)0.0254 (15)0.0148 (12)0.0026 (11)0.0068 (10)0.0013 (10)
C160.0209 (13)0.0144 (12)0.0103 (11)0.0026 (10)0.0023 (10)0.0006 (9)
C170.0148 (12)0.0262 (14)0.0157 (12)0.0012 (11)0.0008 (10)0.0039 (11)
C180.0271 (14)0.0198 (13)0.0136 (12)0.0003 (11)0.0043 (11)0.0019 (10)
C190.0208 (13)0.0175 (12)0.0115 (11)0.0012 (10)0.0006 (10)0.0003 (10)
Geometric parameters (Å, º) top
F1—C151.344 (4)C5—H50.9500
F2—C151.340 (4)C6—C71.401 (4)
F3—C151.326 (3)C6—H60.9500
N1—C71.400 (3)C7—C81.415 (4)
N1—C11.406 (3)C9—C101.393 (4)
N1—C91.427 (3)C9—C141.400 (3)
N2—C171.360 (3)C10—C111.389 (4)
N2—C191.383 (3)C10—H100.9500
N2—C161.466 (3)C11—C121.394 (4)
N3—C171.316 (4)C11—H110.9500
N3—C181.383 (4)C12—C131.387 (4)
C1—C21.365 (4)C12—C151.495 (4)
C1—C161.498 (4)C13—C141.395 (4)
C2—C81.436 (4)C13—H130.9500
C2—H20.9500C14—H140.9500
C3—C41.385 (4)C16—H16A0.9900
C3—C81.401 (4)C16—H16B0.9900
C3—H30.9500C17—H170.9500
C4—C51.416 (4)C18—C191.366 (4)
C4—H40.9500C18—H180.9500
C5—C61.382 (4)C19—H190.9500
C7—N1—C1108.2 (2)C11—C10—H10120.1
C7—N1—C9124.8 (2)C9—C10—H10120.1
C1—N1—C9126.9 (2)C10—C11—C12119.9 (3)
C17—N2—C19106.6 (2)C10—C11—H11120.0
C17—N2—C16125.1 (2)C12—C11—H11120.0
C19—N2—C16127.5 (2)C13—C12—C11120.7 (2)
C17—N3—C18104.4 (2)C13—C12—C15120.2 (2)
C2—C1—N1109.0 (2)C11—C12—C15119.0 (3)
C2—C1—C16127.4 (2)C12—C13—C14119.5 (2)
N1—C1—C16123.4 (2)C12—C13—H13120.2
C1—C2—C8108.2 (2)C14—C13—H13120.2
C1—C2—H2125.9C13—C14—C9119.9 (2)
C8—C2—H2125.9C13—C14—H14120.1
C4—C3—C8118.7 (3)C9—C14—H14120.1
C4—C3—H3120.7F3—C15—F2106.5 (2)
C8—C3—H3120.7F3—C15—F1105.9 (2)
C3—C4—C5121.0 (3)F2—C15—F1105.7 (3)
C3—C4—H4119.5F3—C15—C12113.4 (2)
C5—C4—H4119.5F2—C15—C12112.5 (2)
C6—C5—C4121.5 (3)F1—C15—C12112.2 (2)
C6—C5—H5119.3N2—C16—C1114.8 (2)
C4—C5—H5119.3N2—C16—H16A108.6
C5—C6—C7117.2 (2)C1—C16—H16A108.6
C5—C6—H6121.4N2—C16—H16B108.6
C7—C6—H6121.4C1—C16—H16B108.6
N1—C7—C6129.9 (2)H16A—C16—H16B107.6
N1—C7—C8107.7 (2)N3—C17—N2112.6 (3)
C6—C7—C8122.1 (2)N3—C17—H17123.7
C3—C8—C7119.5 (2)N2—C17—H17123.7
C3—C8—C2133.5 (2)C19—C18—N3111.0 (2)
C7—C8—C2106.8 (2)C19—C18—H18124.5
C10—C9—C14120.2 (2)N3—C18—H18124.5
C10—C9—N1120.5 (2)C18—C19—N2105.3 (2)
C14—C9—N1119.4 (2)C18—C19—H19127.4
C11—C10—C9119.8 (2)N2—C19—H19127.4
C7—N1—C1—C20.6 (3)C14—C9—C10—C111.0 (4)
C9—N1—C1—C2176.1 (2)N1—C9—C10—C11179.8 (2)
C7—N1—C1—C16177.2 (2)C9—C10—C11—C121.2 (4)
C9—N1—C1—C160.4 (4)C10—C11—C12—C130.8 (4)
N1—C1—C2—C81.6 (3)C10—C11—C12—C15178.1 (3)
C16—C1—C2—C8178.0 (2)C11—C12—C13—C140.1 (4)
C8—C3—C4—C51.0 (5)C15—C12—C13—C14177.4 (3)
C3—C4—C5—C60.6 (5)C12—C13—C14—C90.1 (4)
C4—C5—C6—C70.2 (4)C10—C9—C14—C130.4 (4)
C1—N1—C7—C6174.3 (3)N1—C9—C14—C13179.1 (2)
C9—N1—C7—C68.9 (4)C13—C12—C15—F314.2 (4)
C1—N1—C7—C80.6 (3)C11—C12—C15—F3168.5 (3)
C9—N1—C7—C8177.4 (2)C13—C12—C15—F2135.1 (3)
C5—C6—C7—N1172.3 (3)C11—C12—C15—F247.5 (4)
C5—C6—C7—C80.6 (4)C13—C12—C15—F1105.8 (3)
C4—C3—C8—C70.6 (4)C11—C12—C15—F171.6 (4)
C4—C3—C8—C2173.6 (3)C17—N2—C16—C1134.7 (3)
N1—C7—C8—C3174.1 (2)C19—N2—C16—C156.1 (3)
C6—C7—C8—C30.2 (4)C2—C1—C16—N286.5 (3)
N1—C7—C8—C21.5 (3)N1—C1—C16—N297.6 (3)
C6—C7—C8—C2175.8 (2)C18—N3—C17—N21.0 (3)
C1—C2—C8—C3172.8 (3)C19—N2—C17—N31.5 (3)
C1—C2—C8—C71.9 (3)C16—N2—C17—N3172.5 (2)
C7—N1—C9—C10129.0 (3)C17—N3—C18—C190.2 (3)
C1—N1—C9—C1054.7 (4)N3—C18—C19—N20.7 (3)
C7—N1—C9—C1449.7 (4)C17—N2—C19—C181.2 (3)
C1—N1—C9—C14126.5 (3)C16—N2—C19—C18172.0 (2)

Experimental details

Crystal data
Chemical formulaC19H14F3N3
Mr341.33
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)100
a, b, c (Å)10.3732 (17), 7.9960 (13), 37.665 (6)
V3)3124.0 (9)
Z8
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.53 × 0.26 × 0.05
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2004)
Tmin, Tmax0.943, 0.994
No. of measured, independent and
observed [I > 2σ(I)] reflections
30000, 4505, 3217
Rint0.093
(sin θ/λ)max1)0.708
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.079, 0.214, 0.99
No. of reflections4505
No. of parameters226
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.51, 0.38

Computer programs: APEX2 (Bruker, 1998), SAINT (Bruker, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

 

Acknowledgements

This work was supported by the Natural Science Foundation of P. R. China (20562012).

References

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