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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2460.
Published online 2008 November 26. doi:  10.1107/S1600536808037483
PMCID: PMC2959878

2-Amino-1H-benzoimidazol-3-ium 4,4,4-trifluoro-1,3-dioxo-1-phenyl­butan-2-ide

Abstract

In the title compound, C7H8N3 +·C10H6F3O2 , 1H-benzoimidazol-2-amine system adopts a planar conformation with an r.m.s. deviation of 0.0174 Å. The cation and anion in the asymmetric unit are linked by N—H(...)O hydrogen bonds. There are also additional inter­molecular N—H(...)O hydrogen bonds and π–π stacking inter­actions between the phenyl rings of neighbouring anions with centroid–centroid distances of 4.0976 (13) Å.

Related literature

For details of the bioactivity of organofluorine compounds, see: Hermann et al. (2003 [triangle]); Ulrich (2004 [triangle]).

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Object name is e-64-o2460-scheme1.jpg

Experimental

Crystal data

  • C7H8N3 +·C10H6F3O2
  • M r = 349.31
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2460-efi1.jpg
  • a = 16.755 (3) Å
  • b = 10.552 (2) Å
  • c = 18.497 (4) Å
  • V = 3270.0 (11) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 113 (2) K
  • 0.12 × 0.10 × 0.06 mm

Data collection

  • Rigaku Saturn CCD diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2002 [triangle]) T min = 0.986, T max = 0.993
  • 31132 measured reflections
  • 2881 independent reflections
  • 2609 reflections with I > 2σ(I)
  • R int = 0.050

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.107
  • S = 1.06
  • 2881 reflections
  • 243 parameters
  • 5 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2002 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808037483/sj2549sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808037483/sj2549Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the Natural Science Foundation of Henan Province, China (grant No. 082300420110) and the Natural Science Foundation of Henan Province Education Department, China (grant No. 2007150036) for financial support.

supplementary crystallographic information

Comment

Compounds that contain fluorine exhibit particular bioactivity, for example, flumioxazin is a widely used herbicide (Hermann et al., 2003; Ulrich,2004). This led us to pay much attention to the synthesis and structure of similar fluoro-compounds. During the synthesis of trifluoromethylated heterocyclic compounds, an intermediate, the title compound,(I), Fig.1, was isolated and we report its crystal structure here.

The 1H-benzo[d]imizol-2-amine cation adopts a planar conformation with an rms deviation of 0.0174 for the fitted atoms. The phenyl ring is almost perpendicular to the fused heterocyclic rings, with a dihedral angle of 81.84 (4)° between them. The cation and anion in the asymmetric unit are linked by N1—H1B···O1 and N2—H2A···O2 hydrogen bonds.

The crystal packing is further stabilized by additional intermolecular N—H···O hydrogen bonds (Table 1, Fig. 2) and intermolecular π···π stacking interactions between the C5-C10 phenyl rings (symmetry code: 2-x, -y, -z) of neighbouring anions with centroid-to-centroid distances, plane-plane distances and displacement distances of 4.0976 (13), 3.786 and 1.565Å respectively.

Experimental

The title compound was synthesized by the reaction of 4,4,4-trifluoro-1- phenylbutane-1,3-dione (1 mmol) and 1H-benzo[d]imidazol-2-amine (1 mmol) in refluxing ethanol (20 mL) for a certain time (monitored by TLC). Cooling, the reaction mixture slowly to room temperature, gave single crystals suitable for X-ray diffraction.

Refinement

Hydrogen atoms bound to nitrogen atoms were located in a difference Fourier map and were refined with d(N—H) restrained to 0.90 (1) Å and d(H1A···H1B) restrained to 1.50 (1) Å. Other H atoms were placed in calculated positions, d(C—H) = 0.93 Å, and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The asymmetric unit of the title compound, showing 30% probability displacement ellipsoids and the atom-numbering scheme. Hydrogen bonds are drawn as dashed lines.
Fig. 2.
The packing diagram of the title compound. Intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

C7H8N3+·C10H6F3O2F000 = 1440
Mr = 349.31Dx = 1.419 Mg m3
Orthorhombic, PbcaMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 6974 reflections
a = 16.755 (3) Åθ = 2.2–27.9º
b = 10.552 (2) ŵ = 0.12 mm1
c = 18.497 (4) ÅT = 113 (2) K
V = 3270.0 (11) Å3Block, yellow
Z = 80.12 × 0.10 × 0.06 mm

Data collection

Rigaku Saturn CCD diffractometer2881 independent reflections
Radiation source: rotating anode2609 reflections with I > 2σ(I)
Monochromator: confocalRint = 0.050
T = 113(2) Kθmax = 25.0º
ω scansθmin = 2.2º
Absorption correction: multi-scan(CrystalClear; Rigaku/MSC, 2002)h = −19→19
Tmin = 0.986, Tmax = 0.993k = −12→12
31132 measured reflectionsl = −22→21

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.107  w = 1/[σ2(Fo2) + (0.0613P)2 + 0.895P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
2881 reflectionsΔρmax = 0.21 e Å3
243 parametersΔρmin = −0.20 e Å3
5 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0073 (10)

Special details

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)

xyzUiso*/Ueq
F10.74257 (7)0.54639 (12)0.05657 (5)0.0552 (3)
F20.77552 (6)0.66729 (9)0.14532 (6)0.0473 (3)
F30.71669 (6)0.49082 (11)0.16580 (6)0.0467 (3)
O11.01117 (6)0.37243 (10)0.11875 (6)0.0301 (3)
O20.88568 (6)0.49842 (10)0.19269 (6)0.0303 (3)
N11.03832 (8)0.19158 (15)0.23172 (8)0.0379 (4)
N20.90662 (8)0.26462 (13)0.25377 (7)0.0298 (3)
N30.94668 (8)0.09546 (13)0.31266 (7)0.0295 (3)
C10.77211 (10)0.54628 (16)0.12397 (9)0.0335 (4)
C20.85307 (9)0.48052 (14)0.13136 (8)0.0277 (3)
C30.88043 (9)0.40780 (15)0.07420 (8)0.0290 (4)
H30.84670.39550.03490.035*
C40.95774 (9)0.35055 (14)0.07232 (8)0.0264 (3)
C50.97828 (9)0.26266 (14)0.01141 (8)0.0263 (3)
C61.05759 (10)0.25313 (16)−0.01066 (9)0.0324 (4)
H61.09620.30300.01160.039*
C71.07968 (10)0.17084 (17)−0.06508 (10)0.0378 (4)
H71.13270.1665−0.07970.045*
C81.02270 (11)0.09443 (16)−0.09797 (9)0.0368 (4)
H81.03760.0379−0.13410.044*
C90.94389 (10)0.10278 (15)−0.07679 (9)0.0346 (4)
H90.90570.0518−0.09890.042*
C100.92111 (10)0.18696 (15)−0.02263 (8)0.0308 (4)
H100.86780.1928−0.00910.037*
C110.96806 (9)0.18451 (15)0.26443 (8)0.0296 (4)
C120.84329 (9)0.22790 (15)0.29854 (8)0.0275 (4)
C130.76879 (9)0.28105 (17)0.31021 (8)0.0321 (4)
H130.75180.35270.28530.038*
C140.72078 (10)0.22158 (17)0.36124 (9)0.0349 (4)
H140.67050.25480.37100.042*
C150.74579 (10)0.11347 (17)0.39833 (9)0.0339 (4)
H150.71180.07630.43190.041*
C160.82038 (10)0.06027 (15)0.38614 (8)0.0309 (4)
H160.8371−0.01200.41060.037*
C170.86862 (9)0.11999 (14)0.33575 (8)0.0273 (3)
H1A1.0783 (9)0.1439 (16)0.2457 (10)0.046 (5)*
H1B1.0438 (10)0.2461 (14)0.1961 (8)0.043 (5)*
H2A0.9093 (12)0.3377 (13)0.2283 (10)0.051 (6)*
H3A0.9769 (11)0.0317 (15)0.3290 (11)0.051 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
F10.0509 (7)0.0792 (8)0.0356 (6)0.0313 (6)−0.0129 (5)−0.0053 (6)
F20.0462 (6)0.0331 (6)0.0628 (7)0.0093 (4)0.0013 (5)−0.0034 (5)
F30.0293 (5)0.0561 (7)0.0546 (7)−0.0022 (5)0.0024 (5)0.0043 (5)
O10.0292 (6)0.0319 (6)0.0291 (6)−0.0017 (5)−0.0052 (5)−0.0008 (5)
O20.0307 (6)0.0322 (6)0.0279 (6)−0.0019 (5)−0.0042 (4)−0.0015 (5)
N10.0316 (8)0.0461 (9)0.0358 (8)0.0102 (7)0.0039 (6)0.0122 (7)
N20.0306 (7)0.0313 (7)0.0274 (7)0.0048 (6)−0.0006 (5)0.0055 (6)
N30.0298 (7)0.0304 (7)0.0284 (7)0.0056 (6)−0.0008 (5)0.0029 (6)
C10.0353 (9)0.0355 (9)0.0296 (8)0.0026 (7)−0.0016 (7)0.0005 (7)
C20.0275 (8)0.0253 (8)0.0301 (8)−0.0030 (6)−0.0033 (6)0.0048 (6)
C30.0295 (8)0.0312 (8)0.0263 (8)0.0009 (6)−0.0056 (6)0.0006 (6)
C40.0296 (8)0.0239 (8)0.0256 (7)−0.0038 (6)−0.0027 (6)0.0053 (6)
C50.0291 (8)0.0251 (7)0.0249 (7)−0.0002 (6)−0.0030 (6)0.0044 (6)
C60.0285 (8)0.0337 (9)0.0350 (9)−0.0024 (7)−0.0036 (7)−0.0011 (7)
C70.0309 (9)0.0418 (10)0.0407 (9)0.0010 (7)0.0045 (7)−0.0035 (8)
C80.0452 (10)0.0324 (9)0.0327 (9)0.0025 (7)0.0014 (7)−0.0036 (7)
C90.0391 (9)0.0286 (8)0.0360 (9)−0.0057 (7)−0.0058 (7)−0.0025 (7)
C100.0287 (8)0.0306 (8)0.0330 (8)−0.0030 (6)−0.0021 (6)0.0020 (7)
C110.0301 (9)0.0336 (8)0.0250 (8)0.0036 (7)−0.0028 (6)0.0009 (6)
C120.0293 (8)0.0305 (8)0.0227 (7)−0.0001 (6)−0.0027 (6)−0.0021 (6)
C130.0300 (9)0.0369 (9)0.0292 (8)0.0055 (7)−0.0047 (6)−0.0011 (7)
C140.0260 (8)0.0453 (10)0.0332 (9)0.0007 (7)−0.0029 (6)−0.0045 (8)
C150.0300 (8)0.0421 (10)0.0298 (8)−0.0074 (7)−0.0005 (7)−0.0015 (7)
C160.0348 (9)0.0300 (8)0.0279 (8)−0.0032 (7)−0.0049 (6)0.0018 (6)
C170.0279 (8)0.0290 (8)0.0249 (7)0.0008 (6)−0.0056 (6)−0.0033 (6)

Geometric parameters (Å, °)

F1—C11.3415 (19)C5—C101.397 (2)
F2—C11.338 (2)C6—C71.380 (2)
F3—C11.3429 (19)C6—H60.9300
O1—C41.2618 (18)C7—C81.390 (3)
O2—C21.2732 (18)C7—H70.9300
N1—C111.326 (2)C8—C91.380 (2)
N1—H1A0.877 (9)C8—H80.9300
N1—H1B0.879 (9)C9—C101.392 (2)
N2—C111.346 (2)C9—H90.9300
N2—C121.401 (2)C10—H100.9300
N2—H2A0.905 (10)C12—C131.385 (2)
N3—C111.344 (2)C12—C171.396 (2)
N3—C171.400 (2)C13—C141.390 (2)
N3—H3A0.895 (9)C13—H130.9300
C1—C21.530 (2)C14—C151.395 (2)
C2—C31.385 (2)C14—H140.9300
C3—C41.430 (2)C15—C161.388 (2)
C3—H30.9300C15—H150.9300
C4—C51.499 (2)C16—C171.385 (2)
C5—C61.394 (2)C16—H160.9300
C11—N1—H1A120.8 (12)C8—C7—H7120.0
C11—N1—H1B118.1 (11)C9—C8—C7119.73 (16)
H1A—N1—H1B121.1 (14)C9—C8—H8120.1
C11—N2—C12108.60 (13)C7—C8—H8120.1
C11—N2—H2A125.0 (13)C8—C9—C10120.49 (15)
C12—N2—H2A125.5 (13)C8—C9—H9119.8
C11—N3—C17108.79 (13)C10—C9—H9119.8
C11—N3—H3A126.8 (14)C9—C10—C5120.07 (15)
C17—N3—H3A124.4 (14)C9—C10—H10120.0
F2—C1—F1106.81 (13)C5—C10—H10120.0
F2—C1—F3105.99 (13)N1—C11—N3125.36 (14)
F1—C1—F3106.30 (13)N1—C11—N2125.23 (15)
F2—C1—C2111.64 (13)N3—C11—N2109.40 (14)
F1—C1—C2114.24 (14)C13—C12—C17121.81 (14)
F3—C1—C2111.35 (13)C13—C12—N2131.50 (15)
O2—C2—C3128.36 (14)C17—C12—N2106.66 (13)
O2—C2—C1113.13 (14)C12—C13—C14116.39 (15)
C3—C2—C1118.47 (14)C12—C13—H13121.8
C2—C3—C4123.55 (14)C14—C13—H13121.8
C2—C3—H3118.2C13—C14—C15121.95 (15)
C4—C3—H3118.2C13—C14—H14119.0
O1—C4—C3123.29 (14)C15—C14—H14119.0
O1—C4—C5117.51 (13)C16—C15—C14121.39 (15)
C3—C4—C5119.18 (13)C16—C15—H15119.3
C6—C5—C10118.71 (14)C14—C15—H15119.3
C6—C5—C4118.92 (13)C17—C16—C15116.78 (15)
C10—C5—C4122.34 (14)C17—C16—H16121.6
C7—C6—C5120.98 (15)C15—C16—H16121.6
C7—C6—H6119.5C16—C17—C12121.68 (14)
C5—C6—H6119.5C16—C17—N3131.78 (14)
C6—C7—C8120.01 (16)C12—C17—N3106.52 (13)
C6—C7—H7120.0
F2—C1—C2—O248.38 (18)C4—C5—C10—C9−177.14 (14)
F1—C1—C2—O2169.71 (14)C17—N3—C11—N1179.40 (15)
F3—C1—C2—O2−69.86 (17)C17—N3—C11—N2−1.38 (17)
F2—C1—C2—C3−133.69 (15)C12—N2—C11—N1−179.13 (15)
F1—C1—C2—C3−12.4 (2)C12—N2—C11—N31.64 (18)
F3—C1—C2—C3108.07 (16)C11—N2—C12—C13177.01 (16)
O2—C2—C3—C4−7.8 (3)C11—N2—C12—C17−1.26 (17)
C1—C2—C3—C4174.64 (14)C17—C12—C13—C140.3 (2)
C2—C3—C4—O1−8.1 (2)N2—C12—C13—C14−177.71 (16)
C2—C3—C4—C5173.70 (14)C12—C13—C14—C15−0.6 (2)
O1—C4—C5—C6−27.7 (2)C13—C14—C15—C160.3 (2)
C3—C4—C5—C6150.58 (15)C14—C15—C16—C170.3 (2)
O1—C4—C5—C10150.25 (14)C15—C16—C17—C12−0.5 (2)
C3—C4—C5—C10−31.4 (2)C15—C16—C17—N3177.26 (15)
C10—C5—C6—C70.1 (2)C13—C12—C17—C160.2 (2)
C4—C5—C6—C7178.13 (15)N2—C12—C17—C16178.68 (14)
C5—C6—C7—C8−1.0 (3)C13—C12—C17—N3−178.06 (14)
C6—C7—C8—C91.1 (3)N2—C12—C17—N30.42 (16)
C7—C8—C9—C10−0.1 (3)C11—N3—C17—C16−177.45 (16)
C8—C9—C10—C5−0.8 (2)C11—N3—C17—C120.57 (16)
C6—C5—C10—C90.9 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···O2i0.877 (9)2.004 (11)2.7803 (18)146.8 (16)
N3—H3A···O1i0.895 (9)1.949 (13)2.7651 (17)150.9 (19)
N3—H3A···O2i0.895 (9)2.363 (18)2.9912 (18)127.3 (17)
N1—H1B···O10.879 (9)2.030 (10)2.8662 (18)158.4 (16)
N2—H2A···O20.905 (10)1.862 (11)2.7360 (18)161.8 (19)

Symmetry codes: (i) −x+2, y−1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2549).

References

  • Hermann, B., Erwin, H. & Hansjorg, K. (2003). US Patent No. 2 003 176 284.
  • Rigaku/MSC (2002). CrystalClear Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Ulrich, H. (2004). US Patent No. 2 004 033 897.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography