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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2613.
Published online 2009 October 3. doi:  10.1107/S1600536809039051
PMCID: PMC2971400

1-Benzyl-1H-benzimidazole

Abstract

In the title mol­ecule, C14H12N2, the benzimidazole ring system is essentially planar (r.m.s. deviation = 0.024 Å). The dihedral angle between the imidazole ring and the benzyl ring is 85.77 (4)°. In the crystal, mol­ecules are linked into chains along the a axis by C—H(...)N hydrogen bonds. In addition, the packing is stabilized by C—H(...)π inter­actions involving both six-membered rings.

Related literature

For general background to benzimidazole derivatives, see: Ansari & Lal (2009 [triangle]). For the synthesis, see: Hayat et al. (2001 [triangle]).

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Object name is e-65-o2613-scheme1.jpg

Experimental

Crystal data

  • C14H12N2
  • M r = 208.26
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2613-efi1.jpg
  • a = 6.2265 (10) Å
  • b = 8.1740 (13) Å
  • c = 20.975 (4) Å
  • β = 97.839 (2)°
  • V = 1057.5 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 93 K
  • 0.57 × 0.50 × 0.37 mm

Data collection

  • Rigaku SPIDER diffractometer
  • Absorption correction: none
  • 8358 measured reflections
  • 2412 independent reflections
  • 2198 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.038
  • wR(F 2) = 0.093
  • S = 1.00
  • 2412 reflections
  • 145 parameters
  • H-atom parameters constrained
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.25 e Å−3

Data collection: RAPID-AUTO (Rigaku, 2004 [triangle]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP in SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809039051/ci2926sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809039051/ci2926Isup2.hkl

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

Acknowledgments

The authors thank the Centre for Testing and Analysis, Cheng Du Branch of the Chinese Academy of Sciences, for analytical support.

supplementary crystallographic information

Comment

Benzimidazole derivatives are a class of important compounds which exhibit antimicrobial activity (Ansari & Lal, 2009). Here, we report the crystal structure of the title compound.

Bond lengths and angles in the title molecule are normal. The benzimidazole ring system is planar, with a maximum deviation of 0.035 (2)Å for atom C4. The imidazole ring and benzene ring in benzyl group are almost mutually perpendicular, with a dihedral angle of 85.77 (4)% (Fig. 1). The crystal packing is stabilized by C—H···N hydrogen bonds and C—H···π interactions (Cg1 is the centroid of the C11-C16 ring and Cg2 is the centroid of the C4—C9 ring) (Table 1).

Experimental

The title compound was synthesized according to the method reported in the literature (Hayat et al., 2001). Colourless single crystals suitable for X-ray diffraction were obtained by slow evaporation of a methanol solution.

Refinement

All H atoms were placed in calculated positions, with C-H = 0.95 or 0.99 Å, and refined using a riding model, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atomic numbering.

Crystal data

C14H12N2F(000) = 440
Mr = 208.26Dx = 1.308 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3307 reflections
a = 6.2265 (10) Åθ = 3.2–27.5°
b = 8.1740 (13) ŵ = 0.08 mm1
c = 20.975 (4) ÅT = 93 K
β = 97.839 (2)°Block, colourless
V = 1057.5 (3) Å30.57 × 0.50 × 0.37 mm
Z = 4

Data collection

Rigaku SPIDER diffractometer2198 reflections with I > 2σ(I)
Radiation source: Rotating AnodeRint = 0.022
graphiteθmax = 27.5°, θmin = 3.2°
ω scansh = −8→8
8358 measured reflectionsk = −10→10
2412 independent reflectionsl = −27→27

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.093H-atom parameters constrained
S = 1.00w = 1/[σ2(Fo2) + (0.0482P)2 + 0.296P] where P = (Fo2 + 2Fc2)/3
2412 reflections(Δ/σ)max = 0.001
145 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = −0.25 e Å3

Special details

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)

xyzUiso*/Ueq
N10.41468 (13)0.11825 (10)0.58340 (4)0.0151 (2)
N20.08985 (14)0.00680 (11)0.59213 (4)0.0184 (2)
C20.21067 (16)0.08189 (12)0.55458 (5)0.0164 (2)
H20.16020.10860.51100.020*
C40.22460 (16)−0.00841 (12)0.65071 (5)0.0164 (2)
C50.18809 (18)−0.08552 (13)0.70781 (5)0.0206 (2)
H50.0516−0.13290.71220.025*
C60.35775 (19)−0.09021 (14)0.75762 (5)0.0234 (3)
H60.3374−0.14340.79660.028*
C70.55957 (19)−0.01845 (14)0.75220 (5)0.0230 (3)
H70.6720−0.02410.78760.028*
C80.59841 (17)0.06012 (13)0.69652 (5)0.0190 (2)
H80.73380.11030.69290.023*
C90.42797 (16)0.06166 (12)0.64598 (5)0.0153 (2)
C100.58686 (16)0.19667 (13)0.55403 (5)0.0163 (2)
H10A0.54880.19270.50670.020*
H10B0.72230.13340.56530.020*
C110.62877 (16)0.37280 (13)0.57428 (5)0.0148 (2)
C120.47606 (16)0.46721 (13)0.59998 (5)0.0175 (2)
H120.34140.42010.60660.021*
C130.51869 (18)0.63021 (13)0.61606 (5)0.0198 (2)
H130.41380.69360.63390.024*
C140.71437 (17)0.70020 (13)0.60598 (5)0.0187 (2)
H140.74290.81190.61650.022*
C150.86811 (17)0.60677 (13)0.58054 (5)0.0185 (2)
H151.00230.65440.57380.022*
C160.82598 (16)0.44380 (13)0.56497 (5)0.0171 (2)
H160.93220.38010.54780.021*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0142 (4)0.0141 (4)0.0168 (4)−0.0009 (3)0.0017 (3)−0.0012 (3)
N20.0160 (4)0.0162 (4)0.0226 (5)−0.0005 (3)0.0016 (3)0.0004 (4)
C20.0155 (5)0.0136 (5)0.0195 (5)0.0007 (4)−0.0002 (4)−0.0013 (4)
C40.0162 (5)0.0131 (5)0.0201 (5)0.0014 (4)0.0030 (4)−0.0028 (4)
C50.0211 (5)0.0181 (5)0.0239 (5)−0.0002 (4)0.0084 (4)−0.0008 (4)
C60.0305 (6)0.0229 (6)0.0178 (5)0.0026 (5)0.0074 (4)0.0005 (4)
C70.0256 (6)0.0248 (6)0.0176 (5)0.0029 (5)−0.0006 (4)−0.0033 (4)
C80.0171 (5)0.0193 (5)0.0205 (5)−0.0003 (4)0.0015 (4)−0.0040 (4)
C90.0174 (5)0.0119 (5)0.0172 (5)0.0017 (4)0.0037 (4)−0.0028 (4)
C100.0140 (5)0.0167 (5)0.0188 (5)−0.0008 (4)0.0043 (4)−0.0016 (4)
C110.0154 (5)0.0159 (5)0.0129 (5)0.0001 (4)0.0009 (4)0.0012 (4)
C120.0143 (5)0.0187 (5)0.0201 (5)−0.0008 (4)0.0039 (4)0.0000 (4)
C130.0198 (5)0.0173 (5)0.0227 (5)0.0031 (4)0.0048 (4)−0.0009 (4)
C140.0223 (5)0.0143 (5)0.0189 (5)−0.0009 (4)0.0010 (4)0.0005 (4)
C150.0165 (5)0.0198 (5)0.0192 (5)−0.0036 (4)0.0027 (4)0.0019 (4)
C160.0154 (5)0.0196 (5)0.0170 (5)0.0009 (4)0.0044 (4)−0.0001 (4)

Geometric parameters (Å, °)

N1—C21.3630 (13)C8—H80.95
N1—C91.3835 (13)C10—C111.5137 (15)
N1—C101.4560 (13)C10—H10A0.99
N2—C21.3132 (14)C10—H10B0.99
N2—C41.3956 (13)C11—C121.3892 (14)
C2—H20.95C11—C161.3958 (14)
C4—C51.3992 (15)C12—C131.3910 (15)
C4—C91.4055 (14)C12—H120.95
C5—C61.3812 (16)C13—C141.3881 (15)
C5—H50.95C13—H130.95
C6—C71.4053 (17)C14—C151.3870 (15)
C6—H60.95C14—H140.95
C7—C81.3826 (16)C15—C161.3881 (16)
C7—H70.95C15—H150.95
C8—C91.3940 (14)C16—H160.95
C2—N1—C9106.23 (9)N1—C10—C11114.12 (8)
C2—N1—C10127.14 (9)N1—C10—H10A108.7
C9—N1—C10126.61 (8)C11—C10—H10A108.7
C2—N2—C4104.17 (9)N1—C10—H10B108.7
N2—C2—N1114.29 (9)C11—C10—H10B108.7
N2—C2—H2122.9H10A—C10—H10B107.6
N1—C2—H2122.9C12—C11—C16119.02 (10)
N2—C4—C5130.19 (10)C12—C11—C10122.43 (9)
N2—C4—C9109.93 (9)C16—C11—C10118.52 (9)
C5—C4—C9119.80 (10)C11—C12—C13120.53 (10)
C6—C5—C4117.59 (10)C11—C12—H12119.7
C6—C5—H5121.2C13—C12—H12119.7
C4—C5—H5121.2C14—C13—C12120.02 (10)
C5—C6—C7121.82 (10)C14—C13—H13120.0
C5—C6—H6119.1C12—C13—H13120.0
C7—C6—H6119.1C15—C14—C13119.86 (10)
C8—C7—C6121.57 (10)C15—C14—H14120.1
C8—C7—H7119.2C13—C14—H14120.1
C6—C7—H7119.2C14—C15—C16120.05 (10)
C7—C8—C9116.34 (10)C14—C15—H15120.0
C7—C8—H8121.8C16—C15—H15120.0
C9—C8—H8121.8C15—C16—C11120.51 (10)
N1—C9—C8131.71 (10)C15—C16—H16119.7
N1—C9—C4105.38 (9)C11—C16—H16119.7
C8—C9—C4122.85 (10)
C4—N2—C2—N1−0.14 (12)N2—C4—C9—N1−0.51 (11)
C9—N1—C2—N2−0.17 (12)C5—C4—C9—N1176.66 (9)
C10—N1—C2—N2178.24 (9)N2—C4—C9—C8−177.95 (9)
C2—N2—C4—C5−176.38 (11)C5—C4—C9—C8−0.78 (15)
C2—N2—C4—C90.40 (11)C2—N1—C10—C11105.93 (11)
N2—C4—C5—C6176.02 (10)C9—N1—C10—C11−75.97 (12)
C9—C4—C5—C6−0.49 (15)N1—C10—C11—C12−20.55 (13)
C4—C5—C6—C70.97 (16)N1—C10—C11—C16161.34 (9)
C5—C6—C7—C8−0.20 (17)C16—C11—C12—C130.16 (15)
C6—C7—C8—C9−1.03 (16)C10—C11—C12—C13−177.95 (10)
C2—N1—C9—C8177.52 (11)C11—C12—C13—C140.52 (16)
C10—N1—C9—C8−0.91 (17)C12—C13—C14—C15−0.72 (16)
C2—N1—C9—C40.41 (11)C13—C14—C15—C160.24 (16)
C10—N1—C9—C4−178.02 (9)C14—C15—C16—C110.45 (15)
C7—C8—C9—N1−175.17 (10)C12—C11—C16—C15−0.64 (15)
C7—C8—C9—C41.52 (15)C10—C11—C16—C15177.54 (9)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C10—H10B···N2i0.992.503.4890 (14)173
C7—H7···Cg1ii0.952.663.5220 (1)151
C13—H13···Cg2iii0.952.803.5660 (3)139

Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y−1, −z+1; (iii) x, y+1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2926).

References

  • Ansari, K. F. & Lal, C. (2009). Eur. J. Med. Chem.44, 4028–4033. [PubMed]
  • Hayat, S., Atta-ur-Rahman, Choudhary, M. I., Khan, K. M., Schumann, W. & Bayer, E. (2001). Tetrahedron, 57, 9951–9957.
  • Rigaku (2004). RAPID-AUTO Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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