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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1358.
Published online 2009 May 23. doi:  10.1107/S1600536809018546
PMCID: PMC2969630

3-[(1H-Benzimidazol-2-yl)sulfanyl­methyl]benzonitrile

Abstract

In the title compound, C15H11N3S, the dihedral angle between the benzimidazole ring system and the benzene ring is 51.8 (2)°. The crystal structure exhibits inter­molecular N—H(...)N hydrogen bonds which lead to the formation of C(4) chains along the [001] direction.

Related literature

For pharmacological activities of benzimidazole and its derivatives, see: Negwer & Scharnow (2001 [triangle]). For graph-set notation, see: Bernstein et al. (1995 [triangle]).

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Object name is e-65-o1358-scheme1.jpg

Experimental

Crystal data

  • C15H11N3S
  • M r = 265.33
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1358-efi1.jpg
  • a = 15.384 (4) Å
  • b = 9.280 (4) Å
  • c = 9.887 (4) Å
  • β = 101.63 (3)°
  • V = 1382.5 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.22 mm−1
  • T = 292 K
  • 0.35 × 0.30 × 0.25 mm

Data collection

  • Rigaku SCXmini diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 [triangle]) T min = 0.927, T max = 0.947
  • 12254 measured reflections
  • 2711 independent reflections
  • 1926 reflections with I > 2σ(I)
  • R int = 0.052

Refinement

  • R[F 2 > 2σ(F 2)] = 0.070
  • wR(F 2) = 0.184
  • S = 1.13
  • 2711 reflections
  • 172 parameters
  • H-atom parameters constrained
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: CrystalClear (Rigaku, 2005 [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/S1600536809018546/bx2210sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018546/bx2210Isup2.hkl

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

Acknowledgments

This work was supported by financial support from Southeast University for Young Researchers (grant No. 4007041027).

supplementary crystallographic information

Comment

It is well known that Benzimidazole and its derivatives have received much attention due to their versatile pharmacological activities (Negwer & Scharnow, 2001). To further investigate the influence of the bridging ligand on the formation of supramolecular complexes, we designed and prepared a Benzimidazole-containing ligand, and used the ligand to generate some coordination polymers with interesting topologies. Here, we reported the crystal structure of the title compound. The molecular structure of the title compound, C15H11N3S, and the atomic labeling scheme are shown in Fig. 1. In this Structure, the nine-membered benzimidazole ring system C1/N1/C2/C3/C4/C5/C6/C7/N2 is essentially planar. The phenyl ring C9/C10–C14 is connected to the benzimidazole ring system by the SCH2 group. The bond lengths and angles have normal values, the dihedral angle between the benzimidazole ring system and the phenyl substituent is 51.77 (22)°, and the molecules are linked by intermolecular N—H···N hydrogen bonds which leads to the formation chains C(4) along the [001] direction (Bernstein et al., 1995).

Experimental

3-(bromomethyl)benzonitrile (11 mmol) was added to 2-mercaptobenzimidazole (10 mmol) in dry ethanol (25 ml). The mixture was refluxed for 24 h. The reaction mixture was diluted with ethyl acetate (100 ml), and the resulting solid was collected and dissolved in 20 ml of water. 40 ml of a solution of sodium hydrogen carbonate (35 g in 100 ml of water) was added. A white powder was isolated by filtration and dried to give the title compound. Colourless crystals of the title compound suitble for X-ray diffraction were from a solution of 50 mg in 20 ml methanol after 7 d.

Refinement

All H atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (aromatic), 0.97 Å (methylene) or 0.96 Å (methyl) with Uiso(H) = 1.2Ueq(Caromatic, Cmethylene)

Figures

Fig. 1.
The molecular structure of the title compound, showing the atomic numbering scheme. The displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
Packing diagram of the title compound, showing the structure along the a axis.

Crystal data

C15H11N3SF(000) = 552
Mr = 265.33Dx = 1.275 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2386 reflections
a = 15.384 (4) Åθ = 2.6–27.5°
b = 9.280 (4) ŵ = 0.22 mm1
c = 9.887 (4) ÅT = 292 K
β = 101.63 (3)°Prism, colourless
V = 1382.5 (8) Å30.35 × 0.30 × 0.25 mm
Z = 4

Data collection

Rigaku SCXmini diffractometer2711 independent reflections
Radiation source: fine-focus sealed tube1926 reflections with I > 2σ(I)
graphiteRint = 0.052
Detector resolution: 13.6612 pixels mm-1θmax = 26.0°, θmin = 2.6°
ω scansh = −18→18
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −11→11
Tmin = 0.927, Tmax = 0.947l = −12→12
12254 measured reflections

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)] = 0.070Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.184H-atom parameters constrained
S = 1.13w = 1/[σ2(Fo2) + (0.0802P)2 + 0.4001P] where P = (Fo2 + 2Fc2)/3
2711 reflections(Δ/σ)max < 0.001
172 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = −0.16 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
C10.3269 (2)0.2203 (3)0.2414 (3)0.0566 (8)
C20.3718 (2)0.4296 (3)0.3180 (3)0.0541 (8)
C30.3983 (3)0.5528 (3)0.3966 (3)0.0666 (9)
H30.39400.55750.48900.080*
C40.4308 (3)0.6672 (3)0.3330 (3)0.0710 (10)
H40.44840.75050.38340.085*
C50.4379 (3)0.6608 (3)0.1944 (3)0.0684 (9)
H50.46020.73980.15460.082*
C60.4125 (2)0.5406 (3)0.1158 (3)0.0639 (9)
H60.41750.53620.02370.077*
C70.3791 (2)0.4256 (3)0.1795 (3)0.0517 (7)
C80.2071 (3)0.0318 (4)0.3261 (4)0.0835 (11)
H8A0.23300.04080.42360.100*
H8B0.16460.10920.30010.100*
C90.1622 (3)−0.1128 (4)0.2964 (4)0.0772 (10)
C100.1924 (3)−0.2344 (5)0.3728 (5)0.0999 (14)
H100.2388−0.22590.44890.120*
C110.1549 (4)−0.3684 (5)0.3378 (6)0.1166 (17)
H110.1762−0.44930.38970.140*
C120.0852 (4)−0.3812 (5)0.2247 (6)0.1106 (16)
H120.0605−0.47110.19930.133*
C130.0527 (3)−0.2595 (4)0.1495 (5)0.0899 (12)
C140.0911 (3)−0.1256 (4)0.1844 (4)0.0814 (11)
H140.0694−0.04460.13320.098*
C15−0.0208 (4)−0.2675 (6)0.0345 (6)0.1185 (18)
N10.33875 (19)0.2979 (3)0.3553 (2)0.0602 (7)
N20.34898 (18)0.2904 (2)0.1329 (2)0.0572 (7)
H2A0.34500.25720.05070.069*
N3−0.0786 (4)−0.2759 (6)−0.0567 (6)0.161 (2)
S10.29335 (7)0.03901 (9)0.22331 (9)0.0739 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.090 (2)0.0474 (16)0.0342 (14)−0.0029 (15)0.0174 (15)0.0013 (12)
C20.087 (2)0.0441 (14)0.0328 (14)0.0006 (14)0.0159 (14)0.0015 (11)
C30.109 (3)0.0535 (17)0.0404 (16)−0.0015 (17)0.0226 (17)−0.0079 (13)
C40.112 (3)0.0462 (17)0.0565 (19)−0.0052 (18)0.0212 (19)−0.0082 (14)
C50.103 (3)0.0458 (16)0.0602 (19)−0.0037 (17)0.0247 (19)0.0059 (15)
C60.101 (3)0.0558 (18)0.0389 (15)−0.0017 (17)0.0245 (16)0.0057 (13)
C70.083 (2)0.0421 (14)0.0311 (13)0.0052 (14)0.0148 (13)0.0009 (11)
C80.108 (3)0.081 (3)0.067 (2)−0.022 (2)0.031 (2)−0.0129 (19)
C90.095 (3)0.068 (2)0.073 (2)−0.016 (2)0.027 (2)0.0022 (19)
C100.104 (3)0.094 (3)0.100 (3)−0.017 (3)0.018 (3)0.016 (3)
C110.119 (4)0.081 (3)0.146 (5)−0.016 (3)0.017 (4)0.031 (3)
C120.123 (4)0.065 (3)0.149 (5)−0.023 (3)0.040 (4)0.002 (3)
C130.101 (3)0.074 (3)0.095 (3)−0.024 (2)0.021 (3)−0.008 (2)
C140.096 (3)0.066 (2)0.083 (3)−0.010 (2)0.023 (2)−0.0007 (19)
C150.139 (5)0.100 (4)0.112 (4)−0.041 (3)0.018 (4)−0.014 (3)
N10.104 (2)0.0477 (13)0.0330 (12)−0.0047 (13)0.0241 (13)−0.0015 (10)
N20.0971 (19)0.0497 (13)0.0276 (11)−0.0005 (13)0.0189 (12)−0.0020 (10)
N30.159 (5)0.158 (5)0.149 (5)−0.053 (4)−0.010 (4)−0.015 (4)
S10.1199 (8)0.0501 (5)0.0600 (6)−0.0158 (5)0.0378 (5)−0.0082 (4)

Geometric parameters (Å, °)

C1—N11.319 (3)C8—S11.829 (4)
C1—N21.355 (3)C8—H8A0.9700
C1—S11.758 (3)C8—H8B0.9700
C2—C31.396 (4)C9—C101.385 (6)
C2—C71.397 (4)C9—C141.396 (6)
C2—N11.401 (4)C10—C111.386 (6)
C3—C41.379 (4)C10—H100.9300
C3—H30.9300C11—C121.390 (7)
C4—C51.398 (4)C11—H110.9300
C4—H40.9300C12—C131.389 (6)
C5—C61.370 (4)C12—H120.9300
C5—H50.9300C13—C141.389 (5)
C6—C71.390 (4)C13—C151.435 (8)
C6—H60.9300C14—H140.9300
C7—N21.384 (4)C15—N31.135 (7)
C8—C91.510 (5)N2—H2A0.8600
N1—C1—N2113.6 (3)H8A—C8—H8B108.7
N1—C1—S1126.6 (2)C10—C9—C14119.1 (4)
N2—C1—S1119.6 (2)C10—C9—C8121.8 (4)
C3—C2—C7119.7 (3)C14—C9—C8119.0 (4)
C3—C2—N1130.4 (3)C9—C10—C11121.2 (5)
C7—C2—N1109.9 (2)C9—C10—H10119.4
C4—C3—C2118.0 (3)C11—C10—H10119.4
C4—C3—H3121.0C10—C11—C12119.5 (5)
C2—C3—H3121.0C10—C11—H11120.2
C3—C4—C5121.4 (3)C12—C11—H11120.2
C3—C4—H4119.3C13—C12—C11119.8 (4)
C5—C4—H4119.3C13—C12—H12120.1
C6—C5—C4121.4 (3)C11—C12—H12120.1
C6—C5—H5119.3C12—C13—C14120.4 (4)
C4—C5—H5119.3C12—C13—C15121.6 (4)
C5—C6—C7117.2 (3)C14—C13—C15118.0 (4)
C5—C6—H6121.4C13—C14—C9119.9 (4)
C7—C6—H6121.4C13—C14—H14120.0
N2—C7—C6132.4 (3)C9—C14—H14120.0
N2—C7—C2105.3 (2)N3—C15—C13179.0 (7)
C6—C7—C2122.3 (3)C1—N1—C2104.3 (2)
C9—C8—S1106.2 (3)C1—N2—C7107.0 (2)
C9—C8—H8A110.5C1—N2—H2A126.5
S1—C8—H8A110.5C7—N2—H2A126.5
C9—C8—H8B110.5C1—S1—C8102.13 (15)
S1—C8—H8B110.5
C7—C2—C3—C40.0 (5)C11—C12—C13—C15−178.2 (5)
N1—C2—C3—C4178.4 (3)C12—C13—C14—C9−0.6 (7)
C2—C3—C4—C5−0.4 (6)C15—C13—C14—C9179.4 (4)
C3—C4—C5—C60.2 (6)C10—C9—C14—C13−1.1 (6)
C4—C5—C6—C70.3 (5)C8—C9—C14—C13175.6 (4)
C5—C6—C7—N2−179.1 (3)C12—C13—C15—N3−23 (38)
C5—C6—C7—C2−0.6 (5)C14—C13—C15—N3157 (37)
C3—C2—C7—N2179.3 (3)N2—C1—N1—C2−0.4 (4)
N1—C2—C7—N20.6 (4)S1—C1—N1—C2175.5 (3)
C3—C2—C7—C60.5 (5)C3—C2—N1—C1−178.6 (4)
N1—C2—C7—C6−178.2 (3)C7—C2—N1—C1−0.2 (4)
S1—C8—C9—C1088.9 (4)N1—C1—N2—C70.8 (4)
S1—C8—C9—C14−87.8 (4)S1—C1—N2—C7−175.4 (2)
C14—C9—C10—C111.6 (7)C6—C7—N2—C1177.8 (4)
C8—C9—C10—C11−175.0 (4)C2—C7—N2—C1−0.8 (3)
C9—C10—C11—C12−0.4 (8)N1—C1—S1—C841.3 (4)
C10—C11—C12—C13−1.3 (8)N2—C1—S1—C8−143.1 (3)
C11—C12—C13—C141.9 (8)C9—C8—S1—C1170.0 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.861.982.838 (3)174

Symmetry codes: (i) x, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BX2210).

References

  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Negwer, M. & Scharnow, H. G. (2001). Organic Chemical Drugs and Their Synonyms, 8th extensively enlarged ed. Weinheim: Wiley–VCH Verlag GmbH.
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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