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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2947.
Published online 2009 October 31. doi:  10.1107/S1600536809043438
PMCID: PMC2971137

2,2′-Bis(methyl­ene)-3,3′-(2-thioxo-2,3-dihydro-1H-benzimidazole-1,3-di­yl)dipropane­nitrile

Abstract

In the title compound, C15H12N4S, the benzimidazole ring is essentially planar, with a mean deviation of 0.0082 (1) Å from the least-squares plane defined by the nine constituent atoms. In the crystal, inversion dimers linked by pairs of C—H(...)N hydrogen bonds occur.

Related literature

Benzimidazole is a potential precursor in heterocyclic chemistry and the benzimidazol-2-thione ring is present in many pharmacologically active substances, see: Hwa et al. (2008 [triangle]). For ammonium salts from Mannich adducts as precursors for the synthesis of acrylic derivatives carrying functionalized thio­methyl groups, see: M’rabet et al. (2009 [triangle]). For a related structure, see: Khan et al. (2008 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2947-scheme1.jpg

Experimental

Crystal data

  • C15H12N4S
  • M r = 280.35
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2947-efi1.jpg
  • a = 8.6274 (3) Å
  • b = 9.8271 (2) Å
  • c = 9.8271 (2) Å
  • α = 70.553 (2)°
  • β = 89.730 (2)°
  • γ = 67.853 (3)°
  • V = 720.67 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.22 mm−1
  • T = 293 K
  • 0.22 × 0.20 × 0.18 mm

Data collection

  • Enraf–Nonius TurboCAD-4 diffractometer
  • Absorption correction: none
  • 6594 measured reflections
  • 3297 independent reflections
  • 2449 reflections with I > 2σ(I)
  • R int = 0.018
  • 2 standard reflections frequency: 120 min intensity decay: 3%

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.111
  • S = 1.02
  • 3297 reflections
  • 181 parameters
  • H-atom parameters constrained
  • Δρmax = 0.19 e Å−3
  • Δρmin = −0.32 e Å−3

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 [triangle]); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809043438/pv2216sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809043438/pv2216Isup2.hkl

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

supplementary crystallographic information

Comment

Benzimidazole is an important scaffold in heterocyclic chemistry and benzimidazol-2-thione ring is present in many pharmacologically active substances (Hwa et al., 2008). We recently showed that ammonium salts coming from Mannich adducts, constitute precursors interesting for the synthesis of acrylic derivatives carrying functionalized thiomethyle groups (M'rabet et al., 2009). The results obtained encouraged us to try the action of other functionalized thiols, e.g., mercaptobenzimidazole. The analysis of the spectra for the isolated product shows that the nucleophilic attack utilized the two nitrogen atoms of the mercaptobenzimidazole whatever the stoichiometry was used. The compound was identified unequocally as N,N-bis(2-cyanoprop-2-enyl)benzimidazol-2-thione, (I), by the X-ray diffraction analysis.

The bond lengths and angles in the structure of (I) (Fig. 1) are in agreement with the corresponding bond lengths and angles reported for a compound closely related to (I) (Khan, H. et al., 2008) and are within normal ranges (Allen et al., 1987). The benzimidazole ring in (I) is essentially planar with a mean deviation of 0.0028 (1) Å from the least-squares plane defined by the nine constituent atoms. The molecular packing is stabilized by van der Waals interactions and intramolecular (C—H···S) and intermolecular (C—H···N) hydrogen bonds, which link the molecules into dimmers (Table 1 and Fig. 2).

Experimental

To a solution of ammonium salt (12 mmol) in ethanol (50 ml), was added dropwise with stirring 10 mmol of mercaptobenzimidazole. The reaction mixture was stirred for 24 h at room temperature. The residual salt was then filtered and the solvent was removed. The obtained residue was diluted with water (20 ml) and extracted with chloroform. The organic layer was dried over MgSO4 and concentrated under reduced pressure. The product was chromatographed using a silica gel column with 60/40 ether/petroleum ether. The slow evaporation from the solvent afforded crystals of the title compound suitable for X-ray diffraction study.

Refinement

All H atoms were positioned geometrically and treated as riding on the parent atoms [N–H = 0.89, C–H =0.96 Å (CH3 ) with Uiso(H) = 1.5Ueq and C–H = 0.96 Å (Ar–H), with Uiso(H) = 1.5Ueq].

Figures

Fig. 1.
A perspective view of the molecule of (I) with displacement ellipsoids shown at the 30% probability level.
Fig. 2.
Molecular packing in the unit cell of (I) showing H-bonding interactions; H-atoms not involved in H-bonds have been excluded.

Crystal data

C15H12N4SZ = 2
Mr = 280.35F(000) = 292
Triclinic, P1Dx = 1.292 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.6274 (3) ÅCell parameters from 25 reflections
b = 9.8271 (2) Åθ = 9.0–11.0°
c = 9.8271 (2) ŵ = 0.22 mm1
α = 70.553 (2)°T = 293 K
β = 89.730 (2)°Prism, colourless
γ = 67.853 (3)°0.22 × 0.20 × 0.18 mm
V = 720.67 (3) Å3

Data collection

Enraf–Nonius TurboCAD-4 diffractometerRint = 0.018
Radiation source: fine-focus sealed tubeθmax = 28.0°, θmin = 2.2°
graphiteh = −11→11
Nonprofiled ω scansk = −12→12
6594 measured reflectionsl = −12→12
3297 independent reflections2 standard reflections every 120 min
2449 reflections with I > 2σ(I) intensity decay: 3%

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)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.111H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.0547P)2 + 0.1378P] where P = (Fo2 + 2Fc2)/3
3297 reflections(Δ/σ)max = 0.002
181 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = −0.32 e Å3

Special details

Geometry. All e.s.d.'s 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
S10.21056 (7)0.61386 (6)0.54777 (5)0.06747 (18)
N10.12971 (16)0.64019 (15)0.80813 (13)0.0438 (3)
N20.36099 (16)0.43553 (15)0.82525 (13)0.0443 (3)
C20.33686 (19)0.43018 (18)0.96681 (16)0.0429 (3)
C10.19084 (19)0.55980 (18)0.95584 (16)0.0421 (3)
C70.2340 (2)0.56319 (18)0.72744 (16)0.0452 (3)
C90.01720 (18)0.92638 (18)0.74111 (16)0.0447 (3)
C100.1474 (2)0.95298 (19)0.65727 (17)0.0478 (4)
C140.3569 (2)0.1382 (2)0.84115 (19)0.0529 (4)
C130.45594 (19)0.20653 (18)0.74643 (17)0.0455 (3)
C120.5016 (2)0.3244 (2)0.78361 (19)0.0510 (4)
H12A0.59420.26890.86320.061*
H12B0.54050.38230.70000.061*
N30.2515 (2)0.9733 (2)0.59254 (18)0.0649 (4)
C60.1282 (2)0.5886 (2)1.07808 (18)0.0529 (4)
H60.02980.67521.07070.063*
C8−0.0187 (2)0.78626 (19)0.74714 (19)0.0510 (4)
H8A−0.10830.78130.80600.061*
H8B−0.05750.79880.64950.061*
N40.2784 (2)0.0869 (2)0.9192 (2)0.0810 (5)
C30.4283 (2)0.3241 (2)1.10096 (18)0.0563 (4)
H30.52640.23721.10850.068*
C50.2197 (3)0.4820 (2)1.21154 (19)0.0638 (5)
H50.18140.49691.29620.077*
C150.5064 (3)0.1615 (3)0.6360 (2)0.0681 (5)
H15A0.47780.08550.61950.082*
H15B0.57060.20570.57450.082*
C11−0.0631 (2)1.0256 (2)0.8061 (2)0.0638 (5)
H11A−0.03531.11050.79730.077*
H11B−0.14751.01050.86070.077*
C40.3670 (3)0.3534 (2)1.22258 (19)0.0651 (5)
H40.42600.28531.31430.078*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0965 (4)0.0682 (3)0.0385 (2)−0.0351 (3)0.0141 (2)−0.0176 (2)
N10.0492 (7)0.0414 (7)0.0399 (6)−0.0177 (5)0.0080 (5)−0.0138 (5)
N20.0505 (7)0.0423 (7)0.0441 (7)−0.0195 (6)0.0117 (5)−0.0193 (5)
C20.0511 (8)0.0414 (8)0.0432 (7)−0.0239 (7)0.0072 (6)−0.0172 (6)
C10.0502 (8)0.0432 (8)0.0403 (7)−0.0250 (7)0.0090 (6)−0.0166 (6)
C70.0570 (9)0.0446 (8)0.0419 (8)−0.0268 (7)0.0121 (7)−0.0173 (6)
C90.0394 (7)0.0421 (8)0.0441 (8)−0.0114 (6)0.0058 (6)−0.0107 (6)
C100.0486 (9)0.0456 (8)0.0487 (8)−0.0170 (7)0.0085 (7)−0.0181 (7)
C140.0571 (10)0.0575 (10)0.0575 (9)−0.0287 (8)0.0212 (8)−0.0303 (8)
C130.0442 (8)0.0462 (8)0.0505 (8)−0.0196 (7)0.0147 (6)−0.0208 (7)
C120.0476 (8)0.0542 (9)0.0620 (10)−0.0240 (7)0.0193 (7)−0.0295 (8)
N30.0637 (9)0.0732 (11)0.0700 (10)−0.0339 (8)0.0260 (8)−0.0331 (8)
C60.0649 (10)0.0564 (10)0.0522 (9)−0.0317 (8)0.0190 (8)−0.0287 (8)
C80.0446 (8)0.0502 (9)0.0538 (9)−0.0182 (7)0.0051 (7)−0.0142 (7)
N40.0919 (13)0.1025 (14)0.0810 (12)−0.0640 (12)0.0448 (10)−0.0434 (11)
C30.0618 (10)0.0496 (9)0.0524 (9)−0.0208 (8)−0.0045 (8)−0.0136 (8)
C50.0945 (14)0.0776 (13)0.0429 (9)−0.0515 (12)0.0189 (9)−0.0303 (9)
C150.0859 (13)0.0850 (14)0.0663 (11)−0.0532 (12)0.0376 (10)−0.0450 (11)
C110.0618 (11)0.0577 (11)0.0732 (12)−0.0217 (9)0.0246 (9)−0.0272 (9)
C40.0887 (14)0.0639 (11)0.0425 (9)−0.0355 (11)−0.0051 (9)−0.0125 (8)

Geometric parameters (Å, °)

S1—C71.6577 (15)C9—C111.319 (3)
N1—C11.3924 (19)C12—C131.503 (3)
N1—C71.375 (2)C13—C141.434 (2)
N1—C81.452 (2)C13—C151.317 (3)
N2—C21.3922 (19)C3—H30.9300
N2—C71.367 (2)C4—H40.9300
N2—C121.458 (2)C5—H50.9300
N3—C101.138 (3)C6—H60.9300
N4—C141.139 (3)C8—H8A0.9700
C1—C21.386 (2)C8—H8B0.9700
C1—C61.386 (2)C11—H11A0.9300
C2—C31.386 (2)C11—H11B0.9300
C3—C41.378 (3)C12—H12A0.9700
C4—C51.387 (4)C12—H12B0.9700
C5—C61.383 (3)C15—H15A0.9300
C8—C91.504 (3)C15—H15B0.9300
C9—C101.442 (2)
C1—N1—C7109.85 (14)C14—C13—C15119.89 (19)
C1—N1—C8125.42 (14)N4—C14—C13177.6 (2)
C7—N1—C8124.70 (13)C2—C3—H3122.00
C2—N2—C7110.30 (14)C4—C3—H3122.00
C2—N2—C12126.00 (14)C3—C4—H4119.00
C7—N2—C12123.70 (13)C5—C4—H4119.00
N1—C1—C2106.98 (14)C4—C5—H5119.00
N1—C1—C6131.26 (16)C6—C5—H5119.00
C2—C1—C6121.74 (15)C1—C6—H6122.00
N2—C2—C1106.69 (13)C5—C6—H6122.00
N2—C2—C3131.89 (16)N1—C8—H8A109.00
C1—C2—C3121.42 (15)N1—C8—H8B109.00
C2—C3—C4116.90 (18)C9—C8—H8A109.00
C3—C4—C5121.62 (17)C9—C8—H8B109.00
C4—C5—C6121.78 (19)H8A—C8—H8B108.00
C1—C6—C5116.53 (19)C9—C11—H11A120.00
S1—C7—N1127.09 (13)C9—C11—H11B120.00
S1—C7—N2126.73 (13)H11A—C11—H11B120.00
N1—C7—N2106.18 (12)N2—C12—H12A109.00
N1—C8—C9111.91 (15)N2—C12—H12B109.00
C8—C9—C10117.04 (15)C13—C12—H12A109.00
C8—C9—C11124.34 (16)C13—C12—H12B109.00
C10—C9—C11118.62 (16)H12A—C12—H12B108.00
N3—C10—C9179.21 (18)C13—C15—H15A120.00
N2—C12—C13113.07 (15)C13—C15—H15B120.00
C12—C13—C14116.74 (15)H15A—C15—H15B120.00
C12—C13—C15123.33 (19)
C7—N1—C1—C20.2 (2)C2—N2—C12—C13101.76 (19)
C7—N1—C1—C6−178.16 (19)C7—N2—C12—C13−79.4 (2)
C8—N1—C1—C2−177.94 (16)N1—C1—C2—N20.21 (19)
C8—N1—C1—C63.7 (3)N1—C1—C2—C3−179.34 (16)
C1—N1—C7—S1179.15 (14)C6—C1—C2—N2178.77 (16)
C1—N1—C7—N2−0.56 (19)C6—C1—C2—C3−0.8 (3)
C8—N1—C7—S1−2.7 (3)N1—C1—C6—C5178.7 (2)
C8—N1—C7—N2177.61 (15)C2—C1—C6—C50.5 (3)
C1—N1—C8—C978.8 (2)N2—C2—C3—C4−179.3 (2)
C7—N1—C8—C9−99.06 (19)C1—C2—C3—C40.2 (3)
C7—N2—C2—C1−0.6 (2)C2—C3—C4—C50.7 (3)
C7—N2—C2—C3178.92 (19)C3—C4—C5—C6−1.0 (4)
C12—N2—C2—C1178.44 (16)C4—C5—C6—C10.3 (4)
C12—N2—C2—C3−2.1 (3)N1—C8—C9—C1059.16 (19)
C2—N2—C7—S1−179.02 (14)N1—C8—C9—C11−121.4 (2)
C2—N2—C7—N10.69 (19)N2—C12—C13—C14−43.4 (2)
C12—N2—C7—S12.0 (3)N2—C12—C13—C15138.7 (2)
C12—N2—C7—N1−178.34 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C8—H8B···S10.972.773.204 (2)108
C11—H11B···N4i0.932.513.387 (3)158

Symmetry codes: (i) −x, −y+1, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PV2216).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Enraf–Nonius (1994). CAD-4 EXPRESS Enraf–Nonius, Delft, The Netherlands.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Harms, K. & Wocadlo, S. (1995). XCAD4 University of Marburg, Germany.
  • Hwa, J., Singha, R., Hong, S. C., Chang, Y. H., Das, A. R., Vliegen, I., Clercq, E. & Neyts, J. (2008). Antiviral Res.77, 157–162. [PubMed]
  • Khan, H., Badshah, A., Shaheen, F., Gieck, C. & Qureshi, R. A. (2008). Acta Cryst. E64, o1141. [PMC free article] [PubMed]
  • M’rabet, H., Ould M’hamed, M. & El Efrit, M. L. (2009). Synth. Commun.39, 1655–1665.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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