Acta Cryst. (2008). E64, o964 [ doi:10.1107/S1600536808006405 ]
In the title compound, C13H10N2S, the dihedral angle between the imidazole and thiophene rings is 16.89 (19)°, and the double bond adopts an E configuration. In the crystal structure, N-H
N hydrogen bonds link the molecules into rows along b. There is also evidence of weak C-HS interactions.
2-methyl-1H-benzo[d]imidazole (10 mmol, 1.32 g) and thiophene-2-carbaldehyde (45 mmol, 5.04 g) were reacted as a melt at 180°C with stirring for 18 h. Then 20 ml 2-propanol and 1.5 g oxalic acid were added to the reaction mixture, the solution filtered and the precipitate washed with copious quantities of boiling water. The pH was adjusted to 8–9 with ammonia to afford the title compound as a pale-yellow solid powder. Crystals suitable for single-crystal X-ray diffraction studies were obtained by slow evaporation of a solution in ethanol at room temperature over several days.
All carbon-bound H atoms were positioned geometrically, with C—H = 0.93 Å and included in the refinement as riding, withUiso(H) = 1.2Ueq. The H atoms attached to N were found in the difference Fourier map and were subsequently treated as riding atoms, with N—H = 0.86 Å, and Uiso(H) = 1.2Ueq(N).
Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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).
![[Figure 1]](./sj2460fig1thm.gif)
| Fig. 1. The molecular structure of the compound with the atomic numbering scheme. Displacement ellipsoids were drawn at the 30% probability level. |
![[Figure 2]](./sj2460fig2thm.gif)
| Fig. 2. The crystal packing of 1 with hydrogen bonds drawn as dashed lines. |
| C13H10N2S | F000 = 944 |
| Mr = 226.06 | Dx = 1.305 Mg m−3 |
| Orthorhombic, Pnna | Mo Kα radiation λ = 0.71073 Å |
| Hall symbol: -P 2a 2bc | Cell parameters from 14820 reflections |
| a = 12.239 (2) Å | θ = 3.0–29.2º |
| b = 16.389 (3) Å | µ = 0.25 mm−1 |
| c = 11.487 (2) Å | T = 293 (2) K |
| V = 2304.1 (7) Å3 | Block, colorless |
| Z = 8 | 0.15 × 0.10 × 0.07 mm |
| Mercury2 (2x2 bin mode) diffractometer | 2637 independent reflections |
| Radiation source: fine-focus sealed tube | 1360 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.145 |
| Detector resolution: 13.6612 pixels mm-1 | θmax = 27.5º |
| T = 293(2) K | θmin = 3.3º |
| CCD profile fitting scans | h = −15→15 |
| Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | k = −21→21 |
| Tmin = 0.796, Tmax = 1.000 | l = −14→14 |
| 21849 measured reflections |
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.084 | H-atom parameters constrained |
| wR(F2) = 0.214 | w = 1/[σ2(Fo2) + (0.081P)2 + 0.7151P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.07 | (Δ/σ)max < 0.001 |
| 2637 reflections | Δρmax = 0.22 e Å−3 |
| 145 parameters | Δρmin = −0.28 e Å−3 |
| 1 restraint | Extinction correction: none |
| Primary atom site location: structure-invariant direct methods |
| C13H10N2S | V = 2304.1 (7) Å3 |
| Mr = 226.06 | Z = 8 |
| Orthorhombic, Pnna | Mo Kα |
| a = 12.239 (2) Å | µ = 0.25 mm−1 |
| b = 16.389 (3) Å | T = 293 (2) K |
| c = 11.487 (2) Å | 0.15 × 0.10 × 0.07 mm |
| Mercury2 (2x2 bin mode) diffractometer | 2637 independent reflections |
| Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | 1360 reflections with I > 2σ(I) |
| Tmin = 0.796, Tmax = 1.000 | Rint = 0.145 |
| 21849 measured reflections |
| R[F2 > 2σ(F2)] = 0.084 | 1 restraint |
| wR(F2) = 0.214 | H-atom parameters constrained |
| S = 1.07 | Δρmax = 0.22 e Å−3 |
| 2637 reflections | Δρmin = −0.28 e Å−3 |
| 145 parameters |
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. |
| x | y | z | Uiso*/Ueq | Occ. (<1) | |
| S1 | 0.88515 (10) | 0.06908 (7) | 0.51647 (11) | 0.0801 (5) | |
| N1 | 0.6821 (2) | 0.07121 (18) | 0.1000 (3) | 0.0577 (9) | |
| H1B | 0.7264 | 0.0309 | 0.0924 | 0.069* | 0.50 |
| N2 | 0.5945 (2) | 0.17665 (16) | 0.1790 (2) | 0.0452 (7) | |
| H2B | 0.5751 | 0.2134 | 0.2283 | 0.054* | 0.50 |
| C1 | 0.5111 (4) | 0.1178 (3) | −0.1555 (4) | 0.0824 (14) | |
| H1A | 0.4956 | 0.1028 | −0.2319 | 0.099* | |
| C2 | 0.8179 (4) | 0.1317 (3) | 0.7051 (4) | 0.0898 (15) | |
| H2A | 0.8136 | 0.1453 | 0.7836 | 0.108* | |
| C3 | 0.8987 (5) | 0.0855 (3) | 0.6610 (4) | 0.0890 (16) | |
| H3A | 0.9559 | 0.0647 | 0.7053 | 0.107* | |
| C4 | 0.7391 (3) | 0.1583 (3) | 0.6209 (3) | 0.0653 (11) | |
| H4A | 0.6790 | 0.1913 | 0.6364 | 0.078* | |
| C5 | 0.5901 (4) | 0.0750 (3) | −0.0942 (4) | 0.0753 (13) | |
| H5A | 0.6278 | 0.0316 | −0.1277 | 0.090* | |
| C6 | 0.4751 (3) | 0.2076 (2) | 0.0054 (3) | 0.0604 (11) | |
| H6A | 0.4376 | 0.2514 | 0.0381 | 0.073* | |
| C7 | 0.4546 (4) | 0.1825 (3) | −0.1057 (4) | 0.0720 (12) | |
| H7A | 0.4015 | 0.2094 | −0.1492 | 0.086* | |
| C8 | 0.7672 (3) | 0.1264 (2) | 0.5105 (3) | 0.0581 (10) | |
| C9 | 0.7079 (3) | 0.1380 (2) | 0.4039 (3) | 0.0532 (10) | |
| H9A | 0.6461 | 0.1709 | 0.4074 | 0.064* | |
| C10 | 0.6101 (3) | 0.0995 (2) | 0.0186 (3) | 0.0515 (9) | |
| C11 | 0.7328 (3) | 0.1064 (2) | 0.3007 (3) | 0.0526 (10) | |
| H11A | 0.7950 | 0.0740 | 0.2961 | 0.063* | |
| C12 | 0.6700 (3) | 0.1188 (2) | 0.1941 (3) | 0.0479 (9) | |
| C13 | 0.5538 (3) | 0.1655 (2) | 0.0678 (3) | 0.0461 (9) |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| S1 | 0.0830 (9) | 0.0654 (8) | 0.0918 (10) | −0.0012 (6) | −0.0304 (7) | 0.0032 (6) |
| N1 | 0.0607 (19) | 0.0583 (19) | 0.054 (2) | 0.0158 (16) | −0.0072 (15) | −0.0140 (16) |
| N2 | 0.0532 (17) | 0.0401 (16) | 0.0422 (17) | 0.0063 (13) | 0.0015 (13) | −0.0027 (13) |
| C1 | 0.097 (3) | 0.096 (4) | 0.054 (3) | 0.004 (3) | −0.017 (3) | −0.015 (3) |
| C2 | 0.113 (4) | 0.106 (4) | 0.050 (3) | −0.026 (3) | −0.023 (2) | 0.013 (3) |
| C3 | 0.112 (4) | 0.076 (3) | 0.079 (4) | −0.023 (3) | −0.043 (3) | 0.023 (3) |
| C4 | 0.070 (3) | 0.081 (3) | 0.045 (2) | −0.018 (2) | −0.0037 (18) | 0.001 (2) |
| C5 | 0.083 (3) | 0.079 (3) | 0.064 (3) | 0.018 (2) | −0.011 (2) | −0.028 (2) |
| C6 | 0.072 (3) | 0.054 (2) | 0.055 (2) | 0.009 (2) | −0.009 (2) | 0.001 (2) |
| C7 | 0.081 (3) | 0.071 (3) | 0.064 (3) | 0.009 (2) | −0.021 (2) | 0.007 (2) |
| C8 | 0.063 (2) | 0.051 (2) | 0.061 (3) | −0.0153 (19) | −0.014 (2) | 0.0087 (19) |
| C9 | 0.055 (2) | 0.049 (2) | 0.056 (3) | −0.0009 (18) | −0.0023 (18) | 0.0054 (18) |
| C10 | 0.053 (2) | 0.051 (2) | 0.051 (2) | 0.0034 (18) | −0.0051 (18) | −0.0070 (18) |
| C11 | 0.051 (2) | 0.048 (2) | 0.059 (3) | 0.0005 (17) | −0.0004 (19) | −0.0009 (18) |
| C12 | 0.048 (2) | 0.049 (2) | 0.047 (2) | −0.0011 (17) | 0.0016 (17) | 0.0022 (17) |
| C13 | 0.052 (2) | 0.0418 (19) | 0.044 (2) | −0.0023 (17) | 0.0020 (17) | 0.0001 (16) |
| S1—C3 | 1.690 (5) | C4—C8 | 1.415 (5) |
| S1—C8 | 1.723 (4) | C4—H4A | 0.9300 |
| N1—C12 | 1.341 (4) | C5—C10 | 1.379 (5) |
| N1—C10 | 1.366 (4) | C5—H5A | 0.9300 |
| N1—H1B | 0.8600 | C6—C7 | 1.365 (5) |
| N2—C12 | 1.335 (4) | C6—C13 | 1.385 (5) |
| N2—C13 | 1.383 (4) | C6—H6A | 0.9300 |
| N2—H2B | 0.8600 | C7—H7A | 0.9300 |
| C1—C5 | 1.386 (6) | C8—C9 | 1.436 (5) |
| C1—C7 | 1.390 (6) | C9—C11 | 1.329 (5) |
| C1—H1A | 0.9300 | C9—H9A | 0.9300 |
| C2—C3 | 1.344 (6) | C10—C13 | 1.401 (5) |
| C2—C4 | 1.435 (6) | C11—C12 | 1.461 (4) |
| C2—H2A | 0.9300 | C11—H11A | 0.9300 |
| C3—H3A | 0.9300 | ||
| C3—S1—C8 | 92.0 (3) | C7—C6—H6A | 121.3 |
| C12—N1—C10 | 106.4 (3) | C13—C6—H6A | 121.3 |
| C12—N1—H1B | 126.8 | C6—C7—C1 | 121.6 (4) |
| C10—N1—H1B | 126.8 | C6—C7—H7A | 119.2 |
| C12—N2—C13 | 106.0 (3) | C1—C7—H7A | 119.2 |
| C12—N2—H2B | 127.0 | C4—C8—C9 | 126.3 (4) |
| C13—N2—H2B | 127.0 | C4—C8—S1 | 111.7 (3) |
| C5—C1—C7 | 121.6 (4) | C9—C8—S1 | 122.0 (3) |
| C5—C1—H1A | 119.2 | C11—C9—C8 | 126.3 (4) |
| C7—C1—H1A | 119.2 | C11—C9—H9A | 116.8 |
| C3—C2—C4 | 114.3 (4) | C8—C9—H9A | 116.8 |
| C3—C2—H2A | 122.8 | N1—C10—C5 | 131.2 (4) |
| C4—C2—H2A | 122.8 | N1—C10—C13 | 107.7 (3) |
| C2—C3—S1 | 112.8 (4) | C5—C10—C13 | 121.1 (4) |
| C2—C3—H3A | 123.6 | C9—C11—C12 | 125.0 (3) |
| S1—C3—H3A | 123.6 | C9—C11—H11A | 117.5 |
| C8—C4—C2 | 109.2 (4) | C12—C11—H11A | 117.5 |
| C8—C4—H4A | 125.4 | N1—C12—N2 | 112.7 (3) |
| C2—C4—H4A | 125.4 | N1—C12—C11 | 122.5 (3) |
| C1—C5—C10 | 117.0 (4) | N2—C12—C11 | 124.9 (3) |
| C1—C5—H5A | 121.5 | N2—C13—C6 | 131.5 (3) |
| C10—C5—H5A | 121.5 | N2—C13—C10 | 107.3 (3) |
| C7—C6—C13 | 117.5 (4) | C6—C13—C10 | 121.2 (3) |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C11—H11A···S1 | 0.93 | 2.76 | 3.161 (4) | 107 |
| N1—H1B···N1i | 0.86 | 2.01 | 2.865 (6) | 170 |
| N2—H2B···N2ii | 0.86 | 2.11 | 2.906 (5) | 154 |
| Symmetry codes: (i) −x+3/2, −y, z; (ii) x, −y+1/2, −z+1/2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C11—H11A···S1 | 0.93 | 2.76 | 3.161 (4) | 107 |
| N1—H1B···N1i | 0.86 | 2.01 | 2.865 (6) | 170 |
| N2—H2B···N2ii | 0.86 | 2.11 | 2.906 (5) | 154 |
| Symmetry codes: (i) −x+3/2, −y, z; (ii) x, −y+1/2, −z+1/2. |
Huang, X.-C., Zhang, J.-P. & Chen, X.-M. (2003). Chin. Sci. Bull. 48, 1531–1534.
Li, L. & Clarkson, G. J. (2007). Org. Lett. 9, 497–500.
Ozbey, S., Ide, S. & Kendi, E. (1998). J. Mol. Struct. 442, 23–?.
Rigaku (2005). CrystalClear. Version 1.4.0. Rigaku Corporation, Tokyo, Japan.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
Wang, X.-S., Song, Y.-M., Ye, Q. & Xiong, R.-G. (2005). Chin. Sci. Bull. 50, 2317–2340.
Ye, Q., Song, Y.-M., Fu, D.-W., Wang, G.-X. & Xiong, R.-G. (2007). Cryst. Growth Des. 7, 1568–1570.
Ye, Q., Song, Y.-M., Wang, G.-X. & Xiong, R.-G. (2006). J. Am. Chem. Soc. 128, 6554–6555.
It has been generally accepted that imidazole groups play an important role in coordination chemistry (Huang et al., 2003). A flexible ligand readily induces coordination compounds to crystallize in non-centrosymmetric space groups, which makes it possible to investigate their interesting physical properties such as second harmonic generation, ferroelectric and piezoelectric properties (Wang et al., 2005). As a continuation of our work in this field, (Ye et al., 2006, 2007), we have synthesized the title compound, 1, Fig 1.
The title compound, C12H10N2S, was successfully prepared through the reaction between 2-methyl-1H-benzo[d]imidazole and thiophene-2-carbaldehyde. It adopts a trans configuration about the C9?C11 bond and the dihedral angle between the mean plane of the imidazole ring and thiophenyl ring is 16.89 (19)°. The crystal packing is dominated by N—H···N interactions linking the molecules into rows along b, Fig 2. There is also evidence of weak C—H···S interactions.