Acta Cryst. (2009). E65, o557 [ doi:10.1107/S1600536809005315 ]
In the title compound, C13H9N3O2·C3H7NO, the benzimidazole ring system and the benzene ring are essentially coplanar, forming a dihedral angle of 0.86 (5)°. The crystal packing is stabilized by an intermolecular N-H
O hydrogen bond and a ![[pi]](/logos/entities/pi_rmgif.gif)
- stacking interaction with a centroid-centroid separation of 3.685 (4) Å.
The title compound was synthesized by refluxing 4-nitrobenzaldehyde (6.04 g, 4 mmol) and benzene-1,2-diamine (0.43 g, 4 mmol) in 40 ml absolute methanol for 10 h. After cooling to ambient temperature, the yellow solid formed was isolated and dried under vacuum (7.2 g, yield 75%). Single crystals suitable for X-ray structure analysis were obtained by slow evaporation of a dimethylformamide solution in air.
H atoms were placed in calculated positions (N—H = 0.86 Å; C—H = 0.93-0.96 Å), and refined using a riding model approximation with Uiso = 1.2 Ueq(C, N) or 1.5 Ueq(C) for methyl H atoms.
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]](./rz2294fig1thm.gif)
| Fig. 1. The molecular structure of the title compound, showing the atomic numbering scheme and 30% probability displacement ellipsoids. The A suffix for atoms O3, N4, C14, C15 and C16 denotes a transformation of (1 - x, 1 - y, 1 - z). The intermolecular N—H···O hydrogen bond is shown as a dashed line. |
| C13H9N3O2·C3H7NO | Z = 2 |
| Mr = 312.33 | F(000) = 328 |
| Triclinic, P1 | Dx = 1.309 Mg m−3 |
| Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
| a = 6.6228 (13) Å | Cell parameters from 5280 reflections |
| b = 10.601 (2) Å | θ = 3.2–27.4° |
| c = 11.886 (2) Å | µ = 0.09 mm−1 |
| α = 84.534 (10)° | T = 291 K |
| β = 74.13 (2)° | Block, yellow |
| γ = 81.53 (3)° | 0.30 × 0.26 × 0.24 mm |
| V = 792.6 (3) Å3 |
| Rigaku Mercury2 diffractometer | 3102 independent reflections |
| Radiation source: fine-focus sealed tube | 1567 reflections with I > 2σ(I) |
| graphite | Rint = 0.045 |
| Detector resolution: 13.6612 pixels mm-1 | θmax = 26.0°, θmin = 3.2° |
| CCD_Profile_fitting scans | h = −8→8 |
| Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | k = −13→12 |
| Tmin = 0.96, Tmax = 0.98 | l = −14→14 |
| 7352 measured reflections |
| Refinement on F2 | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.060 | Hydrogen site location: inferred from neighbouring sites |
| wR(F2) = 0.138 | H-atom parameters constrained |
| S = 1.01 | w = 1/[σ2(Fo2) + (0.0586P)2] where P = (Fo2 + 2Fc2)/3 |
| 3102 reflections | (Δ/σ)max < 0.001 |
| 210 parameters | Δρmax = 0.12 e Å−3 |
| 0 restraints | Δρmin = −0.19 e Å−3 |
| C13H9N3O2·C3H7NO | γ = 81.53 (3)° |
| Mr = 312.33 | V = 792.6 (3) Å3 |
| Triclinic, P1 | Z = 2 |
| a = 6.6228 (13) Å | Mo Kα radiation |
| b = 10.601 (2) Å | µ = 0.09 mm−1 |
| c = 11.886 (2) Å | T = 291 K |
| α = 84.534 (10)° | 0.30 × 0.26 × 0.24 mm |
| β = 74.13 (2)° |
| Rigaku Mercury2 diffractometer | 3102 independent reflections |
| Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | 1567 reflections with I > 2σ(I) |
| Tmin = 0.96, Tmax = 0.98 | Rint = 0.045 |
| 7352 measured reflections | θmax = 26.0° |
| R[F2 > 2σ(F2)] = 0.060 | H-atom parameters constrained |
| wR(F2) = 0.138 | Δρmax = 0.12 e Å−3 |
| S = 1.01 | Δρmin = −0.19 e Å−3 |
| 3102 reflections | Absolute structure: ? |
| 210 parameters | Flack parameter: ? |
| 0 restraints | Rogers parameter: ? |
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 | ||
| C1 | −0.0895 (4) | 0.3267 (2) | 0.7884 (2) | 0.0599 (6) | |
| C2 | −0.2701 (4) | 0.3902 (2) | 0.8605 (2) | 0.0798 (8) | |
| H2A | −0.2737 | 0.4732 | 0.8809 | 0.096* | |
| C3 | −0.4438 (5) | 0.3249 (3) | 0.9006 (2) | 0.0857 (8) | |
| H3A | −0.5668 | 0.3643 | 0.9497 | 0.103* | |
| C4 | −0.4385 (4) | 0.2011 (2) | 0.8689 (2) | 0.0798 (8) | |
| H4A | −0.5584 | 0.1597 | 0.8973 | 0.096* | |
| C5 | −0.2605 (4) | 0.1383 (2) | 0.7965 (2) | 0.0658 (7) | |
| H5A | −0.2587 | 0.0557 | 0.7756 | 0.079* | |
| C6 | −0.0832 (4) | 0.20250 (19) | 0.75577 (18) | 0.0540 (6) | |
| C7 | 0.2234 (4) | 0.26232 (18) | 0.67137 (18) | 0.0535 (6) | |
| C8 | 0.4421 (4) | 0.26378 (18) | 0.60121 (18) | 0.0520 (6) | |
| C9 | 0.5535 (4) | 0.36846 (19) | 0.5917 (2) | 0.0605 (6) | |
| H9A | 0.4864 | 0.4414 | 0.6308 | 0.073* | |
| C10 | 0.7583 (4) | 0.3659 (2) | 0.5264 (2) | 0.0610 (6) | |
| H10A | 0.8299 | 0.4365 | 0.5202 | 0.073* | |
| C11 | 0.8578 (4) | 0.2568 (2) | 0.46957 (19) | 0.0564 (6) | |
| C12 | 0.7539 (4) | 0.1508 (2) | 0.4773 (2) | 0.0667 (7) | |
| H12A | 0.8226 | 0.0777 | 0.4389 | 0.080* | |
| C13 | 0.5471 (4) | 0.1560 (2) | 0.5427 (2) | 0.0670 (7) | |
| H13A | 0.4757 | 0.0855 | 0.5480 | 0.080* | |
| C14 | 0.7196 (4) | 0.3189 (2) | 0.2083 (2) | 0.0751 (7) | |
| H14A | 0.5807 | 0.3254 | 0.2545 | 0.090* | |
| C15 | 1.0088 (5) | 0.1989 (3) | 0.0766 (3) | 0.1051 (10) | |
| H15A | 1.0684 | 0.2774 | 0.0694 | 0.158* | |
| H15B | 1.0053 | 0.1771 | 0.0006 | 0.158* | |
| H15C | 1.0940 | 0.1320 | 0.1093 | 0.158* | |
| C16 | 0.6700 (5) | 0.1095 (2) | 0.1649 (3) | 0.1028 (10) | |
| H16A | 0.5303 | 0.1337 | 0.2136 | 0.154* | |
| H16B | 0.7355 | 0.0352 | 0.2002 | 0.154* | |
| H16C | 0.6612 | 0.0908 | 0.0891 | 0.154* | |
| N1 | 0.1073 (3) | 0.36303 (15) | 0.73324 (16) | 0.0621 (5) | |
| H1A | 0.1515 | 0.4383 | 0.7376 | 0.074* | |
| N2 | 0.1147 (3) | 0.16428 (15) | 0.68163 (16) | 0.0564 (5) | |
| N3 | 1.0776 (3) | 0.2533 (2) | 0.39914 (18) | 0.0720 (6) | |
| N4 | 0.7958 (3) | 0.21395 (17) | 0.15256 (17) | 0.0647 (6) | |
| O1 | 1.1681 (3) | 0.34815 (17) | 0.39184 (17) | 0.0937 (6) | |
| O2 | 1.1653 (3) | 0.15534 (18) | 0.35180 (19) | 0.1073 (7) | |
| O3 | 0.8186 (3) | 0.40844 (16) | 0.20342 (19) | 0.1109 (8) |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| C1 | 0.0662 (17) | 0.0574 (14) | 0.0553 (15) | −0.0032 (13) | −0.0130 (13) | −0.0147 (12) |
| C2 | 0.086 (2) | 0.0740 (17) | 0.0737 (18) | −0.0067 (16) | −0.0048 (16) | −0.0276 (14) |
| C3 | 0.071 (2) | 0.100 (2) | 0.0763 (19) | −0.0065 (17) | 0.0020 (15) | −0.0251 (16) |
| C4 | 0.076 (2) | 0.0857 (19) | 0.0749 (19) | −0.0169 (15) | −0.0098 (16) | −0.0081 (15) |
| C5 | 0.0683 (18) | 0.0643 (15) | 0.0641 (16) | −0.0103 (14) | −0.0141 (14) | −0.0081 (13) |
| C6 | 0.0637 (16) | 0.0493 (12) | 0.0487 (14) | −0.0006 (11) | −0.0159 (13) | −0.0085 (10) |
| C7 | 0.0644 (17) | 0.0431 (12) | 0.0561 (15) | 0.0000 (11) | −0.0212 (13) | −0.0119 (11) |
| C8 | 0.0579 (15) | 0.0467 (12) | 0.0517 (14) | −0.0007 (11) | −0.0159 (12) | −0.0096 (10) |
| C9 | 0.0636 (17) | 0.0448 (13) | 0.0702 (16) | 0.0021 (11) | −0.0139 (14) | −0.0144 (11) |
| C10 | 0.0647 (17) | 0.0475 (12) | 0.0715 (16) | −0.0054 (11) | −0.0179 (14) | −0.0103 (12) |
| C11 | 0.0571 (15) | 0.0576 (14) | 0.0540 (14) | −0.0015 (12) | −0.0149 (12) | −0.0094 (11) |
| C12 | 0.0693 (18) | 0.0543 (14) | 0.0756 (18) | −0.0022 (13) | −0.0139 (15) | −0.0237 (12) |
| C13 | 0.0667 (18) | 0.0564 (14) | 0.0773 (17) | −0.0107 (12) | −0.0098 (15) | −0.0243 (13) |
| C14 | 0.0786 (19) | 0.0670 (16) | 0.0733 (18) | 0.0010 (15) | −0.0107 (15) | −0.0157 (14) |
| C15 | 0.086 (2) | 0.116 (2) | 0.097 (2) | 0.0080 (18) | −0.0026 (19) | −0.0213 (18) |
| C16 | 0.126 (3) | 0.0753 (18) | 0.118 (3) | −0.0349 (19) | −0.041 (2) | −0.0015 (17) |
| N1 | 0.0643 (13) | 0.0478 (10) | 0.0726 (13) | −0.0072 (9) | −0.0103 (11) | −0.0195 (9) |
| N2 | 0.0595 (13) | 0.0482 (10) | 0.0629 (13) | −0.0041 (9) | −0.0176 (11) | −0.0098 (9) |
| N3 | 0.0658 (15) | 0.0694 (14) | 0.0772 (15) | −0.0028 (12) | −0.0122 (12) | −0.0158 (12) |
| N4 | 0.0693 (14) | 0.0548 (11) | 0.0672 (13) | −0.0039 (10) | −0.0117 (11) | −0.0145 (10) |
| O1 | 0.0768 (13) | 0.0837 (12) | 0.1160 (16) | −0.0240 (11) | −0.0070 (11) | −0.0164 (11) |
| O2 | 0.0802 (14) | 0.0926 (14) | 0.1324 (18) | −0.0057 (11) | 0.0111 (12) | −0.0483 (13) |
| O3 | 0.1330 (19) | 0.0708 (12) | 0.1336 (18) | −0.0294 (12) | −0.0241 (14) | −0.0360 (12) |
| C1—N1 | 1.381 (3) | C10—H10A | 0.9300 |
| C1—C2 | 1.389 (3) | C11—C12 | 1.385 (3) |
| C1—C6 | 1.400 (3) | C11—N3 | 1.464 (3) |
| C2—C3 | 1.379 (3) | C12—C13 | 1.374 (3) |
| C2—H2A | 0.9300 | C12—H12A | 0.9300 |
| C3—C4 | 1.393 (3) | C13—H13A | 0.9300 |
| C3—H3A | 0.9300 | C14—O3 | 1.219 (3) |
| C4—C5 | 1.377 (3) | C14—N4 | 1.313 (3) |
| C4—H4A | 0.9300 | C14—H14A | 0.9300 |
| C5—C6 | 1.392 (3) | C15—N4 | 1.448 (3) |
| C5—H5A | 0.9300 | C15—H15A | 0.9600 |
| C6—N2 | 1.392 (3) | C15—H15B | 0.9600 |
| C7—N2 | 1.327 (2) | C15—H15C | 0.9600 |
| C7—N1 | 1.368 (2) | C16—N4 | 1.454 (3) |
| C7—C8 | 1.462 (3) | C16—H16A | 0.9600 |
| C8—C13 | 1.387 (3) | C16—H16B | 0.9600 |
| C8—C9 | 1.400 (3) | C16—H16C | 0.9600 |
| C9—C10 | 1.364 (3) | N1—H1A | 0.8998 |
| C9—H9A | 0.9300 | N3—O2 | 1.220 (2) |
| C10—C11 | 1.381 (3) | N3—O1 | 1.229 (2) |
| N1—C1—C2 | 132.3 (2) | C12—C11—N3 | 119.2 (2) |
| N1—C1—C6 | 105.77 (19) | C13—C12—C11 | 118.5 (2) |
| C2—C1—C6 | 121.9 (2) | C13—C12—H12A | 120.7 |
| C3—C2—C1 | 117.2 (2) | C11—C12—H12A | 120.7 |
| C3—C2—H2A | 121.4 | C12—C13—C8 | 121.7 (2) |
| C1—C2—H2A | 121.4 | C12—C13—H13A | 119.2 |
| C2—C3—C4 | 121.3 (2) | C8—C13—H13A | 119.2 |
| C2—C3—H3A | 119.4 | O3—C14—N4 | 124.4 (3) |
| C4—C3—H3A | 119.4 | O3—C14—H14A | 117.8 |
| C5—C4—C3 | 121.8 (3) | N4—C14—H14A | 117.8 |
| C5—C4—H4A | 119.1 | N4—C15—H15A | 109.5 |
| C3—C4—H4A | 119.1 | N4—C15—H15B | 109.5 |
| C4—C5—C6 | 117.8 (2) | H15A—C15—H15B | 109.5 |
| C4—C5—H5A | 121.1 | N4—C15—H15C | 109.5 |
| C6—C5—H5A | 121.1 | H15A—C15—H15C | 109.5 |
| C5—C6—N2 | 130.4 (2) | H15B—C15—H15C | 109.5 |
| C5—C6—C1 | 120.1 (2) | N4—C16—H16A | 109.5 |
| N2—C6—C1 | 109.5 (2) | N4—C16—H16B | 109.5 |
| N2—C7—N1 | 112.44 (19) | H16A—C16—H16B | 109.5 |
| N2—C7—C8 | 124.12 (18) | N4—C16—H16C | 109.5 |
| N1—C7—C8 | 123.44 (19) | H16A—C16—H16C | 109.5 |
| C13—C8—C9 | 117.9 (2) | H16B—C16—H16C | 109.5 |
| C13—C8—C7 | 119.0 (2) | C7—N1—C1 | 107.00 (17) |
| C9—C8—C7 | 123.09 (19) | C7—N1—H1A | 126.3 |
| C10—C9—C8 | 121.5 (2) | C1—N1—H1A | 126.7 |
| C10—C9—H9A | 119.3 | C7—N2—C6 | 105.30 (17) |
| C8—C9—H9A | 119.3 | O2—N3—O1 | 122.4 (2) |
| C9—C10—C11 | 119.0 (2) | O2—N3—C11 | 118.7 (2) |
| C9—C10—H10A | 120.5 | O1—N3—C11 | 118.9 (2) |
| C11—C10—H10A | 120.5 | C14—N4—C15 | 120.7 (2) |
| C10—C11—C12 | 121.5 (2) | C14—N4—C16 | 121.4 (2) |
| C10—C11—N3 | 119.3 (2) | C15—N4—C16 | 117.9 (2) |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N1—H1A···O3i | 0.90 | 1.89 | 2.753 (2) | 161 |
| Symmetry codes: (i) −x+1, −y+1, −z+1. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N1—H1A···O3i | 0.90 | 1.89 | 2.753 (2) | 161 |
| Symmetry codes: (i) −x+1, −y+1, −z+1. |
The author thanks Jiangsu Planned Projects for Postdoctoral Research Funds (grant No. 0802003B) and Professor Dr Rengen Xiong.
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Zarrinmayeh, H., Nunes, A. M., Ornstein, P. L., Zimmerman, D. A., Gackenheimer, S. L., Bruns, R. F., Hipskind, P. A., Britton, T. C., Cantrell, B. E. & Gehlert, D. R. (1998). J. Med. Chem. 41, 2709–2719.
Benzimidazole systems continue to attract much attention in chemical synthesis, structural science and applied medicinal research (Zarrinmayeh, et al.,1998; Gallagher et al., 2001; Howarth & Hanlon, 2001). Here we report the crystal structure of the title compound, 1-(2-benzimidazolyl)-4-nitrobenzene dimethylformamide solvate.
The structural analysis shows that in the title compound (Fig. 1) the benzimidazole ring system and the benzene ring are essentially coplanar forming a dihedral angle of 0.86 (5)°. In the imidazole ring, the C7–N2 bond length of 1.327 (2) Å conforms to the value expected for a double bond. The dimethylformamide molecule bridges the benzimidazole ring system, forming an intermolecular N—H···O hydrogen bond (Table 1). The crystal packing is stabilized by aromatic π–π stacking interactions: Cp1···Cp2i = 3.865 (4) Å; perpendicular interplanar distance: 3.374 (3) Å; Cp1···Cp2i offset: 1.481 (3) Å (Cp1 and Cp2 are the centroids of the C1—C7 and C8—C13 aromatic rings, respectively; symmetry code: (i) -1+x, y, z).