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Acta Crystallogr Sect E Struct Rep Online. 2009 March 1; 65(Pt 3): o557.
Published online 2009 February 21. doi:  10.1107/S1600536809005315
PMCID: PMC2968547

1-(1H-Benzimidazol-2-yl)-4-nitro­benzene dimethyl­formamide solvate

Abstract

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 π–π stacking inter­action with a centroid–centroid separation of 3.685 (4) Å.

Related literature

For general background to benzimidazole compounds, see: Zarrinmayeh et al. (1998 [triangle]); Gallagher et al. (2001 [triangle]); Howarth & Hanlon (2001 [triangle]).

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Object name is e-65-0o557-scheme1.jpg

Experimental

Crystal data

  • C13H9N3O2·C3H7NO
  • M r = 312.33
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o557-efi1.jpg
  • a = 6.6228 (13) Å
  • b = 10.601 (2) Å
  • c = 11.886 (2) Å
  • α = 84.534 (10)°
  • β = 74.13 (2)°
  • γ = 81.53 (3)°
  • V = 792.6 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 291 K
  • 0.30 × 0.26 × 0.24 mm

Data collection

  • Rigaku Mercury2 diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 [triangle]) T min = 0.96, T max = 0.98
  • 7352 measured reflections
  • 3102 independent reflections
  • 1567 reflections with I > 2σ(I)
  • R int = 0.045

Refinement

  • R[F 2 > 2σ(F 2)] = 0.060
  • wR(F 2) = 0.138
  • S = 1.01
  • 3102 reflections
  • 210 parameters
  • H-atom parameters constrained
  • Δρmax = 0.12 e Å−3
  • Δρmin = −0.20 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/S1600536809005315/rz2294sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809005315/rz2294Isup2.hkl

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

Acknowledgments

The author thanks Jiangsu Planned Projects for Postdoctoral Research Funds (grant No. 0802003B) and Professor Dr Rengen Xiong.

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

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.

Figures

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 ...

Crystal data

C13H9N3O2·C3H7NOZ = 2
Mr = 312.33F(000) = 328
Triclinic, P1Dx = 1.309 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.6228 (13) ÅCell parameters from 5280 reflections
b = 10.601 (2) Åθ = 3.2–27.4°
c = 11.886 (2) ŵ = 0.09 mm1
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

Data collection

Rigaku Mercury2 diffractometer3102 independent reflections
Radiation source: fine-focus sealed tube1567 reflections with I > 2σ(I)
graphiteRint = 0.045
Detector resolution: 13.6612 pixels mm-1θmax = 26.0°, θmin = 3.2°
CCD_Profile_fitting scansh = −8→8
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −13→12
Tmin = 0.96, Tmax = 0.98l = −14→14
7352 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)] = 0.060Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.138H-atom parameters constrained
S = 1.01w = 1/[σ2(Fo2) + (0.0586P)2] where P = (Fo2 + 2Fc2)/3
3102 reflections(Δ/σ)max < 0.001
210 parametersΔρmax = 0.12 e Å3
0 restraintsΔρmin = −0.19 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
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−0.27370.47320.88090.096*
C3−0.4438 (5)0.3249 (3)0.9006 (2)0.0857 (8)
H3A−0.56680.36430.94970.103*
C4−0.4385 (4)0.2011 (2)0.8689 (2)0.0798 (8)
H4A−0.55840.15970.89730.096*
C5−0.2605 (4)0.1383 (2)0.7965 (2)0.0658 (7)
H5A−0.25870.05570.77560.079*
C6−0.0832 (4)0.20250 (19)0.75577 (18)0.0540 (6)
C70.2234 (4)0.26232 (18)0.67137 (18)0.0535 (6)
C80.4421 (4)0.26378 (18)0.60121 (18)0.0520 (6)
C90.5535 (4)0.36846 (19)0.5917 (2)0.0605 (6)
H9A0.48640.44140.63080.073*
C100.7583 (4)0.3659 (2)0.5264 (2)0.0610 (6)
H10A0.82990.43650.52020.073*
C110.8578 (4)0.2568 (2)0.46957 (19)0.0564 (6)
C120.7539 (4)0.1508 (2)0.4773 (2)0.0667 (7)
H12A0.82260.07770.43890.080*
C130.5471 (4)0.1560 (2)0.5427 (2)0.0670 (7)
H13A0.47570.08550.54800.080*
C140.7196 (4)0.3189 (2)0.2083 (2)0.0751 (7)
H14A0.58070.32540.25450.090*
C151.0088 (5)0.1989 (3)0.0766 (3)0.1051 (10)
H15A1.06840.27740.06940.158*
H15B1.00530.17710.00060.158*
H15C1.09400.13200.10930.158*
C160.6700 (5)0.1095 (2)0.1649 (3)0.1028 (10)
H16A0.53030.13370.21360.154*
H16B0.73550.03520.20020.154*
H16C0.66120.09080.08910.154*
N10.1073 (3)0.36303 (15)0.73324 (16)0.0621 (5)
H1A0.15150.43830.73760.074*
N20.1147 (3)0.16428 (15)0.68163 (16)0.0564 (5)
N31.0776 (3)0.2533 (2)0.39914 (18)0.0720 (6)
N40.7958 (3)0.21395 (17)0.15256 (17)0.0647 (6)
O11.1681 (3)0.34815 (17)0.39184 (17)0.0937 (6)
O21.1653 (3)0.15534 (18)0.35180 (19)0.1073 (7)
O30.8186 (3)0.40844 (16)0.20342 (19)0.1109 (8)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0662 (17)0.0574 (14)0.0553 (15)−0.0032 (13)−0.0130 (13)−0.0147 (12)
C20.086 (2)0.0740 (17)0.0737 (18)−0.0067 (16)−0.0048 (16)−0.0276 (14)
C30.071 (2)0.100 (2)0.0763 (19)−0.0065 (17)0.0020 (15)−0.0251 (16)
C40.076 (2)0.0857 (19)0.0749 (19)−0.0169 (15)−0.0098 (16)−0.0081 (15)
C50.0683 (18)0.0643 (15)0.0641 (16)−0.0103 (14)−0.0141 (14)−0.0081 (13)
C60.0637 (16)0.0493 (12)0.0487 (14)−0.0006 (11)−0.0159 (13)−0.0085 (10)
C70.0644 (17)0.0431 (12)0.0561 (15)0.0000 (11)−0.0212 (13)−0.0119 (11)
C80.0579 (15)0.0467 (12)0.0517 (14)−0.0007 (11)−0.0159 (12)−0.0096 (10)
C90.0636 (17)0.0448 (13)0.0702 (16)0.0021 (11)−0.0139 (14)−0.0144 (11)
C100.0647 (17)0.0475 (12)0.0715 (16)−0.0054 (11)−0.0179 (14)−0.0103 (12)
C110.0571 (15)0.0576 (14)0.0540 (14)−0.0015 (12)−0.0149 (12)−0.0094 (11)
C120.0693 (18)0.0543 (14)0.0756 (18)−0.0022 (13)−0.0139 (15)−0.0237 (12)
C130.0667 (18)0.0564 (14)0.0773 (17)−0.0107 (12)−0.0098 (15)−0.0243 (13)
C140.0786 (19)0.0670 (16)0.0733 (18)0.0010 (15)−0.0107 (15)−0.0157 (14)
C150.086 (2)0.116 (2)0.097 (2)0.0080 (18)−0.0026 (19)−0.0213 (18)
C160.126 (3)0.0753 (18)0.118 (3)−0.0349 (19)−0.041 (2)−0.0015 (17)
N10.0643 (13)0.0478 (10)0.0726 (13)−0.0072 (9)−0.0103 (11)−0.0195 (9)
N20.0595 (13)0.0482 (10)0.0629 (13)−0.0041 (9)−0.0176 (11)−0.0098 (9)
N30.0658 (15)0.0694 (14)0.0772 (15)−0.0028 (12)−0.0122 (12)−0.0158 (12)
N40.0693 (14)0.0548 (11)0.0672 (13)−0.0039 (10)−0.0117 (11)−0.0145 (10)
O10.0768 (13)0.0837 (12)0.1160 (16)−0.0240 (11)−0.0070 (11)−0.0164 (11)
O20.0802 (14)0.0926 (14)0.1324 (18)−0.0057 (11)0.0111 (12)−0.0483 (13)
O30.1330 (19)0.0708 (12)0.1336 (18)−0.0294 (12)−0.0241 (14)−0.0360 (12)

Geometric parameters (Å, °)

C1—N11.381 (3)C10—H10A0.9300
C1—C21.389 (3)C11—C121.385 (3)
C1—C61.400 (3)C11—N31.464 (3)
C2—C31.379 (3)C12—C131.374 (3)
C2—H2A0.9300C12—H12A0.9300
C3—C41.393 (3)C13—H13A0.9300
C3—H3A0.9300C14—O31.219 (3)
C4—C51.377 (3)C14—N41.313 (3)
C4—H4A0.9300C14—H14A0.9300
C5—C61.392 (3)C15—N41.448 (3)
C5—H5A0.9300C15—H15A0.9600
C6—N21.392 (3)C15—H15B0.9600
C7—N21.327 (2)C15—H15C0.9600
C7—N11.368 (2)C16—N41.454 (3)
C7—C81.462 (3)C16—H16A0.9600
C8—C131.387 (3)C16—H16B0.9600
C8—C91.400 (3)C16—H16C0.9600
C9—C101.364 (3)N1—H1A0.8998
C9—H9A0.9300N3—O21.220 (2)
C10—C111.381 (3)N3—O11.229 (2)
N1—C1—C2132.3 (2)C12—C11—N3119.2 (2)
N1—C1—C6105.77 (19)C13—C12—C11118.5 (2)
C2—C1—C6121.9 (2)C13—C12—H12A120.7
C3—C2—C1117.2 (2)C11—C12—H12A120.7
C3—C2—H2A121.4C12—C13—C8121.7 (2)
C1—C2—H2A121.4C12—C13—H13A119.2
C2—C3—C4121.3 (2)C8—C13—H13A119.2
C2—C3—H3A119.4O3—C14—N4124.4 (3)
C4—C3—H3A119.4O3—C14—H14A117.8
C5—C4—C3121.8 (3)N4—C14—H14A117.8
C5—C4—H4A119.1N4—C15—H15A109.5
C3—C4—H4A119.1N4—C15—H15B109.5
C4—C5—C6117.8 (2)H15A—C15—H15B109.5
C4—C5—H5A121.1N4—C15—H15C109.5
C6—C5—H5A121.1H15A—C15—H15C109.5
C5—C6—N2130.4 (2)H15B—C15—H15C109.5
C5—C6—C1120.1 (2)N4—C16—H16A109.5
N2—C6—C1109.5 (2)N4—C16—H16B109.5
N2—C7—N1112.44 (19)H16A—C16—H16B109.5
N2—C7—C8124.12 (18)N4—C16—H16C109.5
N1—C7—C8123.44 (19)H16A—C16—H16C109.5
C13—C8—C9117.9 (2)H16B—C16—H16C109.5
C13—C8—C7119.0 (2)C7—N1—C1107.00 (17)
C9—C8—C7123.09 (19)C7—N1—H1A126.3
C10—C9—C8121.5 (2)C1—N1—H1A126.7
C10—C9—H9A119.3C7—N2—C6105.30 (17)
C8—C9—H9A119.3O2—N3—O1122.4 (2)
C9—C10—C11119.0 (2)O2—N3—C11118.7 (2)
C9—C10—H10A120.5O1—N3—C11118.9 (2)
C11—C10—H10A120.5C14—N4—C15120.7 (2)
C10—C11—C12121.5 (2)C14—N4—C16121.4 (2)
C10—C11—N3119.3 (2)C15—N4—C16117.9 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···O3i0.901.892.753 (2)161

Symmetry codes: (i) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RZ2294).

References

  • Gallagher, J. F., Hanlon, K. & Howarth, J. (2001). Acta Cryst. C57, 1410–1414. [PubMed]
  • Howarth, J. & Hanlon, K. (2001). Tetrahedron Lett.42, 271–274.
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • 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. [PubMed]

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