organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
*Correspondence e-mail: wudh1971@sohu.com

(Received 4 February 2009; accepted 14 February 2009; online 21 February 2009)

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 ππ 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[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.]); Gallagher et al. (2001[Gallagher, J. F., Hanlon, K. & Howarth, J. (2001). Acta Cryst. C57, 1410-1414.]); Howarth & Hanlon (2001[Howarth, J. & Hanlon, K. (2001). Tetrahedron Lett. 42, 271-274.]).

[Scheme 1]

Experimental

Crystal data
  • C13H9N3O2·C3H7NO

  • Mr = 312.33

  • Triclinic, [P \overline 1]

  • 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.96, Tmax = 0.98

  • 7352 measured reflections

  • 3102 independent reflections

  • 1567 reflections with I > 2σ(I)

  • Rint = 0.045

Refinement
  • R[F2 > 2σ(F2)] = 0.060

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯O3i 0.90 1.89 2.753 (2) 161
Symmetry code: (i) -x+1, -y+1, -z+1.

Data collection: CrystalClear (Rigaku, 2005[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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 ππ 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).

Related literature top

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

Experimental top

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 top

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.

Computing details top

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).

Figures top
[Figure 1] 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.
1-(1H-Benzimidazol-2-yl)-4-nitrobenzene dimethylformamide solvate top
Crystal data top
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 top
Rigaku Mercury2
diffractometer
3102 independent reflections
Radiation source: fine-focus sealed tube1567 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.045
Detector resolution: 13.6612 pixels mm-1θmax = 26.0°, θmin = 3.2°
CCD_Profile_fitting scansh = 88
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
k = 1312
Tmin = 0.96, Tmax = 0.98l = 1414
7352 measured reflections
Refinement top
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 = 1.01 w = 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 = 0.20 e Å3
Crystal data top
C13H9N3O2·C3H7NOγ = 81.53 (3)°
Mr = 312.33V = 792.6 (3) Å3
Triclinic, P1Z = 2
a = 6.6228 (13) ÅMo Kα radiation
b = 10.601 (2) ŵ = 0.09 mm1
c = 11.886 (2) ÅT = 291 K
α = 84.534 (10)°0.30 × 0.26 × 0.24 mm
β = 74.13 (2)°
Data collection top
Rigaku Mercury2
diffractometer
3102 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
1567 reflections with I > 2σ(I)
Tmin = 0.96, Tmax = 0.98Rint = 0.045
7352 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0600 restraints
wR(F2) = 0.138H-atom parameters constrained
S = 1.01Δρmax = 0.12 e Å3
3102 reflectionsΔρmin = 0.20 e Å3
210 parameters
Special details top

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) top
xyzUiso*/Ueq
C10.0895 (4)0.3267 (2)0.7884 (2)0.0599 (6)
C20.2701 (4)0.3902 (2)0.8605 (2)0.0798 (8)
H2A0.27370.47320.88090.096*
C30.4438 (5)0.3249 (3)0.9006 (2)0.0857 (8)
H3A0.56680.36430.94970.103*
C40.4385 (4)0.2011 (2)0.8689 (2)0.0798 (8)
H4A0.55840.15970.89730.096*
C50.2605 (4)0.1383 (2)0.7965 (2)0.0658 (7)
H5A0.25870.05570.77560.079*
C60.0832 (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) top
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, º) top
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, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O3i0.901.892.753 (2)161
Symmetry code: (i) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC13H9N3O2·C3H7NO
Mr312.33
Crystal system, space groupTriclinic, P1
Temperature (K)291
a, b, c (Å)6.6228 (13), 10.601 (2), 11.886 (2)
α, β, γ (°)84.534 (10), 74.13 (2), 81.53 (3)
V3)792.6 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.30 × 0.26 × 0.24
Data collection
DiffractometerRigaku Mercury2
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.96, 0.98
No. of measured, independent and
observed [I > 2σ(I)] reflections
7352, 3102, 1567
Rint0.045
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.060, 0.138, 1.01
No. of reflections3102
No. of parameters210
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.12, 0.20

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O3i0.901.892.753 (2)160.9
Symmetry code: (i) x+1, y+1, z+1.
 

Acknowledgements

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

References

First citationGallagher, J. F., Hanlon, K. & Howarth, J. (2001). Acta Cryst. C57, 1410–1414.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationHowarth, J. & Hanlon, K. (2001). Tetrahedron Lett. 42, 271–274.  Google Scholar
First citationRigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZarrinmayeh, 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.  Web of Science CSD CrossRef CAS PubMed Google Scholar

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