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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2011 Jan 15;67(Pt 2):o409. doi: 10.1107/S1600536811001644

2-(1H-Benzimidazol-2-yl)-4-nitro­phenol

Jingya Sun a,*, Xiangdi Tong a
PMCID: PMC3051601  PMID: 21523080

Abstract

The title compound, C13H9N3O3, was prepared by the reaction of 5-nitro­salicyl­aldehyde with 1,2-diamino­benzene in methanol. The whole mol­ecule is approximately planar, with a mean deviation from the plane defined by the non-H atoms of 0.0311 (4) Å, and with a dihedral angle between the benzene ring and the benzimidazole ring system of 1.1 (3)°. An intra­molecular O—H⋯N hydrogen bond occurs. In the crystal, adjacent mol­ecules are linked through inter­molecular N—H⋯O hydrogen bonds, forming centrosymmetric dimers.

Related literature

For Schiff base compounds, see: Miura et al. (2009); Zhao et al. (2010); Karadağ et al. (2011); Bingöl Alpaslan et al. (2010). For bond-length data, see: Allen et al. (1987).graphic file with name e-67-0o409-scheme1.jpg

Experimental

Crystal data

  • C13H9N3O3

  • M r = 255.23

  • Monoclinic, Inline graphic

  • a = 8.117 (3) Å

  • b = 6.769 (2) Å

  • c = 20.842 (3) Å

  • β = 99.235 (2)°

  • V = 1130.2 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.11 mm−1

  • T = 298 K

  • 0.20 × 0.20 × 0.18 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001) T min = 0.978, T max = 0.980

  • 8933 measured reflections

  • 2469 independent reflections

  • 1283 reflections with I > 2σ(I)

  • R int = 0.061

Refinement

  • R[F 2 > 2σ(F 2)] = 0.068

  • wR(F 2) = 0.153

  • S = 1.04

  • 2469 reflections

  • 176 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.14 e Å−3

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811001644/hg2791sup1.cif

e-67-0o409-sup1.cif (15KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811001644/hg2791Isup2.hkl

e-67-0o409-Isup2.hkl (121.3KB, hkl)

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯O2i 0.90 (1) 2.02 (1) 2.898 (3) 164 (3)
O1—H1⋯N1 0.82 1.85 2.590 (3) 149

Symmetry code: (i) Inline graphic.

supplementary crystallographic information

Comment

The condensation reaction between aldehydes with organic primary amines readily forms Schiff bases containing the typical –C=N– groups (Miura et al., 2009; Zhao et al., 2010; Karadağ et al., 2011; Bingöl Alpaslan et al., 2010). In this paper, the title compound (Fig. 1) was prepared by the reaction of 5-nitrosalicylaldehyde with 1,2-diaminobenzene in methanol.

The whole molecule of the compound is approximately planar, with mean deviation from the plane defined by the non-hydrogen atoms of 0.0311 (4) Å, and with the dihedral angle between the benzene ring and the Benzimidazole ring of 1.1 (3)°. All the bond lengths are within normal ranges (Allen et al., 1987). There is an intramolecular O—H···N hydrogen bond in the molecule (Table 1). In the crystal structure, adjacent two molecules are linked through intermolecular N—H···O hydrogen bonds (Table 1) to form a dimer (Fig. 2).

Experimental

5-Nitrosalicylaldehyde (1.0 mmol, 0.167 g) and 1,2-diaminobenzene (0.5 mmol, 0.054 g) were refluxed for 30 min in 30 ml me thanol, and cooled to room temperature to give colorless solid, which was isolated by filtration. Single crystals of the title compound were formed by recrystallization of the solid in methanol.

Refinement

H2 was located in a difference Fourier map and refined isotropically, with the N—H distance restrained to 0.90 (1) Å. The other H atoms were positioned geometrically and refined using the riding-model approximation, with C–H = 0.93 Å, and O–H = 0.82 Å, and Uiso(H) = 1.2Ueq(C) or Uiso(H) = 1.5Ueq(O).

Figures

Fig. 1.

Fig. 1.

The molecular structure of the title compounds with atom labels and the 30% probability displacement ellipsoids. Intramolecular O—H···O hydrogen bond is shown as a dashed line.

Fig. 2.

Fig. 2.

The molecular packing of the title compound. Hydrogen bonds are shown as dashed lines.

Crystal data

C13H9N3O3 F(000) = 528
Mr = 255.23 Dx = 1.500 Mg m3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc Cell parameters from 1124 reflections
a = 8.117 (3) Å θ = 2.5–24.5°
b = 6.769 (2) Å µ = 0.11 mm1
c = 20.842 (3) Å T = 298 K
β = 99.235 (2)° Block, yellow
V = 1130.2 (5) Å3 0.20 × 0.20 × 0.18 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer 2469 independent reflections
Radiation source: fine-focus sealed tube 1283 reflections with I > 2σ(I)
graphite Rint = 0.061
ω scans θmax = 27.0°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2001) h = −10→10
Tmin = 0.978, Tmax = 0.980 k = −8→8
8933 measured reflections l = −26→24

Refinement

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)] = 0.068 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.153 H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0589P)2 + 0.1494P] where P = (Fo2 + 2Fc2)/3
2469 reflections (Δ/σ)max < 0.001
176 parameters Δρmax = 0.20 e Å3
1 restraint Δρmin = −0.14 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)

x y z Uiso*/Ueq
O1 0.7974 (3) 0.7492 (3) 0.12518 (10) 0.0680 (7)
H1 0.8172 0.7776 0.0889 0.102*
O2 0.4484 (3) −0.0641 (3) 0.07368 (10) 0.0687 (7)
O3 0.4555 (3) −0.0423 (3) 0.17662 (11) 0.0764 (8)
N1 0.8286 (3) 0.7006 (4) 0.00445 (12) 0.0547 (7)
N2 0.7411 (3) 0.4267 (3) −0.04913 (12) 0.0495 (7)
N3 0.4870 (3) 0.0226 (4) 0.12571 (12) 0.0520 (7)
C1 0.6985 (3) 0.4551 (4) 0.06634 (13) 0.0425 (7)
C2 0.7228 (4) 0.5722 (4) 0.12303 (15) 0.0477 (8)
C3 0.6712 (4) 0.5046 (5) 0.17926 (14) 0.0562 (9)
H3 0.6878 0.5828 0.2164 0.067*
C4 0.5966 (4) 0.3252 (4) 0.18085 (14) 0.0492 (8)
H4 0.5632 0.2799 0.2189 0.059*
C5 0.5710 (3) 0.2113 (4) 0.12517 (14) 0.0425 (7)
C6 0.6205 (3) 0.2741 (4) 0.06832 (13) 0.0423 (7)
H6 0.6016 0.1950 0.0314 0.051*
C7 0.7560 (3) 0.5267 (4) 0.00778 (14) 0.0461 (7)
C8 0.8628 (4) 0.7151 (4) −0.05876 (14) 0.0484 (8)
C9 0.8092 (3) 0.5440 (4) −0.09285 (15) 0.0475 (7)
C10 0.8259 (4) 0.5165 (5) −0.15689 (15) 0.0594 (9)
H10 0.7902 0.4011 −0.1791 0.071*
C11 0.8983 (4) 0.6692 (5) −0.18671 (16) 0.0645 (10)
H11 0.9114 0.6565 −0.2300 0.077*
C12 0.9518 (4) 0.8413 (5) −0.15324 (18) 0.0694 (10)
H12 0.9996 0.9414 −0.1747 0.083*
C13 0.9354 (4) 0.8666 (5) −0.08904 (17) 0.0645 (9)
H13 0.9719 0.9816 −0.0668 0.077*
H2 0.698 (4) 0.307 (2) −0.0610 (15) 0.080*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0862 (18) 0.0561 (14) 0.0638 (17) −0.0234 (12) 0.0183 (14) −0.0113 (11)
O2 0.1090 (19) 0.0552 (13) 0.0445 (14) −0.0268 (12) 0.0203 (13) −0.0100 (11)
O3 0.122 (2) 0.0662 (15) 0.0487 (14) −0.0165 (14) 0.0369 (14) 0.0101 (12)
N1 0.0620 (18) 0.0552 (15) 0.0460 (17) −0.0161 (13) 0.0055 (13) 0.0067 (13)
N2 0.0588 (17) 0.0435 (14) 0.0465 (16) −0.0102 (12) 0.0096 (13) 0.0012 (13)
N3 0.0713 (18) 0.0478 (15) 0.0403 (16) −0.0029 (13) 0.0192 (13) 0.0019 (13)
C1 0.0475 (18) 0.0399 (16) 0.0387 (17) −0.0038 (14) 0.0033 (14) 0.0005 (13)
C2 0.0458 (18) 0.0434 (17) 0.052 (2) −0.0057 (14) 0.0037 (15) −0.0061 (15)
C3 0.070 (2) 0.058 (2) 0.0413 (19) −0.0124 (17) 0.0117 (16) −0.0126 (16)
C4 0.061 (2) 0.0553 (19) 0.0328 (17) −0.0008 (16) 0.0108 (15) −0.0021 (15)
C5 0.0489 (18) 0.0390 (15) 0.0393 (18) −0.0027 (14) 0.0058 (14) 0.0026 (13)
C6 0.0547 (18) 0.0418 (16) 0.0302 (16) −0.0045 (14) 0.0061 (13) −0.0025 (13)
C7 0.0497 (18) 0.0412 (16) 0.0462 (19) −0.0073 (14) 0.0038 (14) 0.0028 (15)
C8 0.0494 (19) 0.0516 (18) 0.0422 (19) −0.0055 (15) 0.0014 (15) 0.0085 (15)
C9 0.0442 (18) 0.0535 (18) 0.0447 (19) −0.0026 (15) 0.0070 (14) 0.0107 (15)
C10 0.063 (2) 0.065 (2) 0.050 (2) 0.0030 (17) 0.0071 (16) 0.0009 (17)
C11 0.069 (2) 0.082 (3) 0.045 (2) 0.003 (2) 0.0157 (18) 0.0130 (19)
C12 0.070 (2) 0.075 (2) 0.064 (3) −0.009 (2) 0.0121 (19) 0.028 (2)
C13 0.070 (2) 0.061 (2) 0.062 (2) −0.0165 (18) 0.0115 (18) 0.0127 (18)

Geometric parameters (Å, °)

O1—C2 1.340 (3) C3—H3 0.9300
O1—H1 0.8200 C4—C5 1.381 (4)
O2—N3 1.228 (3) C4—H4 0.9300
O3—N3 1.213 (3) C5—C6 1.378 (4)
N1—C7 1.323 (3) C6—H6 0.9300
N1—C8 1.393 (4) C8—C13 1.384 (4)
N2—C7 1.354 (3) C8—C9 1.392 (4)
N2—C9 1.388 (3) C9—C10 1.376 (4)
N2—H2 0.902 (10) C10—C11 1.385 (4)
N3—C5 1.449 (3) C10—H10 0.9300
C1—C6 1.383 (4) C11—C12 1.391 (5)
C1—C2 1.410 (4) C11—H11 0.9300
C1—C7 1.458 (4) C12—C13 1.376 (5)
C2—C3 1.384 (4) C12—H12 0.9300
C3—C4 1.360 (4) C13—H13 0.9300
C2—O1—H1 109.5 C5—C6—H6 120.1
C7—N1—C8 105.7 (2) C1—C6—H6 120.1
C7—N2—C9 107.5 (2) N1—C7—N2 112.1 (2)
C7—N2—H2 132 (2) N1—C7—C1 123.0 (3)
C9—N2—H2 121 (2) N2—C7—C1 124.9 (2)
O3—N3—O2 122.7 (3) C13—C8—C9 120.3 (3)
O3—N3—C5 119.4 (3) C13—C8—N1 130.4 (3)
O2—N3—C5 117.9 (2) C9—C8—N1 109.3 (2)
C6—C1—C2 118.4 (3) C10—C9—N2 132.1 (3)
C6—C1—C7 121.9 (2) C10—C9—C8 122.5 (3)
C2—C1—C7 119.6 (2) N2—C9—C8 105.4 (3)
O1—C2—C3 117.6 (3) C9—C10—C11 116.7 (3)
O1—C2—C1 122.2 (3) C9—C10—H10 121.7
C3—C2—C1 120.2 (3) C11—C10—H10 121.7
C4—C3—C2 120.8 (3) C10—C11—C12 121.4 (3)
C4—C3—H3 119.6 C10—C11—H11 119.3
C2—C3—H3 119.6 C12—C11—H11 119.3
C3—C4—C5 119.1 (3) C13—C12—C11 121.4 (3)
C3—C4—H4 120.5 C13—C12—H12 119.3
C5—C4—H4 120.5 C11—C12—H12 119.3
C6—C5—C4 121.7 (3) C12—C13—C8 117.7 (3)
C6—C5—N3 118.8 (2) C12—C13—H13 121.1
C4—C5—N3 119.6 (3) C8—C13—H13 121.1
C5—C6—C1 119.8 (2)

Hydrogen-bond geometry (Å, °)

D—H···A D—H H···A D···A D—H···A
N2—H2···O2i 0.90 (1) 2.02 (1) 2.898 (3) 164 (3)
O1—H1···N1 0.82 1.85 2.590 (3) 149

Symmetry codes: (i) −x+1, −y, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2791).

References

  1. 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.
  2. Bingöl Alpaslan, Y., Alpaslan, G., Ağar, A. & Işık, Ş. (2010). Acta Cryst. E66, o510. [DOI] [PMC free article] [PubMed]
  3. Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  4. Bruker (2007). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  5. Karadağ, A. T., Atalay, Ş. & Genç, H. (2011). Acta Cryst. E67, o95. [DOI] [PMC free article] [PubMed]
  6. Miura, Y., Aritake, Y. & Akitsu, T. (2009). Acta Cryst. E65, o2381. [DOI] [PMC free article] [PubMed]
  7. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
  8. Zhao, L., Cao, D. & Cui, J. (2010). Acta Cryst. E66, o2204. [DOI] [PMC free article] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811001644/hg2791sup1.cif

e-67-0o409-sup1.cif (15KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811001644/hg2791Isup2.hkl

e-67-0o409-Isup2.hkl (121.3KB, hkl)

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


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