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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o2047.
Published online 2010 July 17. doi:  10.1107/S1600536810027844
PMCID: PMC3007443

2-(1H-Benzimidazol-2-yl)-4,6-dichloro­phenol

Abstract

The title compound, C13H8Cl2N2O, was prepared by the reaction of 3,5-dichloro-2-hy­droxy­benzaldehyde with 1,2-diamino­benzene in methanol at ambient temperature. The title mol­ecule is essentially planar, the mean deviation from the plane of the non-H atoms being 0.037 (2) Å. There is an intra­molecular O—H(...)N hydrogen bond in the mol­ecule. In the crystal, symmetry-related mol­ecules are linked through N—H(...)O hydrogen bonds, forming polymeric chains propagating in [001]. The chains are linked by π–π inter­actions involving the dichloro­phenol ring and the benzoimidazole ring system [centroid–centroid distances = 3.535 (2) and 3.724 (2) Å].

Related literature

For the preparation and crystal structures of some Schiff bases bearing a C=N double bond, see: Jeseentharani et al. (2010 [triangle]); Hamaker et al. (2010 [triangle]); Tanaka et al. (2010 [triangle]); Tunç et al. (2009 [triangle]); Khalaji et al. (2010 [triangle]). For standard bond distances, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2047-scheme1.jpg

Experimental

Crystal data

  • C13H8Cl2N2O
  • M r = 279.11
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2047-efi1.jpg
  • a = 11.850 (3) Å
  • b = 7.446 (3) Å
  • c = 13.947 (2) Å
  • β = 104.261 (3)°
  • V = 1192.7 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.53 mm−1
  • T = 298 K
  • 0.21 × 0.20 × 0.18 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.897, T max = 0.911
  • 6117 measured reflections
  • 2562 independent reflections
  • 1810 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.127
  • S = 1.03
  • 2562 reflections
  • 167 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.26 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; 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 global, I. DOI: 10.1107/S1600536810027844/su2193sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810027844/su2193Isup2.hkl

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

Acknowledgments

The author acknowledges Hunan Yongzhou Vocational College for supporting this work.

supplementary crystallographic information

Comment

The condensation reaction of aldehydes with primary amines readily leads to the formation of Schiff bases bearing a C=N double bond (Jeseentharani et al., 2010; Hamaker et al., 2010; Tanaka et al., 2010; Tunç et al., 2009; Khalaji et al., 2010). Herein, we report on the structure of the title compound, the unexpected result of the Schiff base condensation reaction of 3,5-dichloro-2-hydroxybenzaldehyde with 1,2-diaminobenzene.

The title molecule (Fig. 1) is essentially planar, with the mean deviation from the plane of all the non-H atoms being 0.037 (2) Å. There is an intramolecular O—H···N hydrogen bond (Table 1) in the molecule, as shown in Fig. 1. All the bond lengths are within normal ranges (Allen et al., 1987).

In the crystal symmetry related molecules are linked through an intermolecular N—H···O hydrogen bond to form polymer chains propagating in [001] (Table 1 and Fig. 2). These chains are linked via π–π stacking interactions involving rings N1/N2/C7-C9 and C1-C6 [symmetry operation: 2-x, 2-y, 1-y], with a centroid-to-centroid distance of 3.535 (2) Å, and rings C1-C6 and C8-C13 [symmetry code: 2-x, 1-y, 1-z], with a centroid-to-centroid distance of 3.724 (2)Å.

Experimental

3,5-Dichloro-2-hydroxybenzaldehyde (1 mmol, 0.19 g) and 1,2-diaminobenzene (1 mmol, 0.11 g) were dissolved in methanol (30 ml). The mixture was stirred for 30 mins. at RT to give a yellow solution. Yellow single crystals were obtained by slow evaporation of the solution in air.

Refinement

Atom H1A was located in a difference Fourier map and its positional parameters were refined with a fixed isotropic thermal parameter of 0.08 Å2. The remaining H-atoms were positioned geometrically and refined as riding: C—H = 0.93 Å, O—H = 0.82 Å, with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(O).

Figures

Fig. 1.
The molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probability level. The intramolecular O-H···N hydrogen bond is shown as a dashed line.
Fig. 2.
The crystal packing of the title compound, viewed along the b-axis. The O-H···N and N-H···O hydrogen bonds are shown as dashed lines (see Table 1 for details).

Crystal data

C13H8Cl2N2OF(000) = 568
Mr = 279.11Dx = 1.554 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1560 reflections
a = 11.850 (3) Åθ = 3.0–26.2°
b = 7.446 (3) ŵ = 0.53 mm1
c = 13.947 (2) ÅT = 298 K
β = 104.261 (3)°Block, yellow
V = 1192.7 (6) Å30.21 × 0.20 × 0.18 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer2562 independent reflections
Radiation source: fine-focus sealed tube1810 reflections with I > 2σ(I)
graphiteRint = 0.035
ω scansθmax = 27.0°, θmin = 3.0°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −15→12
Tmin = 0.897, Tmax = 0.911k = −9→9
6117 measured reflectionsl = −12→17

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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.127H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0678P)2] where P = (Fo2 + 2Fc2)/3
2562 reflections(Δ/σ)max = 0.001
167 parametersΔρmax = 0.26 e Å3
1 restraintΔρmin = −0.23 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
Cl11.19596 (6)0.99614 (9)0.79805 (4)0.0505 (2)
Cl21.37522 (5)0.87011 (11)0.48582 (5)0.0602 (3)
N10.91704 (15)0.6598 (3)0.37972 (14)0.0350 (4)
N20.85158 (15)0.7146 (3)0.51409 (13)0.0361 (4)
O10.98220 (14)0.8474 (2)0.67436 (12)0.0469 (4)
H10.92400.80280.63780.070*
C11.05692 (18)0.7881 (3)0.52982 (15)0.0312 (5)
C21.06961 (18)0.8491 (3)0.62790 (16)0.0337 (5)
C31.1788 (2)0.9158 (3)0.67846 (15)0.0345 (5)
C41.27187 (19)0.9217 (3)0.63599 (16)0.0389 (5)
H41.34340.96630.67130.047*
C51.25768 (19)0.8605 (3)0.53975 (17)0.0376 (5)
C61.15119 (19)0.7967 (3)0.48692 (16)0.0360 (5)
H61.14230.75900.42190.043*
C70.94248 (18)0.7206 (3)0.47531 (15)0.0328 (5)
C80.79936 (19)0.6132 (3)0.35518 (16)0.0352 (5)
C90.75956 (18)0.6484 (3)0.44004 (17)0.0365 (5)
C100.6424 (2)0.6198 (4)0.43936 (19)0.0489 (7)
H100.61470.64400.49490.059*
C110.5702 (2)0.5549 (4)0.3542 (2)0.0584 (8)
H110.49220.53460.35200.070*
C120.6117 (2)0.5182 (4)0.2698 (2)0.0596 (8)
H120.56040.47300.21350.071*
C130.7263 (2)0.5474 (3)0.26834 (19)0.0485 (6)
H130.75320.52440.21230.058*
H1A0.968 (2)0.649 (4)0.342 (2)0.080*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0599 (5)0.0604 (4)0.0299 (3)−0.0096 (3)0.0084 (3)−0.0027 (3)
Cl20.0373 (4)0.0907 (6)0.0589 (4)−0.0105 (3)0.0236 (3)−0.0014 (4)
N10.0306 (10)0.0409 (11)0.0340 (10)−0.0020 (8)0.0090 (8)−0.0018 (8)
N20.0306 (10)0.0451 (12)0.0341 (10)0.0002 (9)0.0106 (8)0.0037 (8)
O10.0365 (9)0.0717 (13)0.0367 (9)−0.0072 (8)0.0171 (7)−0.0077 (8)
C10.0297 (11)0.0315 (12)0.0326 (11)0.0013 (9)0.0085 (9)0.0032 (9)
C20.0327 (12)0.0374 (13)0.0326 (11)0.0040 (9)0.0112 (9)0.0065 (9)
C30.0384 (13)0.0367 (13)0.0283 (11)0.0003 (10)0.0077 (9)0.0038 (9)
C40.0318 (13)0.0438 (14)0.0384 (12)−0.0037 (10)0.0034 (10)0.0046 (10)
C50.0303 (12)0.0433 (14)0.0409 (13)0.0004 (10)0.0118 (10)0.0048 (10)
C60.0349 (12)0.0411 (14)0.0338 (11)−0.0007 (10)0.0123 (10)−0.0020 (10)
C70.0331 (12)0.0339 (12)0.0320 (11)0.0028 (10)0.0088 (9)0.0043 (9)
C80.0299 (12)0.0370 (13)0.0382 (12)0.0004 (9)0.0073 (9)0.0048 (10)
C90.0281 (12)0.0399 (13)0.0402 (12)0.0007 (10)0.0058 (10)0.0074 (10)
C100.0343 (13)0.0657 (18)0.0486 (15)−0.0014 (12)0.0138 (11)0.0071 (12)
C110.0297 (13)0.082 (2)0.0626 (18)−0.0054 (14)0.0087 (13)0.0066 (15)
C120.0426 (16)0.075 (2)0.0530 (16)−0.0102 (14)−0.0035 (13)−0.0045 (14)
C130.0425 (15)0.0583 (17)0.0435 (14)−0.0053 (13)0.0082 (11)−0.0039 (12)

Geometric parameters (Å, °)

Cl1—C31.736 (2)C4—C51.388 (3)
Cl2—C51.740 (2)C4—H40.9300
N1—C71.370 (3)C5—C61.379 (3)
N1—C81.395 (3)C6—H60.9300
N1—H1A0.90 (3)C8—C131.393 (3)
N2—C71.320 (3)C8—C91.403 (3)
N2—C91.394 (3)C9—C101.402 (3)
O1—C21.350 (2)C10—C111.369 (4)
O1—H10.8200C10—H100.9300
C1—C61.393 (3)C11—C121.409 (4)
C1—C21.414 (3)C11—H110.9300
C1—C71.470 (3)C12—C131.380 (4)
C2—C31.403 (3)C12—H120.9300
C3—C41.375 (3)C13—H130.9300
C7—N1—C8106.74 (18)C1—C6—H6119.6
C7—N1—H1A125 (2)N2—C7—N1112.43 (19)
C8—N1—H1A128 (2)N2—C7—C1122.80 (19)
C7—N2—C9106.08 (18)N1—C7—C1124.77 (19)
C2—O1—H1109.5C13—C8—N1132.1 (2)
C6—C1—C2119.70 (19)C13—C8—C9122.2 (2)
C6—C1—C7121.93 (19)N1—C8—C9105.67 (19)
C2—C1—C7118.35 (19)N2—C9—C10130.6 (2)
O1—C2—C3118.9 (2)N2—C9—C8109.08 (19)
O1—C2—C1123.35 (19)C10—C9—C8120.3 (2)
C3—C2—C1117.71 (19)C11—C10—C9117.7 (2)
C4—C3—C2122.2 (2)C11—C10—H10121.1
C4—C3—Cl1119.11 (17)C9—C10—H10121.1
C2—C3—Cl1118.67 (17)C10—C11—C12121.4 (2)
C3—C4—C5119.1 (2)C10—C11—H11119.3
C3—C4—H4120.4C12—C11—H11119.3
C5—C4—H4120.4C13—C12—C11121.9 (2)
C6—C5—C4120.4 (2)C13—C12—H12119.0
C6—C5—Cl2120.51 (18)C11—C12—H12119.0
C4—C5—Cl2119.04 (17)C12—C13—C8116.5 (2)
C5—C6—C1120.8 (2)C12—C13—H13121.8
C5—C6—H6119.6C8—C13—H13121.8

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1···N20.821.852.582 (2)148
N1—H1A···O1i0.90 (3)2.39 (2)3.145 (2)143 (3)

Symmetry codes: (i) x, −y+3/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SU2193).

References

  • 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.
  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2007). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Hamaker, C. G., Maryashina, O. S., Daley, D. K. & Wadler, A. L. (2010). J. Chem. Crystallogr.40, 34–39.
  • Jeseentharani, V., Selvakumar, J., Dayalan, A., Varghese, B. & Nagaraja, K. S. (2010). J. Mol. Struct.966, 122–128.
  • Khalaji, A. D., Chermahini, A. N., Fejfarova, K. & Dusek, M. (2010). Struct. Chem.21, 153–157.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Tanaka, K., Shimoura, R. & Caira, M. R. (2010). Tetrahedron Lett.51, 449–452.
  • Tunç, T., Sarı, M., Sadıkoğlu, M. & Büyükgüngör, O. (2009). J. Chem. Crystallogr.39, 672–676.

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