PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 November 1; 66(Pt 11): o2863.
Published online 2010 October 20. doi:  10.1107/S1600536810041243
PMCID: PMC3009370

4-Chloro-2-(6-nitro-1H-benzimidazol-2-yl)phenol N,N-dimethyl­form­amide solvate

Abstract

In the title compound, C13H8ClN3O3·C3H7NO, the benzimidazole and benzene rings make a dihedral angle of 0.63 (11)°. An intra­molecular O—H(...)N hydrogen bond generates an S(6) ring motif. The solvent mol­ecule is hydrogen-bonded to the benzimidazole mol­ecule by inter­molecular N—H(...)O and C—H(...)O hydrogen bonds, generating an R 1 2(7) ring motif. In the crystal, the mol­ecules are arranged into parallel layers perpendicular to the c axis and stabilized by weak π–π inter­actions [centroid–centroid distances in the range 3.4036 (18)–3.5878 (16) Å].

Related literature

For general background to and the biological activity of benzimidazole derivatives, see: Trivedi et al. (2006 [triangle]); White et al. (2004 [triangle]); Garuti et al. (2004 [triangle]). For related structures, see: Eltayeb et al. (2009 [triangle]); Yeap et al. (2009 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2863-scheme1.jpg

Experimental

Crystal data

  • C13H8ClN3O3·C3H7NO
  • M r = 362.77
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2863-efi1.jpg
  • a = 15.200 (2) Å
  • b = 18.355 (2) Å
  • c = 13.279 (3) Å
  • β = 119.232 (2)°
  • V = 3233.1 (9) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.27 mm−1
  • T = 100 K
  • 0.45 × 0.12 × 0.05 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.889, T max = 0.987
  • 14542 measured reflections
  • 3719 independent reflections
  • 2771 reflections with I > 2σ(I)
  • R int = 0.041

Refinement

  • R[F 2 > 2σ(F 2)] = 0.065
  • wR(F 2) = 0.201
  • S = 1.07
  • 3719 reflections
  • 228 parameters
  • H-atom parameters constrained
  • Δρmax = 0.78 e Å−3
  • Δρmin = −0.34 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810041243/ng5046sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810041243/ng5046Isup2.hkl

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

Acknowledgments

The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the RU research grant (815002). HKF and CSY also thank USM for the Research University Grant No. 1001/PFIZIK/811160. AMF thanks the Libyan Government for providing a scholarship.

supplementary crystallographic information

Comment

Benzimidazole and its derivatives are widely used in biological systems (Trivedi et al., 2006). Some derivatives of benzimidazole are used as inhibitors of the DNA-repair enzyme poly (ADP-ribose) polymerase-1 (PARP-1) (White et al., 2004) and antiproliferative activities (Garuti et al., 2004). In view of the biological importance of aforementioned benzimidazole, the crystal structure determination of the title compound was carried out and the result is presented here.

The asymmetric unit of title compound consists of one benzimidazole molecule and one dimethylformamide solvent (Fig. 1). The geometric parameters are comparable to those related structures (Eltayeb et al., 2009; Yeap et al., 2009). The molecular structure of the benzimidazole is essentially planar with the maximum deviation of 0.071 Å for atom O1. An intramolecular O3—H1O3···N2 hydrogen bond generate S(6) ring motif (Bernstein et al., 1995). The solvent molecule is hydrogen-bonded to the benzimidazole molecule by intermolecular N1—H1N1···O4 and C13—H13A···O4 hydrogen bonds generating R12(7) ring motif. In the crystal packing, the molecules are arranged into parallel layers perpendicular to c axis and stabilized by weak π···π interactions [Cg1···Cg1i of 3.4036 (18) Å, Cg1···Cg1ii of 3.5247 (17) Å and Cg1···Cg2i of 3.5878 (16) Å; (i) -x, y, 1/2 - z; (ii) -x, 1 - y, 1 - z. Cg1 and Cg2 are centroids of N1–C1–C6–N2–C7 and C1–C6 rings, respectively].

Experimental

5-Chloro-2-hydroxy benzaldehyde (0.626 g, 4 mmol) was added to the solution of 4-nitrobenzene-1,2-diamine (0.306 g, 2 mmol) in methanol (30 ml). The mixture was refluxed with stirring for 1 h. The resultant solid obtained was then filtered and washed with methanol. Orange plate-shaped single crystals of the title compound suitable for X-ray structure determination was obtained from DMF by slow evaporation at room temperature.

Refinement

The O– and N-bound hydrogen atoms were located from difference Fourier map and refined using a riding model [Uiso(H) = 1.2Ueq (N) or 1.5Ueq(O)]. The rest of hydrogen atoms were positioned geometrically [C–H = 0.93 & 0.96 Å] and refined using a riding model [Uiso(H) = 1.2 & 1.5Ueq(C)]. A rotating-group model were applied for methyl groups.

Figures

Fig. 1.
The molecular structure of title compound with atom labels and 50% probability ellipsoids for non-H atoms. Intramolecular hydrogen bonds are shown as dashed lines.
Fig. 2.
The crystal packing of title compound viewed down b axis, showing the molecules are arranged into parallel layers.

Crystal data

C13H8ClN3O3·C3H7NOF(000) = 1504
Mr = 362.77Dx = 1.491 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 3050 reflections
a = 15.200 (2) Åθ = 2.8–29.6°
b = 18.355 (2) ŵ = 0.27 mm1
c = 13.279 (3) ÅT = 100 K
β = 119.232 (2)°Plate, orange
V = 3233.1 (9) Å30.45 × 0.12 × 0.05 mm
Z = 8

Data collection

Bruker APEXII DUO CCD area-detector diffractometer3719 independent reflections
Radiation source: fine-focus sealed tube2771 reflections with I > 2σ(I)
graphiteRint = 0.041
[var phi] and ω scansθmax = 27.5°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −19→19
Tmin = 0.889, Tmax = 0.987k = −23→23
14542 measured reflectionsl = −17→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)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.201H-atom parameters constrained
S = 1.07w = 1/[σ2(Fo2) + (0.0961P)2 + 7.3038P] where P = (Fo2 + 2Fc2)/3
3719 reflections(Δ/σ)max < 0.001
228 parametersΔρmax = 0.78 e Å3
0 restraintsΔρmin = −0.34 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
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
Cl1−0.29053 (6)0.25697 (4)0.23736 (8)0.0465 (3)
O10.37235 (16)0.53844 (13)0.5412 (2)0.0418 (6)
O20.36636 (17)0.65517 (14)0.5483 (2)0.0444 (6)
O3−0.28130 (16)0.57579 (11)0.23880 (19)0.0362 (5)
H1O3−0.22930.59040.25910.054*
N1−0.00189 (16)0.46895 (13)0.37354 (18)0.0242 (5)
H1N10.00570.42090.37720.029*
N2−0.08820 (17)0.57321 (12)0.33366 (19)0.0245 (5)
N30.32588 (18)0.59601 (15)0.5240 (2)0.0327 (6)
C10.06745 (19)0.52535 (15)0.4062 (2)0.0227 (5)
C20.1718 (2)0.52401 (16)0.4543 (2)0.0261 (6)
H2A0.20850.48090.47190.031*
C30.21629 (19)0.59173 (15)0.4736 (2)0.0250 (6)
C40.1634 (2)0.65760 (16)0.4484 (2)0.0304 (6)
H4A0.19780.70160.46290.036*
C50.0598 (2)0.65720 (16)0.4018 (2)0.0287 (6)
H5A0.02330.70040.38520.034*
C60.0120 (2)0.59004 (15)0.3807 (2)0.0250 (6)
C7−0.09359 (19)0.50080 (15)0.3299 (2)0.0228 (5)
C8−0.18949 (19)0.46199 (14)0.2832 (2)0.0218 (5)
C9−0.2793 (2)0.50277 (16)0.2409 (2)0.0269 (6)
C10−0.3707 (2)0.46580 (18)0.2000 (3)0.0342 (7)
H10A−0.43030.49230.17190.041*
C11−0.3743 (2)0.39127 (18)0.2004 (2)0.0339 (7)
H11A−0.43550.36740.17500.041*
C12−0.2861 (2)0.35177 (17)0.2390 (2)0.0301 (6)
C13−0.1943 (2)0.38598 (15)0.2804 (2)0.0254 (6)
H13A−0.13570.35860.30640.030*
O40.0524 (2)0.32533 (15)0.3936 (3)0.0728 (9)
N40.0760 (2)0.20375 (15)0.4053 (2)0.0374 (6)
C140.0997 (3)0.2715 (2)0.3954 (4)0.0526 (9)
H14A0.15750.27870.38920.063*
C15−0.0141 (3)0.1904 (3)0.4121 (4)0.0611 (11)
H15A−0.03170.23340.43940.092*
H15B−0.00260.15090.46450.092*
H15C−0.06810.17790.33700.092*
C160.1378 (4)0.1427 (2)0.4137 (4)0.0710 (13)
H16A0.19420.15900.40610.106*
H16B0.09890.10850.35340.106*
H16C0.16160.11950.48730.106*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0443 (5)0.0298 (4)0.0618 (5)−0.0138 (3)0.0230 (4)−0.0003 (3)
O10.0249 (11)0.0443 (14)0.0522 (13)−0.0012 (10)0.0157 (10)−0.0013 (10)
O20.0298 (12)0.0452 (14)0.0561 (14)−0.0158 (10)0.0192 (10)−0.0078 (11)
O30.0252 (10)0.0291 (11)0.0515 (13)0.0043 (8)0.0164 (10)−0.0016 (9)
N10.0197 (11)0.0250 (12)0.0278 (11)0.0006 (9)0.0116 (9)0.0019 (9)
N20.0230 (11)0.0238 (12)0.0279 (11)−0.0039 (9)0.0135 (9)−0.0012 (9)
N30.0229 (12)0.0402 (15)0.0341 (12)−0.0047 (11)0.0133 (10)−0.0033 (10)
C10.0209 (12)0.0270 (14)0.0217 (11)−0.0059 (10)0.0115 (10)−0.0023 (10)
C20.0226 (13)0.0301 (15)0.0271 (12)0.0008 (11)0.0134 (10)−0.0006 (10)
C30.0172 (12)0.0326 (15)0.0248 (12)−0.0051 (10)0.0101 (10)−0.0024 (10)
C40.0292 (15)0.0276 (15)0.0334 (14)−0.0087 (11)0.0145 (11)−0.0046 (11)
C50.0273 (14)0.0251 (14)0.0325 (14)0.0016 (11)0.0138 (11)−0.0001 (11)
C60.0235 (13)0.0276 (14)0.0235 (12)−0.0018 (11)0.0112 (10)−0.0020 (10)
C70.0196 (12)0.0290 (14)0.0217 (11)−0.0008 (10)0.0114 (10)0.0009 (10)
C80.0187 (12)0.0248 (14)0.0219 (11)−0.0025 (10)0.0100 (10)−0.0007 (9)
C90.0226 (13)0.0294 (15)0.0281 (13)0.0011 (11)0.0119 (11)0.0008 (10)
C100.0186 (13)0.0455 (19)0.0371 (15)0.0020 (12)0.0124 (12)−0.0009 (13)
C110.0227 (14)0.0443 (18)0.0328 (14)−0.0118 (12)0.0121 (11)−0.0024 (12)
C120.0288 (14)0.0309 (15)0.0299 (13)−0.0094 (12)0.0138 (11)−0.0005 (11)
C130.0213 (13)0.0276 (14)0.0264 (12)−0.0011 (10)0.0110 (10)0.0019 (10)
O40.073 (2)0.0341 (15)0.099 (2)0.0211 (14)0.0322 (18)0.0026 (14)
N40.0405 (15)0.0347 (15)0.0394 (14)−0.0003 (11)0.0214 (12)−0.0028 (11)
C140.048 (2)0.041 (2)0.066 (2)−0.0015 (17)0.0258 (18)0.0046 (17)
C150.048 (2)0.070 (3)0.064 (2)−0.001 (2)0.027 (2)0.009 (2)
C160.092 (4)0.051 (3)0.078 (3)0.023 (2)0.049 (3)0.000 (2)

Geometric parameters (Å, °)

Cl1—C121.741 (3)C8—C131.397 (4)
O1—N31.229 (3)C8—C91.411 (4)
O2—N31.212 (3)C9—C101.396 (4)
O3—C91.341 (3)C10—C111.369 (5)
O3—H1O30.7498C10—H10A0.9300
N1—C71.354 (3)C11—C121.384 (4)
N1—C11.387 (3)C11—H11A0.9300
N1—H1N10.8875C12—C131.376 (4)
N2—C71.331 (4)C13—H13A0.9300
N2—C61.370 (3)O4—C141.216 (5)
N3—C31.463 (3)N4—C141.319 (5)
C1—C21.391 (4)N4—C161.431 (5)
C1—C61.399 (4)N4—C151.437 (5)
C2—C31.378 (4)C14—H14A0.9300
C2—H2A0.9300C15—H15A0.9600
C3—C41.399 (4)C15—H15B0.9600
C4—C51.383 (4)C15—H15C0.9600
C4—H4A0.9300C16—H16A0.9600
C5—C61.388 (4)C16—H16B0.9600
C5—H5A0.9300C16—H16C0.9600
C7—C81.461 (4)
C9—O3—H1O3110.0O3—C9—C8123.1 (2)
C7—N1—C1106.1 (2)C10—C9—C8118.9 (3)
C7—N1—H1N1122.1C11—C10—C9121.2 (3)
C1—N1—H1N1131.8C11—C10—H10A119.4
C7—N2—C6106.1 (2)C9—C10—H10A119.4
O2—N3—O1123.4 (3)C10—C11—C12119.5 (3)
O2—N3—C3119.1 (3)C10—C11—H11A120.3
O1—N3—C3117.5 (2)C12—C11—H11A120.3
N1—C1—C2130.7 (3)C13—C12—C11121.3 (3)
N1—C1—C6106.4 (2)C13—C12—Cl1119.1 (2)
C2—C1—C6122.9 (3)C11—C12—Cl1119.6 (2)
C3—C2—C1114.6 (3)C12—C13—C8119.7 (3)
C3—C2—H2A122.7C12—C13—H13A120.1
C1—C2—H2A122.7C8—C13—H13A120.1
C2—C3—C4124.2 (3)C14—N4—C16123.0 (4)
C2—C3—N3118.6 (3)C14—N4—C15118.9 (3)
C4—C3—N3117.1 (2)C16—N4—C15118.0 (4)
C5—C4—C3119.9 (3)O4—C14—N4125.4 (4)
C5—C4—H4A120.0O4—C14—H14A117.3
C3—C4—H4A120.0N4—C14—H14A117.3
C4—C5—C6117.6 (3)N4—C15—H15A109.5
C4—C5—H5A121.2N4—C15—H15B109.5
C6—C5—H5A121.2H15A—C15—H15B109.5
N2—C6—C5130.4 (3)N4—C15—H15C109.5
N2—C6—C1108.9 (2)H15A—C15—H15C109.5
C5—C6—C1120.8 (2)H15B—C15—H15C109.5
N2—C7—N1112.6 (2)N4—C16—H16A109.5
N2—C7—C8122.2 (2)N4—C16—H16B109.5
N1—C7—C8125.2 (2)H16A—C16—H16B109.5
C13—C8—C9119.4 (2)N4—C16—H16C109.5
C13—C8—C7121.8 (2)H16A—C16—H16C109.5
C9—C8—C7118.8 (2)H16B—C16—H16C109.5
O3—C9—C10118.0 (3)
C7—N1—C1—C2−179.0 (3)C6—N2—C7—C8−179.2 (2)
C7—N1—C1—C60.6 (3)C1—N1—C7—N2−0.9 (3)
N1—C1—C2—C3178.8 (2)C1—N1—C7—C8179.1 (2)
C6—C1—C2—C3−0.8 (4)N2—C7—C8—C13−179.5 (2)
C1—C2—C3—C40.2 (4)N1—C7—C8—C130.4 (4)
C1—C2—C3—N3−180.0 (2)N2—C7—C8—C9−0.2 (4)
O2—N3—C3—C2−175.2 (3)N1—C7—C8—C9179.8 (2)
O1—N3—C3—C23.6 (4)C13—C8—C9—O3−178.9 (2)
O2—N3—C3—C44.6 (4)C7—C8—C9—O31.7 (4)
O1—N3—C3—C4−176.6 (2)C13—C8—C9—C101.7 (4)
C2—C3—C4—C50.5 (4)C7—C8—C9—C10−177.7 (2)
N3—C3—C4—C5−179.3 (2)O3—C9—C10—C11−179.4 (3)
C3—C4—C5—C6−0.7 (4)C8—C9—C10—C110.0 (4)
C7—N2—C6—C5178.3 (3)C9—C10—C11—C12−1.9 (4)
C7—N2—C6—C1−0.4 (3)C10—C11—C12—C132.1 (4)
C4—C5—C6—N2−178.5 (3)C10—C11—C12—Cl1−178.9 (2)
C4—C5—C6—C10.1 (4)C11—C12—C13—C8−0.4 (4)
N1—C1—C6—N2−0.1 (3)Cl1—C12—C13—C8−179.4 (2)
C2—C1—C6—N2179.5 (2)C9—C8—C13—C12−1.5 (4)
N1—C1—C6—C5−179.0 (2)C7—C8—C13—C12177.9 (2)
C2—C1—C6—C50.6 (4)C16—N4—C14—O4−176.2 (4)
C6—N2—C7—N10.8 (3)C15—N4—C14—O41.6 (6)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H1O3···N20.751.902.568 (4)149
N1—H1N1···O40.891.862.736 (4)167
C13—H13A···O40.932.583.472 (5)161

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG5046).

References

  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Eltayeb, N. E., Teoh, S. G., Fun, H.-K., Jebas, S. R. & Adnan, R. (2009). Acta Cryst. E65, o1374–o1375. [PMC free article] [PubMed]
  • Garuti, L., Roberti, M., Pizzirani, D., Pession, A., Leoncini, E., Cenci, V. & Hrelia, S. (2004). Farmaco, 59, 663–668. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]
  • Trivedi, R., De, S. K. & Gibbs, R. A. (2006). J. Mol. Catal. A, 245, 8–11.
  • White, A., Curtin, N. J., Eastman, B., Golding, B. T., Hostomsky, Z., Kyle, S., Li, J., Maegley, K., Skalitzky, D., Webber, S., Yu, X. & Griffin, R. J. (2004). Biorg Med. Chem. Lett.14, 2433–2437. [PubMed]
  • Yeap, C. S., Kargar, H., Kia, R., Jamshidvand, A. & Fun, H.-K. (2009). Acta Cryst. E65, o745–o746. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography