Literature DB >> 24764897

2-(1H-Benzimidazol-2-yl)phenol.

S M Prakash1, A Thiruvalluvar2, S Rosepriya2, N Srinivasan3.   

Abstract

The title mol-ecule, C13H10N2O, is essentially planar, the maximum deviation from the plane of the non-H atoms being 0.016 (2) Å. The imidazole ring makes a dihedral angle of 0.37 (13)° with the attached benzene ring. An intra-molecular O-H⋯N hydrogen bond generates an S(6) ring motif. In the crystal, mol-ecules are linked through N-H⋯O hydrogen bonds, forming chains propagating in [001]. The crystal packing also features four π-π stacking inter-actions involving the imidazole ring, fused benzene ring and attached benzene ring system [centroid-centroid distances = 3.6106 (17), 3.6108 (17), 3.6666 (17) and 3.6668 (17) Å].

Entities:  

Year:  2014        PMID: 24764897      PMCID: PMC3998336          DOI: 10.1107/S1600536814001366

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For applications and general background to substituted benzimidazole derivatives, see: Nakamura et al. (2004 ▶); Su Han & Kim (2001 ▶); Roman et al. 2007 ▶; Congiu et al. 2008 ▶. For related crystal structures, see: Han (2010 ▶); Zhan et al. (2007 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). Note added in proof: a low temperature determination of the same structure has been reported [Konoshima, H., Nagao, S., Kiyota, I., Amimoto, K., Yamamoto, N., Sekine, M., Nakata, M., Furukawa, K. & Sekiya, H. (2012). Phys. Chem. Chem. Phys. 14, 16448–16457].

Experimental

Crystal data

C13H10N2O M = 210.23 Monoclinic, a = 16.864 (4) Å b = 4.7431 (8) Å c = 12.952 (2) Å β = 102.34 (2)° V = 1012.1 (3) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 293 K 0.30 × 0.30 × 0.25 mm

Data collection

Agilent Xcalibur Eos Gemini diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013 ▶) T min = 0.829, T max = 1.000 4073 measured reflections 2338 independent reflections 1184 reflections with I > 2σ(I) R int = 0.037

Refinement

R[F 2 > 2σ(F 2)] = 0.067 wR(F 2) = 0.131 S = 1.03 2338 reflections 150 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.18 e Å−3 Δρmin = −0.17 e Å−3 Data collection: CrysAlis PRO (Agilent, 2013 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR2011 (Burla et al., 2012 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶) and PLATON (Spek, 2009 ▶); software used to prepare material for publication: SHELXL2013 and PLATON. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814001366/hg5377sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814001366/hg5377Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814001366/hg5377Isup3.cdx Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814001366/hg5377Isup4.cml CCDC reference: Additional supporting information: crystallographic information; 3D view; checkCIF report
C13H10N2OF(000) = 440
Mr = 210.23Dx = 1.380 Mg m3
Monoclinic, P21/cMelting point: 386 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 16.864 (4) ÅCell parameters from 612 reflections
b = 4.7431 (8) Åθ = 4.8–23.8°
c = 12.952 (2) ŵ = 0.09 mm1
β = 102.34 (2)°T = 293 K
V = 1012.1 (3) Å3Block, colourless
Z = 40.30 × 0.30 × 0.25 mm
Agilent Xcalibur Eos Gemini diffractometer2338 independent reflections
Radiation source: Enhance (Mo) X-ray Source1184 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.037
Detector resolution: 16.3291 pixels mm-1θmax = 29.2°, θmin = 3.2°
ω scansh = −23→10
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)k = −3→6
Tmin = 0.829, Tmax = 1.000l = −15→17
4073 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.067Hydrogen site location: mixed
wR(F2) = 0.131H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0339P)2] where P = (Fo2 + 2Fc2)/3
2338 reflections(Δ/σ)max < 0.001
150 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = −0.17 e Å3
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
xyzUiso*/Ueq
O260.20929 (12)0.7018 (4)0.54707 (12)0.0640 (8)
N10.25872 (13)0.5474 (4)0.25071 (16)0.0459 (8)
N30.28328 (12)0.4482 (4)0.42170 (14)0.0448 (7)
C20.24046 (15)0.6055 (5)0.34606 (18)0.0420 (8)
C40.38923 (16)0.0807 (5)0.4149 (2)0.0561 (10)
C50.42862 (16)−0.0543 (5)0.3475 (2)0.0603 (11)
C60.41275 (17)0.0093 (6)0.2410 (2)0.0621 (11)
C70.35740 (17)0.2089 (5)0.1985 (2)0.0554 (10)
C80.31718 (15)0.3444 (5)0.26679 (19)0.0438 (9)
C90.33257 (15)0.2825 (5)0.37415 (18)0.0434 (9)
C210.18120 (15)0.8077 (4)0.36215 (19)0.0424 (8)
C220.13653 (15)0.9671 (5)0.28084 (19)0.0512 (9)
C230.08097 (17)1.1585 (5)0.2980 (2)0.0614 (11)
C240.06758 (18)1.1945 (5)0.3980 (3)0.0640 (11)
C250.11064 (18)1.0406 (5)0.4800 (2)0.0617 (11)
C260.16741 (16)0.8493 (5)0.4634 (2)0.0485 (9)
H10.2390 (15)0.643 (5)0.190 (2)0.068 (9)*
H40.400390.037370.486600.0673*
H50.46693−0.191790.373800.0722*
H60.44063−0.086870.197140.0748*
H70.347080.252160.126840.0666*
H220.144740.942540.212660.0613*
H230.052061.265040.242220.0737*
H240.029091.323930.409880.0768*
H250.101381.065680.547620.0741*
H260.238990.587380.526590.0960*
U11U22U33U12U13U23
O260.0835 (16)0.0762 (13)0.0334 (11)0.0152 (10)0.0147 (10)−0.0050 (9)
N10.0540 (15)0.0546 (13)0.0295 (12)−0.0037 (11)0.0100 (10)0.0028 (11)
N30.0511 (14)0.0521 (12)0.0304 (11)0.0005 (11)0.0070 (10)−0.0010 (10)
C20.0486 (16)0.0465 (14)0.0314 (14)−0.0094 (12)0.0095 (12)−0.0032 (12)
C40.0567 (19)0.0620 (17)0.0475 (17)0.0017 (14)0.0068 (14)−0.0017 (14)
C50.0532 (18)0.0608 (17)0.067 (2)0.0028 (14)0.0129 (15)−0.0089 (16)
C60.062 (2)0.0648 (17)0.067 (2)−0.0066 (16)0.0304 (16)−0.0132 (16)
C70.067 (2)0.0610 (17)0.0436 (17)−0.0111 (16)0.0241 (15)−0.0073 (14)
C80.0454 (16)0.0462 (14)0.0410 (15)−0.0080 (13)0.0122 (12)−0.0022 (12)
C90.0443 (16)0.0488 (14)0.0370 (15)−0.0055 (13)0.0087 (12)−0.0015 (12)
C210.0454 (16)0.0424 (13)0.0391 (15)−0.0070 (12)0.0087 (12)−0.0033 (12)
C220.0537 (17)0.0547 (15)0.0440 (17)−0.0030 (14)0.0081 (13)0.0020 (13)
C230.0558 (19)0.0583 (17)0.067 (2)0.0025 (15)0.0062 (16)0.0056 (15)
C240.0547 (19)0.0539 (16)0.085 (2)0.0048 (14)0.0187 (17)−0.0042 (17)
C250.067 (2)0.0645 (18)0.059 (2)0.0004 (16)0.0255 (16)−0.0112 (15)
C260.0534 (18)0.0508 (15)0.0410 (16)−0.0033 (13)0.0092 (13)−0.0051 (13)
O26—C261.355 (3)C21—C261.394 (4)
O26—H260.8200C21—C221.382 (3)
N1—C21.363 (3)C22—C231.357 (4)
N1—C81.362 (3)C23—C241.372 (5)
N3—C91.381 (3)C24—C251.363 (4)
N3—C21.317 (3)C25—C261.369 (4)
N1—H10.91 (2)C4—H40.9300
C2—C211.432 (3)C5—H50.9300
C4—C91.376 (4)C6—H60.9300
C4—C51.364 (4)C7—H70.9300
C5—C61.381 (4)C22—H220.9300
C6—C71.361 (4)C23—H230.9300
C7—C81.383 (4)C24—H240.9300
C8—C91.390 (3)C25—H250.9300
C26—O26—H26109.00C22—C23—C24119.8 (2)
C2—N1—C8107.5 (2)C23—C24—C25120.1 (3)
C2—N3—C9106.09 (19)C24—C25—C26120.4 (3)
C8—N1—H1127.3 (16)O26—C26—C21121.1 (2)
C2—N1—H1124.9 (16)O26—C26—C25118.6 (2)
N1—C2—N3111.4 (2)C21—C26—C25120.3 (2)
N1—C2—C21124.5 (2)C5—C4—H4121.00
N3—C2—C21124.0 (2)C9—C4—H4121.00
C5—C4—C9118.3 (2)C4—C5—H5119.00
C4—C5—C6121.3 (2)C6—C5—H5119.00
C5—C6—C7121.7 (3)C5—C6—H6119.00
C6—C7—C8116.9 (2)C7—C6—H6119.00
N1—C8—C7132.0 (2)C6—C7—H7122.00
C7—C8—C9122.0 (2)C8—C7—H7122.00
N1—C8—C9106.1 (2)C21—C22—H22119.00
C4—C9—C8119.8 (2)C23—C22—H22119.00
N3—C9—C8108.9 (2)C22—C23—H23120.00
N3—C9—C4131.3 (2)C24—C23—H23120.00
C2—C21—C22122.6 (2)C23—C24—H24120.00
C2—C21—C26119.6 (2)C25—C24—H24120.00
C22—C21—C26117.8 (2)C24—C25—H25120.00
C21—C22—C23121.6 (2)C26—C25—H25120.00
C8—N1—C2—N3−0.8 (3)C6—C7—C8—N1−179.1 (3)
C8—N1—C2—C21−179.7 (2)C6—C7—C8—C90.5 (4)
C2—N1—C8—C7180.0 (3)N1—C8—C9—N30.1 (3)
C2—N1—C8—C90.4 (3)N1—C8—C9—C4179.5 (2)
C9—N3—C2—N10.8 (3)C7—C8—C9—N3−179.6 (2)
C9—N3—C2—C21179.7 (2)C7—C8—C9—C4−0.1 (4)
C2—N3—C9—C4−179.9 (3)C2—C21—C22—C23−179.7 (2)
C2—N3—C9—C8−0.6 (3)C26—C21—C22—C230.1 (4)
N1—C2—C21—C22−0.4 (4)C2—C21—C26—O260.1 (4)
N1—C2—C21—C26179.9 (2)C2—C21—C26—C25−179.6 (2)
N3—C2—C21—C22−179.2 (2)C22—C21—C26—O26−179.6 (2)
N3—C2—C21—C261.1 (4)C22—C21—C26—C250.7 (4)
C9—C4—C5—C60.3 (4)C21—C22—C23—C24−0.7 (4)
C5—C4—C9—N3179.0 (3)C22—C23—C24—C250.7 (4)
C5—C4—C9—C8−0.3 (4)C23—C24—C25—C260.0 (4)
C4—C5—C6—C70.1 (4)C24—C25—C26—O26179.6 (2)
C5—C6—C7—C8−0.4 (4)C24—C25—C26—C21−0.7 (4)
D—H···AD—HH···AD···AD—H···A
N1—H1···O26i0.91 (2)1.96 (3)2.851 (3)169 (2)
O26—H26···N30.821.812.551 (3)150
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H1⋯O26i 0.91 (2)1.96 (3)2.851 (3)169 (2)
O26—H26⋯N30.821.812.551 (3)150

Symmetry code: (i) .

  7 in total

1.  Effect of zinc ion on the inhibition of carboxypeptidase A by imidazole-bearing substrate analogues.

Authors:  M S Han; D H Kim
Journal:  Bioorg Med Chem Lett       Date:  2001-06-04       Impact factor: 2.823

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Heme oxygenase inhibition by 2-oxy-substituted 1-(1H-imidazol-1-yl)-4-phenylbutanes: effect of halogen substitution in the phenyl ring.

Authors:  Gheorghe Roman; John G Riley; Jason Z Vlahakis; Robert T Kinobe; James F Brien; Kanji Nakatsu; Walter A Szarek
Journal:  Bioorg Med Chem       Date:  2007-02-22       Impact factor: 3.641

4.  Design, synthesis, and in vitro antitumor activity of new 1,4-diarylimidazole-2-ones and their 2-thione analogues.

Authors:  Cenzo Congiu; Maria Teresa Cocco; Valentina Onnis
Journal:  Bioorg Med Chem Lett       Date:  2007-12-15       Impact factor: 2.823

5.  Imidazole derivatives as new potent and selective 20-HETE synthase inhibitors.

Authors:  Toshio Nakamura; Hiroyuki Kakinuma; Hiroki Umemiya; Hideaki Amada; Noriyuki Miyata; Kazuo Taniguchi; Kagumi Bando; Masakazu Sato
Journal:  Bioorg Med Chem Lett       Date:  2004-01-19       Impact factor: 2.823

6.  2-(1H-Benzimidazol-2-yl)-4,6-dichloro-phenol.

Authors:  Li-Lu Han
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-07-17

7.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  7 in total

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