Literature DB >> 23723856

2-{[2-(Pyridin-4-yl)-1H-benzimidazol-1-yl]meth-yl}phenol.

Mohammed A S Omer1, Jia-Cheng Liu, Chao-Hu Xiao.   

Abstract

In the title compound, C19H15N3O, the benzimidazole ring system makes dihedral angles of 44.36 (7) and 75.67 (7)° with the pyridine and benzene rings, respectively. In the crystal, phenolic O-H⋯N hydrogen bonds to benzimidazole N-atom acceptors give rise to a chain extending along [011].

Entities:  

Year:  2013        PMID: 23723856      PMCID: PMC3648236          DOI: 10.1107/S1600536813009458

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


Related literature

For applications of benzimidazole derivatives as ligands, see: Janiak (2000 ▶); Kühler et al. (2002 ▶); Li et al. (2007 ▶); Carcanague et al. (2002 ▶); Yang et al. (2006 ▶). For the synthesis of the title compound, see: Fellah et al. (2010 ▶). For the structure of a similar compound, see: Kitazume & Ishikawa (1974 ▶).

Experimental

Crystal data

C19H15N3O M = 301.34 Monoclinic, a = 16.1886 (7) Å b = 8.4863 (4) Å c = 21.4316 (10) Å β = 93.756 (4)° V = 2938.0 (2) Å3 Z = 8 Mo Kα radiation μ = 0.09 mm−1 T = 291 K 0.36 × 0.28 × 0.25 mm

Data collection

Agilent SuperNova CCD diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012 ▶) T min = 0.982, T max = 1.000 6104 measured reflections 3010 independent reflections 2398 reflections with I > 2σ(I) R int = 0.026

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.119 S = 1.06 3010 reflections 209 parameters H-atom parameters constrained Δρmax = 0.14 e Å−3 Δρmin = −0.19 e Å−3 Data collection: CrysAlis PRO (Agilent, 2012 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▶); software used to prepare material for publication: OLEX2. Click here for additional data file. Crystal structure: contains datablock(s) globalk, I. DOI: 10.1107/S1600536813009458/zs2254sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813009458/zs2254Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813009458/zs2254Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H15N3OF(000) = 1264
Mr = 301.34Dx = 1.362 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.7107 Å
a = 16.1886 (7) ÅCell parameters from 2313 reflections
b = 8.4863 (4) Åθ = 3.1–28.4°
c = 21.4316 (10) ŵ = 0.09 mm1
β = 93.756 (4)°T = 291 K
V = 2938.0 (2) Å3Block, colourless
Z = 80.36 × 0.28 × 0.25 mm
Agilent SuperNova CCD diffractometer3010 independent reflections
Radiation source: SuperNova (Mo) X-ray Source2398 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.026
Detector resolution: 16.0733 pixels mm-1θmax = 26.4°, θmin = 3.1°
ω scansh = −19→20
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012)k = −10→8
Tmin = 0.982, Tmax = 1.000l = −26→12
6104 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)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0458P)2 + 1.9069P] where P = (Fo2 + 2Fc2)/3
3010 reflections(Δ/σ)max < 0.001
209 parametersΔρmax = 0.14 e Å3
0 restraintsΔρmin = −0.19 e Å3
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.
xyzUiso*/Ueq
O10.14368 (7)0.81061 (16)0.41079 (6)0.0423 (3)
H10.09990.85880.40550.063*
N10.38187 (8)0.62034 (16)0.40429 (6)0.0283 (3)
N20.49801 (8)0.48060 (17)0.39527 (7)0.0336 (4)
N30.32187 (10)0.05156 (18)0.48316 (8)0.0428 (4)
C10.43786 (10)0.7203 (2)0.37809 (8)0.0295 (4)
C20.43205 (11)0.8769 (2)0.35956 (9)0.0389 (4)
H20.38430.93580.36400.047*
C30.50055 (12)0.9406 (3)0.33434 (10)0.0478 (5)
H30.49921.04560.32190.057*
C40.57225 (12)0.8523 (3)0.32683 (10)0.0475 (5)
H40.61700.89930.30910.057*
C50.57749 (11)0.6972 (2)0.34522 (9)0.0417 (5)
H50.62480.63810.33980.050*
C60.50936 (10)0.6314 (2)0.37236 (8)0.0318 (4)
C70.42090 (9)0.47799 (19)0.41279 (8)0.0281 (4)
C80.38405 (10)0.33423 (19)0.43756 (7)0.0283 (4)
C90.30488 (10)0.2814 (2)0.41897 (8)0.0325 (4)
H90.27090.34000.39100.039*
C100.27757 (12)0.1415 (2)0.44250 (9)0.0381 (4)
H100.22470.10750.42920.046*
C110.39780 (12)0.1031 (2)0.50078 (9)0.0433 (5)
H110.42990.04250.52930.052*
C120.43145 (11)0.2401 (2)0.47940 (8)0.0378 (4)
H120.48510.26950.49270.045*
C130.29647 (9)0.6653 (2)0.41536 (8)0.0289 (4)
H13A0.29680.76500.43750.035*
H13B0.27250.58640.44150.035*
C140.24385 (10)0.68048 (19)0.35455 (8)0.0274 (4)
C150.16757 (10)0.75871 (19)0.35461 (8)0.0296 (4)
C160.12004 (11)0.7808 (2)0.29896 (9)0.0365 (4)
H160.07020.83530.29910.044*
C170.14634 (11)0.7224 (2)0.24338 (9)0.0413 (5)
H170.11440.73800.20620.050*
C180.21993 (12)0.6410 (3)0.24306 (9)0.0437 (5)
H180.23700.59900.20600.052*
C190.26815 (10)0.6220 (2)0.29809 (8)0.0355 (4)
H190.31830.56870.29730.043*
U11U22U33U12U13U23
O10.0284 (7)0.0537 (9)0.0450 (7)0.0191 (6)0.0052 (5)−0.0023 (6)
N10.0204 (6)0.0291 (8)0.0358 (8)0.0049 (5)0.0060 (6)0.0042 (6)
N20.0233 (7)0.0334 (8)0.0449 (9)0.0074 (6)0.0073 (6)0.0041 (7)
N30.0508 (10)0.0338 (9)0.0452 (9)0.0011 (8)0.0126 (8)0.0048 (7)
C10.0226 (8)0.0337 (9)0.0324 (8)0.0011 (7)0.0037 (7)0.0031 (7)
C20.0303 (9)0.0353 (10)0.0516 (11)0.0054 (8)0.0064 (8)0.0087 (9)
C30.0403 (11)0.0404 (11)0.0630 (13)−0.0016 (9)0.0064 (10)0.0189 (10)
C40.0314 (10)0.0546 (13)0.0571 (12)−0.0072 (9)0.0088 (9)0.0173 (10)
C50.0225 (8)0.0515 (12)0.0519 (11)0.0033 (8)0.0086 (8)0.0079 (10)
C60.0231 (8)0.0346 (10)0.0378 (9)0.0022 (7)0.0026 (7)0.0050 (8)
C70.0222 (8)0.0306 (9)0.0313 (8)0.0056 (7)0.0017 (6)0.0004 (7)
C80.0297 (8)0.0273 (9)0.0286 (8)0.0056 (7)0.0078 (7)−0.0009 (7)
C90.0300 (9)0.0347 (10)0.0330 (9)0.0033 (7)0.0026 (7)0.0020 (7)
C100.0384 (10)0.0356 (10)0.0411 (10)−0.0040 (8)0.0078 (8)−0.0014 (8)
C110.0453 (11)0.0409 (11)0.0438 (11)0.0093 (9)0.0028 (9)0.0131 (9)
C120.0332 (9)0.0403 (11)0.0394 (10)0.0055 (8)−0.0010 (8)0.0048 (8)
C130.0217 (8)0.0292 (9)0.0366 (9)0.0064 (7)0.0082 (7)0.0014 (7)
C140.0220 (7)0.0244 (8)0.0363 (9)0.0016 (6)0.0061 (7)0.0025 (7)
C150.0226 (8)0.0261 (9)0.0405 (9)0.0022 (7)0.0052 (7)0.0027 (7)
C160.0240 (8)0.0363 (10)0.0489 (11)0.0016 (7)0.0001 (8)0.0074 (8)
C170.0342 (10)0.0499 (12)0.0391 (10)−0.0072 (8)−0.0037 (8)0.0058 (9)
C180.0381 (10)0.0574 (13)0.0363 (10)−0.0058 (9)0.0077 (8)−0.0041 (9)
C190.0257 (8)0.0407 (11)0.0410 (10)0.0024 (8)0.0079 (7)−0.0019 (8)
O1—H10.8200C8—C121.393 (2)
O1—C151.362 (2)C9—H90.9300
N1—C11.387 (2)C9—C101.374 (2)
N1—C71.370 (2)C10—H100.9300
N1—C131.4684 (19)C11—H110.9300
N2—C61.387 (2)C11—C121.376 (3)
N2—C71.327 (2)C12—H120.9300
N3—C101.332 (2)C13—H13A0.9700
N3—C111.336 (3)C13—H13B0.9700
C1—C21.389 (2)C13—C141.515 (2)
C1—C61.394 (2)C14—C151.402 (2)
C2—H20.9300C14—C191.388 (2)
C2—C31.376 (3)C15—C161.389 (2)
C3—H30.9300C16—H160.9300
C3—C41.399 (3)C16—C171.383 (3)
C4—H40.9300C17—H170.9300
C4—C51.375 (3)C17—C181.378 (3)
C5—H50.9300C18—H180.9300
C5—C61.397 (2)C18—C191.380 (3)
C7—C81.472 (2)C19—H190.9300
C8—C91.391 (2)
C15—O1—H1109.5N3—C10—C9124.25 (18)
C1—N1—C13123.64 (13)N3—C10—H10117.9
C7—N1—C1106.57 (13)C9—C10—H10117.9
C7—N1—C13129.68 (14)N3—C11—H11118.0
C7—N2—C6105.34 (14)N3—C11—C12124.03 (17)
C10—N3—C11116.32 (16)C12—C11—H11118.0
N1—C1—C2131.86 (15)C8—C12—H12120.5
N1—C1—C6105.87 (14)C11—C12—C8119.07 (17)
C2—C1—C6122.27 (15)C11—C12—H12120.5
C1—C2—H2121.7N1—C13—H13A109.3
C3—C2—C1116.55 (17)N1—C13—H13B109.3
C3—C2—H2121.7N1—C13—C14111.43 (13)
C2—C3—H3119.0H13A—C13—H13B108.0
C2—C3—C4122.08 (18)C14—C13—H13A109.3
C4—C3—H3119.0C14—C13—H13B109.3
C3—C4—H4119.5C15—C14—C13119.01 (14)
C5—C4—C3121.03 (17)C19—C14—C13122.95 (14)
C5—C4—H4119.5C19—C14—C15118.03 (16)
C4—C5—H5121.1O1—C15—C14117.08 (15)
C4—C5—C6117.82 (17)O1—C15—C16122.82 (15)
C6—C5—H5121.1C16—C15—C14120.10 (16)
N2—C6—C1109.76 (14)C15—C16—H16119.8
N2—C6—C5130.01 (16)C17—C16—C15120.43 (16)
C1—C6—C5120.21 (16)C17—C16—H16119.8
N1—C7—C8125.77 (14)C16—C17—H17120.0
N2—C7—N1112.44 (15)C18—C17—C16119.96 (17)
N2—C7—C8121.79 (14)C18—C17—H17120.0
C9—C8—C7123.44 (15)C17—C18—H18120.2
C9—C8—C12117.26 (16)C17—C18—C19119.66 (18)
C12—C8—C7119.21 (15)C19—C18—H18120.2
C8—C9—H9120.5C14—C19—H19119.1
C10—C9—C8119.06 (16)C18—C19—C14121.77 (17)
C10—C9—H9120.5C18—C19—H19119.1
O1—C15—C16—C17−178.45 (17)C7—N1—C1—C6−0.32 (18)
N1—C1—C2—C3−179.45 (18)C7—N1—C13—C14−104.93 (19)
N1—C1—C6—N2−0.75 (19)C7—N2—C6—C11.54 (19)
N1—C1—C6—C5177.82 (16)C7—N2—C6—C5−176.85 (19)
N1—C7—C8—C944.3 (2)C7—C8—C9—C10176.76 (15)
N1—C7—C8—C12−139.15 (18)C7—C8—C12—C11−177.78 (16)
N1—C13—C14—C15−164.53 (14)C8—C9—C10—N30.7 (3)
N1—C13—C14—C1914.6 (2)C9—C8—C12—C11−1.0 (3)
N2—C7—C8—C9−134.83 (18)C10—N3—C11—C12−0.2 (3)
N2—C7—C8—C1241.7 (2)C11—N3—C10—C9−0.7 (3)
N3—C11—C12—C81.1 (3)C12—C8—C9—C100.2 (2)
C1—N1—C7—N21.36 (19)C13—N1—C1—C23.4 (3)
C1—N1—C7—C8−177.87 (15)C13—N1—C1—C6−176.74 (14)
C1—N1—C13—C1470.6 (2)C13—N1—C7—N2177.48 (15)
C1—C2—C3—C40.8 (3)C13—N1—C7—C8−1.7 (3)
C2—C1—C6—N2179.12 (17)C13—C14—C15—O1−2.9 (2)
C2—C1—C6—C5−2.3 (3)C13—C14—C15—C16176.89 (15)
C2—C3—C4—C5−0.8 (3)C13—C14—C19—C18−178.34 (16)
C3—C4—C5—C6−0.8 (3)C14—C15—C16—C171.8 (3)
C4—C5—C6—N2−179.47 (19)C15—C14—C19—C180.8 (3)
C4—C5—C6—C12.3 (3)C15—C16—C17—C180.3 (3)
C6—N2—C7—N1−1.79 (19)C16—C17—C18—C19−1.8 (3)
C6—N2—C7—C8177.48 (15)C17—C18—C19—C141.2 (3)
C6—C1—C2—C30.7 (3)C19—C14—C15—O1177.92 (16)
C7—N1—C1—C2179.83 (19)C19—C14—C15—C16−2.3 (2)
D—H···AD—HH···AD···AD—H···A
O1—H1···N2i0.821.952.7659 (18)177
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O1—H1⋯N2i 0.821.952.7659 (18)177

Symmetry code: (i) .

  3 in total

1.  A short history of SHELX.

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

2.  Novel structures derived from 2-[[(2-pyridyl)methyl]thio]-1H-benzimidazole as anti-Helicobacter pylori agents, Part 1.

Authors:  Thomas C Kühler; Marianne Swanson; Beritte Christenson; Ann-Charlotte Klintenberg; Bo Lamm; Jonas Fägerhag; Roberto Gatti; Maria Olwegård-Halvarsson; Vladimir Shcherbuchin; Thomas Elebring; Jan-Erik Sjöström
Journal:  J Med Chem       Date:  2002-09-12       Impact factor: 7.446

3.  Novel structures derived from 2-[[(2-pyridyl)methyl]thio]-1H-benzimidazole as anti-Helicobacter pylori agents, Part 2.

Authors:  Daniel Carcanague; Youe-Kong Shue; Mark A Wuonola; Maria Uria-Nickelsen; Camil Joubran; Joseph K Abedi; Jeanette Jones; Thomas C Kühler
Journal:  J Med Chem       Date:  2002-09-12       Impact factor: 7.446

  3 in total

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