Literature DB >> 21754411

1,3-Bis(prop-2-yn-yl)-1H-1,3-benzimid-azol-2(3H)-one.

Younes Ouzidan, Youssef Kandri Rodi, Jerry P Jasinski, Raymond J Butcher, James A Golen, Lahcen El Ammari.   

Abstract

In the title compound, C(13)H(10)N(2)O, the fused-ring system is essentially planar, the largest deviation from the mean plane being 0.015 (1) Å. The two propynyl groups are nearly perpendicular to the benzimidazole plane, making dihedral angles of 85 (3) and 80 (2) °, and point in opposite directions. There are two short inter-molecular C-H⋯O contacts to the carbonyl O atom, one involving the acetyl-enic H atom and the other a H atom of the methyl-ene group.

Entities:  

Year:  2011        PMID: 21754411      PMCID: PMC3089259          DOI: 10.1107/S1600536811012578

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


Related literature

For applications of benzimidazole compounds, see: Gravatt et al. (1994 ▶); Horton et al. (2003 ▶); Kim et al. (1996 ▶); Roth et al. (1997 ▶); Ouzidan et al. (2011 ▶).

Experimental

Crystal data

C13H10N2O M = 210.23 Monoclinic, a = 7.7398 (4) Å b = 17.1869 (9) Å c = 8.4856 (5) Å β = 101.459 (6)° V = 1106.28 (10) Å3 Z = 4 Mo Kα radiation μ = 0.08 mm−1 T = 170 K 0.42 × 0.41 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur E Gemini diffractometer Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009 ▶) T min = 0.966, T max = 0.984 5295 measured reflections 2631 independent reflections 2244 reflections with I > 2σ(I) R int = 0.014

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.104 S = 1.05 2631 reflections 146 parameters H-atom parameters constrained Δρmax = 0.19 e Å−3 Δρmin = −0.16 e Å−3 Data collection: CrysAlis PRO (Oxford Diffraction, 2009 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811012578/gk2361sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811012578/gk2361Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H10N2OF(000) = 440
Mr = 210.23Dx = 1.262 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3141 reflections
a = 7.7398 (4) Åθ = 3.4–32.2°
b = 17.1869 (9) ŵ = 0.08 mm1
c = 8.4856 (5) ÅT = 170 K
β = 101.459 (6)°Block, colorless
V = 1106.28 (10) Å30.42 × 0.41 × 0.20 mm
Z = 4
Oxford Diffraction Xcalibur E Gemini diffractometer2631 independent reflections
Radiation source: Enhance (Mo) X-ray Source2244 reflections with I > 2σ(I)
graphiteRint = 0.014
Detector resolution: 16.1500 pixels mm-1θmax = 27.9°, θmin = 3.4°
ω scansh = −10→10
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −20→22
Tmin = 0.966, Tmax = 0.984l = −11→4
5295 measured reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.104w = 1/[σ2(Fo2) + (0.0447P)2 + 0.2172P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2631 reflectionsΔρmax = 0.19 e Å3
146 parametersΔρmin = −0.16 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.042 (4)
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
O10.19931 (12)0.56190 (5)0.15005 (11)0.0468 (2)
N10.13961 (12)0.46462 (5)0.32281 (11)0.0338 (2)
N20.29126 (12)0.56670 (5)0.42832 (12)0.0356 (2)
C10.20862 (14)0.53446 (6)0.28398 (14)0.0346 (3)
C20.18290 (13)0.45232 (6)0.48810 (13)0.0319 (2)
C30.14722 (15)0.39128 (7)0.58201 (15)0.0400 (3)
H3A0.08260.34700.53620.048*
C40.21003 (18)0.39733 (9)0.74692 (16)0.0493 (3)
H4A0.18710.35650.81530.059*
C50.30518 (18)0.46160 (9)0.81362 (16)0.0524 (4)
H5A0.34630.46380.92670.063*
C60.34172 (16)0.52287 (8)0.71876 (15)0.0447 (3)
H6A0.40730.56690.76460.054*
C70.27878 (14)0.51721 (6)0.55512 (14)0.0337 (3)
C80.06303 (16)0.40760 (7)0.20295 (15)0.0398 (3)
H8A0.01590.43430.10000.048*
H8B−0.03620.38100.23830.048*
C90.19408 (17)0.34996 (7)0.17828 (16)0.0438 (3)
C100.3035 (2)0.30587 (10)0.1615 (2)0.0748 (5)
H100.39270.26990.14790.090*
C110.39412 (16)0.63759 (7)0.43751 (18)0.0443 (3)
H11A0.42080.64840.33020.053*
H11B0.50760.62930.51310.053*
C120.30770 (17)0.70582 (7)0.48968 (16)0.0454 (3)
C130.2472 (2)0.76260 (9)0.5312 (2)0.0678 (5)
H130.19800.80880.56490.081*
U11U22U33U12U13U23
O10.0561 (5)0.0414 (5)0.0426 (5)0.0004 (4)0.0090 (4)0.0060 (4)
N10.0375 (5)0.0275 (4)0.0351 (5)0.0017 (4)0.0043 (4)−0.0037 (4)
N20.0349 (5)0.0290 (5)0.0430 (5)−0.0006 (4)0.0080 (4)−0.0051 (4)
C10.0339 (5)0.0297 (5)0.0405 (6)0.0054 (4)0.0079 (5)−0.0013 (4)
C20.0276 (5)0.0317 (5)0.0363 (6)0.0059 (4)0.0060 (4)−0.0026 (4)
C30.0359 (6)0.0374 (6)0.0481 (7)0.0031 (5)0.0118 (5)0.0028 (5)
C40.0470 (7)0.0577 (8)0.0457 (7)0.0070 (6)0.0150 (6)0.0114 (6)
C50.0489 (7)0.0727 (9)0.0351 (6)0.0086 (7)0.0068 (5)0.0004 (6)
C60.0367 (6)0.0538 (7)0.0419 (7)0.0025 (5)0.0034 (5)−0.0114 (6)
C70.0278 (5)0.0348 (5)0.0390 (6)0.0055 (4)0.0077 (4)−0.0044 (4)
C80.0396 (6)0.0349 (6)0.0413 (6)−0.0008 (5)−0.0003 (5)−0.0066 (5)
C90.0525 (7)0.0328 (6)0.0440 (7)−0.0025 (5)0.0043 (6)−0.0082 (5)
C100.0733 (11)0.0515 (9)0.0976 (14)0.0171 (8)0.0124 (10)−0.0250 (9)
C110.0358 (6)0.0355 (6)0.0628 (8)−0.0057 (5)0.0128 (6)−0.0079 (6)
C120.0447 (7)0.0340 (6)0.0536 (8)−0.0026 (5)0.0002 (6)−0.0054 (5)
C130.0771 (11)0.0436 (8)0.0749 (11)0.0136 (7)−0.0038 (9)−0.0170 (7)
O1—C11.2194 (14)C5—H5A0.9500
N1—C11.3800 (14)C6—C71.3806 (17)
N1—C21.3919 (14)C6—H6A0.9500
N1—C81.4515 (14)C8—C91.4622 (17)
N2—C11.3802 (15)C8—H8A0.9900
N2—C71.3899 (15)C8—H8B0.9900
N2—C111.4491 (14)C9—C101.166 (2)
C2—C31.3782 (16)C10—H100.9500
C2—C71.3965 (15)C11—C121.4615 (17)
C3—C41.3911 (19)C11—H11A0.9900
C3—H3A0.9500C11—H11B0.9900
C4—C51.385 (2)C12—C131.1665 (19)
C4—H4A0.9500C13—H130.9500
C5—C61.388 (2)
C1—N1—C2110.22 (9)C7—C6—H6A121.4
C1—N1—C8122.92 (10)C5—C6—H6A121.4
C2—N1—C8125.91 (9)C6—C7—N2132.11 (11)
C1—N2—C7110.49 (9)C6—C7—C2121.24 (11)
C1—N2—C11122.56 (10)N2—C7—C2106.65 (10)
C7—N2—C11126.50 (10)N1—C8—C9111.07 (10)
O1—C1—N1127.23 (11)N1—C8—H8A109.4
O1—C1—N2127.08 (11)C9—C8—H8A109.4
N1—C1—N2105.69 (10)N1—C8—H8B109.4
C3—C2—N1131.49 (11)C9—C8—H8B109.4
C3—C2—C7121.59 (11)H8A—C8—H8B108.0
N1—C2—C7106.92 (9)C10—C9—C8177.43 (15)
C2—C3—C4117.04 (12)C9—C10—H10180.0
C2—C3—H3A121.5N2—C11—C12114.29 (10)
C4—C3—H3A121.5N2—C11—H11A108.7
C5—C4—C3121.47 (12)C12—C11—H11A108.7
C5—C4—H4A119.3N2—C11—H11B108.7
C3—C4—H4A119.3C12—C11—H11B108.7
C4—C5—C6121.41 (13)H11A—C11—H11B107.6
C4—C5—H5A119.3C13—C12—C11176.21 (15)
C6—C5—H5A119.3C12—C13—H13180.0
C7—C6—C5117.25 (12)
C2—N1—C1—O1177.95 (11)C4—C5—C6—C70.21 (19)
C8—N1—C1—O18.50 (18)C5—C6—C7—N2−179.89 (11)
C2—N1—C1—N2−1.76 (11)C5—C6—C7—C2−0.23 (17)
C8—N1—C1—N2−171.22 (9)C1—N2—C7—C6178.83 (11)
C7—N2—C1—O1−178.10 (11)C11—N2—C7—C66.44 (19)
C11—N2—C1—O1−5.36 (18)C1—N2—C7—C2−0.87 (12)
C7—N2—C1—N11.61 (12)C11—N2—C7—C2−173.26 (10)
C11—N2—C1—N1174.35 (9)C3—C2—C7—C6−0.08 (16)
C1—N1—C2—C3−178.62 (11)N1—C2—C7—C6−179.97 (10)
C8—N1—C2—C3−9.55 (18)C3—C2—C7—N2179.66 (10)
C1—N1—C2—C71.26 (11)N1—C2—C7—N2−0.23 (11)
C8—N1—C2—C7170.33 (10)C1—N1—C8—C993.46 (13)
N1—C2—C3—C4−179.74 (11)C2—N1—C8—C9−74.31 (14)
C7—C2—C3—C40.40 (16)C1—N2—C11—C12105.88 (13)
C2—C3—C4—C5−0.42 (18)C7—N2—C11—C12−82.58 (15)
C3—C4—C5—C60.1 (2)
D—H···AD—HH···AD···AD—H···A
C8—H8A···O1i0.992.423.3096 (15)149
C13—H13···O1ii0.952.343.2252 (17)156
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C8—H8A⋯O1i0.992.423.3096 (15)149
C13—H13⋯O1ii0.952.343.2252 (17)156

Symmetry codes: (i) ; (ii) .

  7 in total

Review 1.  The combinatorial synthesis of bicyclic privileged structures or privileged substructures.

Authors:  Douglas A Horton; Gregory T Bourne; Mark L Smythe
Journal:  Chem Rev       Date:  2003-03       Impact factor: 60.622

2.  A short history of SHELX.

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

3.  1,3-Bis[2-(2-oxo-1,3-oxazolidin-3-yl)eth-yl]-1H-benzimidazol-2(3H)-one.

Authors:  Younes Ouzidan; Youssef Kandri Rodi; Frank R Fronczek; Ramaiyer Venkatraman; Lahcen El Ammari; El Mokhtar Essassi
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-01-12

4.  Synthesis and biological activity of novel nonnucleoside inhibitors of HIV-1 reverse transcriptase. 2-Aryl-substituted benzimidazoles.

Authors:  T Roth; M L Morningstar; P L Boyer; S H Hughes; R W Buckheit; C J Michejda
Journal:  J Med Chem       Date:  1997-12-19       Impact factor: 7.446

5.  1-Nonyl-1H-benzimidazol-2(3H)-one.

Authors:  Younes Ouzidan; Youssef Kandri Rodi; Raymond J Butcher; El Mokhtar Essassi; Lahcen El Ammari
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-01-08

6.  Substituted 2,5'-Bi-1H-benzimidazoles: topoisomerase I inhibition and cytotoxicity.

Authors:  J S Kim; B Gatto; C Yu; A Liu; L F Liu; E J LaVoie
Journal:  J Med Chem       Date:  1996-02-16       Impact factor: 7.446

7.  DNA-directed alkylating agents. 6. Synthesis and antitumor activity of DNA minor groove-targeted aniline mustard analogues of pibenzimol (Hoechst 33258)

Authors:  G L Gravatt; B C Baguley; W R Wilson; W A Denny
Journal:  J Med Chem       Date:  1994-12-09       Impact factor: 7.446

  7 in total
  5 in total

1.  1,3-Bis(2-methyl-prop-2-eno-yl)-1H-benz-imidazol-2(3H)-one.

Authors:  N Haridharan; V Ramkumar
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-05-04

2.  5-Nitro-1-(prop-2-yn-1-yl)-2,3-dihydro-1H-1,3-benzodiazol-2-one.

Authors:  Younes Ouzidan; Youssef Kandri Rodi; Hafid Zouihri; El Mokhtar Essassi; Seik Weng Ng
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-03-31

3.  Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of 1-methyl-3-(prop-2-yn-1-yl)-2,3-di-hydro-1H-1,3-benzo-diazol-2-one.

Authors:  Asmaa Saber; Mohamed Srhir; Tuncer Hökelek; Joel T Mague; Noureddine Hamou Ahabchane; Nada Kheira Sebbar; El Mokhtar Essassi
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2019-11-29

4.  1-(Prop-2-yn-yl)-1H-benzimidazol-2(3H)-one.

Authors:  Younès Ouzidan; Youssef Kandri Rodi; Fouad Ouazzani Chahdi; El Mokhtar Essassi; Mohamed Saadi; Lahcen El Ammari
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-12-22

5.  5-Nitro-1,3-bis-(prop-2-yn-yl)-1H-1,3-benzimidazol-2(3H)-one.

Authors:  Youssef Kandri Rodi; Khalid Misbahi; Abdelkrim El-Ghayoury; Leokadiya Zorina; El Mokhtar Essassi; Lahcen El Ammari
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-06-26
  5 in total

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