Literature DB >> 21582406

4-[1-(4-Cyano-benz-yl)-1H-benzimidazol-2-yl]benzonitrile.

Reza Kia, Hoong-Kun Fun, Hadi Kargar.   

Abstract

In the title compound, C(22)H(14)N(4), a new substituted benzimidazole, three inter-molecular C-H⋯N inter-actions link neighbouring mol-ecules into different dimers with R(2) (2)(12), R(2) (2)(8) and R(2) (2)(24) ring motifs. A fourth C-H⋯N inter-action links neighbouring mol-ecules along the c axis. There is also a short inter-molecular contact between the azomethine (C=N) segment of the benzimidazole ring and one of the C atoms of a neighbouring benzene ring [N⋯C = 3.191 (5), C⋯C = 3.364 (6) Å], which links the mol-ecules along the a axis. The two cyano-benzene rings are almost perpendicular to each other, with an inter-planar angle of 87.70 (7)°. The dihedral angles between the mean planes of the benzimidazole ring and the two outer benzene rings are 36.27 (16) and 86.70 (16)°. In the crystal structure, mol-ecules are stacked down the a axis with centroid-centroid distances of 3.906 (2)-3.912 (2) Å and inter-planar distances of 3.5040 (17) and 3.6235 (17) Å.

Entities:  

Year:  2009        PMID: 21582406      PMCID: PMC2969064          DOI: 10.1107/S1600536809006989

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


Related literature

For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For benzimidazole chemistry, reaction mechanisms and their bioactivity, see, for example: Latif et al. (1983 ▶); Craigo et al. (1999 ▶); Gudmundsson et al. (2000 ▶); Trivedi et al. (2006); Kim et al. (1996 ▶); Ramla et al. (2006 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C22H14N4 M = 334.37 Monoclinic, a = 5.0553 (4) Å b = 17.3437 (10) Å c = 19.6339 (14) Å β = 97.653 (5)° V = 1706.1 (2) Å3 Z = 4 Mo Kα radiation μ = 0.08 mm−1 T = 100 K 0.45 × 0.09 × 0.04 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T min = 0.965, T max = 0.997 15641 measured reflections 2906 independent reflections 1490 reflections with I > 2σ(I) R int = 0.153

Refinement

R[F 2 > 2σ(F 2)] = 0.079 wR(F 2) = 0.169 S = 1.07 2906 reflections 236 parameters H-atom parameters constrained Δρmax = 0.26 e Å−3 Δρmin = −0.35 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809006989/zl2173sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809006989/zl2173Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C22H14N4F(000) = 696
Mr = 334.37Dx = 1.302 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3931 reflections
a = 5.0553 (4) Åθ = 2.4–30.2°
b = 17.3437 (10) ŵ = 0.08 mm1
c = 19.6339 (14) ÅT = 100 K
β = 97.653 (5)°Needle, colourless
V = 1706.1 (2) Å30.45 × 0.09 × 0.04 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer2906 independent reflections
Radiation source: fine-focus sealed tube1490 reflections with I > 2σ(I)
graphiteRint = 0.153
φ and ω scansθmax = 25.0°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −6→6
Tmin = 0.965, Tmax = 0.997k = −20→20
15641 measured reflectionsl = −23→22
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.079H-atom parameters constrained
wR(F2) = 0.169w = 1/[σ2(Fo2) + (0.0473P)2 + 1.9898P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
2906 reflectionsΔρmax = 0.26 e Å3
236 parametersΔρmin = −0.35 e Å3
0 restraintsExtinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0124 (18)
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems 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.
xyzUiso*/Ueq
N10.7041 (7)0.41520 (18)0.10705 (18)0.0222 (9)
N20.8001 (6)0.29462 (17)0.14467 (17)0.0196 (9)
N31.5730 (8)0.3343 (2)−0.1704 (2)0.0366 (11)
N40.1768 (8)−0.0990 (2)0.05749 (19)0.0328 (10)
C10.5702 (8)0.3997 (2)0.1633 (2)0.0205 (10)
C20.3933 (8)0.4456 (2)0.1943 (2)0.0250 (11)
H2A0.35100.49530.17870.030*
C30.2841 (8)0.4148 (2)0.2487 (2)0.0271 (11)
H3A0.16390.44410.26970.033*
C40.3485 (8)0.3408 (2)0.2733 (2)0.0272 (11)
H4A0.27190.32230.31050.033*
C50.5240 (8)0.2944 (2)0.2434 (2)0.0240 (11)
H5A0.56810.24510.25970.029*
C60.6310 (8)0.3255 (2)0.1876 (2)0.0197 (10)
C70.8349 (8)0.3516 (2)0.0971 (2)0.0196 (10)
C80.9937 (8)0.3425 (2)0.0400 (2)0.0183 (10)
C91.0085 (8)0.2747 (2)0.0032 (2)0.0206 (11)
H9A0.91930.23100.01530.025*
C101.1554 (8)0.2718 (2)−0.0515 (2)0.0248 (11)
H10A1.16560.2262−0.07580.030*
C111.2870 (8)0.3372 (2)−0.0697 (2)0.0207 (11)
C121.2703 (8)0.4059 (2)−0.0344 (2)0.0228 (11)
H12A1.35610.4499−0.04730.027*
C131.1248 (8)0.4079 (2)0.0200 (2)0.0229 (11)
H13A1.11350.45380.04390.027*
C140.9363 (8)0.2212 (2)0.1570 (2)0.0221 (11)
H14A0.99870.21670.20570.026*
H14B1.09180.22090.13290.026*
C150.7667 (8)0.1513 (2)0.1346 (2)0.0193 (10)
C160.8439 (8)0.0795 (2)0.1615 (2)0.0232 (11)
H16A0.99620.07510.19350.028*
C170.6958 (8)0.0145 (2)0.1410 (2)0.0256 (11)
H17A0.7492−0.03360.15890.031*
C180.4669 (8)0.0212 (2)0.0936 (2)0.0217 (11)
C190.3883 (8)0.0931 (2)0.0667 (2)0.0228 (11)
H19A0.23490.09780.03510.027*
C200.5388 (8)0.1572 (2)0.0871 (2)0.0208 (10)
H20A0.48690.20520.06870.025*
C211.4437 (9)0.3350 (2)−0.1261 (3)0.0281 (12)
C220.3071 (9)−0.0458 (2)0.0734 (2)0.0256 (11)
U11U22U33U12U13U23
N10.028 (2)0.016 (2)0.023 (2)0.0017 (16)0.0025 (19)−0.0006 (16)
N20.026 (2)0.0127 (19)0.019 (2)0.0003 (15)0.0024 (18)−0.0026 (16)
N30.043 (3)0.031 (2)0.036 (3)−0.0030 (19)0.006 (2)−0.001 (2)
N40.045 (3)0.027 (2)0.027 (2)−0.006 (2)0.006 (2)−0.0006 (18)
C10.026 (2)0.016 (3)0.019 (3)−0.0022 (19)0.003 (2)−0.003 (2)
C20.029 (3)0.015 (2)0.030 (3)0.003 (2)0.000 (2)−0.006 (2)
C30.025 (2)0.031 (3)0.027 (3)−0.004 (2)0.007 (2)−0.006 (2)
C40.032 (3)0.026 (3)0.026 (3)−0.008 (2)0.008 (2)−0.006 (2)
C50.028 (3)0.019 (2)0.024 (3)−0.003 (2)−0.002 (2)−0.003 (2)
C60.024 (2)0.016 (2)0.018 (3)−0.0035 (19)0.001 (2)−0.005 (2)
C70.021 (2)0.017 (2)0.019 (3)−0.0054 (19)−0.005 (2)0.000 (2)
C80.021 (2)0.015 (2)0.019 (3)0.0019 (18)0.001 (2)0.003 (2)
C90.023 (2)0.016 (3)0.023 (3)−0.0008 (18)0.003 (2)0.004 (2)
C100.032 (3)0.022 (3)0.019 (3)0.002 (2)−0.001 (2)−0.001 (2)
C110.022 (2)0.021 (3)0.020 (3)0.0000 (19)0.004 (2)0.005 (2)
C120.031 (3)0.017 (3)0.021 (3)−0.0037 (19)0.004 (2)−0.002 (2)
C130.031 (3)0.015 (2)0.022 (3)0.002 (2)0.002 (2)−0.002 (2)
C140.023 (2)0.021 (2)0.023 (3)0.0009 (19)0.003 (2)0.0011 (19)
C150.023 (3)0.016 (2)0.019 (3)0.0013 (18)0.005 (2)−0.0030 (19)
C160.026 (2)0.020 (2)0.024 (3)−0.001 (2)0.004 (2)0.001 (2)
C170.026 (3)0.019 (2)0.032 (3)0.003 (2)0.004 (3)0.001 (2)
C180.026 (3)0.017 (2)0.024 (3)−0.0035 (19)0.010 (2)−0.004 (2)
C190.021 (2)0.024 (3)0.022 (3)0.000 (2)0.001 (2)0.001 (2)
C200.027 (3)0.015 (2)0.021 (3)0.0006 (19)0.004 (2)−0.0002 (19)
C210.035 (3)0.019 (3)0.030 (3)−0.003 (2)0.003 (3)0.000 (2)
C220.033 (3)0.023 (3)0.022 (3)−0.001 (2)0.007 (2)0.002 (2)
N1—C71.314 (5)C10—C111.385 (5)
N1—C11.397 (5)C10—H10A0.9300
N2—C61.385 (5)C11—C121.387 (5)
N2—C71.387 (5)C11—C211.446 (6)
N2—C141.453 (5)C12—C131.376 (5)
N3—C211.155 (5)C12—H12A0.9300
N4—C221.152 (5)C13—H13A0.9300
C1—C61.391 (5)C14—C151.515 (5)
C1—C21.397 (5)C14—H14A0.9700
C2—C31.375 (6)C14—H14B0.9700
C2—H2A0.9300C15—C201.386 (5)
C3—C41.393 (6)C15—C161.388 (5)
C3—H3A0.9300C16—C171.384 (5)
C4—C51.385 (6)C16—H16A0.9300
C4—H4A0.9300C17—C181.390 (5)
C5—C61.394 (6)C17—H17A0.9300
C5—H5A0.9300C18—C191.391 (5)
C7—C81.472 (6)C18—C221.440 (6)
C8—C91.387 (5)C19—C201.377 (5)
C8—C131.397 (5)C19—H19A0.9300
C9—C101.385 (5)C20—H20A0.9300
C9—H9A0.9300
C7—N1—C1105.2 (3)C10—C11—C21120.6 (4)
C6—N2—C7106.1 (3)C12—C11—C21118.8 (4)
C6—N2—C14123.7 (3)C13—C12—C11119.0 (4)
C7—N2—C14129.6 (3)C13—C12—H12A120.5
C6—C1—C2120.2 (4)C11—C12—H12A120.5
C6—C1—N1109.9 (4)C12—C13—C8121.3 (4)
C2—C1—N1129.8 (4)C12—C13—H13A119.3
C3—C2—C1117.6 (4)C8—C13—H13A119.3
C3—C2—H2A121.2N2—C14—C15114.6 (3)
C1—C2—H2A121.2N2—C14—H14A108.6
C2—C3—C4121.8 (4)C15—C14—H14A108.6
C2—C3—H3A119.1N2—C14—H14B108.6
C4—C3—H3A119.1C15—C14—H14B108.6
C5—C4—C3121.5 (4)H14A—C14—H14B107.6
C5—C4—H4A119.3C20—C15—C16119.3 (4)
C3—C4—H4A119.3C20—C15—C14121.6 (3)
C4—C5—C6116.4 (4)C16—C15—C14119.2 (4)
C4—C5—H5A121.8C17—C16—C15120.4 (4)
C6—C5—H5A121.8C17—C16—H16A119.8
N2—C6—C1106.0 (4)C15—C16—H16A119.8
N2—C6—C5131.6 (4)C16—C17—C18119.7 (4)
C1—C6—C5122.4 (4)C16—C17—H17A120.1
N1—C7—N2112.7 (4)C18—C17—H17A120.1
N1—C7—C8122.6 (4)C17—C18—C19120.0 (4)
N2—C7—C8124.6 (4)C17—C18—C22120.2 (4)
C9—C8—C13118.8 (4)C19—C18—C22119.8 (4)
C9—C8—C7124.0 (4)C20—C19—C18119.6 (4)
C13—C8—C7117.1 (4)C20—C19—H19A120.2
C10—C9—C8120.4 (4)C18—C19—H19A120.2
C10—C9—H9A119.8C19—C20—C15120.9 (4)
C8—C9—H9A119.8C19—C20—H20A119.6
C9—C10—C11119.8 (4)C15—C20—H20A119.6
C9—C10—H10A120.1N3—C21—C11178.5 (5)
C11—C10—H10A120.1N4—C22—C18179.2 (5)
C10—C11—C12120.7 (4)
C7—N1—C1—C61.5 (4)N2—C7—C8—C13−147.4 (4)
C7—N1—C1—C2−177.1 (4)C13—C8—C9—C101.3 (6)
C6—C1—C2—C3−0.1 (6)C7—C8—C9—C10177.7 (4)
N1—C1—C2—C3178.4 (4)C8—C9—C10—C11−0.3 (6)
C1—C2—C3—C40.9 (6)C9—C10—C11—C12−0.9 (6)
C2—C3—C4—C5−0.7 (6)C9—C10—C11—C21179.3 (4)
C3—C4—C5—C6−0.3 (6)C10—C11—C12—C131.2 (6)
C7—N2—C6—C10.4 (4)C21—C11—C12—C13−179.0 (4)
C14—N2—C6—C1172.4 (3)C11—C12—C13—C8−0.2 (6)
C7—N2—C6—C5178.7 (4)C9—C8—C13—C12−1.0 (6)
C14—N2—C6—C5−9.3 (6)C7—C8—C13—C12−177.7 (4)
C2—C1—C6—N2177.5 (3)C6—N2—C14—C1581.2 (5)
N1—C1—C6—N2−1.2 (4)C7—N2—C14—C15−108.9 (4)
C2—C1—C6—C5−1.0 (6)N2—C14—C15—C2020.2 (5)
N1—C1—C6—C5−179.7 (4)N2—C14—C15—C16−160.9 (4)
C4—C5—C6—N2−177.0 (4)C20—C15—C16—C170.2 (6)
C4—C5—C6—C11.1 (6)C14—C15—C16—C17−178.7 (4)
C1—N1—C7—N2−1.3 (4)C15—C16—C17—C18−0.6 (6)
C1—N1—C7—C8177.1 (3)C16—C17—C18—C190.4 (6)
C6—N2—C7—N10.5 (4)C16—C17—C18—C22−178.2 (4)
C14—N2—C7—N1−170.8 (4)C17—C18—C19—C200.2 (6)
C6—N2—C7—C8−177.8 (4)C22—C18—C19—C20178.7 (4)
C14—N2—C7—C810.9 (6)C18—C19—C20—C15−0.6 (6)
N1—C7—C8—C9−142.1 (4)C16—C15—C20—C190.3 (6)
N2—C7—C8—C936.1 (6)C14—C15—C20—C19179.3 (4)
N1—C7—C8—C1334.4 (5)
D—H···AD—HH···AD···AD—H···A
C12—H12A···N1i0.932.623.425 (5)146
C19—H19A···N4ii0.932.573.502 (6)175
C9—H9A···N4iii0.932.713.361 (5)128
C14—H14A···N3iv0.972.573.502 (5)162
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C12—H12A⋯N1i0.932.623.425 (5)146
C19—H19A⋯N4ii0.932.573.502 (6)175
C9—H9A⋯N4iii0.932.713.361 (5)128
C14—H14A⋯N3iv0.972.573.502 (5)162

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  6 in total

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

2.  Synthesis and antiviral evaluation of halogenated beta-D- and -L-erythrofuranosylbenzimidazoles.

Authors:  K S Gudmundsson; J Tidwell; N Lippa; G W Koszalka; N van Draanen; R G Ptak; J C Drach; L B Townsend
Journal:  J Med Chem       Date:  2000-06-15       Impact factor: 7.446

3.  Design of highly active analogues of the pyrrolo[1,2-a]benzimidazole antitumor agents.

Authors:  W A Craigo; B W LeSueur; E B Skibo
Journal:  J Med Chem       Date:  1999-08-26       Impact factor: 7.446

4.  Synthesis and antitumor activity of 1-substituted-2-methyl-5-nitrobenzimidazoles.

Authors:  Mostafa M Ramla; Mohamed A Omar; Abdel-Momen M El-Khamry; Hoda I El-Diwani
Journal:  Bioorg Med Chem       Date:  2006-07-24       Impact factor: 3.641

5.  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

6.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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Authors:  Yiliang Zhao; Clarissa K L Ng
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-09-30

2.  1-[4-(Prop-2-en-1-yl-oxy)benz-yl]-2-[4-(prop-2-en-1-yl-oxy)phen-yl]-1H-benzimidazole.

Authors:  Md Lutfor Rahman; Huey Chong Kwong; Mashitah Mohd Yusoff; Gurumurthy Hegde; Mohamed Ibrahim Mohamed Tahir
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