Literature DB >> 21583223

3-[1-(3-Hydroxy-benz-yl)-1H-benz-imid-azol-2-yl]phenol.

Naser Eltaher Eltayeb, Siang Guan Teoh, Hoong-Kun Fun, Samuel Robinson Jebas, Rohana Adnan.   

Abstract

In the title mol-ecule, C(20)H(16)N(2)O(2), the benzimidazole mean plane forms dihedral angles of 56.55 (3) and 81.65 (4)° with the two benzene rings. In the crystal structure, inter-molecular O-H⋯O and O-H⋯N hydrogen bonds link the mol-ecules into layers parallel to the (101) plane. The crystal packing also exhibits weak inter-molecular C-H⋯O and C-H⋯π inter-actions.

Entities:  

Year:  2009        PMID: 21583223      PMCID: PMC2969736          DOI: 10.1107/S1600536809018698

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


Related literature

For the biological activity of benzimidazole derivatives, see: Demirayak et al. (2002 ▶); Minoura et al. (2004 ▶); Pawar et al. (2004 ▶); Tomei et al. (2003 ▶). For related structures, see: Eltayeb et al. (2007a ▶,b ▶,c ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C20H16N2O2 M = 316.35 Monoclinic, a = 10.5128 (2) Å b = 12.1096 (2) Å c = 12.5235 (2) Å β = 96.948 (1)° V = 1582.61 (5) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.55 × 0.34 × 0.15 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T min = 0.954, T max = 0.987 34106 measured reflections 7426 independent reflections 6004 reflections with I > 2σ(I) R int = 0.040

Refinement

R[F 2 > 2σ(F 2)] = 0.048 wR(F 2) = 0.136 S = 1.05 7426 reflections 225 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.51 e Å−3 Δρmin = −0.29 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/S1600536809018698/cv2563sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018698/cv2563Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H16N2O2F(000) = 664
Mr = 316.35Dx = 1.328 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 8327 reflections
a = 10.5128 (2) Åθ = 2.4–37.2°
b = 12.1096 (2) ŵ = 0.09 mm1
c = 12.5235 (2) ÅT = 100 K
β = 96.948 (1)°Plate, colourless
V = 1582.61 (5) Å30.55 × 0.34 × 0.15 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer7426 independent reflections
Radiation source: fine-focus sealed tube6004 reflections with I > 2σ(I)
graphiteRint = 0.040
φ and ω scansθmax = 36.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −14→17
Tmin = 0.954, Tmax = 0.987k = −20→20
34106 measured reflectionsl = −19→20
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.136H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0723P)2 + 0.2344P] where P = (Fo2 + 2Fc2)/3
7426 reflections(Δ/σ)max < 0.001
225 parametersΔρmax = 0.51 e Å3
0 restraintsΔρmin = −0.29 e Å3
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
O10.60369 (7)0.60548 (5)0.04595 (5)0.01932 (13)
O20.21201 (7)0.70928 (6)0.49193 (6)0.02850 (16)
N10.36876 (7)0.35014 (5)0.31082 (5)0.01366 (12)
N20.55084 (7)0.30903 (6)0.41524 (5)0.01468 (12)
C10.34113 (8)0.26119 (6)0.37376 (6)0.01385 (13)
C20.22644 (8)0.20556 (7)0.38301 (6)0.01625 (14)
H2A0.15020.22470.34150.019*
C30.23254 (9)0.12006 (7)0.45759 (7)0.01787 (15)
H3A0.15810.08200.46760.021*
C40.34872 (9)0.08978 (7)0.51829 (7)0.01903 (16)
H4A0.34970.03080.56590.023*
C50.46206 (9)0.14602 (7)0.50872 (7)0.01765 (15)
H5A0.53880.12550.54860.021*
C60.45615 (8)0.23468 (6)0.43671 (6)0.01408 (13)
C70.49493 (8)0.37658 (6)0.34028 (6)0.01328 (13)
C80.55758 (8)0.47449 (6)0.29966 (6)0.01346 (13)
C90.55681 (8)0.49315 (6)0.18938 (6)0.01442 (13)
H9A0.52140.44110.13980.017*
C100.60956 (8)0.59058 (6)0.15413 (6)0.01466 (14)
C110.66423 (8)0.66833 (7)0.22849 (6)0.01679 (15)
H11A0.69880.73330.20490.020*
C120.66666 (9)0.64783 (7)0.33810 (7)0.01769 (15)
H12A0.70410.69900.38760.021*
C130.61356 (8)0.55155 (7)0.37433 (6)0.01600 (14)
H13A0.61530.53850.44770.019*
C140.27189 (8)0.40916 (7)0.23858 (6)0.01493 (14)
H14A0.21990.35600.19480.018*
H14B0.31440.45560.19070.018*
C150.18581 (8)0.47993 (7)0.29866 (6)0.01546 (14)
C160.05416 (9)0.46392 (8)0.28541 (7)0.02214 (17)
H16A0.01820.40780.24090.027*
C17−0.02425 (10)0.53232 (10)0.33909 (9)0.0298 (2)
H17A−0.11260.52260.32890.036*
C180.02893 (10)0.61473 (9)0.40753 (8)0.0276 (2)
H18A−0.02350.66010.44320.033*
C190.16150 (9)0.62907 (8)0.42254 (7)0.02011 (16)
C200.23951 (8)0.56315 (7)0.36681 (6)0.01647 (14)
H20A0.32760.57460.37500.020*
H1O10.6430 (17)0.6716 (15)0.0307 (14)0.053 (5)*
H1O20.3026 (18)0.6952 (15)0.5216 (14)0.055 (5)*
U11U22U33U12U13U23
O10.0266 (3)0.0181 (3)0.0133 (2)−0.0054 (2)0.0028 (2)0.00132 (19)
O20.0206 (3)0.0285 (3)0.0336 (4)0.0103 (3)−0.0083 (3)−0.0167 (3)
N10.0134 (3)0.0145 (3)0.0127 (3)0.0004 (2)0.0002 (2)0.0011 (2)
N20.0139 (3)0.0155 (3)0.0144 (3)0.0006 (2)0.0007 (2)0.0009 (2)
C10.0148 (3)0.0135 (3)0.0131 (3)−0.0001 (2)0.0012 (3)−0.0002 (2)
C20.0151 (3)0.0170 (3)0.0162 (3)−0.0022 (3)0.0003 (3)−0.0013 (2)
C30.0204 (4)0.0161 (3)0.0173 (3)−0.0041 (3)0.0029 (3)−0.0011 (2)
C40.0242 (4)0.0149 (3)0.0181 (3)−0.0023 (3)0.0027 (3)0.0015 (3)
C50.0197 (4)0.0158 (3)0.0169 (3)0.0008 (3)0.0001 (3)0.0024 (2)
C60.0147 (3)0.0136 (3)0.0137 (3)0.0002 (2)0.0008 (3)−0.0003 (2)
C70.0131 (3)0.0143 (3)0.0124 (3)0.0001 (2)0.0013 (2)−0.0007 (2)
C80.0122 (3)0.0142 (3)0.0140 (3)0.0001 (2)0.0018 (2)−0.0003 (2)
C90.0159 (3)0.0142 (3)0.0131 (3)−0.0019 (2)0.0018 (3)−0.0008 (2)
C100.0154 (3)0.0151 (3)0.0138 (3)−0.0006 (3)0.0026 (3)−0.0001 (2)
C110.0183 (4)0.0148 (3)0.0173 (3)−0.0026 (3)0.0023 (3)−0.0013 (2)
C120.0186 (4)0.0180 (3)0.0165 (3)−0.0035 (3)0.0021 (3)−0.0036 (2)
C130.0161 (4)0.0180 (3)0.0138 (3)−0.0011 (3)0.0016 (3)−0.0019 (2)
C140.0145 (3)0.0177 (3)0.0120 (3)0.0020 (3)−0.0010 (3)0.0002 (2)
C150.0148 (3)0.0176 (3)0.0136 (3)0.0022 (3)0.0000 (3)0.0002 (2)
C160.0145 (4)0.0283 (4)0.0229 (4)0.0005 (3)−0.0007 (3)−0.0069 (3)
C170.0133 (4)0.0409 (6)0.0349 (5)0.0020 (4)0.0017 (4)−0.0144 (4)
C180.0162 (4)0.0369 (5)0.0292 (5)0.0071 (4)0.0002 (3)−0.0126 (4)
C190.0174 (4)0.0217 (4)0.0200 (4)0.0057 (3)−0.0028 (3)−0.0053 (3)
C200.0137 (3)0.0178 (3)0.0172 (3)0.0026 (3)−0.0006 (3)−0.0017 (3)
O1—C101.3607 (10)C9—C101.3977 (11)
O1—H1O10.931 (19)C9—H9A0.9300
O2—C191.3671 (11)C10—C111.3980 (11)
O2—H1O20.994 (19)C11—C121.3922 (11)
N1—C71.3709 (10)C11—H11A0.9300
N1—C11.3861 (10)C12—C131.3922 (11)
N1—C141.4641 (11)C12—H12A0.9300
N2—C71.3275 (10)C13—H13A0.9300
N2—C61.3923 (10)C14—C151.5114 (11)
C1—C21.3981 (11)C14—H14A0.9700
C1—C61.3986 (12)C14—H14B0.9700
C2—C31.3906 (11)C15—C161.3874 (13)
C2—H2A0.9300C15—C201.3951 (11)
C3—C41.4070 (13)C16—C171.3970 (13)
C3—H3A0.9300C16—H16A0.9300
C4—C51.3901 (12)C17—C181.3882 (14)
C4—H4A0.9300C17—H17A0.9300
C5—C61.3987 (11)C18—C191.3944 (14)
C5—H5A0.9300C18—H18A0.9300
C7—C81.4763 (10)C19—C201.3911 (11)
C8—C91.3985 (10)C20—H20A0.9300
C8—C131.3995 (11)
C10—O1—H1O1110.5 (11)C9—C10—C11120.33 (7)
C19—O2—H1O2113.3 (10)C12—C11—C10119.59 (7)
C7—N1—C1106.91 (6)C12—C11—H11A120.2
C7—N1—C14129.07 (7)C10—C11—H11A120.2
C1—N1—C14123.56 (7)C11—C12—C13120.69 (8)
C7—N2—C6105.62 (7)C11—C12—H12A119.7
N1—C1—C2131.58 (8)C13—C12—H12A119.7
N1—C1—C6105.82 (7)C12—C13—C8119.56 (7)
C2—C1—C6122.56 (7)C12—C13—H13A120.2
C3—C2—C1116.37 (8)C8—C13—H13A120.2
C3—C2—H2A121.8N1—C14—C15112.50 (6)
C1—C2—H2A121.8N1—C14—H14A109.1
C2—C3—C4121.56 (8)C15—C14—H14A109.1
C2—C3—H3A119.2N1—C14—H14B109.1
C4—C3—H3A119.2C15—C14—H14B109.1
C5—C4—C3121.52 (8)H14A—C14—H14B107.8
C5—C4—H4A119.2C16—C15—C20119.87 (7)
C3—C4—H4A119.2C16—C15—C14120.66 (7)
C4—C5—C6117.39 (8)C20—C15—C14119.46 (7)
C4—C5—H5A121.3C15—C16—C17119.85 (9)
C6—C5—H5A121.3C15—C16—H16A120.1
N2—C6—C1109.41 (7)C17—C16—H16A120.1
N2—C6—C5130.08 (8)C18—C17—C16120.42 (9)
C1—C6—C5120.50 (7)C18—C17—H17A119.8
N2—C7—N1112.19 (7)C16—C17—H17A119.8
N2—C7—C8124.10 (7)C17—C18—C19119.60 (8)
N1—C7—C8123.52 (7)C17—C18—H18A120.2
C9—C8—C13120.26 (7)C19—C18—H18A120.2
C9—C8—C7121.37 (7)O2—C19—C20121.29 (8)
C13—C8—C7118.31 (7)O2—C19—C18118.63 (8)
C10—C9—C8119.55 (7)C20—C19—C18120.08 (8)
C10—C9—H9A120.2C19—C20—C15120.13 (8)
C8—C9—H9A120.2C19—C20—H20A119.9
O1—C10—C9117.03 (7)C15—C20—H20A119.9
O1—C10—C11122.64 (7)
C7—N1—C1—C2175.17 (8)N1—C7—C8—C13121.97 (8)
C14—N1—C1—C22.30 (12)C13—C8—C9—C10−1.55 (12)
C7—N1—C1—C6−2.40 (8)C7—C8—C9—C10175.65 (7)
C14—N1—C1—C6−175.27 (6)C8—C9—C10—O1−178.61 (7)
N1—C1—C2—C3−178.27 (8)C8—C9—C10—C110.81 (12)
C6—C1—C2—C3−1.05 (11)O1—C10—C11—C12179.82 (8)
C1—C2—C3—C4−1.54 (12)C9—C10—C11—C120.44 (13)
C2—C3—C4—C51.89 (13)C10—C11—C12—C13−0.95 (13)
C3—C4—C5—C60.40 (12)C11—C12—C13—C80.22 (13)
C7—N2—C6—C1−1.16 (8)C9—C8—C13—C121.04 (12)
C7—N2—C6—C5180.00 (8)C7—C8—C13—C12−176.24 (8)
N1—C1—C6—N22.23 (8)C7—N1—C14—C15−98.85 (9)
C2—C1—C6—N2−175.61 (7)C1—N1—C14—C1572.35 (9)
N1—C1—C6—C5−178.80 (7)N1—C14—C15—C16−121.88 (9)
C2—C1—C6—C53.37 (11)N1—C14—C15—C2059.08 (10)
C4—C5—C6—N2175.81 (8)C20—C15—C16—C170.98 (14)
C4—C5—C6—C1−2.93 (11)C14—C15—C16—C17−178.05 (9)
C6—N2—C7—N1−0.41 (8)C15—C16—C17—C18−1.43 (17)
C6—N2—C7—C8174.77 (7)C16—C17—C18—C190.02 (18)
C1—N1—C7—N21.81 (8)C17—C18—C19—O2−178.72 (10)
C14—N1—C7—N2174.16 (7)C17—C18—C19—C201.83 (16)
C1—N1—C7—C8−173.40 (7)O2—C19—C20—C15178.29 (8)
C14—N1—C7—C8−1.05 (11)C18—C19—C20—C15−2.28 (14)
N2—C7—C8—C9130.08 (8)C16—C15—C20—C190.86 (13)
N1—C7—C8—C9−55.28 (11)C14—C15—C20—C19179.91 (8)
N2—C7—C8—C13−52.67 (10)
D—H···AD—HH···AD···AD—H···A
O1—H1O1···O2i0.931 (19)1.712 (19)2.6406 (9)175.4 (17)
O2—H1O2···N2ii0.994 (19)1.646 (19)2.6297 (10)169.7 (16)
C3—H3A···O1iii0.932.573.2987 (10)136
C9—H9A···O1iv0.932.593.4287 (10)150
C12—H12A···Cg1ii0.932.673.4521 (9)142
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1O1⋯O2i0.931 (19)1.712 (19)2.6406 (9)175.4 (17)
O2—H1O2⋯N2ii0.994 (19)1.646 (19)2.6297 (10)169.7 (16)
C3—H3A⋯O1iii0.932.573.2987 (10)136
C9—H9A⋯O1iv0.932.593.4287 (10)150
C12—H12ACg1ii0.932.673.4521 (9)142

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) . Cg1 is the centroid of the ring C1–C6.

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Journal:  Eur J Pharmacol       Date:  2004-06-28       Impact factor: 4.432

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Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-10-20

2.  2-Methyl-6-(6-methyl-1H-benzimidazol-2-yl)phenol-2-methyl-6-(5-methyl-1H-benzimidazol-2-yl)phenol (3/1).

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  3 in total

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