supplementary materials


zs2254 scheme

Acta Cryst. (2013). E69, o700    [ doi:10.1107/S1600536813009458 ]

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

M. A. S. Omer, J. Liu and C. Xiao

Abstract top

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].

Comment top

Supramolecular chemistry based on coordination compounds is a vast area of current research. Benzimidazole derivatives have attracted the attention of many synthetic chemists, due not only to their useful biological activities but also to their strong coordinating abilities as multidentate ligands (Kühler et al., 2002; Carcanague et al., 2002; Yang et al., 2006; Li et al., 2007). In our studies, we synthesized the substituted benzimidazole ligand 2-[2-(pyridin-4-yl)-1H-benzimidazol-1-ylmethyl]phenol, C19H15N3O, derived from the transformation of an unsymmetrical Schiff base and the structure is reported herein.

Within the ligand, the pyridine group is rigidly linked to the central C atom of the benzimidazole group, and the phenol ring is attached via a methylene group to an N-atom (Kitazume & Ishikawa, 1974). The dihedral angles between the pyridine and phenyl rings and the benzimidazole ring are 44.36 (7) and 75.67 (7)°, respectively. These deviations from planarity, in part, may be influenced by intermolecular phenolic O—H···N hydrogen bonds to benzimidazole N-atom acceptors (Table 1), giving one-dimensional chains extending along [110] (Fig. 2). In addition, the crystal structure is stabilized by weak face-to-face ππ stacking interactions involving the pyridine rings, with the shortest centroid to centroid distance between these planes of 3.9624 (10)Å]. This value is within the upper limit of the common range for ππ interactions (Janiak, 2000).

Related literature top

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 top

2-[2-(Pyridin-4-yl)-1H-benzimidazol-1-ylmethyl]phenol was synthesized according to a modification of a previously reported procedure (Fellah et al., 2010). To a solution of o-phenylenediamine (2.16 g, 20 mmol) in ethanol (20 ml), 2-hydroxybenzaldehyde (1.22 g, 10 mmol) dissolved in ethanol (10 ml) was added dropwise. The mixture was stirred at room temperature for 8 h. A yellow precipitate formed and was isolated by filtration. The crude product,[(E)-2((2-aminophenylimino)methyl)], was then crystallized from ethanol and a solution of this product (2.12 g, 10 mmol) and pyridine-4-carbaldehyde (1.07 g, 10 mmol) in ethanol (50 ml) was heated for 10 h under reflux. The reaction mixture was cooled, and a white precipitate of the crude title compound formed and was filtered off (yield 71 wt%). This product was then recrystallized from an aqueous methanol solution (1:1 v/v). Colorless single block crystals of the title compound suitable for X-ray analysis were obtained.

Refinement top

The phenolic H atom was positioned and refined as a freely rotating O—H bond, with a fixed O—H bond length of 0.82 Å and with Uiso(H) = 1.5Ueq(O). Other H atoms were included in calculated positions and refined using a riding-model approximation, with C—H = 0.93 or 0.97 Å for aromatic and methylene H atoms, respectively, and with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); 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 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. Molecular conformation and atom numbering scheme for the title compound, with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] Fig. 2. A perspective view of the packing of the title compound in the unit cell, showing intermolecular hydrogen bonds as dashed lines. For symmetry code (i), see Table 1.
2-{[2-(Pyridin-4-yl)-1H-benzimidazol-1-yl]methyl}phenol top
Crystal data top
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
Data collection top
Agilent SuperNova CCD
diffractometer
3010 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 = 1920
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)
k = 108
Tmin = 0.982, Tmax = 1.000l = 2612
6104 measured reflections
Refinement top
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 = 1.06 w = 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
Crystal data top
C19H15N3OV = 2938.0 (2) Å3
Mr = 301.34Z = 8
Monoclinic, C2/cMo Kα radiation
a = 16.1886 (7) ŵ = 0.09 mm1
b = 8.4863 (4) ÅT = 291 K
c = 21.4316 (10) Å0.36 × 0.28 × 0.25 mm
β = 93.756 (4)°
Data collection top
Agilent SuperNova CCD
diffractometer
3010 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)
2398 reflections with I > 2σ(I)
Tmin = 0.982, Tmax = 1.000Rint = 0.026
6104 measured reflectionsθmax = 26.4°
Refinement top
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.119Δρmax = 0.14 e Å3
S = 1.06Δρmin = 0.19 e Å3
3010 reflectionsAbsolute structure: ?
209 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
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*
Atomic displacement parameters (Å2) top
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)
Geometric parameters (Å, º) top
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—C17178.45 (17)C7—N1—C1—C60.32 (18)
N1—C1—C2—C3179.45 (18)C7—N1—C13—C14104.93 (19)
N1—C1—C6—N20.75 (19)C7—N2—C6—C11.54 (19)
N1—C1—C6—C5177.82 (16)C7—N2—C6—C5176.85 (19)
N1—C7—C8—C944.3 (2)C7—C8—C9—C10176.76 (15)
N1—C7—C8—C12139.15 (18)C7—C8—C12—C11177.78 (16)
N1—C13—C14—C15164.53 (14)C8—C9—C10—N30.7 (3)
N1—C13—C14—C1914.6 (2)C9—C8—C12—C111.0 (3)
N2—C7—C8—C9134.83 (18)C10—N3—C11—C120.2 (3)
N2—C7—C8—C1241.7 (2)C11—N3—C10—C90.7 (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—C8177.87 (15)C13—N1—C1—C6176.74 (14)
C1—N1—C13—C1470.6 (2)C13—N1—C7—N2177.48 (15)
C1—C2—C3—C40.8 (3)C13—N1—C7—C81.7 (3)
C2—C1—C6—N2179.12 (17)C13—C14—C15—O12.9 (2)
C2—C1—C6—C52.3 (3)C13—C14—C15—C16176.89 (15)
C2—C3—C4—C50.8 (3)C13—C14—C19—C18178.34 (16)
C3—C4—C5—C60.8 (3)C14—C15—C16—C171.8 (3)
C4—C5—C6—N2179.47 (19)C15—C14—C19—C180.8 (3)
C4—C5—C6—C12.3 (3)C15—C16—C17—C180.3 (3)
C6—N2—C7—N11.79 (19)C16—C17—C18—C191.8 (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—C162.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N2i0.821.952.7659 (18)177
Symmetry code: (i) x1/2, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N2i0.821.952.7659 (18)177
Symmetry code: (i) x1/2, y+1/2, z.
Acknowledgements top

This work was supported by the Natural Science Foundation of Gansu (grant No. 0710RJ ZA113).

references
References top

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