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The title compound, C25H18ClN3O, results from the intramol­ecular reaction of a difunctional Schiff base in the presence of acid as a catalyst. There is a chiral C atom in the mol­ecule, but the crystal structure is a racemic mixture. There is one strong intermolecular O—H...N hydrogen bond and three weak C—H...N interactions (two intra- and one intermolecular), leading to the formation of a helical chain of mol­ecules.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803009814/fl6035sup1.cif
Contains datablocks global, II

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536803009814/fl6035IIsup2.hkl
Contains datablock II

CCDC reference: 214831

Key indicators

  • Single-crystal X-ray study
  • T = 293 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.034
  • wR factor = 0.092
  • Data-to-parameter ratio = 11.6

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry








Comment top

The preparation of benzimidazoles has attracted some attention due to their variable physiological characteristics, such as anticancer agents, fungicides, antichagasic drugs, inhibitors, and plant-growth regulators (Zhou & Hassner, 2001; Matsuno et al., 2000; Kucukbay et al., 2001; Purygin et al., 2000; Bag et al., 1996).

In general, benzimidazole derivatives are obtained by the reaction of an o-phenylenediamine with a carboxylic acid, ester, amide, nitrile etc., or by the palladium-catalyzed carbonylation, coupling and cyclization of haloaromatics and o-phenylenediamines. Recently, Alajarin and co-workers (Alajarin et al., 1999) described a [4 + 2] intramolecular cycloaddition of ketimines with imines to form benzimidazo[1,2-b]isoquinolines, but it is a tedious procedure requiring expensive reagents. This paper reports a novel method for the synthesis of 1,2-benzimidazoles in good yields by hydrogen transfer cyclization between azomethine groups in the presence of acidic catalysts under mild conditions.

The structure analysis of the title compound, (II), shows that there is a chiral carbon atom in the molecule; however, it crystallizes in the centrosymmetric space group P21/c so its specific rotation is zero. The dihedral angle between the benzimidazole ring and the pyridyl ring is 24.29 (8)°. The bond angles H13—C13—N2, H13—C13—C20 and H13—C13—C14 are 103.2 (8), 110.0 (8) and 105.7 (8)°, respectively. There is one strong intermolecular O—H···N hydrogen bond and three weak C—H···N interactions (two intra- and one intermolecular), leading to the formation of a helical chain of molecules (see Fig. 3).

Experimental top

The title compound, (II), was prepared as follows: in the presence of p-CH3C6H4SO3H, an intramolecular hydrogen-transfer cyclization of 1-N-(phenyl-5-chloro-2-hydroxylphenyl)methylene-2-N-(pyridin-2-yl)methylene −1,2-phenylenedimine was carried out between the two CN bonds of the asymmetrical difunctional Schiff base (I) to give a cyclozation product, (II). The hydrogen on the carbon atom of the aldimine transferred to the carbon atom of ketoimine and formed a chiral center. The specific rotation of the products is 0°. A single-crystal of the title compound was obtained by slow diffusion (1:1 MeOH-MeCN) over a period of one month.

Refinement top

All the C—H and O—H H atoms were found in difference maps and refined isotropically. The bond lengths for C—H are from 0.952 (13)–1.058 (15) Å. The bond length for O—H is 0.99 (2) Å.

Computing details top

Data collection: XSCANS (Bruker, 2000); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. ORTEP representation of title compound, drawn with ellipsoids at the 50% probability level.
[Figure 2] Fig. 2. The crystal packing of title compound, viewed down the b axis.
[Figure 3] Fig. 3. The crystal packing, showing the intermolecular interactions leading to the formation of two helical chains.
3-[(5-Chloro-2-hydroxyphenyl)phenylmethyl]-2-(2-pyridyl)-1H-benzimidazole top
Crystal data top
C25H18ClN3OF(000) = 856
Mr = 411.87Dx = 1.330 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 13.515 (2) Åθ = 2.1–23.2°
b = 9.597 (2) ŵ = 0.21 mm1
c = 16.875 (2) ÅT = 293 K
β = 110.01 (1)°Block, colorless
V = 2056.6 (6) Å30.3 × 0.2 × 0.2 mm
Z = 4
Data collection top
Bruker P4
diffractometer
3129 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.045
Graphite monochromatorθmax = 26.0°, θmin = 1.6°
ω scansh = 1616
Absorption correction: ψ scan
(XPREP; Bruker, 2000)
k = 1111
Tmin = 0.95, Tmax = 0.96l = 1919
10228 measured reflections3 standard reflections every 97 reflections
3982 independent reflections intensity decay: 0.005%
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)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.092All H-atom parameters refined
S = 1.01 w = 1/[σ2(Fo2) + (0.02P)2]
where P = (Fo2 + 2Fc2)/3
3982 reflections(Δ/σ)max < 0.001
343 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = 0.15 e Å3
Crystal data top
C25H18ClN3OV = 2056.6 (6) Å3
Mr = 411.87Z = 4
Monoclinic, P21/cMo Kα radiation
a = 13.515 (2) ŵ = 0.21 mm1
b = 9.597 (2) ÅT = 293 K
c = 16.875 (2) Å0.3 × 0.2 × 0.2 mm
β = 110.01 (1)°
Data collection top
Bruker P4
diffractometer
3129 reflections with I > 2σ(I)
Absorption correction: ψ scan
(XPREP; Bruker, 2000)
Rint = 0.045
Tmin = 0.95, Tmax = 0.963 standard reflections every 97 reflections
10228 measured reflections intensity decay: 0.005%
3982 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0340 restraints
wR(F2) = 0.092All H-atom parameters refined
S = 1.01Δρmax = 0.20 e Å3
3982 reflectionsΔρmin = 0.15 e Å3
343 parameters
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.

Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

3.8274 (0.0129) x + 7.9081 (0.0035) y + 6.1455 (0.0090) z = 3.1747 (0.0027)

* −0.0810 (0.0013) C8 * −0.0222 (0.0016) C9 * 0.0426 (0.0017) C10 * 0.0368 (0.0017) C11 * −0.0277 (0.0012) C12 * 0.0515 (0.0007) N2

Rms deviation of fitted atoms = 0.0477

8.7556 (0.0051) x + 6.5746 (0.0035) y + 1.5415 (0.0053) z = 3.5549 (0.0013)

Angle to previous plane (with approximate e.s.d.) = 24.29 (0.08)

* 0.0174 (0.0013) C1 * −0.0006 (0.0012) C2 * −0.0131 (0.0012) C3 * −0.0076 (0.0012) C4 * 0.0068 (0.0011) C5 * 0.0174 (0.0012) C6 * −0.0196 (0.0010) C7 * 0.0068 (0.0010) N1 * −0.0075 (0.0010) N2

Rms deviation of fitted atoms =0.0123

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
N20.27370 (8)0.13167 (11)0.18508 (6)0.0471 (3)
N10.39468 (9)0.02686 (12)0.18339 (7)0.0547 (3)
C60.28406 (11)0.14024 (14)0.10580 (8)0.0493 (3)
C70.34144 (11)0.02950 (14)0.22825 (8)0.0504 (3)
C10.35919 (11)0.04011 (15)0.10617 (9)0.0534 (3)
C80.35184 (12)0.02258 (15)0.31334 (9)0.0567 (4)
C140.09869 (11)0.18864 (14)0.19490 (8)0.0518 (3)
C200.23141 (11)0.37906 (13)0.19685 (8)0.0490 (3)
C130.21320 (11)0.22933 (13)0.21886 (9)0.0473 (3)
C210.15082 (13)0.46110 (15)0.14484 (9)0.0559 (4)
N30.26999 (11)0.00367 (14)0.33936 (8)0.0674 (4)
C50.23442 (13)0.22136 (16)0.03491 (9)0.0578 (4)
C250.33245 (11)0.43563 (15)0.23018 (9)0.0536 (3)
C150.05079 (12)0.08976 (17)0.13415 (9)0.0604 (4)
C230.26988 (14)0.65271 (18)0.15976 (10)0.0671 (4)
C20.38656 (13)0.01773 (17)0.03450 (10)0.0613 (4)
C220.17066 (13)0.59602 (16)0.12594 (9)0.0621 (4)
C30.33773 (13)0.09732 (18)0.03571 (10)0.0652 (4)
C190.03843 (12)0.25473 (18)0.23605 (10)0.0640 (4)
C40.26306 (14)0.19749 (17)0.03527 (10)0.0637 (4)
C240.35072 (14)0.57270 (17)0.21221 (11)0.0649 (4)
C180.06732 (13)0.2243 (2)0.21586 (12)0.0741 (5)
C160.05565 (14)0.0605 (2)0.11388 (12)0.0749 (5)
C100.4456 (2)0.1491 (2)0.43792 (13)0.0946 (6)
C90.44085 (16)0.0947 (2)0.36024 (12)0.0807 (5)
C170.11394 (15)0.1269 (2)0.15494 (12)0.0777 (5)
C120.27714 (17)0.0583 (2)0.41450 (11)0.0792 (5)
C110.36287 (19)0.1305 (2)0.46453 (13)0.0883 (6)
Cl10.06903 (5)0.69575 (5)0.05804 (3)0.0996 (2)
O10.41034 (8)0.35159 (11)0.28005 (6)0.0625 (3)
H130.2429 (10)0.2156 (13)0.2782 (8)0.047 (3)*
H50.1811 (12)0.2929 (16)0.0350 (9)0.065 (4)*
H210.0784 (13)0.4275 (16)0.1212 (9)0.068 (4)*
H150.0938 (13)0.0354 (16)0.1066 (9)0.067 (4)*
H190.0747 (13)0.3327 (17)0.2798 (10)0.075 (5)*
H230.2850 (14)0.749 (2)0.1481 (11)0.090 (6)*
H240.4235 (14)0.6024 (18)0.2399 (10)0.085 (5)*
H20.4402 (14)0.0545 (18)0.0399 (10)0.082 (5)*
H40.2233 (13)0.2518 (17)0.0894 (10)0.079 (5)*
H30.3580 (12)0.0765 (16)0.0898 (10)0.071 (4)*
H160.0850 (16)0.008 (2)0.0682 (11)0.096 (6)*
H170.1927 (18)0.110 (2)0.1410 (13)0.119 (7)*
H120.2131 (16)0.044 (2)0.4339 (11)0.102 (6)*
H110.3677 (18)0.169 (2)0.5182 (14)0.125 (8)*
H180.1087 (19)0.271 (2)0.2452 (14)0.126 (8)*
H90.4990 (17)0.091 (2)0.3391 (12)0.108 (7)*
H100.516 (2)0.191 (3)0.4730 (17)0.171 (11)*
H1'0.4802 (18)0.397 (2)0.2964 (12)0.114 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N20.0459 (6)0.0445 (6)0.0516 (6)0.0016 (5)0.0177 (5)0.0012 (4)
N10.0484 (7)0.0516 (7)0.0644 (7)0.0020 (5)0.0196 (6)0.0009 (5)
C60.0480 (8)0.0499 (8)0.0513 (7)0.0029 (6)0.0188 (6)0.0042 (6)
C70.0470 (8)0.0454 (8)0.0588 (8)0.0012 (6)0.0183 (6)0.0003 (6)
C10.0488 (8)0.0528 (8)0.0605 (8)0.0038 (6)0.0213 (7)0.0061 (6)
C80.0595 (9)0.0488 (8)0.0624 (8)0.0043 (6)0.0217 (7)0.0060 (6)
C140.0484 (8)0.0490 (8)0.0595 (8)0.0019 (6)0.0204 (6)0.0019 (6)
C200.0507 (8)0.0446 (8)0.0538 (7)0.0006 (6)0.0206 (6)0.0025 (5)
C130.0468 (8)0.0445 (7)0.0522 (8)0.0009 (6)0.0189 (6)0.0011 (5)
C210.0579 (10)0.0475 (8)0.0603 (8)0.0013 (7)0.0176 (7)0.0005 (6)
N30.0707 (9)0.0674 (9)0.0703 (8)0.0051 (7)0.0320 (7)0.0139 (6)
C50.0618 (10)0.0575 (9)0.0534 (8)0.0012 (7)0.0187 (7)0.0022 (6)
C250.0543 (9)0.0494 (8)0.0594 (8)0.0026 (6)0.0226 (7)0.0026 (6)
C150.0549 (9)0.0562 (9)0.0685 (9)0.0083 (7)0.0192 (7)0.0014 (7)
C230.0719 (11)0.0509 (9)0.0784 (10)0.0044 (8)0.0256 (9)0.0013 (8)
C20.0573 (9)0.0646 (10)0.0663 (9)0.0051 (8)0.0268 (8)0.0113 (7)
C220.0686 (10)0.0491 (9)0.0665 (9)0.0032 (7)0.0204 (8)0.0019 (6)
C30.0657 (10)0.0713 (11)0.0622 (9)0.0102 (8)0.0266 (8)0.0103 (7)
C190.0516 (9)0.0682 (10)0.0745 (10)0.0013 (7)0.0247 (8)0.0001 (8)
C40.0678 (10)0.0676 (10)0.0560 (8)0.0080 (8)0.0216 (8)0.0038 (7)
C240.0621 (11)0.0532 (9)0.0796 (10)0.0078 (8)0.0244 (9)0.0022 (7)
C180.0539 (10)0.0790 (12)0.0927 (12)0.0012 (8)0.0292 (9)0.0058 (9)
C160.0585 (10)0.0737 (12)0.0859 (12)0.0151 (8)0.0163 (9)0.0003 (9)
C100.1062 (18)0.0905 (15)0.0810 (13)0.0247 (12)0.0240 (13)0.0258 (10)
C90.0744 (13)0.0865 (13)0.0786 (12)0.0221 (10)0.0227 (10)0.0205 (9)
C170.0543 (11)0.0797 (13)0.0956 (13)0.0102 (9)0.0212 (10)0.0090 (10)
C120.0928 (14)0.0755 (12)0.0767 (11)0.0073 (10)0.0385 (11)0.0171 (9)
C110.1121 (18)0.0791 (14)0.0758 (12)0.0114 (11)0.0349 (12)0.0224 (10)
Cl10.1077 (4)0.0630 (3)0.1041 (4)0.0179 (3)0.0054 (3)0.0200 (2)
O10.0479 (6)0.0586 (6)0.0760 (7)0.0054 (5)0.0149 (5)0.0055 (5)
Geometric parameters (Å, º) top
N2—C71.3688 (17)C15—H151.005 (15)
N2—C61.3945 (16)C23—C221.377 (2)
N2—C131.4802 (16)C23—C241.380 (2)
N1—C71.3252 (17)C23—H230.977 (19)
N1—C11.3833 (17)C2—C31.374 (2)
C6—C51.392 (2)C2—H20.984 (17)
C6—C11.3965 (19)C22—Cl11.7431 (16)
C7—C81.4810 (19)C3—C41.396 (2)
C1—C21.397 (2)C3—H31.058 (15)
C8—N31.3348 (19)C19—C181.382 (2)
C8—C91.379 (2)C19—H191.047 (16)
C14—C151.384 (2)C4—H41.029 (17)
C14—C191.3909 (19)C24—H240.975 (18)
C14—C131.5109 (19)C18—C171.373 (3)
C20—C211.3865 (19)C18—H180.97 (2)
C20—C251.3965 (19)C16—C171.371 (3)
C20—C131.5251 (18)C16—H160.988 (18)
C13—H130.952 (13)C10—C111.352 (3)
C21—C221.382 (2)C10—C91.392 (3)
C21—H210.976 (16)C10—H101.01 (3)
N3—C121.345 (2)C9—H90.97 (2)
C5—C41.385 (2)C17—H171.02 (2)
C5—H50.996 (15)C12—C111.366 (3)
C25—O11.3640 (17)C12—H121.03 (2)
C25—C241.391 (2)C11—H110.96 (2)
C15—C161.389 (2)O1—H1'0.99 (2)
C7—N2—C6106.53 (10)C22—C23—H23122.0 (11)
C7—N2—C13127.27 (11)C24—C23—H23118.6 (11)
C6—N2—C13125.60 (11)C3—C2—C1118.02 (15)
C7—N1—C1105.52 (11)C3—C2—H2126.4 (9)
C5—C6—N2132.88 (13)C1—C2—H2115.6 (9)
C5—C6—C1121.64 (12)C23—C22—C21120.87 (15)
N2—C6—C1105.46 (12)C23—C22—Cl1119.47 (12)
N1—C7—N2112.54 (12)C21—C22—Cl1119.66 (13)
N1—C7—C8121.75 (12)C2—C3—C4120.87 (15)
N2—C7—C8125.59 (12)C2—C3—H3116.7 (8)
N1—C1—C6109.95 (11)C4—C3—H3122.4 (8)
N1—C1—C2129.42 (14)C18—C19—C14120.87 (16)
C6—C1—C2120.62 (14)C18—C19—H19121.3 (9)
N3—C8—C9122.55 (14)C14—C19—H19117.7 (9)
N3—C8—C7117.30 (13)C5—C4—C3122.18 (16)
C9—C8—C7120.04 (14)C5—C4—H4117.5 (9)
C15—C14—C19118.49 (14)C3—C4—H4120.2 (9)
C15—C14—C13123.49 (12)C23—C24—C25120.35 (16)
C19—C14—C13118.01 (12)C23—C24—H24126.3 (11)
C21—C20—C25118.84 (13)C25—C24—H24113.4 (11)
C21—C20—C13122.13 (12)C17—C18—C19119.97 (18)
C25—C20—C13119.03 (12)C17—C18—H18120.0 (14)
N2—C13—C14112.56 (11)C19—C18—H18120.0 (14)
N2—C13—C20110.27 (10)C17—C16—C15120.49 (18)
C14—C13—C20114.47 (11)C17—C16—H16123.9 (11)
N2—C13—H13103.2 (8)C15—C16—H16115.6 (12)
C14—C13—H13105.7 (8)C11—C10—C9119.1 (2)
C20—C13—H13110.0 (8)C11—C10—H10124.9 (16)
C22—C21—C20120.39 (15)C9—C10—H10115.6 (16)
C22—C21—H21117.5 (9)C8—C9—C10118.63 (19)
C20—C21—H21122.1 (9)C8—C9—H9115.3 (12)
C8—N3—C12117.19 (15)C10—C9—H9125.5 (12)
C4—C5—C6116.67 (15)C16—C17—C18119.93 (17)
C4—C5—H5122.0 (8)C16—C17—H17123.0 (12)
C6—C5—H5121.3 (8)C18—C17—H17117.0 (12)
O1—C25—C24122.46 (14)N3—C12—C11123.55 (19)
O1—C25—C20117.42 (13)N3—C12—H12116.6 (11)
C24—C25—C20120.13 (14)C11—C12—H12119.8 (11)
C14—C15—C16120.23 (16)C10—C11—C12119.00 (19)
C14—C15—H15120.0 (9)C10—C11—H11117.7 (14)
C16—C15—H15119.7 (9)C12—C11—H11123.3 (14)
C22—C23—C24119.40 (16)C25—O1—H1'112.0 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···N1i0.99 (2)1.77 (2)2.7520 (16)174.8 (17)
C13—H13···N30.952 (13)2.317 (13)2.9422 (19)122.6 (9)
C15—H15···N21.005 (15)2.513 (15)2.8643 (19)100.0 (10)
C23—H23···N1ii0.977 (19)2.568 (19)3.464 (2)152.5 (14)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC25H18ClN3O
Mr411.87
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)13.515 (2), 9.597 (2), 16.875 (2)
β (°) 110.01 (1)
V3)2056.6 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.21
Crystal size (mm)0.3 × 0.2 × 0.2
Data collection
DiffractometerBruker P4
diffractometer
Absorption correctionψ scan
(XPREP; Bruker, 2000)
Tmin, Tmax0.95, 0.96
No. of measured, independent and
observed [I > 2σ(I)] reflections
10228, 3982, 3129
Rint0.045
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.092, 1.01
No. of reflections3982
No. of parameters343
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.20, 0.15

Computer programs: XSCANS (Bruker, 2000), XSCANS, SHELXTL (Bruker, 2000), SHELXTL.

Selected geometric parameters (Å, º) top
N2—C131.4802 (16)C20—C131.5251 (18)
C14—C131.5109 (19)C13—H130.952 (13)
N2—C13—C14112.56 (11)N2—C13—H13103.2 (8)
N2—C13—C20110.27 (10)C14—C13—H13105.7 (8)
C14—C13—C20114.47 (11)C20—C13—H13110.0 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1'···N1i0.99 (2)1.77 (2)2.7520 (16)174.8 (17)
C13—H13···N30.952 (13)2.317 (13)2.9422 (19)122.6 (9)
C15—H15···N21.005 (15)2.513 (15)2.8643 (19)100.0 (10)
C23—H23···N1ii0.977 (19)2.568 (19)3.464 (2)152.5 (14)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x, y+1, z.
 

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