organic compounds
2-(4-Hydroxyphenyl)-1H-benzimidazol-3-ium chloride monohydrate
aLaboratorio de Biofisica y Biocatálisis, Sección de Estudios de Posgrado e Investigación de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n Casco de Santo Tomás, México, DF 11340, Mexico, bLaboratorio de Investigación en Química, Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria de Biotecnología del Instituto Politécnico Nacional, Av. Acueducto s/n Barrio la laguna Ticoman, México, DF 07340, Mexico, and cCentro de Investigaciones Químicas, Universidad Autonoma del Estado de Hidalgo, km. 4.5 Carretera Pachuca-Tulancingo, Mineral de la Reforma, Hidalgo 42184, Mexico
*Correspondence e-mail: ipadillamar@ipn.mx
The title molecular salt, C13H11N2O+·Cl−·H2O, crystallizes as a monohydrate. In the cation, the phenol and benzimidazole rings are almost coplanar, making a dihedral angle of 3.18 (4)°. The chloride anion and benzimidazole cation are linked by two N+—H⋯Cl− hydrogen bonds, forming chains propagating along [010]. These chains are linked through O—H⋯Cl hydrogen bonds involving the water molecule and the chloride anion, which form a diamond core, giving rise to the formation of two-dimensional networks lying parallel to (10-2). Two π–π interactions involving the imidazolium ring with the benzene and phenol rings [centroid–centroid distances = 3.859 (3) and 3.602 (3) Å, respectively], contribute to this second dimension. A strong O—H⋯O hydrogen bond involving the water molecule and the phenol substituent on the benzimidazole unit links the networks, forming a three-dimensional structure.
Related literature
For biological properties of benzimidazoles and their applications, see: Ansari & Lal (2009); Laryea et al. (2010); Mohan et al. (2011); Refaat (2010); Zhou et al. (2013); Khan et al. (2012). For their use in crystal-engineering, see: Cai et al. (2002). For standard bond lengths, see: Allen et al. (1987). For the structures of benzimidazole halohydrates, see: Akkurt et al. (2010); Baktır et al. (2010). For the microwave synthesis of neutral 4-(1H-benzimidazol-2-yl)phenol, see: Navarrete-Vázquez et al. (2006). For its see: Zhan et al. (2007).
Experimental
Crystal data
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Data collection
Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97, WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).
Supporting information
10.1107/S1600536813023441/su2637sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536813023441/su2637Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536813023441/su2637Isup3.cml
The neutral derivative of the title compound, 4-(1H-benzimidazol-2-yl)phenol, was synthesized following a reported procedure (Navarrete-Vázquez et al., 2006). The reaction of 0.257 g (2.38 mmol) of 1,3-phenylenediamine, 0.290 g (2.38 mmol) of 4-hydroxybenzaldehyde and 0.452 g (2.38 mmol) of Na2S2O5 in 4 ml of DMSO as solvent, heated at 423 K for 15 min in a microwave oven gave a 94% yield of the neutral compound. Colourless block-like crystals of the title compound were obtained by crystallization of this neutral compound in a THF solution with a few drops of an aqueous solution of HCl (10%).
The OH, water and NH H atoms could be located in Fourier difference maps. The water H atoms were refined as riding atoms with Uiso(H)= 1.5Ueq(O). In the final cycles of
the OH, NH and C-bound H atoms were positioned geometrically and treated as riding atoms: O-H = 0.82 Å, N—H = 0.86 Å, C—H = 0.93 Å for CH H atoms, with Uiso(H) = 1.5Ueq(O) and = 1.2Ueq(N,C) for other H atoms.Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell
CrysAlis CCD (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).Fig. 1. The molecular structure of the title compound, with atom labelling. The displacement ellipsoids are drawn at the 30% probability level. | |
Fig. 2. The crystal packing of the title compound viewed along direction [101]. The hydrogen bonds and centroid-centroid interactions are shown as dashed lines (see Table 1 for details). H atoms not involved in hydrogen bonding have been omitted for clarity. |
C13H11N2O+·Cl−·H2O | F(000) = 1104 |
Mr = 264.70 | Dx = 1.376 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 600 reflections |
a = 10.3225 (5) Å | θ = 20–25° |
b = 16.3159 (5) Å | µ = 0.29 mm−1 |
c = 15.4618 (8) Å | T = 293 K |
β = 101.071 (5)° | Block, colourless |
V = 2555.6 (2) Å3 | 0.38 × 0.33 × 0.28 × 0.15 (radius) mm |
Z = 8 |
Oxford Diffraction Xcalibur Ruby Gemini diffractometer | 2519 independent reflections |
Graphite monochromator | 2032 reflections with I > 2σ(I) |
Detector resolution: 10.434 pixels mm-1 | Rint = 0.028 |
ω scans | θmax = 26.2°, θmin = 2.4° |
Absorption correction: for a sphere [the interpolation procedure of (Dwiggins, 1975) was used with some modification] | h = −12→10 |
Tmin = 0.861, Tmax = 0.862 | k = −20→20 |
12720 measured reflections | l = −19→19 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.043 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0595P)2 + 1.2001P] where P = (Fo2 + 2Fc2)/3 |
2519 reflections | (Δ/σ)max = 0.002 |
163 parameters | Δρmax = 0.24 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
C13H11N2O+·Cl−·H2O | V = 2555.6 (2) Å3 |
Mr = 264.70 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 10.3225 (5) Å | µ = 0.29 mm−1 |
b = 16.3159 (5) Å | T = 293 K |
c = 15.4618 (8) Å | 0.38 × 0.33 × 0.28 × 0.15 (radius) mm |
β = 101.071 (5)° |
Oxford Diffraction Xcalibur Ruby Gemini diffractometer | 2519 independent reflections |
Absorption correction: for a sphere [the interpolation procedure of (Dwiggins, 1975) was used with some modification] | 2032 reflections with I > 2σ(I) |
Tmin = 0.861, Tmax = 0.862 | Rint = 0.028 |
12720 measured reflections |
R[F2 > 2σ(F2)] = 0.043 | 0 restraints |
wR(F2) = 0.124 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.24 e Å−3 |
2519 reflections | Δρmin = −0.19 e Å−3 |
163 parameters |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
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. |
x | y | z | Uiso*/Ueq | ||
O13 | −0.24260 (17) | 0.03354 (10) | −0.00034 (11) | 0.0774 (6) | |
N1 | 0.26708 (17) | 0.19303 (9) | 0.25356 (11) | 0.0574 (5) | |
N3 | 0.30346 (16) | 0.06482 (9) | 0.28407 (11) | 0.0555 (5) | |
C2 | 0.2213 (2) | 0.11736 (10) | 0.23396 (13) | 0.0513 (6) | |
C4 | 0.5115 (2) | 0.08213 (13) | 0.39988 (15) | 0.0675 (8) | |
C5 | 0.5938 (3) | 0.14242 (15) | 0.44198 (17) | 0.0740 (9) | |
C6 | 0.5692 (3) | 0.22515 (15) | 0.42173 (17) | 0.0773 (9) | |
C7 | 0.4630 (3) | 0.25048 (13) | 0.35978 (17) | 0.0724 (8) | |
C8 | 0.3799 (2) | 0.19009 (11) | 0.31768 (13) | 0.0565 (6) | |
C9 | 0.4039 (2) | 0.10732 (11) | 0.33766 (13) | 0.0559 (6) | |
C10 | 0.1031 (2) | 0.09650 (11) | 0.17127 (12) | 0.0522 (6) | |
C11 | 0.0230 (2) | 0.15718 (12) | 0.12455 (15) | 0.0647 (7) | |
C12 | −0.0923 (2) | 0.13790 (13) | 0.06684 (15) | 0.0661 (8) | |
C13 | −0.1307 (2) | 0.05700 (13) | 0.05431 (13) | 0.0587 (7) | |
C14 | −0.0528 (2) | −0.00400 (12) | 0.10052 (15) | 0.0643 (7) | |
C15 | 0.0623 (2) | 0.01506 (11) | 0.15739 (14) | 0.0585 (7) | |
O1 | 0.12352 (19) | 0.35642 (11) | 0.39008 (13) | 0.0917 (7) | |
Cl1 | 0.19078 (6) | 0.37204 (3) | 0.19429 (4) | 0.0720 (2) | |
H1 | 0.23133 | 0.23718 | 0.22961 | 0.0688* | |
H3 | 0.29490 | 0.01237 | 0.28299 | 0.0665* | |
H4 | 0.52758 | 0.02694 | 0.41271 | 0.0809* | |
H5 | 0.66666 | 0.12785 | 0.48448 | 0.0888* | |
H6 | 0.62665 | 0.26436 | 0.45120 | 0.0927* | |
H7 | 0.44771 | 0.30569 | 0.34671 | 0.0868* | |
H11 | 0.04805 | 0.21183 | 0.13257 | 0.0776* | |
H12 | −0.14403 | 0.17927 | 0.03646 | 0.0793* | |
H13 | −0.27318 | 0.07238 | −0.03130 | 0.1160* | |
H14 | −0.07904 | −0.05847 | 0.09280 | 0.0771* | |
H15 | 0.11382 | −0.02671 | 0.18711 | 0.0702* | |
H1A | 0.03995 | 0.35369 | 0.36137 | 0.1376* | |
H1B | 0.15177 | 0.35970 | 0.33730 | 0.1376* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O13 | 0.0655 (11) | 0.0665 (10) | 0.0901 (11) | −0.0031 (7) | −0.0101 (8) | −0.0040 (8) |
N1 | 0.0608 (11) | 0.0332 (7) | 0.0725 (10) | 0.0002 (6) | −0.0011 (8) | 0.0030 (6) |
N3 | 0.0593 (11) | 0.0332 (7) | 0.0704 (10) | −0.0001 (6) | 0.0036 (8) | 0.0027 (6) |
C2 | 0.0570 (12) | 0.0358 (8) | 0.0613 (10) | −0.0001 (7) | 0.0116 (9) | 0.0013 (7) |
C4 | 0.0654 (15) | 0.0513 (11) | 0.0802 (14) | 0.0045 (9) | 0.0003 (11) | 0.0078 (10) |
C5 | 0.0639 (16) | 0.0714 (14) | 0.0795 (15) | 0.0028 (11) | −0.0043 (12) | 0.0006 (11) |
C6 | 0.0703 (17) | 0.0622 (13) | 0.0914 (16) | −0.0098 (11) | −0.0043 (12) | −0.0126 (11) |
C7 | 0.0752 (16) | 0.0419 (10) | 0.0929 (15) | −0.0047 (9) | −0.0016 (12) | −0.0066 (10) |
C8 | 0.0580 (13) | 0.0413 (9) | 0.0676 (11) | −0.0001 (8) | 0.0053 (9) | 0.0012 (8) |
C9 | 0.0573 (13) | 0.0423 (9) | 0.0662 (11) | −0.0003 (8) | 0.0072 (9) | 0.0020 (8) |
C10 | 0.0565 (12) | 0.0399 (9) | 0.0596 (10) | 0.0007 (8) | 0.0097 (9) | 0.0016 (7) |
C11 | 0.0710 (15) | 0.0389 (9) | 0.0784 (13) | −0.0029 (9) | −0.0002 (11) | 0.0037 (9) |
C12 | 0.0643 (15) | 0.0545 (11) | 0.0738 (13) | 0.0066 (9) | −0.0010 (11) | 0.0102 (9) |
C13 | 0.0531 (13) | 0.0574 (11) | 0.0633 (11) | −0.0001 (9) | 0.0056 (9) | −0.0040 (8) |
C14 | 0.0651 (14) | 0.0437 (10) | 0.0799 (13) | −0.0025 (9) | 0.0034 (11) | −0.0049 (9) |
C15 | 0.0589 (13) | 0.0410 (9) | 0.0719 (12) | 0.0026 (8) | 0.0030 (10) | 0.0009 (8) |
O1 | 0.0786 (13) | 0.0885 (12) | 0.0977 (13) | −0.0048 (9) | −0.0090 (10) | −0.0099 (10) |
Cl1 | 0.0792 (4) | 0.0328 (3) | 0.0941 (4) | −0.0001 (2) | −0.0079 (3) | 0.0024 (2) |
O13—C13 | 1.349 (3) | C8—C9 | 1.397 (3) |
O13—H13 | 0.8200 | C10—C11 | 1.399 (3) |
O1—H1B | 0.9200 | C10—C15 | 1.398 (3) |
O1—H1A | 0.8900 | C11—C12 | 1.380 (3) |
N1—C8 | 1.378 (3) | C12—C13 | 1.381 (3) |
N1—C2 | 1.336 (2) | C13—C14 | 1.388 (3) |
N3—C9 | 1.383 (3) | C14—C15 | 1.371 (3) |
N3—C2 | 1.342 (2) | C4—H4 | 0.9300 |
N1—H1 | 0.8600 | C5—H5 | 0.9300 |
N3—H3 | 0.8600 | C6—H6 | 0.9300 |
C2—C10 | 1.446 (3) | C7—H7 | 0.9300 |
C4—C5 | 1.379 (3) | C11—H11 | 0.9300 |
C4—C9 | 1.385 (3) | C12—H12 | 0.9300 |
C5—C6 | 1.398 (3) | C14—H14 | 0.9300 |
C6—C7 | 1.374 (4) | C15—H15 | 0.9300 |
C7—C8 | 1.384 (3) | ||
C13—O13—H13 | 109.00 | C10—C11—C12 | 121.57 (18) |
H1A—O1—H1B | 90.00 | C11—C12—C13 | 119.82 (19) |
C2—N1—C8 | 110.15 (16) | C12—C13—C14 | 119.39 (19) |
C2—N3—C9 | 110.09 (15) | O13—C13—C12 | 123.18 (19) |
C2—N1—H1 | 125.00 | O13—C13—C14 | 117.43 (19) |
C8—N1—H1 | 125.00 | C13—C14—C15 | 120.82 (18) |
C2—N3—H3 | 125.00 | C10—C15—C14 | 120.82 (18) |
C9—N3—H3 | 125.00 | C5—C4—H4 | 121.00 |
N1—C2—N3 | 107.61 (17) | C9—C4—H4 | 121.00 |
N1—C2—C10 | 125.87 (17) | C6—C5—H5 | 120.00 |
N3—C2—C10 | 126.51 (16) | C4—C5—H5 | 120.00 |
C5—C4—C9 | 117.1 (2) | C5—C6—H6 | 119.00 |
C4—C5—C6 | 121.0 (3) | C7—C6—H6 | 119.00 |
C5—C6—C7 | 122.2 (2) | C8—C7—H7 | 122.00 |
C6—C7—C8 | 117.0 (2) | C6—C7—H7 | 121.00 |
N1—C8—C7 | 132.49 (18) | C10—C11—H11 | 119.00 |
C7—C8—C9 | 121.1 (2) | C12—C11—H11 | 119.00 |
N1—C8—C9 | 106.40 (16) | C13—C12—H12 | 120.00 |
N3—C9—C4 | 132.57 (17) | C11—C12—H12 | 120.00 |
C4—C9—C8 | 121.68 (18) | C13—C14—H14 | 120.00 |
N3—C9—C8 | 105.76 (17) | C15—C14—H14 | 120.00 |
C11—C10—C15 | 117.56 (18) | C10—C15—H15 | 120.00 |
C2—C10—C15 | 121.15 (17) | C14—C15—H15 | 120.00 |
C2—C10—C11 | 121.25 (17) | ||
C8—N1—C2—N3 | −0.5 (2) | C6—C7—C8—N1 | −179.9 (2) |
C8—N1—C2—C10 | 178.44 (19) | C6—C7—C8—C9 | −0.1 (4) |
C2—N1—C8—C7 | −179.9 (3) | N1—C8—C9—N3 | 0.0 (2) |
C2—N1—C8—C9 | 0.3 (2) | N1—C8—C9—C4 | 179.59 (19) |
C9—N3—C2—N1 | 0.5 (2) | C7—C8—C9—N3 | −179.8 (2) |
C9—N3—C2—C10 | −178.43 (19) | C7—C8—C9—C4 | −0.2 (3) |
C2—N3—C9—C4 | −179.8 (2) | C2—C10—C11—C12 | −177.8 (2) |
C2—N3—C9—C8 | −0.3 (2) | C15—C10—C11—C12 | 0.1 (3) |
N1—C2—C10—C11 | −0.6 (3) | C2—C10—C15—C14 | 177.3 (2) |
N1—C2—C10—C15 | −178.4 (2) | C11—C10—C15—C14 | −0.6 (3) |
N3—C2—C10—C11 | 178.1 (2) | C10—C11—C12—C13 | 0.0 (3) |
N3—C2—C10—C15 | 0.3 (3) | C11—C12—C13—O13 | 179.4 (2) |
C9—C4—C5—C6 | −0.4 (4) | C11—C12—C13—C14 | 0.4 (3) |
C5—C4—C9—N3 | 180.0 (2) | O13—C13—C14—C15 | −179.9 (2) |
C5—C4—C9—C8 | 0.5 (3) | C12—C13—C14—C15 | −0.9 (3) |
C4—C5—C6—C7 | 0.1 (4) | C13—C14—C15—C10 | 1.0 (3) |
C5—C6—C7—C8 | 0.1 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1 | 0.86 | 2.29 | 3.1167 (16) | 162 |
N3—H3···Cl1i | 0.86 | 2.32 | 3.1625 (16) | 168 |
O1—H1A···Cl1ii | 0.89 | 2.39 | 3.266 (2) | 167 |
O1—H1B···Cl1 | 0.92 | 2.33 | 3.243 (2) | 171 |
O13—H13···O1iii | 0.82 | 1.86 | 2.666 (3) | 166 |
Symmetry codes: (i) −x+1/2, y−1/2, −z+1/2; (ii) −x, y, −z+1/2; (iii) x−1/2, −y+1/2, z−1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1 | 0.86 | 2.29 | 3.1167 (16) | 162 |
N3—H3···Cl1i | 0.86 | 2.32 | 3.1625 (16) | 168 |
O1—H1A···Cl1ii | 0.89 | 2.39 | 3.266 (2) | 167 |
O1—H1B···Cl1 | 0.92 | 2.33 | 3.243 (2) | 171 |
O13—H13···O1iii | 0.82 | 1.86 | 2.666 (3) | 166 |
Symmetry codes: (i) −x+1/2, y−1/2, −z+1/2; (ii) −x, y, −z+1/2; (iii) x−1/2, −y+1/2, z−1/2. |
Acknowledgements
The authors gratefully acknowledge financial support from Conacyt and SIP-IPN.
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Benzimidazoles are a class of compounds with a wide variety of biological properties (Mohan et al., 2011; Refaat, 2010; Laryea et al., 2010; Ansari & Lal, 2009) and have applications in crystal-engineering (Cai et al., 2002). Particularly, the neutral derivative of the title compound has recently been reported as having good antimicrobial (Zhou et al., 2013) and β-glucuronidase inhibitory activity (Khan et al., 2012). Herein we report on the crystal structure of the title compound.
The title compound crystallizes as the monohydrate of a hydrochloride salt, Fig. 1. Bond lengths (Allen et al., 1987) and angles are within normal ranges. The phenol and benzimidazole rings are almost coplanar with a dihedral angle of 3.18 (4) °.
One water molecule was included in the asymmetric unit which, besides the chloride anion, directs the organization in the lattice forming hydrogen bonding interactions (Table 1 and Fig. 2), as has been observed in other halohydrates (Akkurt et al., 2010; Baktır et al., 2010).
In the crystal, the chloride anion and the benzimidazole molecule give rise to the first dimension through two N+—H···Cl- interactions (Table 1); forming chains propagating along [010].
The water molecule and chloride anion form a diamond core through O—H···Cl hydrogen bonds, giving rise to the second dimension (Table 1); forming two-dimensional networks lying parallel to plane (10-2).
Two contributions from aromatic systems of the type π–π between the electronic deficient imidazolium ring, [N1/N2/C2/C8/C9 with centroid Cg1], with both electronic rich benzene, [C4-C9 with centroid Cg2], and phenol, [C10-C15 with centroid Cg3], rings contribute to the development in the second dimension [Cg1···Cg2i = 3.6017 (13) Å and Cg1···Cg3ii = 3.8593 (12) Å; symmetry codes: (i) -x+1, y, -z+1/2; (ii) -x, y, -z+1/2].
The third dimension is built by a strong O-H···O hydrogen bond between the water molecule, as the acceptor, with the phenol group of benzimidazole, as donor (Table 1 and Fig. 2); forming a three-dimensional structure.
The molecular structure of the title compound is similar to that of the neutral compound 4-(1H-benzimidazol-2-yl)phenol (Zhan et al., 2007), where the dihedral angle between the benzimidazole ring system and the phenol ring is 8.11 (5) °. In the crystal lattice, only N—H···O and O—H···N (benzimidazole-phenol) hydrogen bonds are present.