Literature DB >> 24427105

2-(4-Hy-droxy-phen-yl)-1H-benzimidazol-3-ium chloride monohydrate.

Jazmin E González-Padilla¹, Martha Cecila Rosales-Hernández¹, Itzia I Padilla-Martínez², Efren V García-Báez², Susana Rojas-Lima³.

Abstract

The title mol-ecular 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 mol-ecule 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 inter-actions 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 mol-ecule and the phenol substituent on the benzimidazole unit links the networks, forming a three-dimensional structure.

Entities: Chemical Disease Species

Year: 2013 PMID： 24427105 PMCID： PMC3884505 DOI： 10.1107/S1600536813023441

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

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 crystal structure, see: Zhan et al. (2007 ▶).

Experimental

Crystal data

C13H11N2O+·Cl−·H2O M = 264.70 Monoclinic, a = 10.3225 (5) Å b = 16.3159 (5) Å c = 15.4618 (8) Å β = 101.071 (5)° V = 2555.6 (2) Å3 Z = 8 Mo Kα radiation μ = 0.29 mm−1 T = 293 K 0.38 × 0.33 × 0.28 × 0.15 (radius) mm

Data collection

Oxford Diffraction Xcalibur Ruby Gemini diffractometer Absorption correction: for a sphere [the interpolation procedure of (Dwiggins, 1975 ▶) was used with some modification] T min = 0.861, T max = 0.862 12720 measured reflections 2519 independent reflections 2032 reflections with I > 2σ(I) R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.043 wR(F 2) = 0.124 S = 1.06 2519 reflections 163 parameters H-atom parameters constrained Δρmax = 0.24 e Å−3 Δρmin = −0.19 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2009 ▶); cell refinement: 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 ▶). Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S1600536813023441/su2637sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813023441/su2637Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813023441/su2637Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₃H₁₁N₂O⁺·Cl⁻·H₂O	F(000) = 1104
M_r = 264.70	D_x = 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	R_int = 0.028
ω scans	θ_max = 26.2°, θ_min = 2.4°
Absorption correction: for a sphere [the interpolation procedure of (Dwiggins, 1975) was used with some modification]	h = −12→10
T_min = 0.861, T_max = 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(F_o²) + (0.0595P)² + 1.2001P] where P = (F_o² + 2F_c²)/3
2519 reflections	(Δ/σ)_max = 0.002
163 parameters	Δρ_max = 0.24 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

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	U_iso*/U_eq
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

Table 1

Hydrogen-bond geometry (Å, °)

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) ; (ii) ; (iii) .

8 in total

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Journal: Eur J Med Chem Date: 2010-03-25 Impact factor: 6.514

2. Synthesis and β-glucuronidase inhibitory potential of benzimidazole derivatives.

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3. A short history of SHELX.

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

4. Characterization of the cytotoxic properties of the benzimidazole fungicides, benomyl and carbendazim, in human tumour cell lines and primary cultures of patient tumour cells.

Authors: Daniel Laryea; Joachim Gullbo; Anders Isaksson; Rolf Larsson; Peter Nygren
Journal: Anticancer Drugs Date: 2010-01 Impact factor: 2.248