Literature DB >> 23424540

2-[4-(Trifluoro-meth-oxy)phen-yl]-1H-benzimidazole.

Nikhath Fathima¹, M S Krishnamurthy, Noor Shahina Begum.

Abstract

In the title compound, C(14)H(9)F(3)N(2)O, the best planes of the benzimidazole group and benzene ring form a dihedral angle of 26.68 (3)°. In the crystal, N-H⋯N hydrogen bonds link the mol-ecules into infinite chains parallel to the c axis. Stacking inter-actions between the benzimidazole groups [centroid-centroid distance = 3.594 (5) Å] assemble the mol-ecules into layers parallel to (100). The trifluoro-methyl group is disordered over three sets of sites with site-occupancy factors of 0.787 (4), 0.107 (7) and 0.106 (7).

Entities: Chemical Disease Gene

Year: 2013 PMID： 23424540 PMCID： PMC3569794 DOI： 10.1107/S1600536813001220

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

Related literature

For therapeutic and medicinal properties of benzimidazole derivatives, see: Chimirri et al. (1991 ▶); Benavides et al. (1995 ▶); Ishihara et al. (1994 ▶); Kubo et al. (1993 ▶). For related structures, see: Jian et al. (2006 ▶); Rashid, Tahir, Yusof et al. (2007 ▶); Rashid, Tahir, Kanwal et al. (2007 ▶).

Experimental

Crystal data

C14H9F3N2O M = 278.23 Monoclinic, a = 14.476 (6) Å b = 9.312 (4) Å c = 9.835 (4) Å β = 108.192 (8)° V = 1259.5 (9) Å3 Z = 4 Mo Kα radiation μ = 0.13 mm−1 T = 296 K 0.18 × 0.16 × 0.16 mm

Data collection

Bruker SMART APEX CCD detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 1998 ▶) T min = 0.978, T max = 0.980 6284 measured reflections 2209 independent reflections 1333 reflections with I > 2σ(I) R int = 0.077

Refinement

R[F 2 > 2σ(F 2)] = 0.064 wR(F 2) = 0.157 S = 1.00 2209 reflections 210 parameters 21 restraints H-atom parameters constrained Δρmax = 0.26 e Å−3 Δρmin = −0.22 e Å−3 Data collection: SMART (Bruker, 1998 ▶); cell refinement: SAINT-Plus (Bruker, 1998 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶) and CAMERON (Watkin et al., 1996 ▶); software used to prepare material for publication: WinGX (Farrugia, 2012 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813001220/gk2550sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813001220/gk2550Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813001220/gk2550Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₄H₉F₃N₂O	F(000) = 568
M_r = 278.23	D_x = 1.467 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2209 reflections
a = 14.476 (6) Å	θ = 2.6–25.0°
b = 9.312 (4) Å	µ = 0.13 mm⁻¹
c = 9.835 (4) Å	T = 296 K
β = 108.192 (8)°	Block, yellow
V = 1259.5 (9) Å³	0.18 × 0.16 × 0.16 mm
Z = 4

Bruker SMART APEX CCD detector diffractometer	2209 independent reflections
Radiation source: fine-focus sealed tube	1333 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.077
ω scans	θ_max = 25.0°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 1998)	h = −17→15
T_min = 0.978, T_max = 0.980	k = −8→11
6284 measured reflections	l = −11→11

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)] = 0.064	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.157	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.0655P)²] where P = (F_o² + 2F_c²)/3
2209 reflections	(Δ/σ)_max = 0.001
210 parameters	Δρ_max = 0.26 e Å⁻³
21 restraints	Δρ_min = −0.22 e Å⁻³

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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	Occ. (<1)
C1	0.3459 (2)	0.8348 (3)	0.4611 (3)	0.0246 (8)
C2	0.3309 (2)	0.9562 (3)	0.3748 (3)	0.0297 (8)
H2	0.3786	0.9857	0.3359	0.036*
C3	0.2445 (2)	1.0344 (4)	0.3460 (4)	0.0361 (9)
H3	0.2352	1.1177	0.2912	0.043*
C4	0.1735 (2)	0.9856 (4)	0.4004 (4)	0.0333 (9)
C6	0.1860 (2)	0.8644 (3)	0.4854 (3)	0.0321 (9)
H6	0.1368	0.8332	0.5206	0.039*
C7	0.2734 (2)	0.7900 (3)	0.5172 (3)	0.0284 (8)
H7	0.2836	0.7097	0.5763	0.034*
C8	0.4390 (2)	0.7578 (3)	0.4969 (3)	0.0245 (8)
C9	0.5675 (2)	0.6361 (3)	0.6072 (3)	0.0260 (8)
C10	0.6411 (2)	0.5565 (3)	0.7050 (3)	0.0316 (9)
H10	0.6339	0.5228	0.7901	0.038*
C11	0.7245 (2)	0.5305 (3)	0.6695 (4)	0.0327 (9)
H11	0.7743	0.4778	0.7323	0.039*
C12	0.7367 (2)	0.5806 (3)	0.5422 (3)	0.0311 (8)
H12	0.7946	0.5624	0.5233	0.037*
C13	0.6639 (2)	0.6567 (3)	0.4443 (3)	0.0277 (8)
H13	0.6709	0.6883	0.3583	0.033*
C14	0.5804 (2)	0.6840 (3)	0.4794 (3)	0.0233 (8)
O1	0.08661 (17)	1.0648 (3)	0.3804 (3)	0.0460 (7)
N1	0.47847 (18)	0.6843 (3)	0.6176 (3)	0.0272 (7)
N2	0.49671 (18)	0.7606 (3)	0.4113 (3)	0.0260 (7)
H21	0.4836	0.8024	0.3295	0.031*
C5	0.0271 (4)	1.0787 (7)	0.2470 (6)	0.0534 (16)	0.787 (4)
F1	−0.0537 (4)	1.1368 (8)	0.2540 (9)	0.0740 (15)	0.787 (4)
F2	0.0616 (3)	1.1639 (8)	0.1658 (6)	0.0954 (17)	0.787 (4)
F3	0.0071 (4)	0.9548 (6)	0.1788 (7)	0.110 (2)	0.787 (4)
C51	0.0312 (14)	1.109 (2)	0.268 (3)	0.047 (6)*	0.107 (7)
F11	−0.0580 (16)	1.145 (3)	0.259 (7)	0.047 (6)*	0.107 (7)
F21	0.0781 (14)	1.2304 (19)	0.261 (3)	0.047 (6)*	0.107 (7)
F31	0.030 (3)	1.033 (3)	0.154 (4)	0.047 (6)*	0.107 (7)
C52	0.010 (2)	1.062 (3)	0.270 (3)	0.056 (7)*	0.106 (7)
F12	−0.066 (4)	1.144 (3)	0.251 (8)	0.056 (7)*	0.106 (7)
F22	−0.0187 (16)	0.928 (2)	0.282 (3)	0.056 (7)*	0.106 (7)
F32	0.037 (4)	1.064 (4)	0.154 (4)	0.056 (7)*	0.106 (7)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0277 (18)	0.0240 (18)	0.0207 (17)	−0.0013 (14)	0.0055 (14)	−0.0033 (14)
C2	0.031 (2)	0.037 (2)	0.0256 (18)	0.0045 (15)	0.0146 (15)	0.0039 (16)
C3	0.040 (2)	0.038 (2)	0.033 (2)	0.0027 (17)	0.0134 (17)	0.0087 (17)
C4	0.030 (2)	0.035 (2)	0.032 (2)	0.0030 (16)	0.0069 (16)	−0.0047 (17)
C6	0.030 (2)	0.033 (2)	0.035 (2)	−0.0056 (15)	0.0115 (16)	−0.0059 (17)
C7	0.033 (2)	0.0275 (19)	0.0244 (18)	−0.0029 (15)	0.0087 (15)	−0.0031 (15)
C8	0.0320 (19)	0.0228 (18)	0.0204 (17)	−0.0048 (14)	0.0105 (15)	−0.0034 (14)
C9	0.0305 (19)	0.0217 (18)	0.0248 (18)	−0.0018 (14)	0.0069 (14)	−0.0029 (14)
C10	0.043 (2)	0.028 (2)	0.0243 (19)	0.0028 (16)	0.0104 (16)	−0.0006 (15)
C11	0.038 (2)	0.0272 (19)	0.030 (2)	0.0044 (16)	0.0060 (16)	−0.0005 (16)
C12	0.032 (2)	0.0268 (19)	0.034 (2)	0.0023 (15)	0.0106 (16)	−0.0014 (16)
C13	0.036 (2)	0.0242 (18)	0.0250 (18)	0.0006 (15)	0.0132 (15)	−0.0037 (15)
C14	0.0318 (19)	0.0179 (17)	0.0206 (17)	−0.0004 (14)	0.0087 (14)	−0.0005 (14)
O1	0.0353 (15)	0.0582 (18)	0.0454 (16)	0.0162 (12)	0.0137 (13)	0.0099 (13)
N1	0.0327 (16)	0.0248 (15)	0.0238 (15)	−0.0002 (12)	0.0085 (12)	−0.0020 (12)
N2	0.0335 (16)	0.0241 (15)	0.0207 (14)	0.0028 (12)	0.0089 (12)	0.0042 (12)
C5	0.038 (3)	0.065 (5)	0.054 (4)	0.012 (3)	0.010 (3)	0.003 (4)
F1	0.026 (2)	0.084 (3)	0.111 (3)	0.0205 (17)	0.021 (2)	0.043 (2)
F2	0.056 (2)	0.154 (5)	0.086 (3)	0.030 (3)	0.034 (2)	0.078 (3)
F3	0.076 (3)	0.085 (3)	0.116 (4)	0.016 (3)	−0.045 (3)	−0.042 (3)

C1—C2	1.390 (4)	C11—C12	1.397 (5)
C1—C7	1.393 (4)	C11—H11	0.9300
C1—C8	1.469 (4)	C12—C13	1.380 (4)
C2—C3	1.397 (4)	C12—H12	0.9300
C2—H2	0.9300	C13—C14	1.380 (4)
C3—C4	1.376 (5)	C13—H13	0.9300
C3—H3	0.9300	C14—N2	1.385 (4)
C4—C6	1.382 (4)	O1—C5	1.332 (6)
C4—O1	1.417 (4)	N2—H21	0.8600
C6—C7	1.391 (4)	C5—F1	1.309 (5)
C6—H6	0.9300	C5—F3	1.321 (7)
C7—H7	0.9300	C5—F2	1.329 (8)
C8—N1	1.334 (4)	C51—F11	1.309 (5)
C8—N2	1.358 (4)	C51—F31	1.321 (7)
C9—N1	1.399 (4)	C51—F21	1.329 (8)
C9—C14	1.400 (4)	C52—F12	1.309 (5)
C9—C10	1.403 (4)	C52—F32	1.321 (7)
C10—C11	1.379 (5)	C52—F22	1.329 (8)
C10—H10	0.9300

C2—C1—C7	119.5 (3)	C10—C11—H11	118.9
C2—C1—C8	120.0 (3)	C12—C11—H11	118.9
C7—C1—C8	120.4 (3)	C13—C12—C11	121.0 (3)
C1—C2—C3	120.5 (3)	C13—C12—H12	119.5
C1—C2—H2	119.8	C11—C12—H12	119.5
C3—C2—H2	119.8	C14—C13—C12	117.2 (3)
C4—C3—C2	118.6 (3)	C14—C13—H13	121.4
C4—C3—H3	120.7	C12—C13—H13	121.4
C2—C3—H3	120.7	C13—C14—N2	132.6 (3)
C3—C4—C6	122.1 (3)	C13—C14—C9	122.6 (3)
C3—C4—O1	120.8 (3)	N2—C14—C9	104.8 (3)
C6—C4—O1	116.9 (3)	C5—O1—C4	117.5 (3)
C4—C6—C7	118.7 (3)	C8—N1—C9	104.3 (3)
C4—C6—H6	120.6	C8—N2—C14	107.8 (3)
C7—C6—H6	120.6	C8—N2—H21	126.1
C6—C7—C1	120.4 (3)	C14—N2—H21	126.1
C6—C7—H7	119.8	F1—C5—F3	109.3 (5)
C1—C7—H7	119.8	F1—C5—F2	107.1 (5)
N1—C8—N2	112.7 (3)	F3—C5—F2	106.3 (6)
N1—C8—C1	124.7 (3)	F1—C5—O1	107.6 (5)
N2—C8—C1	122.5 (3)	F3—C5—O1	112.8 (5)
N1—C9—C14	110.4 (3)	F2—C5—O1	113.6 (5)
N1—C9—C10	129.7 (3)	F11—C51—F31	109.3 (5)
C14—C9—C10	119.9 (3)	F11—C51—F21	107.1 (5)
C11—C10—C9	117.1 (3)	F31—C51—F21	106.3 (6)
C11—C10—H10	121.4	F12—C52—F32	109.3 (5)
C9—C10—H10	121.4	F12—C52—F22	107.1 (5)
C10—C11—C12	122.2 (3)	F32—C52—F22	106.3 (6)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H21···N1ⁱ	0.86	2.07	2.864 (4)	154

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H21⋯N1ⁱ	0.86	2.07	2.864 (4)	154

Symmetry code: (i) .

5 in total

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2. Anti-HIV agents II. Synthesis and in vitro anti-HIV activity of novel 1H,3H-thiazolo[3,4-a]benzimidazoles.

Authors: A Chimirri; S Grasso; A M Monforte; P Monforte; M Zappala
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3. In vivo and in vitro interaction of the novel selective histamine H1 receptor antagonist mizolastine with H1 receptors in the rodent.

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4. Nonpeptide angiotensin II receptor antagonists. Synthesis and biological activity of benzimidazolecarboxylic acids.

Authors: K Kubo; Y Kohara; E Imamiya; Y Sugiura; Y Inada; Y Furukawa; K Nishikawa; T Naka
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5. Effect on gastric mucus of the proton pump inhibitor leminoprazole and its cytoprotective action against ethanol-induced gastric injury in rats.

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