Crystal structure of 2-(4-chloro-3-fluoro­phen­yl)-1H-benzimidazole

Krishnamurthy, M.S.; Begum, N.S.

doi:10.1107/S2056989015008683

organic compounds

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Volume 71| Part 6| June 2015| Pages o387-o388

doi:10.1107/S2056989015008683

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Crystal structure of 2-(4-chloro-3-fluorophenyl)-1H-benzimidazole

M. S. Krishnamurthy ^a and Noor Shahina Begum ^a ^*

^aDepartment of Studies in Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, Karnataka, India
^*Correspondence e-mail: noorsb@rediffmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 11 April 2015; accepted 5 May 2015; online 9 May 2015)

In the title compound, C₁₃H₈ClFN₂, the dihedral angle between the plane of the benzimidazole ring system (r.m.s. deviation = 0.022 Å) and the benzene ring is 26.90 (8)°. The F atom at the meta position of the benzene ring is disordered over two sites in a 0.843 (4):0.157 (4) ratio. In the crystal, molecules are linked by N—H⋯N hydrogen bonds, forming infinite C(4) chains propagating along [010]. In addition, weak C—H⋯π and π–π interactions [shortest centroid–centroid separation = 3.6838 (12) Å] are observed, which link the chains into a three-dimensional network.

Keywords: crystal structure; benzimidazole; fluorine-containing compound; hydrogen bonding; C—H⋯π interactions; π–π interactions.

CCDC reference: 1063160

1. Related literature

For therapeutic and medicinal properties of benzimidazole derivatives, see: Ozden et al. (2004 ); Easmon et al. (2001 ); Thakurdesai et al. (2007 ); Ansari & Lal (2009 ). For the bioactivity of fluorine-containing compounds, see: Ulrich (2004 ). For related structures, see: Fathima et al. (2013 ); Jian et al. (2006 ); Krishnamurthy & Begum (2014 ); Krishnamurthy et al. (2013 ); Rashid et al. 2007 ); Jayamoorthy et al. (2012 ); Yoon et al. (2012 ). Positional disorder is common in many organic compounds containing fluorine in either the ortho or meta position, see: Chopra & Guru Row (2008 ); Nayak et al. (2011 ). For normal C—F bond lengths, see: Zhang et al. (1998 ).

2. Experimental

2.1. Crystal data

C₁₃H₈ClFN₂
M_r = 246.66
Orthorhombic, P b c a
a = 9.2302 (4) Å
b = 9.8500 (4) Å
c = 23.1347 (9) Å
V = 2103.35 (15) Å³
Z = 8
Mo Kα radiation
μ = 0.35 mm⁻¹
T = 100 K
0.18 × 0.16 × 0.16 mm

2.2. Data collection

Bruker SMART APEX CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 1998 ) T_min = 0.940, T_max = 0.946
23308 measured reflections
1844 independent reflections
1606 reflections with I > 2σ(I)
R_int = 0.043

2.3. Refinement

R[F² > 2σ(F²)] = 0.038
wR(F²) = 0.102
S = 0.95
1844 reflections
164 parameters
H-atom parameters constrained
Δρ_max = 0.56 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the N1/C5/C6/N2/C7 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯N1ⁱ	0.88	2.06	2.924 (1)	166
C3—H3⋯Cgⁱⁱ	0.95	2.92	3.700 (3)	140
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z]$ ; (ii) $[x+{\script{1\over 2}}, y, -z+{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; 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).

Supporting information

CCDC reference: 1063160

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015008683/hb7406sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015008683/hb7406Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015008683/hb7406Isup3.cml

checkCIF report

Comment top

Benzimidazole and their derivatives are known to exhibit a wide variety of pharmacological properties. Benzimidazole is an important pharmacophore and a privileged structure in medicinal chemistry encompassing a diverse range of biological activities such as antibacterial (Ozden et al., 2004), anticancer (Easmon et al., 2001), anti-HIV and anti-inflammatory (Ansari & Lal 2009; Thakurdesai et al., 2007). Benzimidazole and its derivatives can also be used as ligands in the field of coordination Chemistry. In addition, compounds which contain fluorine have special bioactivity (Ulrich, 2004). Herein, we report the crystal structure of the title compound. The molecular structure of the title compound C₁₃H₈ClFN₂ is shown in Fig. 1. It is the fluoro-analogue of our previously reported compounds (Fathima et al., 2013; Krishnamurthy et al., 2013; Krishnamurthy & Begum., 2014). The benzimidazole system is essentially planar, with a dihedral angle of 2.251 (6)° between the planes of the benzene ring and its fused imidazole ring. The whole molecule is nonplanar; the dihedral angle between the benzimidazole ring and the benzene ring is 26.898 (1)°. This value is slightly lower than that observed in related compounds (Jian et al., 2006; Krishnamurthy & Begum, 2014). It was observed that the fluorine atom at the meta position is disordered over two sites, the major occupancy refining to 0.843 (4) and minor occupancy is 0.157 (4). In fact, the C—F bond length associated with the major occupancy fluorine is almost close to the standard C—F bond length (1.345 Å) while the minor occupancy fluorine has a bond length lying between normal value of C—H and C—F bond (Zhang et al., 1998). This type of positional disorder is common in many organic compounds containing fluorine in either the ortho or meta position (Chopra et al., 2008; Nayak et al., 2011). In the crystal structure, the molecules are linked by intermolecular N2—H2···N1 hydrogen bonds to form infinite chains parallel to [010] (Table. 1; Fig. 2). In addition, a weak C—H···π interaction of the type C3—H3···Cg (Cg being the centroid of the benzimidazole ring) link chains into layers parallel to [001] and π–π stacking interactions with a centroid—centroid distance of 3.684 (10) Å connect these layers into a three-dimensional network (Fig. 3).

Related literature top

For therapeutic and medicinal properties of benzimidazole derivatives, see: Ozden et al. (2004); Easmon et al. (2001); Thakurdesai et al. (2007); Ansari & Lal (2009). For the bioactivity of fluorine-containing compounds, see: Ulrich (2004). For related structures, see: Fathima et al. (2013); Jian et al. (2006); Krishnamurthy & Begum (2014); Krishnamurthy et al. (2013); Rashid et al. 2007); Jayamoorthy et al. (2012); Yoon et al. (2012). Positional disorder is common in many organic compounds containing fluorine in either the ortho or meta position, see: Chopra & Guru Row (2008); Nayak et al. (2011). For normal C—F bond lengths, see: Zhang et al. (1998).

Experimental top

The title compound was synthesized by refluxing 3-fluoro, 4-chlorobenzaldehyde (20 mmol, 0.28 g) and o-phenyldiamine (20 mmol, 0.22 g) in benzene (3.0 ml) for 6 hrs on a water bath. The reaction mixture was cooled. The solid separated, was filtered and dried (yield = 0.36 g (76%) and M.P. = 526 K). Yellow blocks were obtained by slow evaporation of an ethyl acetate solution.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT (Bruker, 1998); 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).

Figures top

	Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level.
	Fig. 2. Unit cell packing of the title compound showing N—H···N interactions with dotted lines. H-atoms not involved in hydrogen bonding have been excluded.
	Fig. 3. Unit cell packing showing C—H···π and π–π interactions with dotted lines.

2-(4-Chloro-3-fluorophenyl)-1H-benzimidazole top

Crystal data top

C₁₃H₈ClFN₂	F(000) = 1008
M_r = 246.66	D_x = 1.558 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1844 reflections
a = 9.2302 (4) Å	θ = 2.8–25.0°
b = 9.8500 (4) Å	µ = 0.35 mm⁻¹
c = 23.1347 (9) Å	T = 100 K
V = 2103.35 (15) Å³	Block, yellow
Z = 8	0.18 × 0.16 × 0.16 mm

Data collection top

Bruker SMART APEX CCD diffractometer	1844 independent reflections
Radiation source: fine-focus sealed tube	1606 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.043
ω scans	θ_max = 25.0°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 1998)	h = −10→10
T_min = 0.940, T_max = 0.946	k = −11→11
23308 measured reflections	l = −27→27

Refinement top

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)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.102	H-atom parameters constrained
S = 0.95	w = 1/[σ²(F_o²) + (0.0597P)² + 2.5255P] where P = (F_o² + 2F_c²)/3
1844 reflections	(Δ/σ)_max < 0.001
164 parameters	Δρ_max = 0.56 e Å⁻³
0 restraints	Δρ_min = −0.32 e Å⁻³

Crystal data top

C₁₃H₈ClFN₂	V = 2103.35 (15) Å³
M_r = 246.66	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 9.2302 (4) Å	µ = 0.35 mm⁻¹
b = 9.8500 (4) Å	T = 100 K
c = 23.1347 (9) Å	0.18 × 0.16 × 0.16 mm

Data collection top

Bruker SMART APEX CCD diffractometer	1844 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 1998)	1606 reflections with I > 2σ(I)
T_min = 0.940, T_max = 0.946	R_int = 0.043
23308 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	0 restraints
wR(F²) = 0.102	H-atom parameters constrained
S = 0.95	Δρ_max = 0.56 e Å⁻³
1844 reflections	Δρ_min = −0.32 e Å⁻³
164 parameters

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
N1	0.83007 (18)	0.08322 (16)	0.36167 (7)	0.0175 (4)
N2	0.78338 (17)	−0.13986 (16)	0.35704 (7)	0.0175 (4)
H2	0.7371	−0.2172	0.3616	0.021*
Cl1	0.14851 (5)	0.07660 (6)	0.47297 (3)	0.0291 (2)
C1	1.0106 (2)	−0.2127 (2)	0.30462 (9)	0.0198 (5)
H1	0.9910	−0.3073	0.3034	0.024*
C2	1.1337 (2)	−0.1595 (2)	0.28016 (9)	0.0213 (5)
H2A	1.1994	−0.2183	0.2609	0.026*
C3	1.1646 (2)	−0.0202 (2)	0.28307 (9)	0.0222 (5)
H3	1.2509	0.0132	0.2659	0.027*
C4	1.0721 (2)	0.0692 (2)	0.31040 (9)	0.0207 (5)
H4	1.0945	0.1632	0.3128	0.025*
C5	0.9449 (2)	0.01777 (19)	0.33442 (8)	0.0168 (4)
C6	0.9160 (2)	−0.1225 (2)	0.33116 (8)	0.0172 (4)
C7	0.7367 (2)	−0.01515 (19)	0.37430 (8)	0.0161 (4)
C8	0.5944 (2)	0.0055 (2)	0.40055 (9)	0.0175 (4)
C9	0.5678 (2)	0.1165 (2)	0.43598 (9)	0.0182 (4)
H9	0.6435	0.1779	0.4454	0.022*
C11	0.3186 (2)	0.0478 (2)	0.44523 (9)	0.0214 (5)
C13	0.4824 (2)	−0.0846 (2)	0.38887 (9)	0.0223 (5)
H13	0.5008	−0.1617	0.3653	0.027*
C12	0.3456 (2)	−0.0646 (2)	0.41073 (9)	0.0234 (5)
H12	0.2701	−0.1272	0.4023	0.028*	0.843 (4)
F1A	0.2476 (9)	−0.1424 (8)	0.4043 (4)	0.031 (3)	0.157 (4)
C10	0.4302 (2)	0.13632 (19)	0.45723 (9)	0.0187 (4)
H10	0.4116	0.2133	0.4809	0.022*	0.157 (4)
F1	0.40066 (15)	0.24197 (14)	0.49152 (6)	0.0258 (5)	0.843 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0168 (8)	0.0154 (9)	0.0204 (9)	0.0005 (7)	0.0003 (7)	−0.0003 (7)
N2	0.0177 (9)	0.0122 (8)	0.0227 (9)	−0.0010 (7)	0.0020 (7)	0.0006 (7)
Cl1	0.0184 (3)	0.0294 (3)	0.0395 (4)	0.0006 (2)	0.0088 (2)	−0.0051 (2)
C1	0.0235 (11)	0.0152 (10)	0.0208 (10)	0.0036 (8)	0.0000 (9)	0.0009 (8)
C2	0.0229 (11)	0.0212 (11)	0.0199 (11)	0.0070 (9)	0.0007 (9)	−0.0001 (9)
C3	0.0184 (10)	0.0242 (11)	0.0239 (11)	0.0005 (9)	0.0029 (9)	0.0024 (9)
C4	0.0194 (10)	0.0162 (10)	0.0265 (11)	−0.0016 (8)	0.0000 (9)	0.0013 (8)
C5	0.0175 (10)	0.0159 (10)	0.0168 (10)	0.0026 (8)	−0.0007 (8)	0.0008 (8)
C6	0.0176 (10)	0.0182 (10)	0.0157 (10)	0.0018 (8)	−0.0011 (8)	0.0013 (8)
C7	0.0178 (10)	0.0146 (10)	0.0158 (10)	0.0026 (8)	−0.0043 (8)	−0.0017 (8)
C8	0.0190 (10)	0.0154 (9)	0.0180 (10)	0.0016 (8)	0.0000 (8)	0.0018 (8)
C9	0.0184 (10)	0.0157 (9)	0.0206 (10)	0.0002 (8)	0.0002 (8)	0.0023 (8)
C11	0.0189 (10)	0.0229 (11)	0.0226 (11)	0.0019 (9)	0.0030 (9)	0.0037 (9)
C13	0.0226 (11)	0.0185 (10)	0.0257 (12)	−0.0003 (9)	0.0011 (9)	−0.0034 (8)
C12	0.0202 (11)	0.0227 (11)	0.0273 (12)	−0.0027 (9)	0.0005 (9)	−0.0022 (9)
F1A	0.025 (4)	0.029 (5)	0.037 (5)	−0.006 (4)	0.001 (4)	−0.008 (4)
C10	0.0234 (11)	0.0135 (9)	0.0193 (10)	0.0039 (8)	0.0016 (8)	−0.0010 (8)
F1	0.0204 (8)	0.0207 (8)	0.0364 (9)	−0.0002 (6)	0.0054 (6)	−0.0126 (6)

Geometric parameters (Å, º) top

N1—C7	1.329 (3)	C5—C6	1.409 (3)
N1—C5	1.392 (3)	C7—C8	1.461 (3)
N2—C7	1.362 (3)	C8—C9	1.388 (3)
N2—C6	1.374 (3)	C8—C13	1.389 (3)
N2—H2	0.8800	C9—C10	1.376 (3)
Cl1—C11	1.719 (2)	C9—H9	0.9500
C1—C2	1.373 (3)	C11—C10	1.378 (3)
C1—C6	1.389 (3)	C11—C12	1.387 (3)
C1—H1	0.9500	C13—C12	1.375 (3)
C2—C3	1.403 (3)	C13—H13	0.9500
C2—H2A	0.9500	C12—F1A	1.195 (8)
C3—C4	1.380 (3)	C12—H12	0.9500
C3—H3	0.9500	C10—F1	1.337 (2)
C4—C5	1.394 (3)	C10—H10	0.9500
C4—H4	0.9500

C7—N1—C5	104.82 (16)	N2—C7—C8	122.16 (18)
C7—N2—C6	107.33 (16)	C9—C8—C13	119.13 (19)
C7—N2—H2	126.3	C9—C8—C7	120.94 (18)
C6—N2—H2	126.3	C13—C8—C7	119.91 (18)
C2—C1—C6	117.30 (19)	C10—C9—C8	119.06 (19)
C2—C1—H1	121.4	C10—C9—H9	120.5
C6—C1—H1	121.4	C8—C9—H9	120.5
C1—C2—C3	121.41 (19)	C10—C11—C12	119.13 (19)
C1—C2—H2A	119.3	C10—C11—Cl1	120.18 (16)
C3—C2—H2A	119.3	C12—C11—Cl1	120.69 (17)
C4—C3—C2	121.40 (19)	C12—C13—C8	121.35 (19)
C4—C3—H3	119.3	C12—C13—H13	119.3
C2—C3—H3	119.3	C8—C13—H13	119.3
C3—C4—C5	118.11 (19)	F1A—C12—C13	123.9 (4)
C3—C4—H4	120.9	F1A—C12—C11	116.6 (4)
C5—C4—H4	120.9	C13—C12—C11	119.4 (2)
N1—C5—C4	130.80 (18)	C13—C12—H12	120.3
N1—C5—C6	109.54 (17)	C11—C12—H12	120.3
C4—C5—C6	119.63 (18)	F1—C10—C9	120.70 (18)
N2—C6—C1	132.36 (19)	F1—C10—C11	117.39 (18)
N2—C6—C5	105.50 (17)	C9—C10—C11	121.90 (19)
C1—C6—C5	122.12 (18)	C9—C10—H10	119.0
N1—C7—N2	112.82 (17)	C11—C10—H10	119.0
N1—C7—C8	124.92 (17)

C6—C1—C2—C3	1.5 (3)	N2—C7—C8—C9	156.49 (19)
C1—C2—C3—C4	−0.3 (3)	N1—C7—C8—C13	150.8 (2)
C2—C3—C4—C5	−1.1 (3)	N2—C7—C8—C13	−25.3 (3)
C7—N1—C5—C4	178.2 (2)	C13—C8—C9—C10	−1.8 (3)
C7—N1—C5—C6	0.2 (2)	C7—C8—C9—C10	176.41 (18)
C3—C4—C5—N1	−176.6 (2)	C9—C8—C13—C12	1.3 (3)
C3—C4—C5—C6	1.2 (3)	C7—C8—C13—C12	−176.97 (19)
C7—N2—C6—C1	−178.1 (2)	C8—C13—C12—F1A	−176.2 (5)
C7—N2—C6—C5	0.3 (2)	C8—C13—C12—C11	−0.1 (3)
C2—C1—C6—N2	176.80 (19)	C10—C11—C12—F1A	175.8 (5)
C2—C1—C6—C5	−1.4 (3)	Cl1—C11—C12—F1A	−4.0 (5)
N1—C5—C6—N2	−0.3 (2)	C10—C11—C12—C13	−0.6 (3)
C4—C5—C6—N2	−178.58 (17)	Cl1—C11—C12—C13	179.62 (17)
N1—C5—C6—C1	178.26 (18)	C8—C9—C10—F1	179.91 (18)
C4—C5—C6—C1	0.0 (3)	C8—C9—C10—C11	1.2 (3)
C5—N1—C7—N2	0.0 (2)	C12—C11—C10—F1	−178.73 (18)
C5—N1—C7—C8	−176.36 (18)	Cl1—C11—C10—F1	1.1 (3)
C6—N2—C7—N1	−0.2 (2)	C12—C11—C10—C9	0.0 (3)
C6—N2—C7—C8	176.25 (17)	Cl1—C11—C10—C9	179.80 (16)
N1—C7—C8—C9	−27.5 (3)

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the N1/C5/C6/N2/C7 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1ⁱ	0.88	2.06	2.924 (1)	166
C3—H3···Cgⁱⁱ	0.95	2.92	3.700 (3)	140

Symmetry codes: (i) −x+3/2, y−1/2, z; (ii) x+1/2, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the N1/C5/C6/N2/C7 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1ⁱ	0.88	2.061	2.924 (1)	166
C3—H3···Cgⁱⁱ	0.95	2.924	3.700 (3)	140

Symmetry codes: (i) −x+3/2, y−1/2, z; (ii) x+1/2, y, −z+1/2.

Acknowledgements

MSK is thankful to the University Grants Commission (UGC), India, for the UGC–BSR meritorious fellowship.

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Volume 71| Part 6| June 2015| Pages o387-o388

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