Crystal structure of 2-(4-chloro-3-fluoro-phen-yl)-1H-benzimidazole.

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, mol-ecules 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 inter-actions [shortest centroid-centroid separation = 3.6838 (12) Å] are observed, which link the chains into a three-dimensional network.

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 ▸).

Experimental

Crystal data

C13H8ClFN2

M = 246.66

Orthorhombic,

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

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

Refinement

R[F 2 > 2σ(F 2)] = 0.038

wR(F 2) = 0.102

S = 0.95

1844 reflections

164 parameters

H-atom parameters constrained

Δρmax = 0.56 e Å−3

Δρmin = −0.32 e Å−3

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 ▸).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015008683/hb7406sup1.cif

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

Click here for additional data file.

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

Click here for additional data file.

. DOI: 10.1107/S2056989015008683/hb7406fig1.tif

The mol­ecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level.

Click here for additional data file.

. DOI: 10.1107/S2056989015008683/hb7406fig2.tif

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.

Click here for additional data file.

. DOI: 10.1107/S2056989015008683/hb7406fig3.tif

Unit cell packing showing C—H⋯π and π–π inter­actions with dotted lines.

CCDC reference: 1063160

Additional supporting information: crystallographic information; 3D view; checkCIF report

C13H8ClFN2	F(000) = 1008
Mr = 246.66	Dx = 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

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

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(Fo2) + (0.0597P)2 + 2.5255P] where P = (Fo2 + 2Fc2)/3
1844 reflections	(Δ/σ)max < 0.001
164 parameters	Δρmax = 0.56 e Å−3
0 restraints	Δρmin = −0.32 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	Uiso*/Ueq	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)

	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)

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)

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

Table 1

Hydrogen-bond geometry (, )

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

DHA	DH	HA	D A	DHA
N2H2N1i	0.88	2.06	2.924(1)	166
C3H3Cg ii	0.95	2.92	3.700(3)	140

Symmetry codes: (i) ; (ii) .