2-(3,4-Di­fluoro­phen­yl)-1H-benzimidazole

Krishnamurthy, M.S.; Fathima, N.; Nagarajaiah, H.; Begum, N.S.

doi:10.1107/S1600536813028559

organic compounds

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doi:10.1107/S1600536813028559

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2-(3,4-Difluorophenyl)-1H-benzimidazole

M. S. Krishnamurthy,^a Nikhath Fathima,^a H. Nagarajaiah ^a and Noor Shahina Begum ^a ^*

^aDepartment of Chemistry, Bangalore University, Bangalore 560 001, India
^*Correspondence e-mail: noorsb@rediffmail.com

(Received 1 October 2013; accepted 17 October 2013; online 23 October 2013)

In the title molecule, C₁₃H₈F₂N₂, the dihedral angle between the benzimidazole ring system and the difluoro-substituted benzene ring is 30.0 (1)°. In the crystal, molecules are linked by N—H⋯N hydrogen bonds, forming chains along [010]. In addition, weak C—H⋯F hydrogen bonds connect chains into a two-dimensional network parallel to (001). A weak C—H⋯π interaction is observed between an H atom of the benzimidazole ring sytem and the π system of the difluoro-substituted benzene ring.

CCDC reference: 966933

Related literature

For the therapeutic and medicinal properties of benzimidazole derivatives, see: Chimirri et al. (1991 ); Ishihara et al. (1994 ); Kubo et al. (1993 ). For related structures, see: Rashid et al. (2007 ); Jayamoorthy et al. (2012 ); Yoon et al. (2012 ); Fathima et al. (2013 ).

Experimental

Crystal data

C₁₃H₈F₂N₂
M_r = 230.21
Orthorhombic, P b c a
a = 8.7195 (17) Å
b = 9.9454 (19) Å
c = 23.389 (4) Å
V = 2028.2 (7) Å³
Z = 8
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 100 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 = 0.982, T_max = 0.984
13072 measured reflections
2209 independent reflections
1558 reflections with I > 2σ(I)
R_int = 0.067

Refinement

R[F² > 2σ(F²)] = 0.059
wR(F²) = 0.156
S = 1.01
2209 reflections
154 parameters
H-atom parameters constrained
Δρ_max = 0.47 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the ring C9–C13 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N2ⁱ	0.88	2.04	2.874 (3)	158
C13—H13⋯F2ⁱⁱ	0.95	2.51	3.379 (3)	153
C3—H3A⋯Cgⁱⁱⁱ	0.95	2.89	3.529 (3)	125
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (iii) $[x+{\script{1\over 2}}, y, -z+{\script{1\over 2}}]$ .

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).

Supporting information

CCDC reference: 966933

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536813028559/lh5659sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813028559/lh5659Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813028559/lh5659Isup3.cml

checkCIF report

Comment top

Benzimidazole is a bicyclic heterocycle system consisting of two nitrogen atoms and fused phenyl ring. It shows wide variety of pharmacological activities such as antihypertensive (Kubo et al., 1993), anti-HIV (Chimirri et al., 1991), antiulcer (Ishihara et al., 1994). The bond lengths and bond angles of the benzimidazole moiety in the title compound are in good agreement with those observed in other benzimidazole derivatives (Jayamoorthy et al., 2012; Yoon et al., 2012).

The molecular structure of the title compound is shown in Fig. 1. The dihedral angle between the benzimidazole ring system and difluoro-substituted benzene ring is 30.0 (1)°. This value is slightly larger than for the benzene ring with a trifluoromethoxy substituent at the para position (Fathima et al., 2013), and slightly smaller for a ring with a fluorine atom at the para position (Rashid et al., 2007). In the crystal, molecules are linked by intermolecular N1—H1···N2ⁱ and C9—H9···F2ⁱⁱ hydrogen bonds (see Table 1 for symmetry codes). The former interaction forms extended chains parallel to the b-axis and the latter results in one-dimensional chains along the a-axis (Fig. 2). Overall a two-dimensional network parallel to (001) is formed. In addition, a weak C—H···π interaction of the type C3—H3A···Cg (Cg being the centroid of the ring C9—C13 ring) is observed (Table 1).

Related literature top

For the therapeutic and medicinal properties of benzimidazole derivatives, see: Chimirri et al. (1991); Ishihara et al. (1994); Kubo et al. (1993). For related structures, see: Rashid et al. (2007); Jayamoorthy et al. (2012); Yoon et al. (2012); Fathima et al. (2013).

Experimental top

The title compound was synthesized by refluxing 3,4-difluorobenzaldehyde (20 mmol,0.28 g) and o-phenyldiamine (20 mmol,0.22 g) in benzene (3.0 ml) for 6hrs on a water bath. The reaction mixture was cooled. The solid separated, was filtered and dried (Yield; 0.34 g (75%) and M.P. 533 K). Yellow crystals of the title compound were obtained by slow evaporation of a solution of the title compound in ethyl acetate.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus (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. H atoms are presented as small spheres of arbitrary radius.
	Fig. 2. Part of the crystal structure showing intermolecular hydrogen bonds with dashed lines. H-atoms not involved in hydrogen bonds have been excluded. The atoms N2 and F2 are related by the symmetry operators (-x+3/2, y+1/2, z) and (x+1/2, -y+3/2, -z+1) respectively.

2-(3,4-Difluorophenyl)-1H-benzimidazole top

Crystal data top

C₁₃H₈F₂N₂	F(000) = 944
M_r = 230.21	D_x = 1.508 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 2209 reflections
a = 8.7195 (17) Å	θ = 2.9–27.0°
b = 9.9454 (19) Å	µ = 0.12 mm⁻¹
c = 23.389 (4) Å	T = 100 K
V = 2028.2 (7) Å³	Block, yellow
Z = 8	0.18 × 0.16 × 0.16 mm

Data collection top

Bruker SMART APEX CCD detector diffractometer	2209 independent reflections
Radiation source: fine-focus sealed tube	1558 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.067
ω scans	θ_max = 27.0°, θ_min = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 1998)	h = −11→10
T_min = 0.982, T_max = 0.984	k = −11→12
13072 measured reflections	l = −28→29

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)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.156	H-atom parameters constrained
S = 1.01	w = 1/[σ²(F_o²) + (0.0725P)² + 2.7172P] where P = (F_o² + 2F_c²)/3
2209 reflections	(Δ/σ)_max < 0.001
154 parameters	Δρ_max = 0.47 e Å⁻³
0 restraints	Δρ_min = −0.31 e Å⁻³

Crystal data top

C₁₃H₈F₂N₂	V = 2028.2 (7) Å³
M_r = 230.21	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 8.7195 (17) Å	µ = 0.12 mm⁻¹
b = 9.9454 (19) Å	T = 100 K
c = 23.389 (4) Å	0.18 × 0.16 × 0.16 mm

Data collection top

Bruker SMART APEX CCD detector diffractometer	2209 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 1998)	1558 reflections with I > 2σ(I)
T_min = 0.982, T_max = 0.984	R_int = 0.067
13072 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.059	0 restraints
wR(F²) = 0.156	H-atom parameters constrained
S = 1.01	Δρ_max = 0.47 e Å⁻³
2209 reflections	Δρ_min = −0.31 e Å⁻³
154 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
F1	0.14852 (18)	0.58743 (18)	0.48006 (8)	0.0366 (5)
F2	0.38138 (19)	0.75233 (17)	0.50344 (7)	0.0341 (5)
N1	0.8188 (2)	0.5958 (2)	0.36510 (9)	0.0174 (5)
H1	0.8081	0.6819	0.3727	0.021*
N2	0.7666 (2)	0.3748 (2)	0.36264 (9)	0.0182 (5)
C1	0.9394 (3)	0.5363 (2)	0.33662 (11)	0.0177 (5)
C2	0.7191 (3)	0.4952 (2)	0.37920 (10)	0.0160 (5)
C3	1.1638 (3)	0.4987 (3)	0.28151 (11)	0.0211 (6)
H3A	1.2526	0.5311	0.2624	0.025*
C4	1.1307 (3)	0.3607 (3)	0.28051 (11)	0.0219 (6)
H4	1.1975	0.3017	0.2605	0.026*
C5	1.0038 (3)	0.3082 (3)	0.30778 (11)	0.0204 (6)
H5	0.9838	0.2143	0.3076	0.025*
C6	0.9064 (3)	0.3973 (2)	0.33543 (11)	0.0175 (5)
C7	1.0692 (3)	0.5888 (3)	0.30993 (11)	0.0212 (6)
H7	1.0918	0.6822	0.3111	0.025*
C8	0.5694 (3)	0.5218 (2)	0.40631 (11)	0.0185 (5)
C9	0.4478 (3)	0.4362 (3)	0.39494 (12)	0.0228 (6)
H9	0.4632	0.3615	0.3703	0.027*
C10	0.3033 (3)	0.4573 (3)	0.41895 (13)	0.0268 (6)
H10	0.2201	0.3988	0.4106	0.032*
C11	0.2849 (3)	0.5654 (3)	0.45506 (12)	0.0233 (6)
C12	0.4062 (3)	0.6501 (3)	0.46667 (12)	0.0216 (6)
C13	0.5477 (3)	0.6304 (2)	0.44261 (11)	0.0188 (5)
H13	0.6298	0.6902	0.4507	0.023*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0223 (9)	0.0372 (10)	0.0504 (11)	−0.0001 (7)	0.0114 (8)	−0.0089 (8)
F2	0.0312 (9)	0.0280 (9)	0.0430 (10)	0.0038 (8)	0.0066 (8)	−0.0127 (8)
N1	0.0202 (11)	0.0083 (9)	0.0236 (11)	0.0000 (8)	0.0013 (9)	−0.0010 (8)
N2	0.0216 (11)	0.0125 (10)	0.0204 (11)	0.0017 (9)	−0.0007 (9)	−0.0011 (8)
C1	0.0205 (13)	0.0122 (11)	0.0204 (13)	0.0040 (10)	−0.0022 (10)	0.0001 (10)
C2	0.0184 (12)	0.0117 (11)	0.0178 (12)	−0.0012 (10)	−0.0026 (10)	0.0017 (9)
C3	0.0179 (12)	0.0194 (13)	0.0261 (14)	0.0004 (11)	0.0063 (11)	0.0005 (11)
C4	0.0233 (13)	0.0178 (13)	0.0247 (14)	0.0055 (11)	0.0006 (11)	0.0001 (11)
C5	0.0245 (13)	0.0128 (12)	0.0240 (13)	0.0013 (10)	−0.0030 (11)	0.0002 (10)
C6	0.0185 (12)	0.0134 (12)	0.0205 (13)	−0.0027 (10)	−0.0031 (10)	0.0023 (10)
C7	0.0252 (14)	0.0113 (12)	0.0270 (14)	−0.0007 (10)	0.0031 (11)	0.0012 (10)
C8	0.0206 (13)	0.0146 (12)	0.0202 (13)	−0.0004 (10)	−0.0031 (10)	0.0047 (10)
C9	0.0278 (14)	0.0150 (12)	0.0257 (14)	−0.0007 (11)	0.0017 (11)	−0.0045 (11)
C10	0.0221 (14)	0.0246 (14)	0.0337 (15)	−0.0055 (12)	−0.0037 (12)	0.0003 (12)
C11	0.0164 (13)	0.0255 (14)	0.0281 (14)	0.0026 (11)	0.0041 (11)	0.0033 (11)
C12	0.0233 (13)	0.0134 (12)	0.0280 (15)	0.0041 (10)	−0.0010 (11)	−0.0011 (10)
C13	0.0183 (13)	0.0125 (12)	0.0257 (14)	−0.0008 (10)	−0.0002 (11)	0.0022 (10)

Geometric parameters (Å, º) top

F1—C11	1.344 (3)	C4—H4	0.9500
F2—C12	1.349 (3)	C5—C6	1.388 (4)
N1—C2	1.366 (3)	C5—H5	0.9500
N1—C1	1.378 (3)	C7—H7	0.9500
N1—H1	0.8800	C8—C9	1.386 (4)
N2—C2	1.326 (3)	C8—C13	1.386 (4)
N2—C6	1.393 (3)	C9—C10	1.396 (4)
C1—C7	1.394 (4)	C9—H9	0.9500
C1—C6	1.412 (3)	C10—C11	1.376 (4)
C2—C8	1.474 (4)	C10—H10	0.9500
C3—C7	1.388 (4)	C11—C12	1.379 (4)
C3—C4	1.403 (4)	C12—C13	1.371 (4)
C3—H3A	0.9500	C13—H13	0.9500
C4—C5	1.380 (4)

C2—N1—C1	106.7 (2)	C3—C7—C1	117.1 (2)
C2—N1—H1	126.6	C3—C7—H7	121.5
C1—N1—H1	126.6	C1—C7—H7	121.5
C2—N2—C6	105.2 (2)	C9—C8—C13	119.5 (2)
N1—C1—C7	132.4 (2)	C9—C8—C2	118.9 (2)
N1—C1—C6	105.9 (2)	C13—C8—C2	121.6 (2)
C7—C1—C6	121.6 (2)	C8—C9—C10	121.4 (2)
N2—C2—N1	113.1 (2)	C8—C9—H9	119.3
N2—C2—C8	124.4 (2)	C10—C9—H9	119.3
N1—C2—C8	122.4 (2)	C11—C10—C9	118.0 (2)
C7—C3—C4	121.2 (2)	C11—C10—H10	121.0
C7—C3—H3A	119.4	C9—C10—H10	121.0
C4—C3—H3A	119.4	F1—C11—C10	119.8 (2)
C5—C4—C3	121.8 (2)	F1—C11—C12	119.5 (2)
C5—C4—H4	119.1	C10—C11—C12	120.6 (2)
C3—C4—H4	119.1	F2—C12—C13	120.9 (2)
C4—C5—C6	117.7 (2)	F2—C12—C11	117.6 (2)
C4—C5—H5	121.1	C13—C12—C11	121.4 (2)
C6—C5—H5	121.1	C12—C13—C8	119.1 (2)
C5—C6—N2	130.2 (2)	C12—C13—H13	120.5
C5—C6—C1	120.6 (2)	C8—C13—H13	120.5
N2—C6—C1	109.1 (2)

C2—N1—C1—C7	176.2 (3)	C6—C1—C7—C3	0.7 (4)
C2—N1—C1—C6	−0.7 (3)	N2—C2—C8—C9	−26.6 (4)
C6—N2—C2—N1	−0.5 (3)	N1—C2—C8—C9	148.7 (2)
C6—N2—C2—C8	175.3 (2)	N2—C2—C8—C13	153.6 (2)
C1—N1—C2—N2	0.7 (3)	N1—C2—C8—C13	−31.1 (4)
C1—N1—C2—C8	−175.1 (2)	C13—C8—C9—C10	0.5 (4)
C7—C3—C4—C5	−0.3 (4)	C2—C8—C9—C10	−179.4 (2)
C3—C4—C5—C6	1.6 (4)	C8—C9—C10—C11	−0.8 (4)
C4—C5—C6—N2	175.1 (2)	C9—C10—C11—F1	−178.5 (2)
C4—C5—C6—C1	−1.6 (4)	C9—C10—C11—C12	0.4 (4)
C2—N2—C6—C5	−177.0 (3)	F1—C11—C12—F2	0.3 (4)
C2—N2—C6—C1	0.0 (3)	C10—C11—C12—F2	−178.5 (2)
N1—C1—C6—C5	177.8 (2)	F1—C11—C12—C13	179.2 (2)
C7—C1—C6—C5	0.5 (4)	C10—C11—C12—C13	0.4 (4)
N1—C1—C6—N2	0.4 (3)	F2—C12—C13—C8	178.2 (2)
C7—C1—C6—N2	−176.8 (2)	C11—C12—C13—C8	−0.7 (4)
C4—C3—C7—C1	−0.8 (4)	C9—C8—C13—C12	0.3 (4)
N1—C1—C7—C3	−175.7 (3)	C2—C8—C13—C12	−179.9 (2)

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the ring C9–C13 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N2ⁱ	0.88	2.04	2.874 (3)	158
C13—H13···F2ⁱⁱ	0.95	2.51	3.379 (3)	153
C3—H3A···Cgⁱⁱⁱ	0.95	2.89	3.529 (3)	125

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

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the ring C9–C13 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N2ⁱ	0.88	2.04	2.874 (3)	158
C13—H13···F2ⁱⁱ	0.95	2.51	3.379 (3)	153
C3—H3A···Cgⁱⁱⁱ	0.95	2.89	3.529 (3)	125

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

Acknowledgements

NSB is thankful to the University Grants Commission (UGC), India, for financial assistance.

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