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

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.

Related literature

For the therapeutic and medicinal properties of benzimidazole derivatives, see: Chimirri et al. (1991[Chimirri, A., Grasso, S., Monforte, A. M., Monforte, P. & Zappala, M. (1991). Il Farmaco, 46, 925-933.]); Ishihara et al. (1994[Ishihara, K., Ichikawa, T., Komuro, Y., Ohara, S. & Hotta, K. (1994). Arzneim. Forsch. Drug. Res. 44, 827-830.]); Kubo et al. (1993[Kubo, K., Kohara, Y., Imamia, E., Sugiura, Y., Inada, Y., Furukawa, Y., Nishikawa, K. & Naka, T. (1993). J. Med. Chem. 36, 2182-2195.]). For related structures, see: Rashid et al. (2007[Rashid, N., Tahir, M. K., Kanwal, S., Yusof, N. M. & Yamin, B. M. (2007). Acta Cryst. E63, o1402-o1403.]); Jayamoorthy et al. (2012[Jayamoorthy, K., Rosepriya, S., Thiruvalluvar, A., Jayabharathi, J. & Butcher, R. J. (2012). Acta Cryst. E68, o2708.]); Yoon et al. (2012[Yoon, Y. K., Ali, M. A., Choon, T. S., Arshad, S. & Razak, I. A. (2012). Acta Cryst. E68, o2715-o2716.]); Fathima et al. (2013[Fathima, N., Krishnamurthy, M. S. & Begum, N. S. (2013). Acta Cryst. E69, o264.]).

[Scheme 1]

Experimental

Crystal data
  • C13H8F2N2

  • Mr = 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[Bruker. (1998). SMART, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconcin, USA.]) Tmin = 0.982, Tmax = 0.984

  • 13072 measured reflections

  • 2209 independent reflections

  • 1558 reflections with I > 2σ(I)

  • Rint = 0.067

Refinement
  • R[F2 > 2σ(F2)] = 0.059

  • wR(F2) = 0.156

  • S = 1.01

  • 2209 reflections

  • 154 parameters

  • H-atom parameters constrained

  • Δρmax = 0.47 e Å−3

  • Δρmin = −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 DA 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—H3ACgiii 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[Bruker. (1998). SMART, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconcin, USA.]); cell refinement: SAINT-Plus (Bruker, 1998[Bruker. (1998). SMART, SAINT-Plus and SADABS. Bruker AXS Inc., Madison, Wisconcin, USA.]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, University of Oxford, England.]); software used to prepare material for publication: WinGX (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Supporting information


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.

Refinement top

The H atoms were placed in calculated positions and refined in a riding-model approximation with C—H = 0.93 Å, N—H = 0.86 Å and with Uiso(H) = 1.2Ueq(N/C).

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
[Figure 1] 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.
[Figure 2] 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
C13H8F2N2F(000) = 944
Mr = 230.21Dx = 1.508 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 2209 reflections
a = 8.7195 (17) Åθ = 2.9–27.0°
b = 9.9454 (19) ŵ = 0.12 mm1
c = 23.389 (4) ÅT = 100 K
V = 2028.2 (7) Å3Block, yellow
Z = 80.18 × 0.16 × 0.16 mm
Data collection top
Bruker SMART APEX CCD detector
diffractometer
2209 independent reflections
Radiation source: fine-focus sealed tube1558 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.067
ω scansθmax = 27.0°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Bruker, 1998)
h = 1110
Tmin = 0.982, Tmax = 0.984k = 1112
13072 measured reflectionsl = 2829
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.156H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0725P)2 + 2.7172P]
where P = (Fo2 + 2Fc2)/3
2209 reflections(Δ/σ)max < 0.001
154 parametersΔρmax = 0.47 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C13H8F2N2V = 2028.2 (7) Å3
Mr = 230.21Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 8.7195 (17) ŵ = 0.12 mm1
b = 9.9454 (19) ÅT = 100 K
c = 23.389 (4) Å0.18 × 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)
Tmin = 0.982, Tmax = 0.984Rint = 0.067
13072 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0590 restraints
wR(F2) = 0.156H-atom parameters constrained
S = 1.01Δρmax = 0.47 e Å3
2209 reflectionsΔρmin = 0.31 e Å3
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
xyzUiso*/Ueq
F10.14852 (18)0.58743 (18)0.48006 (8)0.0366 (5)
F20.38138 (19)0.75233 (17)0.50344 (7)0.0341 (5)
N10.8188 (2)0.5958 (2)0.36510 (9)0.0174 (5)
H10.80810.68190.37270.021*
N20.7666 (2)0.3748 (2)0.36264 (9)0.0182 (5)
C10.9394 (3)0.5363 (2)0.33662 (11)0.0177 (5)
C20.7191 (3)0.4952 (2)0.37920 (10)0.0160 (5)
C31.1638 (3)0.4987 (3)0.28151 (11)0.0211 (6)
H3A1.25260.53110.26240.025*
C41.1307 (3)0.3607 (3)0.28051 (11)0.0219 (6)
H41.19750.30170.26050.026*
C51.0038 (3)0.3082 (3)0.30778 (11)0.0204 (6)
H50.98380.21430.30760.025*
C60.9064 (3)0.3973 (2)0.33543 (11)0.0175 (5)
C71.0692 (3)0.5888 (3)0.30993 (11)0.0212 (6)
H71.09180.68220.31110.025*
C80.5694 (3)0.5218 (2)0.40631 (11)0.0185 (5)
C90.4478 (3)0.4362 (3)0.39494 (12)0.0228 (6)
H90.46320.36150.37030.027*
C100.3033 (3)0.4573 (3)0.41895 (13)0.0268 (6)
H100.22010.39880.41060.032*
C110.2849 (3)0.5654 (3)0.45506 (12)0.0233 (6)
C120.4062 (3)0.6501 (3)0.46667 (12)0.0216 (6)
C130.5477 (3)0.6304 (2)0.44261 (11)0.0188 (5)
H130.62980.69020.45070.023*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0223 (9)0.0372 (10)0.0504 (11)0.0001 (7)0.0114 (8)0.0089 (8)
F20.0312 (9)0.0280 (9)0.0430 (10)0.0038 (8)0.0066 (8)0.0127 (8)
N10.0202 (11)0.0083 (9)0.0236 (11)0.0000 (8)0.0013 (9)0.0010 (8)
N20.0216 (11)0.0125 (10)0.0204 (11)0.0017 (9)0.0007 (9)0.0011 (8)
C10.0205 (13)0.0122 (11)0.0204 (13)0.0040 (10)0.0022 (10)0.0001 (10)
C20.0184 (12)0.0117 (11)0.0178 (12)0.0012 (10)0.0026 (10)0.0017 (9)
C30.0179 (12)0.0194 (13)0.0261 (14)0.0004 (11)0.0063 (11)0.0005 (11)
C40.0233 (13)0.0178 (13)0.0247 (14)0.0055 (11)0.0006 (11)0.0001 (11)
C50.0245 (13)0.0128 (12)0.0240 (13)0.0013 (10)0.0030 (11)0.0002 (10)
C60.0185 (12)0.0134 (12)0.0205 (13)0.0027 (10)0.0031 (10)0.0023 (10)
C70.0252 (14)0.0113 (12)0.0270 (14)0.0007 (10)0.0031 (11)0.0012 (10)
C80.0206 (13)0.0146 (12)0.0202 (13)0.0004 (10)0.0031 (10)0.0047 (10)
C90.0278 (14)0.0150 (12)0.0257 (14)0.0007 (11)0.0017 (11)0.0045 (11)
C100.0221 (14)0.0246 (14)0.0337 (15)0.0055 (12)0.0037 (12)0.0003 (12)
C110.0164 (13)0.0255 (14)0.0281 (14)0.0026 (11)0.0041 (11)0.0033 (11)
C120.0233 (13)0.0134 (12)0.0280 (15)0.0041 (10)0.0010 (11)0.0011 (10)
C130.0183 (13)0.0125 (12)0.0257 (14)0.0008 (10)0.0002 (11)0.0022 (10)
Geometric parameters (Å, º) top
F1—C111.344 (3)C4—H40.9500
F2—C121.349 (3)C5—C61.388 (4)
N1—C21.366 (3)C5—H50.9500
N1—C11.378 (3)C7—H70.9500
N1—H10.8800C8—C91.386 (4)
N2—C21.326 (3)C8—C131.386 (4)
N2—C61.393 (3)C9—C101.396 (4)
C1—C71.394 (4)C9—H90.9500
C1—C61.412 (3)C10—C111.376 (4)
C2—C81.474 (4)C10—H100.9500
C3—C71.388 (4)C11—C121.379 (4)
C3—C41.403 (4)C12—C131.371 (4)
C3—H3A0.9500C13—H130.9500
C4—C51.380 (4)
C2—N1—C1106.7 (2)C3—C7—C1117.1 (2)
C2—N1—H1126.6C3—C7—H7121.5
C1—N1—H1126.6C1—C7—H7121.5
C2—N2—C6105.2 (2)C9—C8—C13119.5 (2)
N1—C1—C7132.4 (2)C9—C8—C2118.9 (2)
N1—C1—C6105.9 (2)C13—C8—C2121.6 (2)
C7—C1—C6121.6 (2)C8—C9—C10121.4 (2)
N2—C2—N1113.1 (2)C8—C9—H9119.3
N2—C2—C8124.4 (2)C10—C9—H9119.3
N1—C2—C8122.4 (2)C11—C10—C9118.0 (2)
C7—C3—C4121.2 (2)C11—C10—H10121.0
C7—C3—H3A119.4C9—C10—H10121.0
C4—C3—H3A119.4F1—C11—C10119.8 (2)
C5—C4—C3121.8 (2)F1—C11—C12119.5 (2)
C5—C4—H4119.1C10—C11—C12120.6 (2)
C3—C4—H4119.1F2—C12—C13120.9 (2)
C4—C5—C6117.7 (2)F2—C12—C11117.6 (2)
C4—C5—H5121.1C13—C12—C11121.4 (2)
C6—C5—H5121.1C12—C13—C8119.1 (2)
C5—C6—N2130.2 (2)C12—C13—H13120.5
C5—C6—C1120.6 (2)C8—C13—H13120.5
N2—C6—C1109.1 (2)
C2—N1—C1—C7176.2 (3)C6—C1—C7—C30.7 (4)
C2—N1—C1—C60.7 (3)N2—C2—C8—C926.6 (4)
C6—N2—C2—N10.5 (3)N1—C2—C8—C9148.7 (2)
C6—N2—C2—C8175.3 (2)N2—C2—C8—C13153.6 (2)
C1—N1—C2—N20.7 (3)N1—C2—C8—C1331.1 (4)
C1—N1—C2—C8175.1 (2)C13—C8—C9—C100.5 (4)
C7—C3—C4—C50.3 (4)C2—C8—C9—C10179.4 (2)
C3—C4—C5—C61.6 (4)C8—C9—C10—C110.8 (4)
C4—C5—C6—N2175.1 (2)C9—C10—C11—F1178.5 (2)
C4—C5—C6—C11.6 (4)C9—C10—C11—C120.4 (4)
C2—N2—C6—C5177.0 (3)F1—C11—C12—F20.3 (4)
C2—N2—C6—C10.0 (3)C10—C11—C12—F2178.5 (2)
N1—C1—C6—C5177.8 (2)F1—C11—C12—C13179.2 (2)
C7—C1—C6—C50.5 (4)C10—C11—C12—C130.4 (4)
N1—C1—C6—N20.4 (3)F2—C12—C13—C8178.2 (2)
C7—C1—C6—N2176.8 (2)C11—C12—C13—C80.7 (4)
C4—C3—C7—C10.8 (4)C9—C8—C13—C120.3 (4)
N1—C1—C7—C3175.7 (3)C2—C8—C13—C12179.9 (2)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the ring C9–C13 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1···N2i0.882.042.874 (3)158
C13—H13···F2ii0.952.513.379 (3)153
C3—H3A···Cgiii0.952.893.529 (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···AD—HH···AD···AD—H···A
N1—H1···N2i0.882.042.874 (3)158
C13—H13···F2ii0.952.513.379 (3)153
C3—H3A···Cgiii0.952.893.529 (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.

References

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