2-Methyl-5,6-dinitro­benzimidazolium chloride

Dinçer, S.; Gönülalan, G.; Tercan, B.; Hökelek, T.

doi:10.1107/S1600536811008105

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 67| Part 4| April 2011| Pages o806-o807

doi:10.1107/S1600536811008105

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2-Methyl-5,6-dinitrobenzimidazolium chloride

Sebla Dinçer,^a Gonca Gönülalan,^a Barış Tercan ^b and Tuncer Hökelek ^c ^*

^aDepartment of Chemistry, Ankara University, 06100 Tandoğan, Ankara, Turkey, ^bDepartment of Physics, Karabük University, 78050, Karabük, Turkey, and ^cDepartment of Physics, Hacettepe University, 06800 Beytepe, Ankara, Turkey
^*Correspondence e-mail: merzifon@hacettepe.edu.tr

(Received 2 March 2011; accepted 3 March 2011; online 9 March 2011)

In the title compound, C₈H₇N₄O₄⁺·Cl⁻, the cation possesses twofold symmetry, with the twofold axis bisecting the 2-methyl-5,6-dinitrobenzimidazolium cation. The methyl H atoms are disordered about this twofold axis and were assigned equal half-occupancies. The chloride anion also lies on a twofold axis. In the crystal, N—H⋯Cl and C—H⋯O hydrogen bonds link the ions to form a three-dimensional network.

Related literature

For literature on the antitumour, anthelmintic, antibacterial, virucidal and fungicidal properties of benzimidazole derivatives, see: Refaat (2010 ); Laryea et al. (2010 ); Horton et al. (2003 ); Spasov et al. (1999 ); Soula & Luu-Duc (1986 ). For literature on the coordination and corrosion inhibitor abilities of the benzimidazoles, see: Kuznetsov & Kazansky (2008 ); Subramanyam & Mayanna (1985 ). For literature on the use of benzimidazole derivatives as photographic materials and dyes, see: Hoffmann et al. (2011 ); Alamgir et al. (2007 ). For a related structure, see: Hökelek et al. (2002 ).

Experimental

Crystal data

C₈H₇N₄O₄⁺·Cl⁻
M_r = 258.63
Orthorhombic, C 222₁
a = 4.9453 (1) Å
b = 20.4691 (4) Å
c = 10.4543 (3) Å
V = 1058.25 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.37 mm⁻¹
T = 100 K
0.46 × 0.40 × 0.20 mm

Data collection

Bruker Kappa APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2001 ) T_min = 0.848, T_max = 0.929
3043 measured reflections
1302 independent reflections
1264 reflections with I > 2σ(I)
R_int = 0.016

Refinement

R[F² > 2σ(F²)] = 0.024
wR(F²) = 0.062
S = 1.11
1302 reflections
83 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.16 e Å⁻³
Absolute structure: Flack (1983 ), 517 Friedel pairs
Flack parameter: 0.10 (6)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯Cl1	0.86 (2)	2.15 (2)	3.008 (1)	172.5 (18)
C2—H2⋯O1ⁱ	0.93	2.51	3.339 (2)	150
Symmetry code: (i) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Data collection: APEX2 (Bruker, 2007 ); cell refinement: SAINT (Bruker, 2007); 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, 1997 ) and Mercury (Macrae et al., 2006 ); software used to prepare material for publication: WinGX (Farrugia, 1999 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811008105/su2261sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811008105/su2261Isup2.hkl

checkCIF report

Comment top

Benzimidazole derivatives are privileged structures in pharmaceutical chemistry because of their biological activities and clinical applications. They exhibit antitumor, anthelmintic, antibacterial, virucidal and fungucidal properties (Refaat, 2010; Laryea et al., 2010; Horton et al., 2003; Spasov et al., 1999; Soula & Luu-Duc, 1986). In addition to their biological activities, a review of the literature reveals that there are numerous studies including the coordination and corrosion inhibitor abilities of benzimidazoles (Kuznetsov & Kazansky, 2008; Subramanyam & Mayanna, 1985). Some of these derivatives, particularly nitro derivatives, are used as photographic materials in photography and on the other hand, the development of the chemistry of the benzimidazole dyes has been remarkable (Hoffmann et al., 2011; Alamgir et al., 2007). As a part of our ongoing investigations of benzimidazole derivatives, the title compound was synthesized and its crystal structure is reported herein.

The asymmetric unit of the title compound, (Fig. 1), contains one half of each component. It consists of an imidazole ring with the one CH₃ and two NO₂ groups bonded at positions 2, 5 and 6, respectively, and one chloride anion. Both the 2-methyl-5,6-dinitrobenzimidazolium moiety and the chloride anion lie on twofold axes. The methyl H atoms are disordered about the twofold axis with equal half occupancies.

In the crystal of the title compound N—H···Cl hydrogen bonds link the cations to form zigzag chains propagating in [001]. There are also C—H···O hydrogen bonds linking these chains to form a three-dimensional network (Table 1 and Fig. 2).

The crystal structure of a similar benzimidazole derivative, (C₇H₄N₄O₄).H₂O, has been reported (Hökelek et al., 2002).

Related literature top

For literature on the antitumour, anthelmintic, antibacterial, virucidal and fungicidal properties of benzimidazole derivatives, see: Refaat (2010); Laryea et al. (2010); Horton et al. (2003); Spasov et al. (1999); Soula & Luu-Duc (1986). For literature on the coordination and corrosion inhibitor abilities of the benzimidazoles, see: Kuznetsov & Kazansky (2008); Subramanyam & Mayanna (1985). For literature on the use of benzimidazole derivatives as photographic materials and dyes, see: Hoffmann et al. (2011); Alamgir et al. (2007). For a related structure, see: Hökelek et al. (2002).

Experimental top

For the preparation of the title compound a solution of 2-methyl-5-nitro- benzimidazole (3.0 g) in sulphuric acid (3.0 ml) was treated with nitric acid (6.0 ml) and refluxed for 3 h, then poured onto ice. The precipitate was filtered off and washed with cold water. Hydrogen chloride was passed into a suspension of the crude dinitro product in warm water. After cooling, the precipitate was filtered and crystallized from ethanol to give yellow block-like crystals of the the title compound (m.p. 507-512 K).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); 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, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top

	Fig. 1. The molecular structure of the title compound with the displacement ellipsoids drawn at the 50% probability level. The N-H···Cl hydrogen bond is shown as a dashed line.
	Fig. 2. A view along the a-axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines [H-atoms not involved in hydrogen bonding have been omitted for clarity].

2-Methyl-5,6-dinitrobenzimidazolium chloride top

Crystal data top

C₈H₇N₄O₄⁺·Cl⁻	F(000) = 528
M_r = 258.63	D_x = 1.623 Mg m⁻³
Orthorhombic, C222₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2c 2	Cell parameters from 2425 reflections
a = 4.9453 (1) Å	θ = 2.8–28.2°
b = 20.4691 (4) Å	µ = 0.37 mm⁻¹
c = 10.4543 (3) Å	T = 100 K
V = 1058.25 (4) Å³	Block, yellow
Z = 4	0.46 × 0.40 × 0.20 mm

Data collection top

Bruker Kappa APEXII CCD area-detector diffractometer	1302 independent reflections
Radiation source: fine-focus sealed tube	1264 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.016
ϕ and ω scans	θ_max = 28.3°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −6→6
T_min = 0.848, T_max = 0.929	k = −20→26
3043 measured reflections	l = −13→13

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.024	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.062	w = 1/[σ²(F_o²) + (0.0335P)² + 0.4282P] where P = (F_o² + 2F_c²)/3
S = 1.11	(Δ/σ)_max < 0.001
1302 reflections	Δρ_max = 0.27 e Å⁻³
83 parameters	Δρ_min = −0.16 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 517 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.10 (6)

Crystal data top

C₈H₇N₄O₄⁺·Cl⁻	V = 1058.25 (4) Å³
M_r = 258.63	Z = 4
Orthorhombic, C222₁	Mo Kα radiation
a = 4.9453 (1) Å	µ = 0.37 mm⁻¹
b = 20.4691 (4) Å	T = 100 K
c = 10.4543 (3) Å	0.46 × 0.40 × 0.20 mm

Data collection top

Bruker Kappa APEXII CCD area-detector diffractometer	1302 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2001)	1264 reflections with I > 2σ(I)
T_min = 0.848, T_max = 0.929	R_int = 0.016
3043 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.024	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.062	Δρ_max = 0.27 e Å⁻³
S = 1.11	Δρ_min = −0.16 e Å⁻³
1302 reflections	Absolute structure: Flack (1983), 517 Friedel pairs
83 parameters	Absolute structure parameter: 0.10 (6)
0 restraints

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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)
Cl1	0.38240 (8)	0.0000	0.5000	0.02165 (12)
O1	0.9799 (2)	0.31462 (5)	0.62135 (10)	0.0235 (2)
O2	0.5726 (2)	0.27552 (5)	0.60594 (10)	0.0234 (2)
N1	0.8093 (2)	0.27227 (6)	0.64031 (11)	0.0174 (2)
N2	0.8329 (2)	0.03251 (5)	0.68250 (10)	0.0133 (2)
H2A	0.712 (4)	0.0200 (10)	0.628 (2)	0.035 (6)*
C1	0.8975 (3)	0.21173 (6)	0.70323 (11)	0.0143 (2)
C2	0.7865 (3)	0.15455 (7)	0.65679 (12)	0.0146 (3)
H2	0.6486	0.1545	0.5963	0.018*
C3	0.8933 (3)	0.09724 (6)	0.70596 (11)	0.0124 (2)
C4	1.0000	−0.00475 (10)	0.7500	0.0143 (3)
C5	1.0000	−0.07722 (10)	0.7500	0.0207 (4)
H5A	0.8609	−0.0929	0.6937	0.031*	0.50
H5B	0.9666	−0.0929	0.8351	0.031*	0.50
H5C	1.1726	−0.0929	0.7211	0.031*	0.50

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.01317 (19)	0.0379 (3)	0.01385 (18)	0.000	0.000	−0.00422 (19)
O1	0.0284 (5)	0.0159 (5)	0.0261 (5)	−0.0007 (4)	0.0058 (4)	0.0042 (4)
O2	0.0231 (5)	0.0213 (5)	0.0259 (5)	0.0069 (4)	−0.0046 (4)	0.0017 (4)
N1	0.0222 (6)	0.0145 (5)	0.0156 (5)	0.0036 (5)	0.0015 (4)	0.0010 (4)
N2	0.0137 (5)	0.0129 (5)	0.0133 (5)	−0.0011 (4)	0.0006 (4)	−0.0010 (4)
C1	0.0145 (6)	0.0127 (6)	0.0157 (5)	0.0026 (5)	0.0030 (5)	0.0019 (4)
C2	0.0133 (5)	0.0169 (6)	0.0137 (5)	0.0015 (5)	0.0000 (4)	0.0009 (5)
C3	0.0129 (5)	0.0125 (6)	0.0117 (5)	−0.0009 (5)	0.0026 (5)	−0.0007 (4)
C4	0.0145 (7)	0.0154 (9)	0.0131 (7)	0.000	0.0035 (6)	0.000
C5	0.0250 (10)	0.0110 (9)	0.0261 (10)	0.000	0.0025 (8)	0.000

Geometric parameters (Å, º) top

N1—O1	1.2259 (16)	C2—H2	0.9300
N1—O2	1.2260 (16)	C3—C3ⁱ	1.401 (3)
N1—C1	1.4692 (17)	C4—N2	1.3275 (16)
N2—C3	1.3801 (16)	C4—N2ⁱ	1.3275 (16)
N2—H2A	0.86 (2)	C4—C5	1.483 (3)
C1—C1ⁱ	1.409 (3)	C5—H5A	0.9600
C2—C1	1.3808 (18)	C5—H5B	0.9600
C2—C3	1.3855 (18)	C5—H5C	0.9600

O1—N1—O2	124.84 (12)	N2—C3—C2	131.66 (12)
O1—N1—C1	117.67 (11)	N2—C3—C3ⁱ	106.24 (7)
O2—N1—C1	117.41 (11)	C2—C3—C3ⁱ	122.08 (8)
C3—N2—H2A	123.5 (14)	N2ⁱ—C4—N2	109.87 (17)
C4—N2—C3	108.82 (12)	N2ⁱ—C4—C5	125.07 (9)
C4—N2—H2A	127.6 (14)	N2—C4—C5	125.07 (9)
C1ⁱ—C1—N1	121.63 (7)	C4—C5—H5A	109.5
C2—C1—N1	116.07 (11)	C4—C5—H5B	109.5
C2—C1—C1ⁱ	122.02 (8)	C4—C5—H5C	109.5
C1—C2—C3	115.83 (12)	H5A—C5—H5B	109.5
C1—C2—H2	122.1	H5A—C5—H5C	109.5
C3—C2—H2	122.1	H5B—C5—H5C	109.5

O1—N1—C1—C1ⁱ	33.8 (2)	C3—C2—C1—N1	172.73 (11)
O1—N1—C1—C2	−140.30 (13)	C3—C2—C1—C1ⁱ	−1.3 (2)
O2—N1—C1—C1ⁱ	−149.18 (15)	C1—C2—C3—N2	179.82 (13)
O2—N1—C1—C2	36.76 (17)	C1—C2—C3—C3ⁱ	−2.1 (2)
C4—N2—C3—C2	177.52 (13)	N2ⁱ—C4—N2—C3	0.32 (6)
C4—N2—C3—C3ⁱ	−0.81 (16)	C5—C4—N2—C3	−179.68 (6)

Symmetry code: (i) −x+2, y, −z+3/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···Cl1	0.86 (2)	2.15 (2)	3.008 (1)	172.5 (18)
C2—H2···O1ⁱⁱ	0.93	2.51	3.339 (2)	150

Symmetry code: (ii) x−1/2, −y+1/2, −z+1.

Experimental details

Crystal data
Chemical formula	C₈H₇N₄O₄⁺·Cl⁻
M_r	258.63
Crystal system, space group	Orthorhombic, C222₁
Temperature (K)	100
a, b, c (Å)	4.9453 (1), 20.4691 (4), 10.4543 (3)
V (Å³)	1058.25 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.37
Crystal size (mm)	0.46 × 0.40 × 0.20

Data collection
Diffractometer	Bruker Kappa APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.848, 0.929
No. of measured, independent and observed [I > 2σ(I)] reflections	3043, 1302, 1264
R_int	0.016
(sin θ/λ)_max (Å⁻¹)	0.667

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.024, 0.062, 1.11
No. of reflections	1302
No. of parameters	83
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.16
Absolute structure	Flack (1983), 517 Friedel pairs
Absolute structure parameter	0.10 (6)

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···Cl1	0.86 (2)	2.15 (2)	3.008 (1)	172.5 (18)
C2—H2···O1ⁱ	0.93	2.51	3.339 (2)	149.5

Symmetry code: (i) x−1/2, −y+1/2, −z+1.

Acknowledgements

The authors are indebted to Anadolu University and the Medicinal Plants and Medicine Research Centre of Anadolu University, Eskişehir, Turkey, for the use of the X-ray diffractometer.

References

Alamgir, M., Black, D. S. C. & Kumar, N. (2007). Top. Heterocycl. Chem. 9, 87–118. CrossRef CAS Google Scholar
Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838. CrossRef CAS IUCr Journals Google Scholar
Flack, H. D. (1983). Acta Cryst. A39, 876–881. CrossRef CAS Web of Science IUCr Journals Google Scholar
Hoffmann, H. S., Stefani, V., Benvenutti, E. V., Costa, T. M. H. & Gallas, M. R. (2011). Mater. Chem. Phys. 126, 97–101. Web of Science CrossRef CAS Google Scholar
Hökelek, T., Dinçer, S. & Kılıç, E. (2002). Cryst. Res. Technol. 37, 1138–1142. CSD CrossRef CAS Google Scholar
Horton, D. A., Bourne, G. T. & Smythe, M. L. (2003). Chem. Rev. 103, 893–930. Web of Science CrossRef PubMed CAS Google Scholar
Kuznetsov, Y. I. & Kazansky, L. P. (2008). Russ. Chem. Rev. 77, 219–232. CrossRef CAS Google Scholar
Laryea, D., Gullbo, J., Isakssoon, A., Larsson, R. & Nygren, P. (2010). Anti-Cancer Drugs, 21, 33–42. Web of Science CrossRef PubMed CAS Google Scholar
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453–457. Web of Science CrossRef CAS IUCr Journals Google Scholar
Refaat, H. M. (2010). Eur. J. Med. Chem. 45, 2949–2956. Web of Science CrossRef CAS PubMed Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Soula, C. & Luu-Duc, C. (1986). Lyon Pharm. 37, 297–302. CAS Google Scholar
Spasov, A. A., Yozhitsa, I. N., Bugaeva, L. I. & Anisimova, V. A. (1999). Pharm. Chem. J. 33, 232–243. CrossRef CAS Google Scholar
Subramanyam, N. C. & Mayanna, S. M. (1985). Corros. Sci. 25, 163–169. CrossRef CAS Google Scholar