2-Methyl-5-nitro-1H-benzimidazole monohydrate

Abstract

In the title compound, C₈H₇N₃O₂·H₂O, the 2-methyl-5-nitro-1H-benzimidazole mol­ecule, excluding the methyl H atoms, is approximately planar, with a maximum deviation of 0.137 (1) Å. The crystal structure is stabilized by water mol­ecules via N—H⋯O(water), O(water)—H⋯O and O(water)—H⋯N hydrogen bonds, forming sheets parallel to the (100) plane. A short inter­molecular contact between the benzene and imidazole rings, with a centroid–centroid distance of 3.6419 (10) Å, indicates a π–π inter­action.

Related literature

For general background to and the potential biological activity of benzimidazole derivatives, see: Puratchikody et al. (2008 ▶); Tonelli et al. (2010 ▶); Shingalapur et al. (2010 ▶); Refaat (2010 ▶); Lazer et al. (1987 ▶). For the preparation of the title compound, see: Umare et al. (2008 ▶); Singh & Pathak (2008 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶). For standard bond-length data, see: Allen et al. (1987 ▶). For related structures, see: Eltayeb et al. (2009 ▶); Arumugam et al. (2010 ▶).

Experimental

Crystal data

• C₈H₇N₃O₂·H₂O

• M _r = 195.18

• Triclinic,

• a = 6.9051 (10) Å

• b = 7.1309 (11) Å

• c = 10.0653 (15) Å

• α = 79.421 (3)°

• β = 73.062 (3)°

• γ = 67.517 (3)°

• V = 436.61 (11) ų

• Z = 2

• Mo Kα radiation

• μ = 0.12 mm⁻¹

• T = 100 K

• 0.52 × 0.19 × 0.14 mm

Data collection

• Bruker SMART APEXII DUO CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.942, T _max = 0.984

• 6312 measured reflections

• 1784 independent reflections

• 1506 reflections with I > 2σ(I)

• R _int = 0.032

Refinement

• R[F ² > 2σ(F ²)] = 0.040

• wR(F ²) = 0.115

• S = 1.06

• 1784 reflections

• 140 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.30 e Å⁻³

• Δρ_min = −0.35 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536811019027/is2711Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N1⋯O1Wi	0.91 (3)	1.84 (2)	2.7347 (18)	170 (2)
O1W—H1W1⋯O2ii	0.831 (19)	2.06 (2)	2.8737 (17)	168.5 (19)
O1W—H2W1⋯N2iii	0.92 (3)	1.86 (3)	2.7808 (18)	177.2 (17)

Symmetry codes: (i) ; (ii) ; (iii) .

supplementary crystallographic information

Comment

benzimidazoles are aromatic heterocylic organic compounds of wide biological importance. They are reported as antimicrobial (Puratchikody et al., 2008), antiviral (Tonelli et al., 2010), anticancer (Refaat, 2010), anti-inflammatory (Lazer et al., 1987) and anti-diabetic (Shingalapur et al., 2010) agents.

The molecular structure of the title compound is shown in Fig. 1. The 2-methyl-5-nitro-1H-benzimidazole molecule (O1/O2/N1-N3/C1-C8), excluding methyl H atoms, is almost planar, with a maximum deviation of 0.137 (1) Å for atom O2. Bond lengths (Allen et al., 1987) and angles are within normal ranges and comparable to related structures (Eltayeb et al., 2009; Arumugam et al., 2010).

The crystal structure (Fig. 2) is stabilized by water molecules via intermolecular N1—H1N1···O1W, O1W—H1W1···O2 and O1W—H2W1···N2 hydrogen bonds to form sheets parallel to the (100) plane. The crystal packing is further consolidated by π–π stacking interactions between the centroids of N1/N2/C2/C3/C8 (Cg1) and C3–C8 (Cg2) rings, with Cg1···Cg2ⁱⁱⁱ distance of 3.6419 (10) Å [symmetry code: (iii) -x, 1 - y, -z].

Experimental

4-Nitro-o-phenylenediamine (1.53 g) was well dissolved in acetic acid and refluxed on a heating mantle for 6 h. The reaction mixture was dried on rotavapor at low pressure to give the solid mass which was then crystallized with alcohol-chloroform (1:1 v/v) mixture to give the brownish crystals of title compound (Umare et al., 2008; Singh & Pathak, 2008), yield 50%, m.p. 496-498 K. Melting point was taken on Thermo Fisher digital melting point apparatus of IA9000 series and is uncorrected.

Refinement

O- and N-bound H atoms were located in a difference Fourier map and refined freely [O—H = 0.83 (2)–0.92 (3) Å, N1—H1N1 = 0.91 (2) Å]. The remaining H atoms were positioned geometrically and refined using a riding model with C—H = 0.93 or 0.96 Å, and with U_iso(H) = 1.2 or 1.5U_eq(C). A rotating-group model was applied for the methyl group. The highest residual electron density peak is located at 0.66 Å from C3 and the deepest hole is located at 0.67 Å from N3.

Figures

Fig. 1.

The molecular structure of the title compound showing 50% probability displacement ellipsoids for non-H atoms.

Fig. 2.

The crystal structure of the title compound, viewed along the a axis. H atoms not involved in hydrogen bonds (dashed lines) have been omitted for clarity.

Crystal data

C8H7N3O2·H2O	Z = 2
Mr = 195.18	F(000) = 204
Triclinic, P1	Dx = 1.485 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.9051 (10) Å	Cell parameters from 2800 reflections
b = 7.1309 (11) Å	θ = 3.1–29.8°
c = 10.0653 (15) Å	µ = 0.12 mm−1
α = 79.421 (3)°	T = 100 K
β = 73.062 (3)°	Needle, brown
γ = 67.517 (3)°	0.52 × 0.19 × 0.14 mm
V = 436.61 (11) Å3

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer	1784 independent reflections
Radiation source: fine-focus sealed tube	1506 reflections with I > 2σ(I)
graphite	Rint = 0.032
φ and ω scans	θmax = 26.5°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −8→8
Tmin = 0.942, Tmax = 0.984	k = −8→8
6312 measured reflections	l = −12→12

Refinement

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)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ2(Fo2) + (0.0635P)2 + 0.1355P] where P = (Fo2 + 2Fc2)/3
1784 reflections	(Δ/σ)max = 0.001
140 parameters	Δρmax = 0.30 e Å−3
0 restraints	Δρmin = −0.35 e Å−3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.23733 (19)	−0.19984 (17)	0.30176 (12)	0.0281 (3)
O2	0.2283 (2)	0.0307 (2)	0.41865 (11)	0.0350 (3)
N1	0.26105 (19)	0.47231 (19)	−0.17804 (12)	0.0176 (3)
N2	0.2160 (2)	0.17912 (19)	−0.18388 (12)	0.0190 (3)
N3	0.2355 (2)	−0.0294 (2)	0.30934 (13)	0.0220 (3)
C1	0.2320 (3)	0.4036 (2)	−0.40419 (15)	0.0248 (4)
H1A	0.1500	0.3383	−0.4285	0.037*
H1B	0.3773	0.3594	−0.4608	0.037*
H1C	0.1669	0.5486	−0.4198	0.037*
C2	0.2349 (2)	0.3487 (2)	−0.25514 (15)	0.0186 (3)
C3	0.2308 (2)	0.1917 (2)	−0.05118 (14)	0.0167 (3)
C4	0.2203 (2)	0.0559 (2)	0.06588 (15)	0.0183 (3)
H4A	0.1994	−0.0652	0.0652	0.022*
C5	0.2426 (2)	0.1109 (2)	0.18391 (15)	0.0185 (3)
C6	0.2731 (2)	0.2924 (2)	0.19023 (15)	0.0189 (3)
H6A	0.2881	0.3206	0.2726	0.023*
C7	0.2808 (2)	0.4286 (2)	0.07407 (15)	0.0187 (3)
H7A	0.2995	0.5504	0.0760	0.022*
C8	0.2594 (2)	0.3764 (2)	−0.04673 (15)	0.0168 (3)
O1W	0.28031 (19)	0.83785 (17)	0.68930 (12)	0.0244 (3)
H1N1	0.265 (3)	0.598 (4)	−0.212 (2)	0.036 (5)*
H1W1	0.269 (3)	0.877 (3)	0.608 (2)	0.036 (5)*
H2W1	0.257 (4)	0.949 (4)	0.734 (2)	0.052 (6)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0388 (7)	0.0180 (6)	0.0275 (6)	−0.0098 (5)	−0.0114 (5)	0.0032 (5)
O2	0.0605 (8)	0.0352 (7)	0.0160 (6)	−0.0209 (6)	−0.0151 (5)	0.0003 (5)
N1	0.0242 (6)	0.0138 (7)	0.0168 (6)	−0.0068 (5)	−0.0075 (5)	−0.0017 (5)
N2	0.0259 (6)	0.0153 (6)	0.0177 (6)	−0.0062 (5)	−0.0089 (5)	−0.0028 (5)
N3	0.0248 (7)	0.0214 (7)	0.0194 (7)	−0.0065 (5)	−0.0076 (5)	−0.0004 (5)
C1	0.0349 (8)	0.0219 (8)	0.0186 (8)	−0.0083 (7)	−0.0104 (6)	−0.0017 (6)
C2	0.0212 (7)	0.0157 (7)	0.0191 (7)	−0.0040 (6)	−0.0069 (6)	−0.0042 (6)
C3	0.0185 (7)	0.0161 (7)	0.0162 (7)	−0.0041 (6)	−0.0064 (5)	−0.0036 (5)
C4	0.0211 (7)	0.0137 (7)	0.0211 (8)	−0.0056 (6)	−0.0062 (5)	−0.0033 (6)
C5	0.0197 (7)	0.0179 (8)	0.0163 (7)	−0.0043 (6)	−0.0061 (5)	0.0000 (6)
C6	0.0203 (7)	0.0206 (8)	0.0165 (7)	−0.0049 (6)	−0.0066 (5)	−0.0051 (6)
C7	0.0203 (7)	0.0166 (7)	0.0216 (7)	−0.0061 (6)	−0.0066 (6)	−0.0057 (6)
C8	0.0179 (7)	0.0146 (7)	0.0177 (7)	−0.0041 (5)	−0.0053 (5)	−0.0030 (5)
O1W	0.0428 (7)	0.0166 (6)	0.0191 (6)	−0.0125 (5)	−0.0127 (5)	−0.0008 (5)

Geometric parameters (Å, °)

O1—N3	1.2271 (18)	C3—C4	1.384 (2)
O2—N3	1.2334 (17)	C3—C8	1.414 (2)
N1—C2	1.3660 (18)	C4—C5	1.383 (2)
N1—C8	1.3710 (19)	C4—H4A	0.9300
N1—H1N1	0.91 (2)	C5—C6	1.404 (2)
N2—C2	1.320 (2)	C6—C7	1.378 (2)
N2—C3	1.3905 (18)	C6—H6A	0.9300
N3—C5	1.4609 (19)	C7—C8	1.3973 (19)
C1—C2	1.483 (2)	C7—H7A	0.9300
C1—H1A	0.9600	O1W—H1W1	0.83 (2)
C1—H1B	0.9600	O1W—H2W1	0.92 (3)
C1—H1C	0.9600
C2—N1—C8	107.18 (12)	N2—C3—C8	109.57 (13)
C2—N1—H1N1	122.1 (13)	C5—C4—C3	116.11 (13)
C8—N1—H1N1	130.4 (13)	C5—C4—H4A	121.9
C2—N2—C3	104.83 (12)	C3—C4—H4A	121.9
O1—N3—O2	123.11 (13)	C4—C5—C6	124.00 (14)
O1—N3—C5	119.20 (13)	C4—C5—N3	117.95 (13)
O2—N3—C5	117.69 (13)	C6—C5—N3	118.05 (13)
C2—C1—H1A	109.5	C7—C6—C5	119.80 (13)
C2—C1—H1B	109.5	C7—C6—H6A	120.1
H1A—C1—H1B	109.5	C5—C6—H6A	120.1
C2—C1—H1C	109.5	C6—C7—C8	117.33 (14)
H1A—C1—H1C	109.5	C6—C7—H7A	121.3
H1B—C1—H1C	109.5	C8—C7—H7A	121.3
N2—C2—N1	113.13 (13)	N1—C8—C7	132.77 (14)
N2—C2—C1	124.88 (13)	N1—C8—C3	105.30 (12)
N1—C2—C1	121.98 (13)	C7—C8—C3	121.93 (14)
C4—C3—N2	129.61 (13)	H1W1—O1W—H2W1	109 (2)
C4—C3—C8	120.82 (13)
C3—N2—C2—N1	−0.04 (16)	O2—N3—C5—C6	9.3 (2)
C3—N2—C2—C1	179.09 (13)	C4—C5—C6—C7	0.4 (2)
C8—N1—C2—N2	0.05 (16)	N3—C5—C6—C7	179.98 (12)
C8—N1—C2—C1	−179.10 (13)	C5—C6—C7—C8	−0.6 (2)
C2—N2—C3—C4	179.60 (14)	C2—N1—C8—C7	179.43 (15)
C2—N2—C3—C8	0.01 (15)	C2—N1—C8—C3	−0.04 (15)
N2—C3—C4—C5	179.45 (13)	C6—C7—C8—N1	−179.40 (14)
C8—C3—C4—C5	−1.0 (2)	C6—C7—C8—C3	0.0 (2)
C3—C4—C5—C6	0.4 (2)	C4—C3—C8—N1	−179.62 (12)
C3—C4—C5—N3	−179.17 (12)	N2—C3—C8—N1	0.02 (15)
O1—N3—C5—C4	9.0 (2)	C4—C3—C8—C7	0.8 (2)
O2—N3—C5—C4	−171.14 (13)	N2—C3—C8—C7	−179.52 (12)
O1—N3—C5—C6	−170.60 (13)

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O1Wi	0.91 (3)	1.84 (2)	2.7347 (18)	170 (2)
O1W—H1W1···O2ii	0.831 (19)	2.06 (2)	2.8737 (17)	168.5 (19)
O1W—H2W1···N2iii	0.92 (3)	1.86 (3)	2.7808 (18)	177.2 (17)

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