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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 6| June 2011| Pages o1523-o1524
doi:10.1107/S1600536811019027

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

Raza Murad Ghalib,a Rokiah Hashim,a Othman Sulaiman,a Ching Kheng Quahb‡ and Hoong-Kun Funb*§

aSchool of Industrial Technology, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my

(Received 10 May 2011; accepted 19 May 2011; online 25 May 2011)

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[Puratchikody, A., Nagalakshmi, G. & Doble, M. (2008). Chem. Pharm. Bull. 56, 273-281.]); Tonelli et al. (2010[Tonelli, M., Simone, M., Tasso, B., Novelli, F., Boido, V., Sparatore, F., Paglietti, G., Pricl, S., Giliberti, G., Blois, S., Ibba, C., Sanna, G., Loddo, R. & La Colla, P. (2010). Bioorg. Med. Chem. 18, 2937-2953.]); Shingalapur et al. (2010[Shingalapur, R. V., Hosamani, K. M., Keri, R. S. & Hugar, M. H. (2010). Eur. J. Med. Chem. 45, 1753-1759.]); Refaat (2010[Refaat, H. M. (2010). Eur. J. Med. Chem. 45, 2949-2956.]); Lazer et al. (1987[Lazer, E. S., Matteo, M. R. & Possanza, G. J. (1987). J. Med. Chem. 30, 726-729.]). For the preparation of the title compound, see: Umare et al. (2008[Umare, V. D., Ingle, V. N. & Wanare, R. K. (2008). Indian J. Heterocycl. Chem. 17, 253-256.]); Singh & Pathak (2008[Singh, J. & Pathak, D. P. (2008). Orient. J. Chem. 24, 175-180.]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]). For standard bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). For related structures, see: Eltayeb et al. (2009[Eltayeb, N. E., Teoh, S. G., Quah, C. K., Fun, H.-K. & Adnan, R. (2009). Acta Cryst. E65, o1613-o1614.]); Arumugam et al. (2010[Arumugam, N., Abdul Rahim, A. S., Osman, H., Quah, C. K. & Fun, H.-K. (2010). Acta Cryst. E66, o2412-o2413.]).

[Scheme 1]

Experimental

Crystal data

  • C8H7N3O2·H2O

  • Mr = 195.18

  • Triclinic, [P \overline 1]

  • 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) Å3

  • 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[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.942, Tmax = 0.984

  • 6312 measured reflections

  • 1784 independent reflections

  • 1506 reflections with I > 2σ(I)

  • Rint = 0.032
Refinement

  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.115

  • S = 1.06

  • 1784 reflections

  • 140 parameters

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

  • Δρmax = 0.30 e Å−3

  • Δρmin = −0.35 e Å−3

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) x, y, z-1; (ii) x, y+1, z; (iii) x, y+1, z+1.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811019027/is2711sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811019027/is2711Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811019027/is2711Isup3.cml

checkCIF report


Comment top

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].

Related literature top

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 top

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 top

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 Uiso(H) = 1.2 or 1.5Ueq(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.

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing 50% probability displacement ellipsoids for non-H atoms.
[Figure 2] 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.
2-Methyl-5-nitro-1H-benzimidazole monohydrate top
Crystal data top
C8H7N3O2·H2OZ = 2
Mr = 195.18F(000) = 204
Triclinic, P1Dx = 1.485 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.9051 (10) ÅCell parameters from 2800 reflections
b = 7.1309 (11) Åθ = 3.1–29.8°
c = 10.0653 (15) ŵ = 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 top
Bruker SMART APEXII DUO CCD area-detector
diffractometer		1784 independent reflections
Radiation source: fine-focus sealed tube1506 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
ϕ and ω scansθmax = 26.5°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		h = −8→8
Tmin = 0.942, Tmax = 0.984k = −8→8
6312 measured reflectionsl = −12→12
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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H 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 parametersΔρmax = 0.30 e Å−3
0 restraintsΔρmin = −0.35 e Å−3
Crystal data top
C8H7N3O2·H2Oγ = 67.517 (3)°
Mr = 195.18V = 436.61 (11) Å3
Triclinic, P1Z = 2
a = 6.9051 (10) ÅMo Kα radiation
b = 7.1309 (11) ŵ = 0.12 mm−1
c = 10.0653 (15) ÅT = 100 K
α = 79.421 (3)°0.52 × 0.19 × 0.14 mm
β = 73.062 (3)°
Data collection top
Bruker SMART APEXII DUO CCD area-detector
diffractometer		1784 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		1506 reflections with I > 2σ(I)
Tmin = 0.942, Tmax = 0.984Rint = 0.032
6312 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.115H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.30 e Å−3
1784 reflectionsΔρmin = −0.35 e Å−3
140 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
O10.23733 (19)−0.19984 (17)0.30176 (12)0.0281 (3)
O20.2283 (2)0.0307 (2)0.41865 (11)0.0350 (3)
N10.26105 (19)0.47231 (19)−0.17804 (12)0.0176 (3)
N20.2160 (2)0.17912 (19)−0.18388 (12)0.0190 (3)
N30.2355 (2)−0.0294 (2)0.30934 (13)0.0220 (3)
C10.2320 (3)0.4036 (2)−0.40419 (15)0.0248 (4)
H1A0.15000.3383−0.42850.037*
H1B0.37730.3594−0.46080.037*
H1C0.16690.5486−0.41980.037*
C20.2349 (2)0.3487 (2)−0.25514 (15)0.0186 (3)
C30.2308 (2)0.1917 (2)−0.05118 (14)0.0167 (3)
C40.2203 (2)0.0559 (2)0.06588 (15)0.0183 (3)
H4A0.1994−0.06520.06520.022*
C50.2426 (2)0.1109 (2)0.18391 (15)0.0185 (3)
C60.2731 (2)0.2924 (2)0.19023 (15)0.0189 (3)
H6A0.28810.32060.27260.023*
C70.2808 (2)0.4286 (2)0.07407 (15)0.0187 (3)
H7A0.29950.55040.07600.022*
C80.2594 (2)0.3764 (2)−0.04673 (15)0.0168 (3)
O1W0.28031 (19)0.83785 (17)0.68930 (12)0.0244 (3)
H1N10.265 (3)0.598 (4)−0.212 (2)0.036 (5)*
H1W10.269 (3)0.877 (3)0.608 (2)0.036 (5)*
H2W10.257 (4)0.949 (4)0.734 (2)0.052 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0388 (7)0.0180 (6)0.0275 (6)−0.0098 (5)−0.0114 (5)0.0032 (5)
O20.0605 (8)0.0352 (7)0.0160 (6)−0.0209 (6)−0.0151 (5)0.0003 (5)
N10.0242 (6)0.0138 (7)0.0168 (6)−0.0068 (5)−0.0075 (5)−0.0017 (5)
N20.0259 (6)0.0153 (6)0.0177 (6)−0.0062 (5)−0.0089 (5)−0.0028 (5)
N30.0248 (7)0.0214 (7)0.0194 (7)−0.0065 (5)−0.0076 (5)−0.0004 (5)
C10.0349 (8)0.0219 (8)0.0186 (8)−0.0083 (7)−0.0104 (6)−0.0017 (6)
C20.0212 (7)0.0157 (7)0.0191 (7)−0.0040 (6)−0.0069 (6)−0.0042 (6)
C30.0185 (7)0.0161 (7)0.0162 (7)−0.0041 (6)−0.0064 (5)−0.0036 (5)
C40.0211 (7)0.0137 (7)0.0211 (8)−0.0056 (6)−0.0062 (5)−0.0033 (6)
C50.0197 (7)0.0179 (8)0.0163 (7)−0.0043 (6)−0.0061 (5)0.0000 (6)
C60.0203 (7)0.0206 (8)0.0165 (7)−0.0049 (6)−0.0066 (5)−0.0051 (6)
C70.0203 (7)0.0166 (7)0.0216 (7)−0.0061 (6)−0.0066 (6)−0.0057 (6)
C80.0179 (7)0.0146 (7)0.0177 (7)−0.0041 (5)−0.0053 (5)−0.0030 (5)
O1W0.0428 (7)0.0166 (6)0.0191 (6)−0.0125 (5)−0.0127 (5)−0.0008 (5)
Geometric parameters (Å, º) top
O1—N31.2271 (18)C3—C41.384 (2)
O2—N31.2334 (17)C3—C81.414 (2)
N1—C21.3660 (18)C4—C51.383 (2)
N1—C81.3710 (19)C4—H4A0.9300
N1—H1N10.91 (2)C5—C61.404 (2)
N2—C21.320 (2)C6—C71.378 (2)
N2—C31.3905 (18)C6—H6A0.9300
N3—C51.4609 (19)C7—C81.3973 (19)
C1—C21.483 (2)C7—H7A0.9300
C1—H1A0.9600O1W—H1W10.83 (2)
C1—H1B0.9600O1W—H2W10.92 (3)
C1—H1C0.9600
C2—N1—C8107.18 (12)N2—C3—C8109.57 (13)
C2—N1—H1N1122.1 (13)C5—C4—C3116.11 (13)
C8—N1—H1N1130.4 (13)C5—C4—H4A121.9
C2—N2—C3104.83 (12)C3—C4—H4A121.9
O1—N3—O2123.11 (13)C4—C5—C6124.00 (14)
O1—N3—C5119.20 (13)C4—C5—N3117.95 (13)
O2—N3—C5117.69 (13)C6—C5—N3118.05 (13)
C2—C1—H1A109.5C7—C6—C5119.80 (13)
C2—C1—H1B109.5C7—C6—H6A120.1
H1A—C1—H1B109.5C5—C6—H6A120.1
C2—C1—H1C109.5C6—C7—C8117.33 (14)
H1A—C1—H1C109.5C6—C7—H7A121.3
H1B—C1—H1C109.5C8—C7—H7A121.3
N2—C2—N1113.13 (13)N1—C8—C7132.77 (14)
N2—C2—C1124.88 (13)N1—C8—C3105.30 (12)
N1—C2—C1121.98 (13)C7—C8—C3121.93 (14)
C4—C3—N2129.61 (13)H1W1—O1W—H2W1109 (2)
C4—C3—C8120.82 (13)
C3—N2—C2—N1−0.04 (16)O2—N3—C5—C69.3 (2)
C3—N2—C2—C1179.09 (13)C4—C5—C6—C70.4 (2)
C8—N1—C2—N20.05 (16)N3—C5—C6—C7179.98 (12)
C8—N1—C2—C1−179.10 (13)C5—C6—C7—C8−0.6 (2)
C2—N2—C3—C4179.60 (14)C2—N1—C8—C7179.43 (15)
C2—N2—C3—C80.01 (15)C2—N1—C8—C3−0.04 (15)
N2—C3—C4—C5179.45 (13)C6—C7—C8—N1−179.40 (14)
C8—C3—C4—C5−1.0 (2)C6—C7—C8—C30.0 (2)
C3—C4—C5—C60.4 (2)C4—C3—C8—N1−179.62 (12)
C3—C4—C5—N3−179.17 (12)N2—C3—C8—N10.02 (15)
O1—N3—C5—C49.0 (2)C4—C3—C8—C70.8 (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, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O1Wi0.91 (3)1.84 (2)2.7347 (18)170 (2)
O1W—H1W1···O2ii0.831 (19)2.06 (2)2.8737 (17)168.5 (19)
O1W—H2W1···N2iii0.92 (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.

Experimental details

Crystal data
Chemical formulaC8H7N3O2·H2O
Mr195.18
Crystal system, space groupTriclinic, P1
Temperature (K)100
a, b, c (Å)6.9051 (10), 7.1309 (11), 10.0653 (15)
α, β, γ (°)79.421 (3), 73.062 (3), 67.517 (3)
V (Å3)436.61 (11)
Z2
Radiation typeMo Kα
µ (mm−1)0.12
Crystal size (mm)0.52 × 0.19 × 0.14
Data collection
DiffractometerBruker SMART APEXII DUO CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.942, 0.984
No. of measured, independent and
observed [I > 2σ(I)] reflections		6312, 1784, 1506
Rint0.032
(sin θ/λ)max (Å−1)0.628
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.115, 1.06
No. of reflections1784
No. of parameters140
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.30, −0.35

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O1Wi0.91 (3)1.84 (2)2.7347 (18)170 (2)
O1W—H1W1···O2ii0.831 (19)2.06 (2)2.8737 (17)168.5 (19)
O1W—H2W1···N2iii0.92 (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.
 

Footnotes

‡Thomson Reuters ResearcherID: A-5525-2009.

§Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

We would like to acknowledge Universiti Sains Malaysia (USM) for the University Grant 1001/PTEKIND/8140152. HKF and CKQ also thank USM for the Research University Grant (No. 1001/PFIZIK/811160).

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CrossRef Web of Science Google Scholar
 First citationArumugam, N., Abdul Rahim, A. S., Osman, H., Quah, C. K. & Fun, H.-K. (2010). Acta Cryst. E66, o2412–o2413.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationBruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
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ISSN: 2056-9890
Volume 67| Part 6| June 2011| Pages o1523-o1524
doi:10.1107/S1600536811019027
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