1-Methyl-2-methyl-sulfanyl-6-nitro-1H-benzimidazole.

The mol-ecule of the title compound, C9H9N3O2S, is built up from fused five- and six-membered rings connected to methyl-sulfanyl and nitro groups, respectively. The mean plane through the fused ring system is inclined slightly relative to the plane passing through the nitro group [dihedral angle = 3.6 (2)°]. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds and π-π inter-actions between imidazole rings [inter-centroid distance = 3.667 (3) Å], forming a three-dimensional network.

Related literature

For the biological activity of benzimidazoles, see: Achar et al. (2010 ▶); Boiani & Gonzalez (2005 ▶); Ishida et al. (2006 ▶); Kamal et al. (2008 ▶); Kus et al. (2004 ▶); LaPlante et al. (2004 ▶).

Experimental

Crystal data

C9H9N3O2S

M = 223.25

Monoclinic,

a = 11.7213 (4) Å

b = 11.8991 (4) Å

c = 7.3025 (3) Å

β = 103.523 (1)°

V = 990.26 (6) Å3

Z = 4

Mo Kα radiation

μ = 0.31 mm−1

T = 296 K

0.42 × 0.31 × 0.26 mm

Data collection

Bruker X8 APEX diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.658, T max = 0.746

11751 measured reflections

2772 independent reflections

2350 reflections with I > 2σ(I)

R int = 0.025

Refinement

R[F 2 > 2σ(F 2)] = 0.039

wR(F 2) = 0.116

S = 1.07

2772 reflections

136 parameters

H-atom parameters constrained

Δρmax = 0.34 e Å−3

Δρmin = −0.19 e Å−3

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); 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, 2012 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶) and publCIF (Westrip, 2010 ▶).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S1600536814004723/tk5298sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814004723/tk5298Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814004723/tk5298Isup3.cml

CCDC reference: 989365

Additional supporting information: crystallographic information; 3D view; checkCIF report

C9H9N3O2S	F(000) = 464
Mr = 223.25	Dx = 1.497 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2772 reflections
a = 11.7213 (4) Å	θ = 2.5–29.6°
b = 11.8991 (4) Å	µ = 0.31 mm−1
c = 7.3025 (3) Å	T = 296 K
β = 103.523 (1)°	Block, colourless
V = 990.26 (6) Å3	0.42 × 0.31 × 0.26 mm
Z = 4

Bruker X8 APEX diffractometer	2772 independent reflections
Radiation source: fine-focus sealed tube	2350 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.025
φ and ω scans	θmax = 29.6°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −16→16
Tmin = 0.658, Tmax = 0.746	k = −16→15
11751 measured reflections	l = −10→8

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.116	H-atom parameters constrained
S = 1.07	w = 1/[σ2(Fo2) + (0.0644P)2 + 0.2102P] where P = (Fo2 + 2Fc2)/3
2772 reflections	(Δ/σ)max = 0.001
136 parameters	Δρmax = 0.34 e Å−3
0 restraints	Δρmin = −0.19 e Å−3

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > σ(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.

	x	y	z	Uiso*/Ueq
C1	0.37904 (11)	0.74865 (11)	0.42804 (17)	0.0319 (3)
C2	0.21992 (11)	0.66649 (11)	0.29323 (17)	0.0315 (3)
C3	0.13098 (12)	0.58951 (11)	0.2205 (2)	0.0385 (3)
H3	0.1435	0.5126	0.2365	0.046*
C4	0.02393 (12)	0.63119 (12)	0.1243 (2)	0.0388 (3)
H4	−0.0373	0.5820	0.0752	0.047*
C5	0.00707 (11)	0.74680 (12)	0.10023 (18)	0.0344 (3)
C6	0.09247 (11)	0.82662 (11)	0.17081 (17)	0.0331 (3)
H6	0.0793	0.9034	0.1538	0.040*
C7	0.19868 (11)	0.78276 (10)	0.26849 (16)	0.0295 (3)
C8	0.58418 (14)	0.64247 (14)	0.5740 (2)	0.0502 (4)
H8A	0.6651	0.6472	0.6400	0.075*
H8B	0.5788	0.6101	0.4518	0.075*
H8C	0.5424	0.5961	0.6440	0.075*
C9	0.32546 (14)	0.95396 (12)	0.3712 (3)	0.0487 (4)
H9A	0.2561	0.9940	0.3088	0.073*
H9B	0.3884	0.9716	0.3123	0.073*
H9C	0.3470	0.9756	0.5013	0.073*
N1	0.30262 (9)	0.83409 (9)	0.35759 (15)	0.0326 (2)
N2	0.33342 (10)	0.64715 (10)	0.39349 (16)	0.0353 (2)
N3	−0.10606 (11)	0.78650 (12)	−0.00931 (19)	0.0451 (3)
O1	−0.17998 (12)	0.71648 (13)	−0.0807 (2)	0.0775 (5)
O2	−0.12317 (11)	0.88741 (11)	−0.02760 (19)	0.0610 (3)
S1	0.52130 (3)	0.78014 (3)	0.54830 (5)	0.04086 (13)

	U11	U22	U33	U12	U13	U23
C1	0.0322 (6)	0.0338 (6)	0.0290 (6)	−0.0034 (5)	0.0058 (4)	−0.0008 (5)
C2	0.0328 (6)	0.0299 (6)	0.0312 (6)	−0.0036 (4)	0.0066 (4)	−0.0010 (4)
C3	0.0407 (7)	0.0282 (6)	0.0445 (7)	−0.0073 (5)	0.0062 (5)	−0.0029 (5)
C4	0.0351 (6)	0.0374 (7)	0.0426 (7)	−0.0098 (5)	0.0062 (5)	−0.0089 (6)
C5	0.0290 (6)	0.0422 (7)	0.0312 (6)	−0.0004 (5)	0.0053 (5)	−0.0059 (5)
C6	0.0342 (6)	0.0306 (6)	0.0340 (6)	0.0001 (5)	0.0068 (5)	−0.0027 (5)
C7	0.0311 (6)	0.0291 (6)	0.0281 (5)	−0.0047 (4)	0.0067 (4)	−0.0022 (4)
C8	0.0382 (7)	0.0525 (9)	0.0537 (9)	0.0044 (6)	−0.0016 (6)	−0.0025 (7)
C9	0.0460 (8)	0.0291 (7)	0.0657 (10)	−0.0091 (6)	0.0024 (7)	−0.0022 (6)
N1	0.0318 (5)	0.0282 (5)	0.0356 (5)	−0.0054 (4)	0.0032 (4)	−0.0020 (4)
N2	0.0338 (5)	0.0316 (5)	0.0379 (5)	−0.0027 (4)	0.0033 (4)	0.0007 (4)
N3	0.0337 (6)	0.0560 (8)	0.0427 (6)	0.0032 (5)	0.0032 (5)	−0.0095 (5)
O1	0.0439 (7)	0.0760 (10)	0.0950 (11)	−0.0049 (6)	−0.0193 (7)	−0.0228 (8)
O2	0.0467 (6)	0.0567 (8)	0.0720 (8)	0.0149 (5)	−0.0012 (6)	−0.0006 (6)
S1	0.0342 (2)	0.0423 (2)	0.0412 (2)	−0.00665 (13)	−0.00108 (13)	−0.00503 (13)

C1—N2	1.3210 (17)	C6—H6	0.9300
C1—N1	1.3730 (17)	C7—N1	1.3819 (15)
C1—S1	1.7342 (13)	C8—S1	1.7882 (17)
C2—N2	1.3796 (16)	C8—H8A	0.9600
C2—C3	1.3960 (17)	C8—H8B	0.9600
C2—C7	1.4098 (18)	C8—H8C	0.9600
C3—C4	1.379 (2)	C9—N1	1.4504 (17)
C3—H3	0.9300	C9—H9A	0.9600
C4—C5	1.395 (2)	C9—H9B	0.9600
C4—H4	0.9300	C9—H9C	0.9600
C5—C6	1.3888 (18)	N3—O2	1.2196 (18)
C5—N3	1.4578 (18)	N3—O1	1.2270 (18)
C6—C7	1.3841 (17)
N2—C1—N1	113.95 (11)	S1—C8—H8A	109.5
N2—C1—S1	126.34 (11)	S1—C8—H8B	109.5
N1—C1—S1	119.71 (10)	H8A—C8—H8B	109.5
N2—C2—C3	129.35 (12)	S1—C8—H8C	109.5
N2—C2—C7	110.56 (11)	H8A—C8—H8C	109.5
C3—C2—C7	120.09 (12)	H8B—C8—H8C	109.5
C4—C3—C2	117.86 (12)	N1—C9—H9A	109.5
C4—C3—H3	121.1	N1—C9—H9B	109.5
C2—C3—H3	121.1	H9A—C9—H9B	109.5
C3—C4—C5	120.27 (12)	N1—C9—H9C	109.5
C3—C4—H4	119.9	H9A—C9—H9C	109.5
C5—C4—H4	119.9	H9B—C9—H9C	109.5
C6—C5—C4	123.99 (12)	C1—N1—C7	105.98 (10)
C6—C5—N3	117.79 (13)	C1—N1—C9	127.50 (11)
C4—C5—N3	118.20 (12)	C7—N1—C9	126.52 (12)
C7—C6—C5	114.64 (12)	C1—N2—C2	104.24 (11)
C7—C6—H6	122.7	O2—N3—O1	122.70 (14)
C5—C6—H6	122.7	O2—N3—C5	118.97 (13)
N1—C7—C6	131.58 (12)	O1—N3—C5	118.32 (14)
N1—C7—C2	105.28 (11)	C1—S1—C8	100.32 (7)
C6—C7—C2	123.13 (11)

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8A···O1i	0.96	2.53	3.393 (2)	150
C3—H3···O2ii	0.93	2.65	3.3038 (19)	128
C9—H9A···O2iii	0.96	2.67	3.563 (2)	155

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C8—H8A⋯O1i	0.96	2.53	3.393 (2)	150
C3—H3⋯O2ii	0.93	2.65	3.3038 (19)	128
C9—H9A⋯O2iii	0.96	2.67	3.563 (2)	155

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