1-Methyl-2-methyl­sulfanyl-6-nitro-1H-benzimidazole

El Ghozlani, M.; Rakib, E.M.; Medaghri-Alaoui, A.; Saadi, M.; El Ammari, L.

doi:10.1107/S1600536814004723

organic compounds

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Volume 70| Part 4| April 2014| Page o407

doi:10.1107/S1600536814004723

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1-Methyl-2-methylsulfanyl-6-nitro-1H-benzimidazole

Mohamed El Ghozlani,^a ^* El Mostapha Rakib,^a Abdelouahid Medaghri-Alaoui,^a Mohamed Saadi ^b and Lahcen El Ammari ^b

^aLaboratoire de Chimie Organique et Analytique, Université Sultan Moulay Slimane, Faculté des Sciences et Techniques, Béni-Mellal, BP 523, Morocco, and ^bLaboratoire de Chimie du Solide Appliquée, Faculté des Sciences, Université Mohammed V-Agdal, Avenue Ibn Battouta, BP 1014, Rabat, Morocco
^*Correspondence e-mail: m_elghozlani@yahoo.fr

(Received 27 February 2014; accepted 1 March 2014; online 8 March 2014)

The molecule of the title compound, C₉H₉N₃O₂S, is built up from fused five- and six-membered rings connected to methylsulfanyl 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, molecules are linked by C—H⋯O hydrogen bonds and π–π interactions between imidazole rings [inter-centroid distance = 3.667 (3) Å], forming a three-dimensional network.

CCDC reference: 989365

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_r = 223.25
Monoclinic, P 2₁ /c
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[F² > 2σ(F²)] = 0.039
wR(F²) = 0.116
S = 1.07
2772 reflections
136 parameters
H-atom parameters constrained
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.19 e Å⁻³

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) x+1, y, z+1; (ii) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) -x, -y+2, -z.

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 ).

Supporting information

CCDC reference: 989365

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

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

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

checkCIF report

Structural commentary top

Benzimidazole derivatives are of wide interest because of their diverse biological activities and clinical applications. This fused-ring system exhibits a broad spectrum of biological activities, that is, anti-cancer, anti-viral, anti-bacterial, anti-inflammatory, anti-oxidant and anti-leukaemic (LaPlante et al., 2004; Ishida et al., 2006; Boiani & Gonzalez, 2005; Achar et al., 2010; Kus et al., 2004; Kamal et al., 2008).

The molecule of the title compound, C₉H₉N₃O₂S, is formed by a fused five- and six-membered rings as shown in Fig.1. The mean plane through the fused ring system (N1,N2,C1 to C7) is slightly inclined relative to the mean plane passing through the nitro group with a dihedral angle of 3.6 (2)°. In the crystal, molecules are linked by C—H···O hydrogen bonds and π–π interactions between indazole rings [inter-centroid distance = 3.667 (3) Å], forming a three-dimensional network as shown in Fig.2 and Table 1.

Synthesis and crystallization top

To a solution of 5-nitro-1H-benzimidazole-2-thiol (5.12 mmol) in DMSO (15 ml) was added potassium carbonate (5.2 mmol). After 15 min. at 298 K, methyl iodide (7.68 mmol) was added drop wise. Upon disappearance of the starting material, as indicated by TLC, the resulting mixture was evaporated. The crude material was dissolved with EtOAc (60 ml), washed with water and brine, dried over MgSO₄ and the solvent was evaporated in vacuo. The resulting residue was purified by column chromatography (EtOAc/hexane 3/7). The title compound was recrystallized from acetone at room temperature giving colourless crystals (M.pt: 475 K, yield: 47%).

Refinement top

H atoms were located in a difference map and treated as riding with C–H = 0.96 Å and C–H = 0.93 Å for methyl- and aromatic-H, respectively. All hydrogen with U_iso(H) = 1.5 U_eq for methyl-H and U_iso(H) = 1.2 U_eq for aromatic-H.

Related literature top

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).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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).

Figures top

	Fig. 1. Plot of the molecule of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.
	Fig. 2. Partial crystal packing for the title compound showing molecules linked by π–π interactions and hydrogen bonds (dashed lines).

1-Methyl-2-methylsulfanyl-6-nitro-1H-benzimidazole top

Crystal data top

C₉H₉N₃O₂S	F(000) = 464
M_r = 223.25	D_x = 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

Data collection top

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

Refinement top

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(F_o²) + (0.0644P)² + 0.2102P] where P = (F_o² + 2F_c²)/3
2772 reflections	(Δ/σ)_max = 0.001
136 parameters	Δρ_max = 0.34 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₉H₉N₃O₂S	V = 990.26 (6) Å³
M_r = 223.25	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 11.7213 (4) Å	µ = 0.31 mm⁻¹
b = 11.8991 (4) Å	T = 296 K
c = 7.3025 (3) Å	0.42 × 0.31 × 0.26 mm
β = 103.523 (1)°

Data collection top

Bruker X8 APEX diffractometer	2772 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	2350 reflections with I > 2σ(I)
T_min = 0.658, T_max = 0.746	R_int = 0.025
11751 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.116	H-atom parameters constrained
S = 1.07	Δρ_max = 0.34 e Å⁻³
2772 reflections	Δρ_min = −0.19 e Å⁻³
136 parameters

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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)

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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) x+1, y, z+1; (ii) −x, y−1/2, −z+1/2; (iii) −x, −y+2, −z.

Hydrogen-bond geometry (Å, º) top

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) x+1, y, z+1; (ii) −x, y−1/2, −z+1/2; (iii) −x, −y+2, −z.

Acknowledgements

The authors thank the Unit of Support for Technical and Scientific Research (UATRS, CNRST) for the X-ray measurements.

References

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 70| Part 4| April 2014| Page o407

doi:10.1107/S1600536814004723

Open

access