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

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ISSN: 2056-9890

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

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 ππ inter­actions 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[Achar, K. C. S., Hosamani, K. M. & Seetharamareddy, H. R. (2010). Eur. J. Med. Chem. 45, 2048-2054.]); Boiani & Gonzalez (2005[Boiani, M. & Gonzalez, M. (2005). Mini Rev. Med. Chem. 5, 409-424.]); Ishida et al. (2006[Ishida, T., Suzuki, T., Hirashima, S., Mizutani, K., Yoshida, A., Ando, I., Ikeda, S., Adachi, T. & Hashimoto, H. (2006). Bioorg. Med. Chem. Lett. 16, 1859-1863.]); Kamal et al. (2008[Kamal, A., Kumar, P. P., Sreekanth, K., Seshadri, B. N. & Ramulu, P. (2008). Bioorg. Med. Chem. Lett. 18, 2594-2598.]); Kus et al. (2004[Kus, C., Ayhan-KIlcIgil, G., Eke, B. C. & Iscan, M. (2004). Arch. Pharm. Res. 27, 156-163.]); LaPlante et al. (2004[LaPlante, S. R., Jakalian, A., Aubry, N., Bousquet, Y., Ferland, J. M., Gillard, J., Lefebvre, S., Poirier, M., Tsantrizos, Y. S., Kukolj, G. & Beaulieu, P. L. (2004). Angew. Chem. Int. Ed. 43, 4306-4311.]).

[Scheme 1]

Experimental

Crystal data
  • C9H9N3O2S

  • Mr = 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[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.658, Tmax = 0.746

  • 11751 measured reflections

  • 2772 independent reflections

  • 2350 reflections with I > 2σ(I)

  • Rint = 0.025

Refinement
  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[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: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


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 ππ 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 Uiso(H) = 1.5 Ueq for methyl-H and Uiso(H) = 1.2 Ueq 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
[Figure 1] 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.
[Figure 2] Fig. 2. Partial crystal packing for the title compound showing molecules linked by ππ interactions and hydrogen bonds (dashed lines).
1-Methyl-2-methylsulfanyl-6-nitro-1H-benzimidazole top
Crystal data top
C9H9N3O2SF(000) = 464
Mr = 223.25Dx = 1.497 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2772 reflections
a = 11.7213 (4) Åθ = 2.5–29.6°
b = 11.8991 (4) ŵ = 0.31 mm1
c = 7.3025 (3) ÅT = 296 K
β = 103.523 (1)°Block, colourless
V = 990.26 (6) Å30.42 × 0.31 × 0.26 mm
Z = 4
Data collection top
Bruker X8 APEX
diffractometer
2772 independent reflections
Radiation source: fine-focus sealed tube2350 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
ϕ and ω scansθmax = 29.6°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 1616
Tmin = 0.658, Tmax = 0.746k = 1615
11751 measured reflectionsl = 108
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)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.116H-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 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = 0.19 e Å3
Crystal data top
C9H9N3O2SV = 990.26 (6) Å3
Mr = 223.25Z = 4
Monoclinic, P21/cMo Kα radiation
a = 11.7213 (4) ŵ = 0.31 mm1
b = 11.8991 (4) ÅT = 296 K
c = 7.3025 (3) Å0.42 × 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)
Tmin = 0.658, Tmax = 0.746Rint = 0.025
11751 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.116H-atom parameters constrained
S = 1.07Δρmax = 0.34 e Å3
2772 reflectionsΔρmin = 0.19 e Å3
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
xyzUiso*/Ueq
C10.37904 (11)0.74865 (11)0.42804 (17)0.0319 (3)
C20.21992 (11)0.66649 (11)0.29323 (17)0.0315 (3)
C30.13098 (12)0.58951 (11)0.2205 (2)0.0385 (3)
H30.14350.51260.23650.046*
C40.02393 (12)0.63119 (12)0.1243 (2)0.0388 (3)
H40.03730.58200.07520.047*
C50.00707 (11)0.74680 (12)0.10023 (18)0.0344 (3)
C60.09247 (11)0.82662 (11)0.17081 (17)0.0331 (3)
H60.07930.90340.15380.040*
C70.19868 (11)0.78276 (10)0.26849 (16)0.0295 (3)
C80.58418 (14)0.64247 (14)0.5740 (2)0.0502 (4)
H8A0.66510.64720.64000.075*
H8B0.57880.61010.45180.075*
H8C0.54240.59610.64400.075*
C90.32546 (14)0.95396 (12)0.3712 (3)0.0487 (4)
H9A0.25610.99400.30880.073*
H9B0.38840.97160.31230.073*
H9C0.34700.97560.50130.073*
N10.30262 (9)0.83409 (9)0.35759 (15)0.0326 (2)
N20.33342 (10)0.64715 (10)0.39349 (16)0.0353 (2)
N30.10606 (11)0.78650 (12)0.00931 (19)0.0451 (3)
O10.17998 (12)0.71648 (13)0.0807 (2)0.0775 (5)
O20.12317 (11)0.88741 (11)0.02760 (19)0.0610 (3)
S10.52130 (3)0.78014 (3)0.54830 (5)0.04086 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0322 (6)0.0338 (6)0.0290 (6)0.0034 (5)0.0058 (4)0.0008 (5)
C20.0328 (6)0.0299 (6)0.0312 (6)0.0036 (4)0.0066 (4)0.0010 (4)
C30.0407 (7)0.0282 (6)0.0445 (7)0.0073 (5)0.0062 (5)0.0029 (5)
C40.0351 (6)0.0374 (7)0.0426 (7)0.0098 (5)0.0062 (5)0.0089 (6)
C50.0290 (6)0.0422 (7)0.0312 (6)0.0004 (5)0.0053 (5)0.0059 (5)
C60.0342 (6)0.0306 (6)0.0340 (6)0.0001 (5)0.0068 (5)0.0027 (5)
C70.0311 (6)0.0291 (6)0.0281 (5)0.0047 (4)0.0067 (4)0.0022 (4)
C80.0382 (7)0.0525 (9)0.0537 (9)0.0044 (6)0.0016 (6)0.0025 (7)
C90.0460 (8)0.0291 (7)0.0657 (10)0.0091 (6)0.0024 (7)0.0022 (6)
N10.0318 (5)0.0282 (5)0.0356 (5)0.0054 (4)0.0032 (4)0.0020 (4)
N20.0338 (5)0.0316 (5)0.0379 (5)0.0027 (4)0.0033 (4)0.0007 (4)
N30.0337 (6)0.0560 (8)0.0427 (6)0.0032 (5)0.0032 (5)0.0095 (5)
O10.0439 (7)0.0760 (10)0.0950 (11)0.0049 (6)0.0193 (7)0.0228 (8)
O20.0467 (6)0.0567 (8)0.0720 (8)0.0149 (5)0.0012 (6)0.0006 (6)
S10.0342 (2)0.0423 (2)0.0412 (2)0.00665 (13)0.00108 (13)0.00503 (13)
Geometric parameters (Å, º) top
C1—N21.3210 (17)C6—H60.9300
C1—N11.3730 (17)C7—N11.3819 (15)
C1—S11.7342 (13)C8—S11.7882 (17)
C2—N21.3796 (16)C8—H8A0.9600
C2—C31.3960 (17)C8—H8B0.9600
C2—C71.4098 (18)C8—H8C0.9600
C3—C41.379 (2)C9—N11.4504 (17)
C3—H30.9300C9—H9A0.9600
C4—C51.395 (2)C9—H9B0.9600
C4—H40.9300C9—H9C0.9600
C5—C61.3888 (18)N3—O21.2196 (18)
C5—N31.4578 (18)N3—O11.2270 (18)
C6—C71.3841 (17)
N2—C1—N1113.95 (11)S1—C8—H8A109.5
N2—C1—S1126.34 (11)S1—C8—H8B109.5
N1—C1—S1119.71 (10)H8A—C8—H8B109.5
N2—C2—C3129.35 (12)S1—C8—H8C109.5
N2—C2—C7110.56 (11)H8A—C8—H8C109.5
C3—C2—C7120.09 (12)H8B—C8—H8C109.5
C4—C3—C2117.86 (12)N1—C9—H9A109.5
C4—C3—H3121.1N1—C9—H9B109.5
C2—C3—H3121.1H9A—C9—H9B109.5
C3—C4—C5120.27 (12)N1—C9—H9C109.5
C3—C4—H4119.9H9A—C9—H9C109.5
C5—C4—H4119.9H9B—C9—H9C109.5
C6—C5—C4123.99 (12)C1—N1—C7105.98 (10)
C6—C5—N3117.79 (13)C1—N1—C9127.50 (11)
C4—C5—N3118.20 (12)C7—N1—C9126.52 (12)
C7—C6—C5114.64 (12)C1—N2—C2104.24 (11)
C7—C6—H6122.7O2—N3—O1122.70 (14)
C5—C6—H6122.7O2—N3—C5118.97 (13)
N1—C7—C6131.58 (12)O1—N3—C5118.32 (14)
N1—C7—C2105.28 (11)C1—S1—C8100.32 (7)
C6—C7—C2123.13 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8A···O1i0.962.533.393 (2)150
C3—H3···O2ii0.932.653.3038 (19)128
C9—H9A···O2iii0.962.673.563 (2)155
Symmetry codes: (i) x+1, y, z+1; (ii) x, y1/2, z+1/2; (iii) x, y+2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C8—H8A···O1i0.962.533.393 (2)150
C3—H3···O2ii0.932.653.3038 (19)128
C9—H9A···O2iii0.962.673.563 (2)155
Symmetry codes: (i) x+1, y, z+1; (ii) x, y1/2, 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

First citationAchar, K. C. S., Hosamani, K. M. & Seetharamareddy, H. R. (2010). Eur. J. Med. Chem. 45, 2048–2054.  Web of Science CrossRef CAS PubMed Google Scholar
First citationBoiani, M. & Gonzalez, M. (2005). Mini Rev. Med. Chem. 5, 409–424.  Web of Science CrossRef PubMed CAS Google Scholar
First citationBruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationIshida, T., Suzuki, T., Hirashima, S., Mizutani, K., Yoshida, A., Ando, I., Ikeda, S., Adachi, T. & Hashimoto, H. (2006). Bioorg. Med. Chem. Lett. 16, 1859–1863.  Web of Science CrossRef PubMed CAS Google Scholar
First citationKamal, A., Kumar, P. P., Sreekanth, K., Seshadri, B. N. & Ramulu, P. (2008). Bioorg. Med. Chem. Lett. 18, 2594–2598.  Web of Science CrossRef PubMed CAS Google Scholar
First citationKus, C., Ayhan-KIlcIgil, G., Eke, B. C. & Iscan, M. (2004). Arch. Pharm. Res. 27, 156–163.  Web of Science CrossRef PubMed CAS Google Scholar
First citationLaPlante, S. R., Jakalian, A., Aubry, N., Bousquet, Y., Ferland, J. M., Gillard, J., Lefebvre, S., Poirier, M., Tsantrizos, Y. S., Kukolj, G. & Beaulieu, P. L. (2004). Angew. Chem. Int. Ed. 43, 4306–4311.  Web of Science CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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