organic compounds
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
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
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Data collection: APEX2 (Bruker, 2009); cell 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
10.1107/S1600536814004723/tk5298sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814004723/tk5298Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814004723/tk5298Isup3.cml
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.
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
(EtOAc/hexane 3/7). The title compound was recrystallized from acetone at room temperature giving colourless crystals (M.pt: 475 K, yield: 47%).Data collection: APEX2 (Bruker, 2009); cell
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).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 |
C9H9N3O2S | V = 990.26 (6) Å3 |
Mr = 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)° |
Bruker X8 APEX diffractometer | 2772 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 2350 reflections with I > 2σ(I) |
Tmin = 0.658, Tmax = 0.746 | Rint = 0.025 |
11751 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.116 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.34 e Å−3 |
2772 reflections | Δρmin = −0.19 e Å−3 |
136 parameters |
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 |
Symmetry codes: (i) x+1, y, z+1; (ii) −x, y−1/2, −z+1/2; (iii) −x, −y+2, −z. |
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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