organic compounds
E)-2-(4-methylphenyl)ethenyl]-4-nitro-1H-imidazole
of 1-methyl-2-[(aLaboratoire des Produits Naturels d'Origine Végétale et de Synthèse Organique, PHYSYNOR, Université Constantine 1, 25000 Constantine, Algeria, bUnité de Recherche de Chimie de l'Environnement et Moléculaire Structurale (CHEMS), Université Constantine 1, 25000 , Algeria, and cDépartement Sciences de la Matière, Faculté des Sciences Exactes et Sciences de la Nature et de la Vie, Université Oum El Bouaghi, Algeria
*Correspondence e-mail: bouacida_sofiane@yahoo.fr
In the title molecule, C13H13N3O2, the planes of the benzene and imidazole rings form a dihedral angle of 7.72 (5)°. In the crystal, molecules are linked by weak C—H⋯N and C—H⋯O hydrogen bonds, forming layers parallel to (100). A weak C—H⋯π interaction connects these layers into a three-dimensional network. A π–π stacking interaction, with a centroid–centroid distance of 3.5373 (9) Å, is also observed.
Keywords: crystal structure; imidazoles; nitroimidazoles; pharmacophore; hydrogen bonding; π–π stacking interactions.
CCDC reference: 1016150
1. Related literature
For the synthesis and applications of imidazole derivatives, see: Mamedov et al. (2011); De Luca (2006); Teimouri & Chermahini (2011); Achar et al. (2010); Özkay et al. (2010); Shingalapur et al. (2009); Bhatia & Shanbhag (1984); Hoffer & Grunberg (1974). For the biological activity of nitroimidazole derivatives, see: Trivedi et al. (2011); Leitsch et al. (2011); Luo et al. (2010); Saadeh et al. (2009); Thompson et al. (2009); Carvalho et al. (2006); Alliouche et al. (2014); Hunkeler et al. (1981); Tanigawara et al. (1999).
2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2006); cell SAINT (Bruker, 2006); data reduction: SAINT; program(s) used to solve structure: SIR2002 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg & Berndt, 2001); software used to prepare material for publication: WinGX (Farrugia, 2012).
Supporting information
CCDC reference: 1016150
10.1107/S1600536814017243/lh5721sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814017243/lh5721Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814017243/lh5721Isup3.cml
The title compound (I) was obtained as yellow solid in 94% yield by heating the corresponding 5-nitroisomer at 433K in nitrobenzene in presence of methyl iodide as catalyst, during 24 h. Suitable crystals were obtained by slow evaporation of a solution of the title compound in water/methanol solution at room temperature.
All non-H atoms were refined with anisotropic atomic displacement parameters. All H atoms were located in difference Fourier maps but were introduced in calculated positions and treated as riding on their parent atom (with C—H = 0.93 and 0.96 Å and Uiso(H) = 1.5 or 1.2Ueq(C).
Data collection: APEX2 (Bruker, 2006); cell
SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SIR2002 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg & Berndt, 2001); software used to prepare material for publication: WinGX (Farrugia, 2012).Fig. 1. The molecular structure structure of the title compound with displacement ellipsoids drawn at the 50% probability level. | |
Fig. 2. The crystal packing of (I) viewed along the c axis showing weak C—H···O hydrogen bonds as dashed lines. | |
Fig. 3. The crystal packing of (I) viewed along the a axis showing weak C—H···O and C—H···N hydrogen bonds as dashed lines. |
C13H13N3O2 | F(000) = 512 |
Mr = 243.26 | Dx = 1.35 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 6402 reflections |
a = 7.1774 (8) Å | θ = 2.3–25.1° |
b = 15.7931 (16) Å | µ = 0.09 mm−1 |
c = 10.7901 (11) Å | T = 150 K |
β = 101.798 (6)° | Needle, colorless |
V = 1197.3 (2) Å3 | 0.16 × 0.06 × 0.05 mm |
Z = 4 |
Bruker APEXII diffractometer | 1958 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.025 |
CCD rotation images, thin slices scans | θmax = 25.1°, θmin = 2.6° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2002) | h = −8→8 |
Tmin = 0.891, Tmax = 1.000 | k = −18→18 |
9856 measured reflections | l = −12→12 |
2113 independent reflections |
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)] = 0.035 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.094 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0455P)2 + 0.712P] where P = (Fo2 + 2Fc2)/3 |
2113 reflections | (Δ/σ)max = 0.005 |
165 parameters | Δρmax = 0.36 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
C13H13N3O2 | V = 1197.3 (2) Å3 |
Mr = 243.26 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.1774 (8) Å | µ = 0.09 mm−1 |
b = 15.7931 (16) Å | T = 150 K |
c = 10.7901 (11) Å | 0.16 × 0.06 × 0.05 mm |
β = 101.798 (6)° |
Bruker APEXII diffractometer | 2113 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2002) | 1958 reflections with I > 2σ(I) |
Tmin = 0.891, Tmax = 1.000 | Rint = 0.025 |
9856 measured reflections |
R[F2 > 2σ(F2)] = 0.035 | 0 restraints |
wR(F2) = 0.094 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.36 e Å−3 |
2113 reflections | Δρmin = −0.31 e Å−3 |
165 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 | ||
N2 | 0.41984 (15) | 0.20989 (7) | 0.58571 (10) | 0.0142 (3) | |
O1B | 0.58852 (16) | 0.36479 (6) | 0.59448 (9) | 0.0234 (3) | |
O1A | 0.62422 (14) | 0.36871 (6) | 0.79969 (9) | 0.0214 (3) | |
N3 | 0.37372 (15) | 0.13617 (7) | 0.75347 (10) | 0.0136 (3) | |
N1 | 0.56745 (16) | 0.33418 (7) | 0.69608 (10) | 0.0154 (3) | |
C12 | 0.16578 (19) | −0.08459 (9) | 0.37141 (12) | 0.0173 (3) | |
H12 | 0.1714 | −0.0947 | 0.457 | 0.021* | |
C1 | 0.47447 (18) | 0.25439 (8) | 0.69479 (12) | 0.0138 (3) | |
C7 | 0.20697 (18) | −0.00361 (8) | 0.33138 (12) | 0.0148 (3) | |
C3 | 0.35902 (18) | 0.13706 (8) | 0.62364 (12) | 0.0136 (3) | |
C9 | 0.15285 (19) | −0.05791 (9) | 0.11606 (13) | 0.0177 (3) | |
H9 | 0.1512 | −0.0485 | 0.0308 | 0.021* | |
C5 | 0.29083 (19) | 0.06490 (8) | 0.54450 (12) | 0.0157 (3) | |
H5 | 0.265 | 0.0148 | 0.5831 | 0.019* | |
C2 | 0.44778 (18) | 0.21119 (8) | 0.79988 (12) | 0.0141 (3) | |
H2 | 0.4744 | 0.2293 | 0.8837 | 0.017* | |
C11 | 0.11685 (19) | −0.14954 (9) | 0.28511 (13) | 0.0187 (3) | |
H11 | 0.0879 | −0.2025 | 0.3138 | 0.022* | |
C6 | 0.26340 (18) | 0.06724 (8) | 0.41831 (12) | 0.0157 (3) | |
H6 | 0.2821 | 0.1192 | 0.3821 | 0.019* | |
C10 | 0.10965 (19) | −0.13770 (9) | 0.15583 (13) | 0.0182 (3) | |
C4 | 0.3300 (2) | 0.06497 (8) | 0.82950 (12) | 0.0169 (3) | |
H4A | 0.4249 | 0.0217 | 0.8324 | 0.025* | |
H4B | 0.2073 | 0.0424 | 0.7921 | 0.025* | |
H4C | 0.3293 | 0.0841 | 0.9139 | 0.025* | |
C13 | 0.0545 (2) | −0.20885 (10) | 0.06267 (14) | 0.0255 (3) | |
H13A | −0.0782 | −0.2215 | 0.055 | 0.038* | |
H13B | 0.1287 | −0.2582 | 0.092 | 0.038* | |
H13C | 0.0779 | −0.1923 | −0.0184 | 0.038* | |
C8 | 0.19843 (19) | 0.00802 (9) | 0.20157 (12) | 0.0168 (3) | |
H8 | 0.224 | 0.0613 | 0.1722 | 0.02* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N2 | 0.0171 (6) | 0.0135 (6) | 0.0119 (5) | 0.0024 (4) | 0.0024 (4) | −0.0006 (4) |
O1B | 0.0390 (6) | 0.0180 (5) | 0.0150 (5) | −0.0046 (4) | 0.0093 (4) | 0.0023 (4) |
O1A | 0.0312 (6) | 0.0174 (5) | 0.0144 (5) | −0.0033 (4) | 0.0019 (4) | −0.0040 (4) |
N3 | 0.0162 (6) | 0.0129 (6) | 0.0118 (5) | 0.0014 (4) | 0.0033 (4) | 0.0011 (4) |
N1 | 0.0199 (6) | 0.0129 (6) | 0.0136 (6) | 0.0026 (4) | 0.0037 (4) | −0.0001 (4) |
C12 | 0.0190 (7) | 0.0184 (7) | 0.0135 (6) | 0.0014 (5) | 0.0016 (5) | 0.0007 (5) |
C1 | 0.0164 (6) | 0.0116 (6) | 0.0135 (6) | 0.0027 (5) | 0.0034 (5) | −0.0002 (5) |
C7 | 0.0122 (6) | 0.0175 (7) | 0.0147 (6) | 0.0012 (5) | 0.0024 (5) | −0.0013 (5) |
C3 | 0.0137 (6) | 0.0148 (7) | 0.0123 (6) | 0.0031 (5) | 0.0028 (5) | 0.0012 (5) |
C9 | 0.0153 (7) | 0.0249 (7) | 0.0130 (6) | 0.0016 (5) | 0.0030 (5) | −0.0021 (5) |
C5 | 0.0172 (7) | 0.0139 (6) | 0.0163 (7) | 0.0003 (5) | 0.0040 (5) | −0.0001 (5) |
C2 | 0.0164 (6) | 0.0134 (6) | 0.0126 (6) | 0.0028 (5) | 0.0028 (5) | −0.0015 (5) |
C11 | 0.0182 (7) | 0.0150 (7) | 0.0216 (7) | 0.0007 (5) | 0.0014 (5) | 0.0013 (5) |
C6 | 0.0158 (7) | 0.0142 (7) | 0.0176 (7) | 0.0002 (5) | 0.0043 (5) | 0.0010 (5) |
C10 | 0.0126 (6) | 0.0207 (7) | 0.0202 (7) | 0.0029 (5) | 0.0008 (5) | −0.0055 (6) |
C4 | 0.0211 (7) | 0.0165 (7) | 0.0136 (6) | −0.0008 (5) | 0.0049 (5) | 0.0029 (5) |
C13 | 0.0260 (8) | 0.0249 (8) | 0.0238 (8) | −0.0004 (6) | 0.0009 (6) | −0.0088 (6) |
C8 | 0.0157 (7) | 0.0181 (7) | 0.0170 (7) | −0.0003 (5) | 0.0043 (5) | 0.0011 (5) |
N2—C3 | 1.3244 (17) | C9—C10 | 1.387 (2) |
N2—C1 | 1.3581 (17) | C9—H9 | 0.93 |
O1B—N1 | 1.2354 (15) | C5—C6 | 1.3358 (19) |
O1A—N1 | 1.2357 (15) | C5—H5 | 0.93 |
N3—C2 | 1.3522 (17) | C2—H2 | 0.93 |
N3—C3 | 1.3832 (16) | C11—C10 | 1.398 (2) |
N3—C4 | 1.4631 (16) | C11—H11 | 0.93 |
N1—C1 | 1.4246 (17) | C6—H6 | 0.93 |
C12—C11 | 1.3816 (19) | C10—C13 | 1.5057 (19) |
C12—C7 | 1.4006 (19) | C4—H4A | 0.96 |
C12—H12 | 0.93 | C4—H4B | 0.96 |
C1—C2 | 1.3700 (18) | C4—H4C | 0.96 |
C7—C8 | 1.4015 (19) | C13—H13A | 0.96 |
C7—C6 | 1.4632 (18) | C13—H13B | 0.96 |
C3—C5 | 1.4479 (18) | C13—H13C | 0.96 |
C9—C8 | 1.3853 (19) | C8—H8 | 0.93 |
C3—N2—C1 | 103.69 (11) | N3—C2—H2 | 128 |
C2—N3—C3 | 108.00 (11) | C1—C2—H2 | 128 |
C2—N3—C4 | 125.37 (11) | C12—C11—C10 | 121.71 (13) |
C3—N3—C4 | 126.51 (11) | C12—C11—H11 | 119.1 |
O1B—N1—O1A | 123.54 (11) | C10—C11—H11 | 119.1 |
O1B—N1—C1 | 118.65 (11) | C5—C6—C7 | 126.59 (13) |
O1A—N1—C1 | 117.80 (11) | C5—C6—H6 | 116.7 |
C11—C12—C7 | 120.71 (12) | C7—C6—H6 | 116.7 |
C11—C12—H12 | 119.6 | C9—C10—C11 | 117.74 (12) |
C7—C12—H12 | 119.6 | C9—C10—C13 | 121.09 (13) |
N2—C1—C2 | 113.28 (12) | C11—C10—C13 | 121.16 (13) |
N2—C1—N1 | 121.19 (11) | N3—C4—H4A | 109.5 |
C2—C1—N1 | 125.23 (12) | N3—C4—H4B | 109.5 |
C12—C7—C8 | 117.33 (12) | H4A—C4—H4B | 109.5 |
C12—C7—C6 | 123.28 (12) | N3—C4—H4C | 109.5 |
C8—C7—C6 | 119.36 (12) | H4A—C4—H4C | 109.5 |
N2—C3—N3 | 111.11 (11) | H4B—C4—H4C | 109.5 |
N2—C3—C5 | 126.46 (12) | C10—C13—H13A | 109.5 |
N3—C3—C5 | 122.40 (11) | C10—C13—H13B | 109.5 |
C8—C9—C10 | 120.94 (12) | H13A—C13—H13B | 109.5 |
C8—C9—H9 | 119.5 | C10—C13—H13C | 109.5 |
C10—C9—H9 | 119.5 | H13A—C13—H13C | 109.5 |
C6—C5—C3 | 122.75 (12) | H13B—C13—H13C | 109.5 |
C6—C5—H5 | 118.6 | C9—C8—C7 | 121.55 (13) |
C3—C5—H5 | 118.6 | C9—C8—H8 | 119.2 |
N3—C2—C1 | 103.93 (11) | C7—C8—H8 | 119.2 |
C3—N2—C1—C2 | −0.46 (15) | C3—N3—C2—C1 | 0.06 (14) |
C3—N2—C1—N1 | 173.57 (11) | C4—N3—C2—C1 | 176.18 (12) |
O1B—N1—C1—N2 | 3.97 (18) | N2—C1—C2—N3 | 0.25 (15) |
O1A—N1—C1—N2 | −175.44 (11) | N1—C1—C2—N3 | −173.49 (12) |
O1B—N1—C1—C2 | 177.24 (12) | C7—C12—C11—C10 | 1.1 (2) |
O1A—N1—C1—C2 | −2.16 (19) | C3—C5—C6—C7 | 175.78 (12) |
C11—C12—C7—C8 | −0.70 (19) | C12—C7—C6—C5 | 2.8 (2) |
C11—C12—C7—C6 | −178.70 (12) | C8—C7—C6—C5 | −175.12 (13) |
C1—N2—C3—N3 | 0.48 (14) | C8—C9—C10—C11 | −1.05 (19) |
C1—N2—C3—C5 | −177.57 (12) | C8—C9—C10—C13 | 178.22 (12) |
C2—N3—C3—N2 | −0.35 (14) | C12—C11—C10—C9 | −0.2 (2) |
C4—N3—C3—N2 | −176.42 (11) | C12—C11—C10—C13 | −179.50 (13) |
C2—N3—C3—C5 | 177.79 (12) | C10—C9—C8—C7 | 1.5 (2) |
C4—N3—C3—C5 | 1.73 (19) | C12—C7—C8—C9 | −0.57 (19) |
N2—C3—C5—C6 | −7.0 (2) | C6—C7—C8—C9 | 177.51 (12) |
N3—C3—C5—C6 | 175.11 (12) |
Cg is the centroid of the C7–C12 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···N2i | 0.93 | 2.49 | 3.3702 (17) | 159 |
C4—H4C···O1Bi | 0.96 | 2.54 | 3.2676 (17) | 133 |
C13—H13B···O1Aii | 0.96 | 2.59 | 3.5347 (19) | 168 |
C4—H4B···Cgiii | 0.96 | 2.61 | 3.4336 (16) | 144 |
Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+1, −y, −z+1; (iii) −x, −y+1, −z+1. |
Cg is the centroid of the C7–C12 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···N2i | 0.93 | 2.49 | 3.3702 (17) | 159.00 |
C4—H4C···O1Bi | 0.96 | 2.54 | 3.2676 (17) | 133.00 |
C13—H13B···O1Aii | 0.96 | 2.59 | 3.5347 (19) | 168.00 |
C4—H4B···Cgiii | 0.96 | 2.61 | 3.4336 (16) | 144.00 |
Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x+1, −y, −z+1; (iii) −x, −y+1, −z+1. |
Acknowledgements
We are grateful to all personnel of the PHYSYNOR Laboratory, Universite Constantine 1, Algeria, for their assistance. Thanks are due to the MESRS (Ministére de l'Enseignement Supérieur et de la Recherche Scientifique, Algérie) for financial support.
References
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The imidazole nucleus is an important pharmacophore found in a large number of natural products and synthetic compounds with a wide range of applications which make imidazole derivatives a subject of extensive investigations (Mamedov, et al., 2011; De Luca, 2006; Tanigawara, et al., 1999; Hunkeler, et al., 1981). For example, many synthetic imidazole derivatives are present in a number of bioactive compounds such as fungicides, herbicides, bactericides, anti-inflammators, analgesics and anticancers (Teimouri, et al., 2011; Achar, et al., 2010; Özkay, et al., 2010; Shingalapur, et al., 2009). Nitroimidazoles are a particular class of imidazoles principally composed of bioactive substances where their spectrum of action is closely associated with the position of the nitro group on the imidazole ring. Due to their significant biological activity, 5-nitroimidazoles are widely used in medicine as bactericide and parasiticide agents, some of them possess an original activity spectrum especially towards protozoa and strict anaerobic bacteria (Trivedi, et al., 2011; Bhatia, et al., 1984; Hoffer et al., 1974), and others exhibit cytotoxic and radiosensitization activities in vitro and in vivo (Leitsch, et al., 2011; Luo, et al., 2010). However, only few biological properties of 4-nitroimidazoles have been reported in the literature (Saadeh, et al., 2009; Thompson, et al., 2009; Carvalho, et al., 2006). The transposition of a nitro group in 5-nitroimidazoles is a known reaction and constitutes an efficient synthetic procedure of 4-nitroisomers. However, only few examples of this reaction are described using methyl iodide as catalyst (Alliouche, et al. 2014). We report in this paper, the synthesis and structure determination of (E)-1-methyl-2-[(4-methylphenyl)-1-ethenyl]-5-nitroimidazole (I). The later was easily prepared from its 5-nitro isomer via an intramolecular transposition of the nitro group. The reaction was carried out in nitrobenzene at 433K using catalytic amount of methyl iodide.
The molecular structure of (I) is shown in Fig. 1. The benzene and imidazole ring form a dihedral angle of 7.72 (5)°. The crystal packing can be described as double zig-zag layers parallel to (100) (Fig. 2) which are stabilized by weak C—H···N and C—H···O hydrogen bonds. A weak C—H···π interaction links the layers forming a three-dimensional network (Fig. 2 and Fig. 3). The crystal structure features one π–π stacking interaction: Cg1—Cg2 (-x, -y, 1-z) = 3.5373 (9) Å Where, Cg1 is the centroid of the imidazole ring (C1/C2/N3/C3/N2) and Cg2 is is the centroid of the phenyl ring (C7/C8/C9/C10/C11/C12).