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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 70| Part 9| September 2014| Pages o966-o967

Crystal structure of (E)-1-methyl-2-[2-(2-methoxphen­yl)ethen­yl]-4-nitro-1H-imidazole

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

Edited by P. C. Healy, Griffith University, Australia (Received 19 July 2014; accepted 25 July 2014; online 1 August 2014)

In the asymmetric unit of the title compound, C13H13N3O3, the 2-(2-methoxphen­yl)ethenyl unit is connected to the methyl-nitro­imidazole 1-methyl-4-nitro-1H-imidazole moiety. The mol­ecule is quasi-planar and the planes of the two rings form a dihedral angle of 0.92 (11)°. The crystal packing can be described as layers parallel to the (011) plane, stabilized by inter­molecular C—H⋯O hydrogen bonding, resulting in the formation of an infinite three-dimensional network linking these layers. Strong ππ stacking inter­actions are observed, viz. benzene–benzene, imidazole–imidazole and benzene–imidazole rings, with centroid–centroid distances of 3.528 (2), 3.457 (2) and 3.544 (2) Å, respectively. Intensity statistics indicated twinning by non-merohedry, with refined weighs of the twin components of 0.3687:0.6313.

1. Related literature

For the synthesis and applications of this important class of compounds, see: Hori et al. (1997[Hori, H., Jin, C. Z., Kiyono, M., Kasai, S., Shimamura, M. & Inayama, S. (1997). Bioorg. Med. Chem. 5, 591-599.]); Bourdin-Trunz et al. (2011[Bourdin-Trunz, B., Jedrysiak, R., Tweats, D., Brun, R., Kaiser, M., Suwiński, J. & Torreele, E. (2011). Eur. J. Med. Chem. 46, 1524-1534.]). For our previous work on imidazole derivatives, see: Alliouche et al. (2014[Alliouche, H., Bouraiou, A., Bouacida, S., Bahnous, M., Roisnel, T. & Belfaitah, A. (2014). Lett. Org. Chem. 11, 174-179.]); Zama et al. (2013[Zama, S., Bouraiou, A., Bouacida, S., Roisnel, T. & Belfaitah, A. (2013). Acta Cryst. E69, o837-o838.]); Bahnous et al. (2012[Bahnous, M., Bouraiou, A., Bouacida, S., Roisnel, T. & Belfaitah, A. (2012). Acta Cryst. E68, o1391.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C13H13N3O3

  • Mr = 259.26

  • Triclinic, [P \overline 1]

  • a = 7.9339 (18) Å

  • b = 8.1994 (19) Å

  • c = 10.452 (3) Å

  • α = 68.877 (17)°

  • β = 75.037 (17)°

  • γ = 76.182 (17)°

  • V = 604.7 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 150 K

  • 0.19 × 0.12 × 0.08 mm

2.2. Data collection

  • Bruker APEXII diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2002[Sheldrick, G. M. (2002). SADABS. University of Göttingen, Germany.]) Tmin = 0.754, Tmax = 1.000

  • 5177 measured reflections

  • 5177 independent reflections

  • 3712 reflections with I > 2σ(I)

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.088

  • wR(F2) = 0.282

  • S = 1.06

  • 5171 reflections

  • 176 parameters

  • H-atom parameters constrained

  • Δρmax = 0.49 e Å−3

  • Δρmin = −0.42 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C3—H3⋯O2i 0.93 2.45 3.271 (4) 147
C4—H4B⋯O1ii 0.96 2.53 3.465 (5) 165
C6—H6⋯O3 0.93 2.31 2.685 (4) 103
C6—H6⋯N2 0.93 2.60 2.935 (4) 102
Symmetry codes: (i) -x, -y+1, -z+1; (ii) x, y+1, z.

Data collection: APEX2 (Bruker, 2006[Bruker (2006). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2006[Bruker (2006). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR2002 (Burla et al., 2005[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381-388.]); 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.]) and DIAMOND (Brandenburg & Berndt, 2001[Brandenburg, K. & Berndt, M. (2001). DIAMOND. Crystal Impact, Bonn, Germany.]); software used to prepare material for publication: WinGX (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Supporting information


Comment top

Nitroimidazoles are a class of N-heterocyclic compounds which have a wide range of applications in the drug synthesis (Hori, et al., 1997) In fact, Metronidazole (Flagyl) and related N-1 substituted 5-nitroimidazoles such as Tinidazole (Fasigyne), Ornidazole (Tiberal) and Secnidazole (Secnol) still commonly used in medicine. Despite their fewer biological activities compared with 5-nitroimidazoles, a number of 4-nitroimidazoles were reported to exhibit antileishmanial, antiamebic and anti-parasitic activities (Bourdin-Trunz, et al. 2011). However, only some limited investigations have been carried out using methyl iodide (Alliouche, et al. 2014). In previous work, we have reported the synthesis and structure determination of some new heterocyclic compounds bearing an imidazole unit (Zama, et al., 2013; Bahnous, et al., 2012). Herein, we describe the synthesis and the structure determination of (E)-1-methyl-2-[(2-methoxphenyl)-1-ethenyl]-4-nitroimidazole resulting from the intramolecular transposition reaction of its 5-nitro isomer in the presence of catalytic amounts of methyl iodide in nitrobenzene. The molecular geometry and the atom-numbering scheme of (I) are shown in Fig. 1. In the asymmetric unit of title compound the methoxphenyl-1-ethenyl unit is linked to methyl-nitroimidazole moiety. The molecule is quasi-planar and the two rings of phenyl and imidazol form a dihedral angle of 0.92 (11)°. The crystal packing can be described as layers parallel to (011) plane, along the a axis (Fig. 2). It is stabilized by intermolecular hydrogen bond C—H···O, resulting in the formation of an infinite three-dimensional network linking these layers together and reinforcing cohesion in the structure (Fig. 2). Hydrogen-bonding parameters are listed in Table 1. Strong π-π stacking interactions are observed between phenyl-phenyl, imidazol-imidazol and phenyl-imidazol rings, distances centroid-centroid are CgCg = 3.528 (2), 3.457 (2) and 3.544 (2) Å respetively. The crystal used was a non-merohedral twin, the refined ratio of twin components being 0.3687:0.6313.

Related literature top

For the synthesis and applications of this important class of compounds, see: Hori et al. (1997); Bourdin-Trunz et al. (2011). For our previous work on imidazole derivatives, see: Alliouche et al. (2014); Zama et al. (2013); Bahnous et al. (2012).

Experimental top

The title compound was obtained as a yellow-green solid in 83% of yield by heating a solution of (E)-1-methyl-2-[(2-methoxphenyl)-1-ethenyl]-5-nitroimidazole in nitrobenzene at 160°C during 24 h in the presence of catalytic amount of CH3I. Suitable crystal of compound (I) was obtained by slow evaporation from a water/methanol solution at room temperature, and X-ray crystallographic analysis confirmed the structural assignment (Fig. 1).

Refinement top

All non-H atoms were refined with anisotropic atomic displacement parameters. All H atoms were localized on Fourier maps but introduced in calculated positions and treated as riding on their parent C or N atom. (with C—H = 0.93 and 0.96 Å and Uiso(H) = 1.5 or 1.2 (carrier atom).

Computing details top

Data collection: APEX2 (Bruker, 2006); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. The structure of the title compound with the atomic labelling scheme. Displacement are drawn at the 50% probability level.
[Figure 2] Fig. 2. A diagram of the layered crystal packing of (I) viewed down the a axis and showing hydrogen bond [C—H···O] as dashed line.
1-Methyl-2-[(E)-2-(2-methoxphenyl)ethenyl]-4-nitro-1H-imidazole top
Crystal data top
C13H13N3O3Z = 2
Mr = 259.26F(000) = 272
Triclinic, P1Dx = 1.424 Mg m3
a = 7.9339 (18) ÅMo Kα radiation, λ = 0.71073 Å
b = 8.1994 (19) ÅCell parameters from 1356 reflections
c = 10.452 (3) Åθ = 2.7–24.6°
α = 68.877 (17)°µ = 0.10 mm1
β = 75.037 (17)°T = 150 K
γ = 76.182 (17)°Block, yellow
V = 604.7 (2) Å30.19 × 0.12 × 0.08 mm
Data collection top
Bruker APEXII
diffractometer
3712 reflections with I > 2σ(I)
Graphite monochromatorRint = 0
CCD rotation images, thin slices scansθmax = 25.3°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2002)
h = 99
Tmin = 0.754, Tmax = 1.000k = 99
5177 measured reflectionsl = 1212
5177 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.088H-atom parameters constrained
wR(F2) = 0.282 w = 1/[σ2(Fo2) + (0.1745P)2 + 0.1919P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
5171 reflectionsΔρmax = 0.49 e Å3
176 parametersΔρmin = 0.42 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.045 (12)
Crystal data top
C13H13N3O3γ = 76.182 (17)°
Mr = 259.26V = 604.7 (2) Å3
Triclinic, P1Z = 2
a = 7.9339 (18) ÅMo Kα radiation
b = 8.1994 (19) ŵ = 0.10 mm1
c = 10.452 (3) ÅT = 150 K
α = 68.877 (17)°0.19 × 0.12 × 0.08 mm
β = 75.037 (17)°
Data collection top
Bruker APEXII
diffractometer
5177 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2002)
3712 reflections with I > 2σ(I)
Tmin = 0.754, Tmax = 1.000Rint = 0
5177 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0880 restraints
wR(F2) = 0.282H-atom parameters constrained
S = 1.06Δρmax = 0.49 e Å3
5171 reflectionsΔρmin = 0.42 e Å3
176 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
O10.4178 (3)0.2400 (3)0.2786 (3)0.0256 (6)
O31.0969 (3)0.6148 (3)0.0846 (2)0.0219 (6)
O20.1531 (3)0.2922 (3)0.3961 (3)0.0238 (6)
N10.3026 (4)0.3303 (4)0.3420 (3)0.0167 (7)
N20.5059 (3)0.5331 (4)0.2979 (3)0.0162 (7)
N30.3292 (3)0.7076 (3)0.4156 (3)0.0134 (6)
C10.3460 (4)0.4809 (4)0.3545 (3)0.0142 (7)
C20.4934 (4)0.6726 (4)0.3362 (3)0.0125 (7)
C50.6299 (4)0.7796 (5)0.3004 (3)0.0172 (8)
H50.60180.88670.3190.021*
C60.7973 (4)0.7279 (4)0.2408 (3)0.0151 (7)
H60.81980.61870.22610.018*
C70.9464 (4)0.8227 (4)0.1968 (3)0.0139 (7)
C81.1027 (4)0.7634 (4)0.1144 (3)0.0159 (8)
C131.2438 (4)0.5580 (5)0.0106 (4)0.0273 (9)
H13C1.26220.65420.09610.041*
H13A1.220.46040.02960.041*
H13B1.34780.52140.02990.041*
C40.2711 (4)0.8439 (5)0.4845 (3)0.0196 (8)
H4A0.14650.85080.52150.029*
H4B0.29480.95630.4180.029*
H4C0.33390.8140.55910.029*
C30.2328 (4)0.5873 (4)0.4277 (3)0.0139 (7)
H30.1170.57780.47440.017*
C91.2469 (4)0.8506 (5)0.0702 (3)0.0207 (8)
H91.3490.810.01540.025*
C101.2392 (5)0.9970 (5)0.1072 (3)0.0233 (8)
H101.33691.05440.07810.028*
C111.0871 (4)1.0600 (5)0.1876 (3)0.0211 (8)
H111.08181.16020.21160.025*
C120.9434 (4)0.9723 (5)0.2317 (3)0.0199 (8)
H120.84181.01440.28630.024*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0232 (13)0.0238 (14)0.0331 (14)0.0046 (11)0.0055 (11)0.0199 (12)
O30.0169 (13)0.0238 (14)0.0257 (13)0.0036 (10)0.0029 (10)0.0135 (11)
O20.0142 (13)0.0280 (15)0.0313 (14)0.0066 (11)0.0037 (11)0.0154 (12)
N10.0173 (15)0.0150 (15)0.0183 (14)0.0021 (12)0.0013 (12)0.0077 (12)
N20.0144 (14)0.0181 (15)0.0159 (14)0.0007 (12)0.0022 (11)0.0070 (12)
N30.0139 (14)0.0113 (14)0.0162 (13)0.0006 (11)0.0005 (11)0.0083 (11)
C10.0135 (16)0.0166 (17)0.0122 (16)0.0007 (13)0.0053 (13)0.0032 (13)
C20.0120 (16)0.0162 (17)0.0099 (14)0.0020 (13)0.0029 (13)0.0043 (13)
C50.0170 (18)0.0181 (17)0.0207 (17)0.0027 (14)0.0072 (14)0.0086 (15)
C60.0155 (17)0.0144 (17)0.0177 (16)0.0010 (14)0.0055 (13)0.0084 (14)
C70.0154 (17)0.0165 (17)0.0089 (15)0.0037 (14)0.0028 (13)0.0018 (13)
C80.0143 (17)0.0193 (18)0.0134 (16)0.0016 (14)0.0034 (14)0.0047 (14)
C130.0200 (19)0.033 (2)0.0253 (19)0.0037 (17)0.0043 (15)0.0167 (17)
C40.0171 (17)0.0219 (18)0.0232 (17)0.0021 (15)0.0010 (14)0.0137 (15)
C30.0126 (17)0.0178 (18)0.0129 (15)0.0037 (14)0.0026 (13)0.0058 (13)
C90.0150 (17)0.029 (2)0.0163 (17)0.0043 (15)0.0043 (14)0.0036 (15)
C100.026 (2)0.030 (2)0.0173 (17)0.0148 (16)0.0081 (15)0.0020 (16)
C110.0237 (19)0.025 (2)0.0201 (17)0.0062 (16)0.0086 (15)0.0092 (16)
C120.0187 (18)0.025 (2)0.0176 (17)0.0039 (15)0.0067 (14)0.0068 (15)
Geometric parameters (Å, º) top
O1—N11.241 (3)C7—C81.406 (4)
O3—C81.375 (4)C8—C91.383 (5)
O3—C131.429 (4)C13—H13C0.96
O2—N11.236 (3)C13—H13A0.96
N1—C11.415 (4)C13—H13B0.96
N2—C21.317 (4)C4—H4A0.96
N2—C11.354 (4)C4—H4B0.96
N3—C31.339 (4)C4—H4C0.96
N3—C21.380 (4)C3—H30.93
N3—C41.464 (4)C9—C101.372 (5)
C1—C31.380 (4)C9—H90.93
C2—C51.445 (5)C10—C111.386 (5)
C5—C61.351 (5)C10—H100.93
C5—H50.93C11—C121.382 (5)
C6—C71.455 (5)C11—H110.93
C6—H60.93C12—H120.93
C7—C121.394 (5)
C8—O3—C13117.1 (3)O3—C13—H13A109.5
O2—N1—O1122.5 (3)H13C—C13—H13A109.5
O2—N1—C1119.0 (3)O3—C13—H13B109.5
O1—N1—C1118.4 (3)H13C—C13—H13B109.5
C2—N2—C1103.9 (3)H13A—C13—H13B109.5
C3—N3—C2108.4 (2)N3—C4—H4A109.5
C3—N3—C4124.7 (3)N3—C4—H4B109.5
C2—N3—C4126.7 (3)H4A—C4—H4B109.5
N2—C1—C3112.9 (3)N3—C4—H4C109.5
N2—C1—N1123.0 (3)H4A—C4—H4C109.5
C3—C1—N1124.1 (3)H4B—C4—H4C109.5
N2—C2—N3111.1 (3)N3—C3—C1103.7 (3)
N2—C2—C5125.9 (3)N3—C3—H3128.1
N3—C2—C5123.0 (3)C1—C3—H3128.1
C6—C5—C2121.7 (3)C10—C9—C8120.0 (3)
C6—C5—H5119.2C10—C9—H9120
C2—C5—H5119.2C8—C9—H9120
C5—C6—C7127.7 (3)C9—C10—C11120.6 (3)
C5—C6—H6116.1C9—C10—H10119.7
C7—C6—H6116.1C11—C10—H10119.7
C12—C7—C8117.2 (3)C12—C11—C10119.2 (3)
C12—C7—C6123.3 (3)C12—C11—H11120.4
C8—C7—C6119.5 (3)C10—C11—H11120.4
O3—C8—C9124.8 (3)C11—C12—C7121.9 (3)
O3—C8—C7114.1 (3)C11—C12—H12119
C9—C8—C7121.1 (3)C7—C12—H12119
O3—C13—H13C109.5
C2—N2—C1—C30.3 (3)C13—O3—C8—C96.8 (5)
C2—N2—C1—N1178.3 (3)C13—O3—C8—C7173.6 (3)
O2—N1—C1—N2179.5 (3)C12—C7—C8—O3179.6 (3)
O1—N1—C1—N21.5 (4)C6—C7—C8—O30.6 (4)
O2—N1—C1—C32.0 (5)C12—C7—C8—C90.1 (5)
O1—N1—C1—C3176.9 (3)C6—C7—C8—C9179.8 (3)
C1—N2—C2—N30.1 (3)C2—N3—C3—C10.6 (3)
C1—N2—C2—C5179.2 (3)C4—N3—C3—C1175.4 (3)
C3—N3—C2—N20.5 (3)N2—C1—C3—N30.5 (3)
C4—N3—C2—N2175.4 (3)N1—C1—C3—N3178.1 (3)
C3—N3—C2—C5178.9 (3)O3—C8—C9—C10179.3 (3)
C4—N3—C2—C55.3 (5)C7—C8—C9—C100.3 (5)
N2—C2—C5—C610.8 (5)C8—C9—C10—C110.7 (5)
N3—C2—C5—C6170.0 (3)C9—C10—C11—C120.8 (5)
C2—C5—C6—C7178.6 (3)C10—C11—C12—C70.5 (5)
C5—C6—C7—C1211.0 (5)C8—C7—C12—C110.1 (5)
C5—C6—C7—C8168.8 (3)C6—C7—C12—C11179.7 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O2i0.932.453.271 (4)147
C4—H4B···O1ii0.962.533.465 (5)165
C6—H6···O30.932.312.685 (4)103
C6—H6···N20.932.602.935 (4)102
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O2i0.93002.45003.271 (4)147.00
C4—H4B···O1ii0.96002.53003.465 (5)165.00
C6—H6···O30.93002.31002.685 (4)103.00
C6—H6···N20.93002.60002.935 (4)102.00
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1, z.
 

Acknowledgements

We are grateful to the 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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Volume 70| Part 9| September 2014| Pages o966-o967
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