supplementary materials


yk2093 scheme

Acta Cryst. (2013). E69, o837-o838    [ doi:10.1107/S1600536813011914 ]

Methyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate

S. Zama, A. Bouraiou, S. Bouacida, T. Roisnel and A. Belfaitah

Abstract top

In the crystal of the title compound, C7H9N3O4, molecules are linked by weak C-H...O hydrogen bonds into chains along the a-axis direction. The dihedral angle between the ring and the nitro group is 3.03 (6), while that between the ring and the acetate group is 85.01 (3)°.

Comment top

The chemistry of imidazole occupies an extremely important position within the family of five-membered heterocyclic compounds. Synthesis of imidazole derivatives has attracted great interest in recent years due to their broad spectrum of biological activities (Gaonkar et al., 2009). For a few decades, nitroimdazoles have been the subject of much interest because of their properties. Nitroimidazoles, such as metronidazole, misonidazole, ornidazole, secnidazole and etamidazole, are commonly used as therapeutic agents against a variety of protozoan and bacterial infections of humans and animals (Olender et al., 2009). The compounds with nitro group at position 4 are usually less active than the corresponding 5-nitro derivatives. The structures of nitroimidazoles have been studied more thoroughly by X-ray and 13C NMR and can be explained by wide application of these compounds, especially in medicine. The problem of structural identification of 1-substituted nitroimidazoles by NMR spectroscopy has been considered in many works (Larina & Lopyrev, 2009). In previous work, we have reported the synthesis and structure determination of some new heterocyclic compounds bearing an imidazole unit (Chelghoum et al., 2011; Bahnous et al., 2012). Herein, we report the synthesis and single-crystal X-ray structure of methyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate, (I).

The molecular geometry and the atom-numbering scheme of (I) are shown in Fig. 1. The asymmetric unit of (I)consists of 2-methyl-4-nitro-1H-imidazol linked to methyl acetate. The crystal packing can be described as crossed layers in zigzag parallel to the (110) plane. (Fig. 2). It is stabilized by C—H···O and C—H···N hydrogen bond (Table 1), weak N—O···π interactions and ππ stacking interactions between imidazole rings with a centroid–centroid distance of 4.6619 (6)Å. These interaction bonds link the molecules within the layers and also link the layers together, reinforcing the cohesion of the structure.

Related literature top

For the synthesis of the title compound, see: Pavlik et al. (2011); Kasai et al. (2001). For the structural identification of nitroimidazoles, see: Larina & Lopyrev (2009). For biological activities of this class of compounds, see: Gaonkar et al. (2009); Olender et al. (2009). For our previous work on imidazole derivatives, see: Chelghoum et al. (2011); Bahnous et al. (2012).

Experimental top

Methyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate, (I), was obtained from reaction of methyl bromoacetate and 4(5)-nitro-2-methylimidazole in presence of potassium carbonate in DMF. Crystals suitable for X-ray analysis were obtained by slow evaporation of a chloroform–carbon tetrachloride solution.

Refinement top

All non-H atoms were refined with anisotropic atomic displacement parameters. Approximate positions for all the H atoms were first obtained from the difference electron-density map. However, the H atoms were situated into idealized positions and the H atoms have been refined within the riding-atom approximation. The applied constraints were as follows: Caryl—Haryl = 0.95 Å, Cmethylene—Hmethylene = 0.99 Å and Cmethyl—Hmethyl = 0.98 Å. The idealized methyl group was allowed to rotate about the C—C bond during the refinement by application of the command AFIX 137 in SHELXL97 (Sheldrick, 2008). Uiso(Hmethyl) = 1.5Ueq(Cmethyl) or Uiso(Haryl or Hmethylene) = 1.2Ueq(Caryl or Cmethylene).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); 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) and CRYSCAL (local program).

Figures top
[Figure 1] Fig. 1. A view of the title molecule with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small spheres of arbitrary radius.
[Figure 2] Fig. 2. The crossed layers in the structure of the title compound, viewed down the c axis.
[Figure 3] Fig. 3. A diagram of the layered crystal packing of the title compound, viewed down the a axis and showing hydrogen bonds as dashed lines.
Methyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate top
Crystal data top
C7H9N3O4F(000) = 416
Mr = 199.17Dx = 1.509 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3719 reflections
a = 4.6619 (2) Åθ = 3.8–27.5°
b = 17.3256 (7) ŵ = 0.13 mm1
c = 11.1490 (4) ÅT = 150 K
β = 103.204 (2)°Prism, colourless
V = 876.70 (6) Å30.35 × 0.3 × 0.12 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer
1753 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
CCD rotation images, thin slices scansθmax = 27.5°, θmin = 3.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2002)
h = 65
Tmin = 0.937, Tmax = 0.985k = 2222
7665 measured reflectionsl = 1413
1991 independent reflections
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)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.088H-atom parameters constrained
S = 1.09 w = 1/[σ2(Fo2) + (0.0409P)2 + 0.2051P]
where P = (Fo2 + 2Fc2)/3
1991 reflections(Δ/σ)max = 0.002
129 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = 0.21 e Å3
Crystal data top
C7H9N3O4V = 876.70 (6) Å3
Mr = 199.17Z = 4
Monoclinic, P21/cMo Kα radiation
a = 4.6619 (2) ŵ = 0.13 mm1
b = 17.3256 (7) ÅT = 150 K
c = 11.1490 (4) Å0.35 × 0.3 × 0.12 mm
β = 103.204 (2)°
Data collection top
Bruker APEXII CCD
diffractometer
1991 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2002)
1753 reflections with I > 2σ(I)
Tmin = 0.937, Tmax = 0.985Rint = 0.030
7665 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.034H-atom parameters constrained
wR(F2) = 0.088Δρmax = 0.26 e Å3
S = 1.09Δρmin = 0.21 e Å3
1991 reflectionsAbsolute structure: ?
129 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
C10.6041 (3)0.02718 (8)0.85178 (13)0.0358 (3)
H1A0.56680.06890.79090.054*
H1B0.58280.04690.93170.054*
H1C0.80460.00750.85960.054*
O20.39315 (19)0.03498 (5)0.81191 (8)0.0303 (2)
C30.4191 (2)0.06977 (6)0.70857 (10)0.0215 (2)
O40.58536 (18)0.05011 (5)0.64611 (8)0.0268 (2)
C50.2106 (3)0.13799 (6)0.67831 (10)0.0227 (2)
H5A0.00690.11940.64590.027*
H5B0.21440.16840.75380.027*
N60.3015 (2)0.18625 (5)0.58664 (8)0.0199 (2)
C70.2472 (2)0.17282 (6)0.46184 (10)0.0201 (2)
N80.4024 (2)0.21960 (5)0.40814 (8)0.0215 (2)
C90.5615 (2)0.26266 (6)0.50325 (10)0.0199 (2)
C100.5056 (2)0.24382 (6)0.61419 (10)0.0211 (2)
H100.58920.26570.69250.025*
C110.0408 (3)0.11215 (7)0.39924 (11)0.0277 (3)
H11A0.00540.12110.31010.042*
H11B0.14110.11410.42920.042*
H11C0.13270.06130.41720.042*
N120.7683 (2)0.31975 (5)0.48349 (9)0.0228 (2)
O130.80836 (19)0.32840 (5)0.37915 (8)0.0315 (2)
O140.8988 (2)0.35710 (5)0.57330 (8)0.0361 (2)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0406 (7)0.0303 (7)0.0373 (7)0.0065 (6)0.0110 (6)0.0126 (6)
O20.0335 (5)0.0293 (5)0.0315 (5)0.0039 (4)0.0143 (4)0.0106 (4)
C30.0218 (5)0.0203 (5)0.0228 (5)0.0043 (4)0.0061 (4)0.0001 (4)
O40.0290 (4)0.0248 (4)0.0293 (4)0.0039 (3)0.0124 (4)0.0003 (3)
C50.0231 (6)0.0243 (6)0.0235 (6)0.0000 (4)0.0112 (4)0.0016 (4)
N60.0223 (5)0.0196 (4)0.0191 (5)0.0021 (4)0.0075 (4)0.0002 (3)
C70.0198 (5)0.0208 (5)0.0197 (5)0.0062 (4)0.0045 (4)0.0001 (4)
N80.0232 (5)0.0230 (5)0.0185 (5)0.0051 (4)0.0054 (4)0.0013 (4)
C90.0215 (5)0.0177 (5)0.0215 (5)0.0037 (4)0.0068 (4)0.0014 (4)
C100.0243 (5)0.0198 (5)0.0200 (5)0.0003 (4)0.0067 (4)0.0009 (4)
C110.0265 (6)0.0282 (6)0.0276 (6)0.0002 (5)0.0043 (5)0.0051 (5)
N120.0238 (5)0.0212 (5)0.0245 (5)0.0040 (4)0.0080 (4)0.0037 (4)
O130.0340 (5)0.0365 (5)0.0279 (5)0.0001 (4)0.0154 (4)0.0069 (4)
O140.0417 (6)0.0349 (5)0.0318 (5)0.0141 (4)0.0084 (4)0.0049 (4)
Geometric parameters (Å, º) top
C1—O21.4578 (15)C7—N81.3178 (15)
C1—H1A0.98C7—C111.4869 (16)
C1—H1B0.98N8—C91.3682 (15)
C1—H1C0.98C9—C101.3607 (15)
O2—C31.3299 (13)C9—N121.4329 (14)
C3—O41.2036 (13)C10—H100.95
C3—C51.5183 (16)C11—H11A0.98
C5—N61.4564 (14)C11—H11B0.98
C5—H5A0.99C11—H11C0.98
C5—H5B0.99N12—O131.2287 (12)
N6—C101.3641 (15)N12—O141.2302 (13)
N6—C71.3760 (14)
O2—C1—H1A109.5N8—C7—N6111.22 (10)
O2—C1—H1B109.5N8—C7—C11125.81 (10)
H1A—C1—H1B109.5N6—C7—C11122.96 (10)
O2—C1—H1C109.5C7—N8—C9103.89 (9)
H1A—C1—H1C109.5C10—C9—N8113.02 (10)
H1B—C1—H1C109.5C10—C9—N12125.50 (10)
C3—O2—C1114.24 (9)N8—C9—N12121.46 (10)
O4—C3—O2124.82 (11)C9—C10—N6103.85 (10)
O4—C3—C5123.76 (10)C9—C10—H10128.1
O2—C3—C5111.41 (9)N6—C10—H10128.1
N6—C5—C3109.20 (9)C7—C11—H11A109.5
N6—C5—H5A109.8C7—C11—H11B109.5
C3—C5—H5A109.8H11A—C11—H11B109.5
N6—C5—H5B109.8C7—C11—H11C109.5
C3—C5—H5B109.8H11A—C11—H11C109.5
H5A—C5—H5B108.3H11B—C11—H11C109.5
C10—N6—C7108.01 (9)O13—N12—O14123.54 (10)
C10—N6—C5124.16 (9)O13—N12—C9118.87 (10)
C7—N6—C5126.63 (10)O14—N12—C9117.58 (9)
C1—O2—C3—O44.91 (17)C11—C7—N8—C9178.43 (10)
C1—O2—C3—C5175.23 (10)C7—N8—C9—C100.55 (12)
O4—C3—C5—N615.79 (15)C7—N8—C9—N12178.05 (9)
O2—C3—C5—N6164.35 (9)N8—C9—C10—N60.03 (12)
C3—C5—N6—C1086.81 (12)N12—C9—C10—N6178.57 (10)
C3—C5—N6—C779.17 (13)C7—N6—C10—C90.58 (12)
C10—N6—C7—N80.99 (12)C5—N6—C10—C9168.78 (10)
C5—N6—C7—N8168.81 (10)C10—C9—N12—O13176.38 (10)
C10—N6—C7—C11178.38 (10)N8—C9—N12—O132.04 (15)
C5—N6—C7—C1110.55 (16)C10—C9—N12—O142.92 (16)
N6—C7—N8—C90.92 (11)N8—C9—N12—O14178.66 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5A···O4i0.992.303.2350 (16)156
Symmetry code: (i) x1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5A···O4i0.992.303.2350 (16)156.0
Symmetry code: (i) x1, y, z.
Acknowledgements top

The authors are grateful to all the personnel of the research team `Synthèse de molécules à objectif thérapeutique' of the PHYSYNOR Laboratory, Université Constantine, Algeria, for their assistance. Thanks are due to the MESRS (Ministére de l'Enseignement Supérieur et de la Recherche Scientifique, Algerie) for financial support.

references
References top

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