Crystal structure of 1-[(1-methyl-5-nitro-1H-imidazol-2-yl)meth­yl]pyridinium iodide

Roumaissa Belguedj; Abdelmalek Bouraiou; Hocine Merazig; Ali Belfaitah; Sofiane Bouacida

doi:10.1107/S2056989015001541

. 2015 Jan 28;71(Pt 2):o133–o134. doi: 10.1107/S2056989015001541

Crystal structure of 1-[(1-methyl-5-nitro-1H-imidazol-2-yl)methyl]pyridinium iodide

Roumaissa Belguedj ^a, Abdelmalek Bouraiou ^a, Hocine Merazig ^a, Ali Belfaitah ^b, Sofiane Bouacida ^a,^c,^*

PMCID: PMC4384567 PMID: 25878869

Abstract

In the title salt, C₁₀H₁₁N₄O₂ ⁺·I⁻, the asymmetric unit consists of a pyridinium cation bearning a (1-methyl-5-nitro-1H-imidazol-2-yl)methyl group at the N position and an iodide anion. The imidazole ring is quasiplanar, with a maxiumum deviation of 0.0032 (16) Å, and forms a dihedral angle of 67.39 (6)° with the plane of the pyridinium ring. The crystal packing can be described as alternating zigzag layers of cations parallel to the (001) plane, which are sandwiched by the iodide ions. The structure features two types of hydrogen bonds (C—H⋯O and C—H⋯I), viz. cation–anion and cation–cation, which lead to the form ation of a three-dimensional network.

Keywords: crystal structure, imidazole, pyridinium, iodide, hydrogen bonding

Related literature

For the synthesis and applications of imidazole derivatives, see: Upcroft & Upcroft (2001 ▸); Çelik & Ateş (2006 ▸); Boyer (1986 ▸); Olender et al. (2009 ▸); Gaonkar et al. (2009 ▸); Larina & Lopyrev (2009 ▸). For our previous work on this type of chemistry, see: Zama et al. (2013 ▸); Alliouche et al. (2014 ▸); Bahnous et al. (2012 ▸). For the synthesis of the title compound, see: Albright & Shepherd (1973 ▸). graphic file with name e-71-0o133-scheme1.jpg

Experimental

Crystal data

C₁₀H₁₁N₄O₂ ⁺·I⁻
M _r = 346.13
Monoclinic,
a = 11.035 (7) Å
b = 9.073 (6) Å
c = 12.859 (8) Å
β = 91.69 (2)°
V = 1286.8 (14) Å³
Z = 4
Mo Kα radiation
μ = 2.49 mm⁻¹
T = 295 K
0.14 × 0.12 × 0.11 mm

Data collection

Bruker APEXII diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2002 ▸) T _min = 0.615, T _max = 0.745
22502 measured reflections
6134 independent reflections
3669 reflections with I > 2σ(I)
R _int = 0.030

Refinement

R[F ² > 2σ(F ²)] = 0.029
wR(F ²) = 0.067
S = 0.99
6134 reflections
155 parameters
H-atom parameters constrained
Δρ_max = 1.14 e Å⁻³
Δρ_min = −0.89 e Å⁻³

Data collection: APEX2 (Bruker, 2011 ▸); cell refinement: SAINT (Bruker, 2011 ▸); data reduction: SAINT; program(s) used to solve structure: SIR2002 (Burla et al., 2003 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2015 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸) and DIAMOND (Brandenburg, 2006 ▸); software used to prepare material for publication: WinGX (Farrugia, 2012 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989015001541/hg5425sup1.cif

e-71-0o133-sup1.cif^{(21.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015001541/hg5425Isup2.hkl

e-71-0o133-Isup2.hkl^{(294.2KB, hkl)}

Click here for additional data file.^{(4.7KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015001541/hg5425Isup3.cml

Click here for additional data file.^{(1.3MB, tif)}

. DOI: 10.1107/S2056989015001541/hg5425fig1.tif

(Farrugia, 2012). The molecule structure of the title compound with the atomic labelling scheme. Displacement are drawn at the 50% probability level. H atoms are represented as small spheres of arbitrary radius.

Click here for additional data file.^{(1.5MB, tif)}

via a . DOI: 10.1107/S2056989015001541/hg5425fig2.tif

(Brandenburg, 2006). Alternating layers parallel to (001) plane of (I) sandwiched by iodide ions viewed via a axis

Click here for additional data file.^{(1.9MB, tif)}

via b . DOI: 10.1107/S2056989015001541/hg5425fig3.tif

(Brandenburg, 2006). Crystal packing of (I) viewed via b axis showing hydrogen bond as dashed lines [C—H⋯I in red and C—H⋯O in black]

CCDC reference: 1045139

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C10H10O2ⁱ	0.93	2.51	3.138(3)	125
C5H5AI1ⁱⁱ	0.97	3.04	3.807(3)	137
C7H7I1ⁱⁱⁱ	0.93	3.04	3.854(3)	147

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) .

Acknowledgments

Thanks are due to MESRS and the DG–RSDT (Ministère de l’Enseignement Supérieur et de la Recherche Scientifique et la Direction Générale de la Recherche - Algérie) for financial support.

supplementary crystallographic information

S1. Comment

1. Chemical Context

Nitroheterocyclic drugs have drawn a continuing interest over the years due to efficient use in the treatment of various anaerobic pathogenic bacterial and protozoal infections (Upcroft & Upcroft, 2001; Çelik & Ates, 2006). Nitroimidazole derivatives have been the subject of much research because of their properties. Depending on the nature and the position of substituents or the nitro group, the nitroimidazole derivatives can posses various pharmacological action (Boyer, 1986). 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; Gaonkar et al. 2009; Larina & Lopyrev 2009). In previous work, we have reported the synthesis and structure determination of some new heterocyclic compounds bearing a nitroimidazole entity (Zama et al., 2013; Alliouche et al., 2014; Bahnous et al., 2012). Herein, we report the synthesis and single-crystal X-ray structure of 1-((1-methyl-5-nitro-1H-imidazol-2-yl)methyl)pyridinium iodide, (I).

2. Structural commentary

The molecule structure of (I), and the atomic numbering used, is illustrated in Fig. 1. The asymmetric unit of (I) consists of pyridinium cation bearing a 1-methyl-5-nitro-1H-imidazol-2-yl)methyl group at N position, and the iodide anion. The imidazol ring is quasiplanar with maxiumum deviation of 0.0032 (16) Å at C1 atom; and form dihedral angle of 67.39 (6)° with pyridinium ring. The crystal packing can be described by alternating layers in zigzag parallel to (001) plane of cations group, which are sandwiched by iodide ions (Fig. 2).

3. Supramolecular features

The crystal packing is mostly governed by classical hydrogen bonds (Fig. 3). Atoms C2, C5, C7, C10 and O2 of the cation participate in the formation of intramolecular [C—H···O and C—H···I] hydrogen bonds (Table 1). In this structure, we observe two types of hydrogen bonds, viz. cation-anion, cation-cation which form a three-dimensional network. The intramolecular hydrogen bond interactions C—H···O are also observed in cations moities. however the centroid to centroid distance between the phenyl rings are too long (4.430 (3) Å) for considering π-π interactions. These interactions link the molecules within the layers and also link the layers together and reinforcing the cohesion of the ionic structure.

S2. Experimental

The 1-((1-methyl-5-nitro-1H-imidazol-2-yl)methyl)pyridinium iodide, I, was prepared from 1,2-dimethyl-5-nitro-1H-imidazole in presence of iodine and pyridine as solvent according to described procedure (Albright & Shepherd, 1973). The colorless crystals of the title compound used for the X-ray diffraction study were obtained from aqueous solution of I.