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

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.


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-5nitro-1H-imidazol-2-yl)methyl)pyridinium iodide, (I).

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).

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.
The colorless crystals of the title compound used for the X-ray diffraction study were obtained from aqueous solution of I.

Special details
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 F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.