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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 71| Part 2| February 2015| Pages 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 Belfaitahb and Sofiane Bouacidaa,c*

aUnité de Recherche de Chimie de l'Environnement et Moléculaire Structurale, CHEMS, Université Constantine1, 25000 , Algeria, bEquipe de Synthèse de Molécules à Objectif Thérapeutique, Laboratoire des Produits Naturels d'Origine Végétale et de Synthèse Organique, Université Constantine 1, Constantine 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 January 2015; accepted 23 January 2015; online 28 January 2015)

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.

CCDC reference: 1045139

1. Related literature

For the synthesis and applications of imidazole derivatives, see: Upcroft & Upcroft (2001[Upcroft, P. & Upcroft, J. A. (2001). Clin. Microbiol. Rev. 14, 150-164.]); Çelik & Ateş (2006[Çelik, A. & Ateş, N. A. (2006). Drug Chem. Toxicol. 29, 85-94.]); Boyer (1986[Boyer, J. H. (1986). Nitroazoles, pp. 165-166. Deerfield Beach, Florida: VCH Publishers, Inc.]); Olender et al. (2009[Olender, D., Żwawiak, J., Lukianchuk, V., Lesyk, R., Kropacz, A., Fojutowski, A. & Zaprutko, L. (2009). Eur. J. Med. Chem. 44, 645-652.]); Gaonkar et al. (2009[Gaonkar, S. L., Lokanatha Rai, K. M. & Suchetha Shetty, N. (2009). Med. Chem. Res. 18, 221-230.]); Larina & Lopyrev (2009[Larina, L. & Lopyrev, V. (2009). In Nitroazoles: Synthesis, Structure and Applications, in Topics in Applied Chemistry, edited by A. Katritzky & G. J. Sabongi. Berlin: Springer.]). For our previous work on this type of chemistry, see: Zama et al. (2013[Zama, S., Bouraiou, A., Bouacida, S., Roisnel, T. & Belfaitah, A. (2013). Acta Cryst. E69, o837-o838.]); Alliouche et al. (2014[Alliouche, H., Bouraiou, A., Bouacida, S., Bahnous, M., Roisnel, T. & Belfaitah, A. (2014). Lett. Org. Chem. 11, 174-179.]); Bahnous et al. (2012[Bahnous, M., Bouraiou, A., Bouacida, S., Roisnel, T. & Belfaitah, A. (2012). Acta Cryst. E68, o1391.]). For the synthesis of the title compound, see: Albright & Shepherd (1973[Albright, J. D. & Shepherd, R. G. (1973). J. Heterocycl. Chem. 10, 899-907.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C10H11N4O2+·I−

  • Mr = 346.13

  • Monoclinic, P 21 /c

  • 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

2.2. Data collection

  • Bruker APEXII diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2002[Sheldrick, G. M. (2002). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.615, Tmax = 0.745

  • 22502 measured reflections

  • 6134 independent reflections

  • 3669 reflections with I > 2σ(I)

  • Rint = 0.030

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.029

  • wR(F2) = 0.067

  • S = 0.99

  • 6134 reflections

  • 155 parameters

  • H-atom parameters constrained

  • Δρmax = 1.14 e Å−3

  • Δρmin = −0.89 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C10—H10⋯O2i 0.93 2.51 3.138 (3) 125
C5—H5A⋯I1ii 0.97 3.04 3.807 (3) 137
C7—H7⋯I1iii 0.93 3.04 3.854 (3) 147
Symmetry codes: (i) x, y+1, z; (ii) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2011[Bruker (2011). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2011[Bruker (2011). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR2002 (Burla et al., 2003[Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). 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

CCDC reference: 1045139

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

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

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

checkCIF report


Comment top

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.

Related literature top

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).

Experimental top

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.

Refinement top

The H atoms were localized on Fourier maps but introduced in calculated positions and treated as riding on their parent atom (C) with C—H = 0.93 Å (aromatic), C—H = 0.97 Å (methylene) and C—H = 0.96 Å (methyl) with Uiso(H) = 1.2 or 1.5Ueq(C).

Computing details top

Data collection: APEX2 (Bruker, 2011); cell refinement: SAINT (Bruker, 2011); data reduction: SAINT (Bruker, 2011); 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).

Figures top
[Figure 1] Fig. 1. (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.
[Figure 2] Fig. 2. (Brandenburg, 2006). Alternating layers parallel to (001) plane of (I) sandwiched by iodide ions viewed via a axis
[Figure 3] Fig. 3. (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]
1-[(1-Methyl-5-nitro-1H-imidazol-2-yl)methyl]pyridinium iodide top
Crystal data top
C10H11N4O2+·I−F(000) = 672
Mr = 346.13Dx = 1.787 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 11.035 (7) ÅCell parameters from 6343 reflections
b = 9.073 (6) Åθ = 2.8–29.3°
c = 12.859 (8) ŵ = 2.49 mm−1
β = 91.69 (2)°T = 295 K
V = 1286.8 (14) Å3Prism, colorless
Z = 40.14 × 0.12 × 0.11 mm
Data collection top
Bruker APEXII
diffractometer		6134 independent reflections
Radiation source: Enraf–Nonius FR5903669 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
CCD rotation images, thick slices scansθmax = 36.5°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2002)		h = −18→17
Tmin = 0.615, Tmax = 0.745k = −14→14
22502 measured reflectionsl = −21→21
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)] = 0.029Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.067H-atom parameters constrained
S = 0.99 w = 1/[σ2(Fo2) + (0.0275P)2]
where P = (Fo2 + 2Fc2)/3
6134 reflections(Δ/σ)max = 0.006
155 parametersΔρmax = 1.14 e Å−3
0 restraintsΔρmin = −0.89 e Å−3
Crystal data top
C10H11N4O2+·I−V = 1286.8 (14) Å3
Mr = 346.13Z = 4
Monoclinic, P21/cMo Kα radiation
a = 11.035 (7) ŵ = 2.49 mm−1
b = 9.073 (6) ÅT = 295 K
c = 12.859 (8) Å0.14 × 0.12 × 0.11 mm
β = 91.69 (2)°
Data collection top
Bruker APEXII
diffractometer		6134 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2002)		3669 reflections with I > 2σ(I)
Tmin = 0.615, Tmax = 0.745Rint = 0.030
22502 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0290 restraints
wR(F2) = 0.067H-atom parameters constrained
S = 0.99Δρmax = 1.14 e Å−3
6134 reflectionsΔρmin = −0.89 e Å−3
155 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
C10.53170 (14)−0.02548 (17)0.12964 (12)0.0288 (3)
C20.75852 (17)−0.0764 (2)0.10429 (18)0.0469 (5)
H2A0.8317−0.02350.12170.07*
H2B0.755−0.09650.0310.07*
H2C0.7577−0.16760.14210.07*
C30.65440 (15)0.15859 (18)0.15888 (12)0.0299 (3)
C40.46650 (16)0.09581 (18)0.15569 (14)0.0361 (4)
H40.38260.09950.16030.043*
C50.76681 (16)0.25171 (19)0.16974 (12)0.0353 (4)
H5A0.75840.32020.2270.042*
H5B0.83610.1890.18550.042*
C60.87603 (16)0.2915 (2)0.01029 (14)0.0458 (4)
H60.92140.20790.02680.055*
C70.8991 (2)0.3696 (3)−0.07726 (17)0.0563 (5)
H70.96040.3395−0.12060.068*
C80.8319 (3)0.4928 (3)−0.10157 (16)0.0633 (6)
H80.84890.5479−0.16030.076*
C90.7398 (3)0.5340 (2)−0.03922 (18)0.0698 (7)
H90.69220.6156−0.05620.084*
C100.7181 (2)0.4539 (2)0.04885 (16)0.0520 (5)
H100.65560.4810.0920.062*
N10.48460 (14)−0.16821 (16)0.10430 (11)0.0361 (3)
N20.65316 (11)0.01303 (14)0.13202 (9)0.0278 (3)
N30.54387 (13)0.21140 (15)0.17398 (11)0.0377 (3)
N40.78797 (12)0.33517 (15)0.07265 (10)0.0323 (3)
O10.37309 (12)−0.17941 (15)0.09568 (11)0.0516 (3)
O20.55464 (14)−0.27106 (14)0.09207 (13)0.0594 (4)
I11.107377 (10)0.089936 (13)0.189052 (9)0.04248 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0291 (8)0.0313 (8)0.0262 (7)−0.0053 (6)0.0025 (6)0.0001 (6)
C20.0322 (10)0.0468 (11)0.0620 (12)0.0067 (8)0.0072 (9)−0.0108 (9)
C30.0317 (8)0.0315 (8)0.0268 (7)−0.0030 (6)0.0042 (6)0.0000 (6)
C40.0269 (8)0.0405 (9)0.0412 (9)−0.0011 (7)0.0070 (7)−0.0027 (7)
C50.0376 (9)0.0392 (9)0.0291 (7)−0.0098 (7)0.0012 (7)0.0012 (7)
C60.0322 (9)0.0637 (12)0.0416 (10)−0.0018 (9)0.0049 (8)0.0067 (9)
C70.0492 (12)0.0784 (15)0.0417 (10)−0.0130 (11)0.0102 (9)0.0030 (11)
C80.1028 (19)0.0505 (12)0.0368 (10)−0.0304 (13)0.0066 (11)0.0034 (10)
C90.123 (2)0.0316 (10)0.0558 (13)0.0119 (12)0.0106 (14)0.0052 (11)
C100.0778 (16)0.0293 (8)0.0498 (11)0.0068 (10)0.0161 (10)−0.0007 (9)
N10.0418 (9)0.0356 (7)0.0311 (7)−0.0086 (6)0.0038 (6)−0.0016 (6)
N20.0259 (7)0.0309 (7)0.0267 (6)0.0000 (5)0.0039 (5)0.0005 (5)
N30.0354 (8)0.0333 (7)0.0449 (8)−0.0005 (6)0.0095 (6)−0.0049 (6)
N40.0349 (8)0.0312 (7)0.0310 (6)−0.0096 (6)0.0028 (6)−0.0037 (6)
O10.0413 (8)0.0544 (8)0.0589 (8)−0.0164 (6)−0.0041 (6)−0.0063 (7)
O20.0606 (9)0.0336 (7)0.0847 (11)−0.0003 (7)0.0177 (8)−0.0112 (7)
I10.03084 (7)0.04881 (8)0.04816 (8)0.00945 (5)0.00730 (5)0.00972 (5)
Geometric parameters (Å, º) top
C1—C41.362 (2)C5—H5B0.97
C1—N21.385 (2)C6—N41.338 (2)
C1—N11.429 (2)C6—C71.360 (3)
C2—N21.470 (2)C6—H60.93
C2—H2A0.96C7—C81.373 (3)
C2—H2B0.96C7—H70.93
C2—H2C0.96C8—C91.365 (4)
C3—N31.330 (2)C8—H80.93
C3—N21.365 (2)C9—C101.373 (3)
C3—C51.504 (2)C9—H90.93
C4—N31.368 (2)C10—N41.355 (2)
C4—H40.93C10—H100.93
C5—N41.484 (2)N1—O21.225 (2)
C5—H5A0.97N1—O11.236 (2)
C4—C1—N2107.98 (14)C7—C6—H6120
C4—C1—N1126.65 (15)C6—C7—C8119.9 (2)
N2—C1—N1125.37 (14)C6—C7—H7120
N2—C2—H2A109.5C8—C7—H7120
N2—C2—H2B109.5C9—C8—C7119.7 (2)
H2A—C2—H2B109.5C9—C8—H8120.1
N2—C2—H2C109.5C7—C8—H8120.1
H2A—C2—H2C109.5C8—C9—C10119.4 (2)
H2B—C2—H2C109.5C8—C9—H9120.3
N3—C3—N2112.53 (14)C10—C9—H9120.3
N3—C3—C5122.78 (15)N4—C10—C9119.7 (2)
N2—C3—C5124.69 (15)N4—C10—H10120.2
C1—C4—N3109.28 (16)C9—C10—H10120.2
C1—C4—H4125.4O2—N1—O1123.78 (15)
N3—C4—H4125.4O2—N1—C1119.53 (15)
N4—C5—C3110.99 (13)O1—N1—C1116.69 (15)
N4—C5—H5A109.4C3—N2—C1104.61 (13)
C3—C5—H5A109.4C3—N2—C2126.38 (14)
N4—C5—H5B109.4C1—N2—C2128.85 (14)
C3—C5—H5B109.4C3—N3—C4105.60 (14)
H5A—C5—H5B108C6—N4—C10121.25 (16)
N4—C6—C7119.9 (2)C6—N4—C5119.21 (15)
N4—C6—H6120C10—N4—C5119.53 (15)
N2—C1—C4—N30.4 (2)C5—C3—N2—C2−3.1 (2)
N1—C1—C4—N3−179.70 (15)C4—C1—N2—C3−0.60 (17)
N3—C3—C5—N4−83.61 (19)N1—C1—N2—C3179.51 (14)
N2—C3—C5—N495.79 (18)C4—C1—N2—C2−176.19 (17)
N4—C6—C7—C8−0.1 (3)N1—C1—N2—C23.9 (3)
C6—C7—C8—C9−1.8 (3)N2—C3—N3—C4−0.35 (19)
C7—C8—C9—C101.9 (4)C5—C3—N3—C4179.12 (15)
C8—C9—C10—N4−0.1 (4)C1—C4—N3—C3−0.1 (2)
C4—C1—N1—O2−173.00 (17)C7—C6—N4—C102.1 (3)
N2—C1—N1—O26.9 (2)C7—C6—N4—C5−177.91 (17)
C4—C1—N1—O17.2 (2)C9—C10—N4—C6−2.0 (3)
N2—C1—N1—O1−172.89 (15)C9—C10—N4—C5178.00 (19)
N3—C3—N2—C10.59 (17)C3—C5—N4—C6−105.28 (18)
C5—C3—N2—C1−178.86 (14)C3—C5—N4—C1074.8 (2)
N3—C3—N2—C2176.33 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2C···O20.962.502.861 (3)102
C10—H10···O2i0.932.513.138 (3)125
C5—H5A···I1ii0.973.043.807 (3)137
C7—H7···I1iii0.933.043.854 (3)147
Symmetry codes: (i) x, y+1, z; (ii) −x+2, y+1/2, −z+1/2; (iii) x, −y+1/2, z−1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2C···O20.96002.50002.861 (3)102.00
C10—H10···O2i0.93002.51003.138 (3)125.00
C5—H5A···I1ii0.97003.04003.807 (3)137.00
C7—H7···I1iii0.93003.04003.854 (3)147.00
Symmetry codes: (i) x, y+1, z; (ii) −x+2, y+1/2, −z+1/2; (iii) x, −y+1/2, z−1/2.
 

Acknowledgements

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.

References

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ISSN: 2056-9890
Volume 71| Part 2| February 2015| Pages o133-o134
doi:10.1107/S2056989015001541
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