2-Methoxy-1-methyl-4-nitro-1H-imidazole

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1 University of Wollongong Research Online Australian Institute for Innovative Materials - Papers Australian Institute for Innovative Materials Methoxy-1-methyl-4-nitro-1H-imidazole Maciej Kubicki Adam Mickiewicz University Pawel Wagner University of Wollongong, pawel@uow.edu.au Publication Details Kubicki, M. & Wagner, P. (2007). 2-Methoxy-1-methyl-4-nitro-1H-imidazole. Acta Crystallographica Section E: Structure Reports Online, 63 (7), o3120. Research Online is the open access institutional repository for the University of Wollongong. For further information contact the UOW Library: research-pubs@uow.edu.au

2 2-Methoxy-1-methyl-4-nitro-1H-imidazole Abstract The molecule of the title compound, C 5 H 7 N 3 O 3, is approximately planar. The maximum deviation from the least-squares plane calculated for all non-h atoms is (2) Å. The dihedral angles between the mean plane of the imidazole ring [planar within (6) Å] and the planes of the nitro and methoxy groups are 2.9 (1) and 1.2 (1), respectively. The molecules are held together by weak C H...N and C H...O interactions and by van der Waals forces. Keywords 1, 2, 1h, nitro, 4, methyl, imidazole, methoxy Disciplines Engineering Physical Sciences and Mathematics Publication Details Kubicki, M. & Wagner, P. (2007). 2-Methoxy-1-methyl-4-nitro-1H-imidazole. Acta Crystallographica Section E: Structure Reports Online, 63 (7), o3120. This journal article is available at Research Online:

3 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN Methoxy-1-methyl-4-nitro-1H-imidazole Maciej Kubicki a * and Paweł Wagner b a Department of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, Poznań, Poland, and b Nanomaterials Research Centre and, MacDiarmid Institute for Advanced Materials and Nanotechnology, Massey University, Private Bag , Palmerston North, New Zealand Correspondence mkubicki@amu.edu.pl b = (13) Å c = (8) Å = (7) V = (10) Å 3 Z =4 Data collection Kuma KM-4 CCD four-circle diffractometer Absorption correction: multi-scan (SORTAV; Blessing, 1989) T min = 0.988, T max = Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections Mo K radiation = 0.13 mm 1 T = 90 (1) K mm 6537 measured reflections 1791 independent reflections 1514 reflections with I > 2(I) R int = parameters All H-atom parameters refined max = 0.25 e Å 3 min = 0.32 e Å 3 Received 31 May 2007; accepted 4 June 2007 Key indicators: single-crystal X-ray study; T = 90 K; mean (C C) = Å; R factor = 0.033; wr factor = 0.091; data-to-parameter ratio = The molecule of the title compound, C 5 H 7 N 3 O 3, is approximately planar. The maximum deviation from the least-squares plane calculated for all non-h atoms is (2) Å. The dihedral angles between the mean plane of the imidazole ring [planar within (6) Å] and the planes of the nitro and methoxy groups are 2.9 (1) and 1.2 (1), respectively. The molecules are held together by weak C HN and C HO interactions and by van der Waals forces. Related literature This is a part of our studies of intermolecular interactions in 4- nitroimidazole derivatives (e.g. Kubicki, 2004, and references therein). Related literature: Kulkarni et al. (1987); Suwiński & Wagner (2007). Table 1 Hydrogen-bond geometry (Å, ). D HA D H HA DA D HA C11 H11AO42 i (15) (15) (13) (11) C11 H11CO41 ii (17) (17) (13) (12) C5 H5N3 ii (14) (14) (12) (11) C21 H21CO2 iii (15) (15) (13) (11) Symmetry codes: (i) x þ 1; y þ 1 2 ; z þ 3 2 ; (ii) x; y þ 3 2 ; z þ 1 2 ; (iii) x þ 3; y þ 2; z þ 1. Data collection: CrysAlis CCD (Oxford Diffraction, 2002); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989); software used to prepare material for publication: SHELXL97. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FB2054). Experimental Crystal data C 5 H 7 N 3 O 3 M r = Monoclinic, P2 1 =c a = (4) Å References Blessing, R. H. (1989). J. Appl. Cryst. 22, Kubicki, M. (2004). J. Mol. Struct. 696, Kulkarni, S., Grimmett, M. R., Hanton, L. R. & Simpson, J. (1987). Aust. J. Chem. 40, Oxford Diffraction (2002). CrysAlis CCD and CrysAlis RED. Version Oxford Diffraction, Wrocław, Poland. Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany. Siemens (1989). Stereochemical Workstation Operation Manual. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA. Suwiński, J. & Wagner, P. (2007). In preparation. o3120 # 2007 International Union of Crystallography doi: /s Acta Cryst. (2007). E63, o3120

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5 Acta Cryst. (2007). E63, o3120 [ doi: /s ] 2-Methoxy-1-methyl-4-nitro-1H-imidazole M. Kubicki and P. Wagner Comment The molecule of 1-methyl-2-methoxy-4-nitroimidazole, (I), (Fig. 1, Scheme 1) is almost planar, contrary to its analogue 1-methyl-4-nitro-5-methoxyimidazole, (II), that was determined at 100 K (Kulkarni et al., 1987; CCDC ). In (II) the methoxy and and the nitro groups are twisted by (14) and by 7.90 (12), respectively. These larger twists are obviously concomitant to the steric interactions that have a profound effect on the crystal packing. In (I), there are weak hydrogen bonds that interconnect molecules into layers (Fig. 2). In (II), on the other hand, the C H A interactions (A = O or N) are somewhat stronger (the H O distances are in the range 2.38 Å 2.57 Å, H N is 2.54 Å. Additionally, a π-π interaction with the interplanar distance of (2)Å (the distance between the ring centroids is (2) Å) is also present in the structure of (II). Experimental The title compound was synthesized by ipso nucleophilic replacement of nitro group from 2,4-dinitro-1-methyl imidazole in methanol-sodium methoxide solution with a yield (ca. 54%). The detailed synthesis will be described elsewhere (Suwiński & Wagner, 2007). Refinement All the hydrogen atoms were discernible in the difference Fourier maps and were freely refined. Figures Fig. 1. Title molecule with anisotropic displacement parameters at the 50% probability level. The hydrogen atoms are drawn as spheres with arbitrary radii. Fig. 2. The layer of the title molecules with C H O and C H N hydrogen bonds depicted as dashed lines. The view is approximately along the direction [100]. Symmetry codes: (i) x,y,z; (ii): x,3/2 y,1/2 + z; (iii) x,3/2 y,-1/2 + z; (iv) 1 x,-1/2 + y,3/2 z; (v) 1 x,1 y,1 z; (vi) 1 x,-1/2 + y,1/2 z. sup-1

6 2-Methoxy-1-methyl-4-nitro-1H-imidazole Crystal data C 5 H 7 N 3 O 3 F 000 = 328 M r = Monoclinic, P2 1 /c Hall symbol: -P 2ybc D x = Mg m 3 Mo Kα radiation λ = Å a = (4) Å θ = 3 24º b = (13) Å c = (8) Å β = (7)º V = (10) Å 3 Z = 4 Cell parameters from 5503 reflections µ = 0.13 mm 1 T = 90 (1) K Prism, colourless mm Data collection Kuma KM-4 CCD four-circle diffractometer Radiation source: fine-focus sealed tube Monochromator: graphite R int = T = 90(1) K θ max = 30.0º ω scans θ min = 3.2º Absorption correction: multi-scan (SORTAV; Blessing, 1989) T min = 0.988, T max = independent reflections 1514 reflections with I > 2σ(I) h = 5 5 k = measured reflections l = 7 15 Refinement Refinement on F 2 Secondary atom site location: difference Fourier map Least-squares matrix: full Hydrogen site location: difference Fourier map R[F 2 > 2σ(F 2 )] = All H-atom parameters refined wr(f 2 ) = w = 1/[σ 2 (F 2 o ) + (0.0584P) P] where P = (F 2 o + 2F 2 c )/3 S = 1.08 (Δ/σ) max = reflections Δρ max = 0.25 e Å parameters Δρ min = 0.32 e Å 3 Primary atom site location: structure-invariant direct methods Extinction correction: none 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 sup-2

7 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 > 2sigma(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. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq N (2) (6) (7) (19) C (3) (7) (9) (2) H11A (4) (9) (12) (3)* H11B (4) (10) (13) (4)* H11C (4) (11) (15) (4)* C (2) (6) (8) (2) O (18) (5) (6) (18) C (3) (7) (9) (2) H21A (3) (9) (12) (3)* H21B (3) (9) (12) (3)* H21C (4) (10) (13) (3)* N (2) (5) (7) (19) C (2) (6) (8) (2) N (2) (6) (7) (19) O (2) (5) (7) (2) O (19) (5) (7) (19) C (2) (6) (8) (2) H (3) (9) (12) (3)* Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 N (4) (4) (4) (3) (3) (3) C (5) (5) (5) (4) (4) (4) C (4) (5) (4) (3) (3) (3) O (4) (4) (3) (3) (3) (2) C (5) (5) (4) (4) (3) (3) N (4) (4) (4) (3) (3) (3) C (4) (4) (4) (3) (3) (3) N (4) (4) (4) (3) (3) (3) O (4) (4) (4) (3) (3) (3) O (4) (4) (4) (3) (3) (3) C (4) (5) (4) (3) (3) (3) Geometric parameters (Å, ) N1 C (12) C21 H21A (14) N1 C (13) C21 H21B (14) sup-3

8 N1 C (12) C21 H21C (15) C11 H11A (15) N3 C (12) C11 H11B (17) C4 C (13) C11 H11C (17) C4 N (13) C2 N (13) N4 O (11) C2 O (12) N4 O (11) O2 C (11) C5 H (14) C2 N1 C (8) H21A C21 H21B (11) C2 N1 C (8) O2 C21 H21C (8) C5 N1 C (8) H21A C21 H21C (12) N1 C11 H11A (8) H21B C21 H21C (11) N1 C11 H11B (9) C2 N3 C (8) H11A C11 H11B (13) C5 C4 N (9) N1 C11 H11C (10) C5 C4 N (9) H11A C11 H11C (13) N3 C4 N (8) H11B C11 H11C (13) O41 N4 O (9) N3 C2 O (8) O41 N4 C (8) N3 C2 N (8) O42 N4 C (8) O2 C2 N (8) C4 C5 N (8) C2 O2 C (7) C4 C5 H (9) O2 C21 H21A (8) N1 C5 H (9) O2 C21 H21B (8) C5 N1 C2 N (11) C2 N3 C4 N (8) C11 N1 C2 N (9) C5 C4 N4 O (9) C5 N1 C2 O (8) N3 C4 N4 O (13) C11 N1 C2 O (14) C5 C4 N4 O (14) N3 C2 O2 C (13) N3 C4 N4 O (8) N1 C2 O2 C (8) N3 C4 C5 N (11) O2 C2 N3 C (9) N4 C4 C5 N (9) N1 C2 N3 C (10) C2 N1 C5 C (10) C2 N3 C4 C (11) C11 N1 C5 C (9) Hydrogen-bond geometry (Å, ) D H A D H H A D A D H A C11 H11A O42 i (15) (15) (13) (11) C11 H11C O41 ii (17) (17) (13) (12) C5 H5 N3 ii (14) (14) (12) (11) C21 H21C O2 iii (15) (15) (13) (11) Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x, y+3/2, z+1/2; (iii) x+3, y+2, z+1. sup-4

9 Fig. 1 sup-5

10 Fig. 2 sup-6

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