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The imidazole and pyridine rings in the title compound, C9H8N4O4, are twisted with respect to one another, with a dihedral angle of 48.30 (4)°. The nitro group is almost coplanar with the imidazole plane. The crystal packing involves some weak C—H...N and C—H...O hydrogen bonds, of which the strongest, between the imidazole CH group and a nitro O atom [H...O 2.396 (15) Å], forms a centrosymmetric dimer.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807023884/rk2016sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807023884/rk2016Isup2.hkl
Contains datablock I

CCDC reference: 657731

Key indicators

  • Single-crystal X-ray study
  • T = 291 K
  • Mean [sigma](C-C) = 0.002 Å
  • R factor = 0.041
  • wR factor = 0.123
  • Data-to-parameter ratio = 16.6

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT480_ALERT_4_C Long H...A H-Bond Reported H14 .. N13 .. 2.75 Ang.
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

Almost identical crystal packing was observed in the crystal structure of 1-(4-methylphenyl)-2-methyl-4-nitroimidazole (Kowalski, 1995), which crystallizes in similar unit cell (8.259 (2) Å, 7.805 (2) Å, 16.774 (3) Å). Also, there are close analogies between the intermolecular contacts in these structures. Another similar unit cell was used to describe 1-phenyl-2-methyl-4-nitroimidazole (Kowalski, 1995). In this case, however, only the projection along b-direction might be compared to the former cases; the packing along other directions looks quite different. In this case there is less intermolecular contacts in the crystal structure. This comparison might be regarded as another argument in favour of the role played by C—H···O and C—H···N hydrogen bonds in the determination of the crystal packing.

Related literature top

This is a part of our studies of intermolecular interactions in 4-nitroimidazole derivatives that started with 1-phenyl-4-nitroimidazole (Kubicki et al., 2001, 2002). Similar packing schemes and unit-cell parameters were found in 1-phenyl- and 1-(p-methylphenyl)-2-methyl-4-nitroimidazole (Kowalski, 1995). For related literature, see: Suwiński & Szczepankiewicz (1991).

Experimental top

The title compound was synthesized by aromatic nucleophilic sybstitution ANRORC according to procedure described before (Suwiński & Szczepankiewicz, 1991).

Refinement top

Isotropic displacement parameters for hydrogen atoms were calculeted as 1.2 (1.4 for the methyl group) times the Ueq value of the appropriate carrier atom.

Structure description top

Almost identical crystal packing was observed in the crystal structure of 1-(4-methylphenyl)-2-methyl-4-nitroimidazole (Kowalski, 1995), which crystallizes in similar unit cell (8.259 (2) Å, 7.805 (2) Å, 16.774 (3) Å). Also, there are close analogies between the intermolecular contacts in these structures. Another similar unit cell was used to describe 1-phenyl-2-methyl-4-nitroimidazole (Kowalski, 1995). In this case, however, only the projection along b-direction might be compared to the former cases; the packing along other directions looks quite different. In this case there is less intermolecular contacts in the crystal structure. This comparison might be regarded as another argument in favour of the role played by C—H···O and C—H···N hydrogen bonds in the determination of the crystal packing.

This is a part of our studies of intermolecular interactions in 4-nitroimidazole derivatives that started with 1-phenyl-4-nitroimidazole (Kubicki et al., 2001, 2002). Similar packing schemes and unit-cell parameters were found in 1-phenyl- and 1-(p-methylphenyl)-2-methyl-4-nitroimidazole (Kowalski, 1995). For related literature, see: Suwiński & Szczepankiewicz (1991).

Computing details top

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 (Siemens ,1989); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. Anisotropic displacement ellipsoid representation (at the 50% probability level) of the molecule 1 (Siemens, 1989), together with numbering scheme. The hydrogen atoms are drawn as spheres with arbitrary radii.
[Figure 2] Fig. 2. The crystal packing as seen along [010] direction. Weak hydrogen bonds are depicted as dashed lines.
2-Methyl-4-nitro-1-(3-pyridyl)-1H-imidazole top
Crystal data top
C9H8N4O2F(000) = 424
Mr = 204.19Dx = 1.524 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3725 reflections
a = 8.1315 (12) Åθ = 3–23°
b = 7.3189 (10) ŵ = 0.11 mm1
c = 15.104 (3) ÅT = 291 K
β = 98.178 (14)°Prism, colourless
V = 889.8 (3) Å30.5 × 0.4 × 0.1 mm
Z = 4
Data collection top
KUMA KM4CCD four-circle
diffractometer
1892 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.018
Graphite monochromatorθmax = 29.6°, θmin = 5.1°
ω scanh = 911
5973 measured reflectionsk = 109
2311 independent reflectionsl = 1920
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.041H-atom parameters constrained
wR(F2) = 0.123 w = 1/[σ2(Fo2) + (0.0731P)2 + 0.1177P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2311 reflectionsΔρmax = 0.23 e Å3
139 parametersΔρmin = 0.19 e Å3
0 restraintsExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.049 (8)
Crystal data top
C9H8N4O2V = 889.8 (3) Å3
Mr = 204.19Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.1315 (12) ŵ = 0.11 mm1
b = 7.3189 (10) ÅT = 291 K
c = 15.104 (3) Å0.5 × 0.4 × 0.1 mm
β = 98.178 (14)°
Data collection top
KUMA KM4CCD four-circle
diffractometer
1892 reflections with I > 2σ(I)
5973 measured reflectionsRint = 0.018
2311 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.123H-atom parameters constrained
S = 1.06Δρmax = 0.23 e Å3
2311 reflectionsΔρmin = 0.19 e Å3
139 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
N10.63363 (11)0.17729 (13)0.85813 (6)0.0313 (2)
C110.64183 (13)0.15842 (14)0.76563 (7)0.0312 (2)
C120.50520 (15)0.10274 (17)0.70904 (8)0.0397 (3)
H120.40730.08120.73250.048*
N130.50567 (14)0.07805 (17)0.62254 (7)0.0483 (3)
C140.64606 (18)0.10848 (19)0.59085 (8)0.0476 (3)
H140.64770.09190.52990.057*
C150.78857 (17)0.16272 (19)0.64222 (9)0.0453 (3)
H150.88500.18210.61700.054*
C160.78730 (14)0.18828 (17)0.73201 (8)0.0387 (3)
H160.88270.22490.76910.046*
C20.51425 (13)0.26370 (16)0.89872 (7)0.0337 (3)
C210.37448 (16)0.3658 (2)0.85117 (8)0.0453 (3)
H21A0.34060.45850.88980.063*
H21B0.28340.28400.83340.063*
H21C0.40760.42210.79910.063*
N30.54348 (11)0.24577 (14)0.98488 (6)0.0372 (2)
C40.68361 (13)0.14672 (16)0.99900 (7)0.0344 (3)
N40.75007 (12)0.09068 (15)1.08599 (7)0.0416 (3)
O410.67792 (13)0.13436 (17)1.14800 (6)0.0582 (3)
O420.87520 (12)0.00099 (17)1.09452 (7)0.0598 (3)
C50.74372 (13)0.10265 (15)0.92353 (7)0.0343 (3)
H50.83900.03620.91760.041*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0286 (4)0.0398 (5)0.0251 (4)0.0019 (3)0.0023 (3)0.0022 (3)
C110.0336 (5)0.0343 (5)0.0262 (5)0.0004 (4)0.0059 (4)0.0009 (4)
C120.0362 (6)0.0530 (7)0.0300 (5)0.0047 (5)0.0052 (4)0.0034 (4)
N130.0498 (6)0.0659 (7)0.0289 (5)0.0043 (5)0.0042 (4)0.0064 (4)
C140.0597 (8)0.0559 (8)0.0290 (5)0.0035 (6)0.0131 (5)0.0010 (5)
C150.0469 (7)0.0521 (7)0.0413 (6)0.0014 (5)0.0213 (5)0.0034 (5)
C160.0354 (6)0.0428 (6)0.0390 (6)0.0026 (4)0.0091 (4)0.0004 (5)
C20.0300 (5)0.0433 (6)0.0277 (5)0.0026 (4)0.0036 (4)0.0024 (4)
C210.0394 (6)0.0584 (8)0.0369 (6)0.0146 (5)0.0013 (5)0.0004 (5)
N30.0331 (5)0.0508 (6)0.0274 (4)0.0040 (4)0.0037 (3)0.0019 (4)
C40.0302 (5)0.0449 (6)0.0270 (5)0.0005 (4)0.0001 (4)0.0013 (4)
N40.0352 (5)0.0567 (6)0.0308 (5)0.0026 (4)0.0021 (4)0.0058 (4)
O410.0555 (6)0.0917 (8)0.0270 (4)0.0024 (5)0.0043 (4)0.0054 (4)
O420.0460 (5)0.0805 (8)0.0496 (6)0.0150 (5)0.0043 (4)0.0147 (5)
C50.0299 (5)0.0407 (6)0.0314 (5)0.0021 (4)0.0008 (4)0.0000 (4)
Geometric parameters (Å, º) top
N1—C51.3505 (14)C16—H160.9300
N1—C21.3738 (13)C2—N31.2960 (14)
N1—C111.4149 (13)C2—C211.4608 (16)
C11—C121.3642 (16)C21—H21A0.9600
C11—C161.3696 (15)C21—H21B0.9600
C12—N131.3195 (15)C21—H21C0.9600
C12—H120.9300N3—C41.3418 (14)
N13—C141.3181 (18)C4—C51.3419 (15)
C14—C151.359 (2)C4—N41.4089 (14)
C14—H140.9300N4—O421.2102 (14)
C15—C161.3707 (17)N4—O411.2165 (14)
C15—H150.9300C5—H50.9300
C5—N1—C2107.26 (9)N3—C2—N1111.18 (10)
C5—N1—C11124.28 (9)N3—C2—C21124.35 (10)
C2—N1—C11128.40 (9)N1—C2—C21124.46 (10)
C12—C11—C16118.99 (10)C2—C21—H21A109.5
C12—C11—N1119.95 (10)C2—C21—H21B109.5
C16—C11—N1121.00 (10)H21A—C21—H21B109.5
N13—C12—C11122.99 (11)C2—C21—H21C109.5
N13—C12—H12118.5H21A—C21—H21C109.5
C11—C12—H12118.5H21B—C21—H21C109.5
C14—N13—C12117.46 (11)C2—N3—C4104.15 (9)
N13—C14—C15123.66 (11)N3—C4—C5113.49 (10)
N13—C14—H14118.2N3—C4—N4120.66 (10)
C15—C14—H14118.2C5—C4—N4125.77 (11)
C14—C15—C16118.62 (11)O42—N4—O41123.64 (11)
C14—C15—H15120.7O42—N4—C4117.76 (11)
C16—C15—H15120.7O41—N4—C4118.59 (11)
C11—C16—C15118.27 (11)C4—C5—N1103.91 (9)
C11—C16—H16120.9C4—C5—H5128.0
C15—C16—H16120.9N1—C5—H5128.0
C5—N1—C11—C12129.18 (12)C5—N1—C2—C21178.35 (12)
C2—N1—C11—C1247.68 (16)C11—N1—C2—C214.36 (19)
C5—N1—C11—C1648.21 (16)N1—C2—N3—C40.08 (13)
C2—N1—C11—C16134.93 (12)C21—C2—N3—C4178.71 (12)
C16—C11—C12—N130.83 (19)C2—N3—C4—C50.31 (14)
N1—C11—C12—N13178.27 (11)C2—N3—C4—N4176.59 (10)
C11—C12—N13—C140.3 (2)N3—C4—N4—O42178.79 (11)
C12—N13—C14—C150.2 (2)C5—C4—N4—O422.28 (19)
N13—C14—C15—C160.3 (2)N3—C4—N4—O410.16 (18)
C12—C11—C16—C150.74 (18)C5—C4—N4—O41176.67 (12)
N1—C11—C16—C15178.15 (11)N3—C4—C5—N10.57 (13)
C14—C15—C16—C110.23 (19)N4—C4—C5—N1176.15 (11)
C5—N1—C2—N30.44 (13)C2—N1—C5—C40.58 (12)
C11—N1—C2—N3176.85 (10)C11—N1—C5—C4176.84 (10)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C12—H12···O41i0.932.573.2872 (16)135
C14—H14···N13ii0.932.753.5557 (17)145
C15—H15···N3iii0.932.583.4342 (16)153
C5—H5···O42iv0.932.373.2358 (16)155
Symmetry codes: (i) x+1, y, z+2; (ii) x+1, y, z+1; (iii) x+1/2, y+1/2, z1/2; (iv) x+2, y, z+2.

Experimental details

Crystal data
Chemical formulaC9H8N4O2
Mr204.19
Crystal system, space groupMonoclinic, P21/n
Temperature (K)291
a, b, c (Å)8.1315 (12), 7.3189 (10), 15.104 (3)
β (°) 98.178 (14)
V3)889.8 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.5 × 0.4 × 0.1
Data collection
DiffractometerKUMA KM4CCD four-circle
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5973, 2311, 1892
Rint0.018
(sin θ/λ)max1)0.694
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.123, 1.06
No. of reflections2311
No. of parameters139
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.23, 0.19

Computer programs: CrysAlis CCD (Oxford Diffraction, 2002), CrysAlis CCD, CrysAlis RED (Oxford Diffraction, 2002), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), Stereochemical Workstation (Siemens ,1989), SHELXL97.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C12—H12···O41i0.932.573.2872 (16)134.7
C14—H14···N13ii0.932.753.5557 (17)144.8
C15—H15···N3iii0.932.583.4342 (16)153.1
C5—H5···O42iv0.932.373.2358 (16)154.6
Symmetry codes: (i) x+1, y, z+2; (ii) x+1, y, z+1; (iii) x+1/2, y+1/2, z1/2; (iv) x+2, y, z+2.
 

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