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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2164.
Published online 2009 August 15. doi:  10.1107/S1600536809031894
PMCID: PMC2969872

3-Meth­oxy-4-[3-(2-methyl-4-nitro-1H-imidazol-1-yl)prop­oxy]benzaldehyde

Abstract

In the title mol­ecule, C15H17N3O5, the dihedral angle between the benzene and imidazole rings is 3.69 (2)°. The crystal structure is stabilized by weak inter­molecular C—H(...)O hydrogen bonds and π–π stacking inter­actions with a centroid–centroid distance of 3.614 (1) Å.

Related literature

For general background to the biological activity of nitro­imidazole and its derivatives, see:Demirayak et al. (1999 [triangle]); Huang et al. (2007 [triangle]); Olender et al. (2009 [triangle]). For the synthetic procedure, see: Khalafi-Nezhad et al. (2005 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2164-scheme1.jpg

Experimental

Crystal data

  • C15H17N3O5
  • M r = 319.32
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2164-efi1.jpg
  • a = 9.4885 (14) Å
  • b = 13.048 (2) Å
  • c = 12.745 (2) Å
  • β = 101.120 (3)°
  • V = 1548.3 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 173 K
  • 0.28 × 0.24 × 0.2 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.971, T max = 0.979
  • 7761 measured reflections
  • 3329 independent reflections
  • 2329 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.043
  • wR(F 2) = 0.130
  • S = 1.03
  • 3329 reflections
  • 210 parameters
  • H-atom parameters constrained
  • Δρmax = 0.27 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg & Putz, 1999 [triangle]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809031894/lh2876sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809031894/lh2876Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We thank Southwest University (SWUB2006018, XSGX0602 and SWUF2007023) and the Natural Science Foundation of Chongqing (2007BB5369) for financial support.

supplementary crystallographic information

Comment

Nitroimidazole and its derivatives possess several biological activities such as radiosensitizer, anti-tuberculosis and antimicrobial (Demirayak et al., 1999; Huang et al., 2007; Olender et al., 2009). In view of the therapeutic potentials of nitroimidazole derivatives, we are interested in the research and development of nitroimidazole compounds as drugs. Herein we report the crystal structure of the title compound (I).

The stucture of the title compound (I) is shown in Fig 1. In the molecule the dihedral angle between the benzene and imidazole rings is 3.69 (2)°. The crystal structure is stabilized by weak intermolecular C—H···O hydrogen bonds and significant π–π stacking interactions with a centroid to centroid ditance of 3.614 (1)Å between benzene and imidazole rings related by the symmetry operator (1/2-x, 1/2+y, 1/2-z).

Experimental

Compound (I) was synthesized according to the procedure of Khalafi-Nezhad et al. (2005). Single crystals used in X-ray diffraction studies were grown by slow evaporation at room temperature of solutions of (I) in ethyl acetate and dichlormethane mixtures.

Refinement

Hydrogen atoms were placed in calculated positions with C—H = 0.95Å (aromatic), 0.99Å (methylene) and 0.98Å (methyl) with Uiso(H) = 1.2Ueq(C) (aromatic and methylene C) or 1.5Ueq(C) (methyl C).

Figures

Fig. 1.
The molecular structure of (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C15H17N3O5F(000) = 672
Mr = 319.32Dx = 1.370 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3149 reflections
a = 9.4885 (14) Åθ = 2.3–26.9°
b = 13.048 (2) ŵ = 0.10 mm1
c = 12.745 (2) ÅT = 173 K
β = 101.120 (3)°Block, colorless
V = 1548.3 (4) Å30.28 × 0.24 × 0.2 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer3329 independent reflections
Radiation source: fine-focus sealed tube2329 reflections with I > 2σ(I)
graphiteRint = 0.022
[var phi] and ω scansθmax = 27.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −7→12
Tmin = 0.971, Tmax = 0.979k = −15→16
7761 measured reflectionsl = −13→16

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H-atom parameters constrained
S = 1.03w = 1/[σ2(Fo2) + (0.0623P)2 + 0.3992P] where P = (Fo2 + 2Fc2)/3
3329 reflections(Δ/σ)max < 0.001
210 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = −0.19 e Å3

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 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)

xyzUiso*/Ueq
C10.2645 (2)1.03088 (14)−0.03024 (16)0.0502 (5)
H10.23441.09010.00280.060*
C20.21471 (17)0.93177 (12)0.00141 (13)0.0363 (4)
C30.25719 (18)0.84045 (12)−0.04102 (14)0.0381 (4)
H30.31930.8421−0.09120.046*
C40.3482 (2)0.65169 (17)−0.1102 (2)0.0691 (7)
H4A0.31070.6882−0.17690.104*
H4B0.36810.5803−0.12620.104*
H4C0.43700.6847−0.07370.104*
C50.20870 (17)0.74857 (12)−0.00975 (13)0.0346 (4)
C60.11391 (16)0.74686 (11)0.06315 (12)0.0305 (3)
C70.07388 (17)0.83703 (11)0.10519 (13)0.0322 (4)
H70.01140.83590.15510.039*
C80.12529 (17)0.92983 (12)0.07433 (13)0.0347 (4)
H80.09850.99210.10380.042*
C9−0.01627 (18)0.64126 (12)0.16566 (14)0.0360 (4)
H9A−0.10900.67750.14400.043*
H9B0.03440.66990.23460.043*
C10−0.04042 (17)0.52728 (12)0.17563 (14)0.0378 (4)
H10A−0.11070.51520.22250.045*
H10B−0.08000.49810.10430.045*
C110.0990 (2)0.47573 (13)0.2218 (2)0.0616 (6)
H11A0.17210.49660.18020.074*
H11B0.13160.49990.29620.074*
C120.16148 (17)0.29675 (13)0.16772 (13)0.0384 (4)
C130.2589 (2)0.33135 (16)0.09670 (16)0.0560 (5)
H13A0.29360.27170.06240.084*
H13B0.34070.36800.13900.084*
H13C0.20660.37720.04170.084*
C140.01304 (17)0.30668 (12)0.28026 (15)0.0403 (4)
H14−0.04750.33040.32640.048*
C150.04200 (16)0.20834 (11)0.25747 (13)0.0326 (4)
N10.09014 (14)0.36345 (10)0.22222 (12)0.0417 (4)
N20.13429 (14)0.20076 (10)0.18821 (11)0.0346 (3)
N3−0.01634 (15)0.11998 (11)0.29957 (12)0.0404 (4)
O10.34061 (19)1.04390 (12)−0.09476 (13)0.0758 (5)
O20.24432 (13)0.65445 (9)−0.04271 (11)0.0493 (4)
O30.06945 (12)0.65190 (8)0.08547 (10)0.0376 (3)
O40.02197 (15)0.03485 (9)0.27613 (12)0.0544 (4)
O5−0.10418 (15)0.13411 (11)0.35800 (12)0.0611 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0631 (12)0.0379 (10)0.0515 (11)−0.0115 (8)0.0156 (10)0.0021 (8)
C20.0422 (9)0.0306 (8)0.0360 (9)−0.0055 (7)0.0074 (7)0.0004 (7)
C30.0385 (9)0.0378 (9)0.0404 (9)−0.0086 (7)0.0139 (7)−0.0058 (7)
C40.0556 (12)0.0577 (13)0.1071 (19)−0.0074 (10)0.0486 (13)−0.0360 (13)
C50.0327 (8)0.0294 (8)0.0427 (9)−0.0027 (6)0.0097 (7)−0.0106 (7)
C60.0306 (8)0.0248 (7)0.0355 (8)−0.0027 (6)0.0046 (6)−0.0010 (6)
C70.0370 (8)0.0285 (8)0.0327 (8)0.0011 (6)0.0106 (7)−0.0008 (6)
C80.0420 (9)0.0249 (8)0.0365 (9)0.0012 (6)0.0057 (7)−0.0022 (6)
C90.0391 (9)0.0279 (8)0.0435 (9)−0.0007 (7)0.0140 (7)0.0017 (7)
C100.0375 (9)0.0284 (8)0.0483 (10)−0.0015 (7)0.0106 (7)0.0036 (7)
C110.0487 (11)0.0249 (9)0.0984 (17)−0.0025 (8)−0.0175 (11)0.0050 (9)
C120.0367 (8)0.0364 (9)0.0391 (9)−0.0067 (7)−0.0004 (7)0.0046 (7)
C130.0567 (12)0.0595 (12)0.0517 (12)−0.0214 (10)0.0102 (10)0.0122 (10)
C140.0356 (8)0.0316 (9)0.0529 (11)0.0045 (7)0.0065 (8)−0.0035 (8)
C150.0321 (8)0.0273 (8)0.0384 (9)0.0018 (6)0.0068 (7)0.0007 (6)
N10.0360 (8)0.0254 (7)0.0597 (10)−0.0008 (6)−0.0008 (7)0.0048 (6)
N20.0368 (7)0.0309 (7)0.0370 (7)−0.0023 (6)0.0092 (6)0.0003 (6)
N30.0445 (8)0.0319 (7)0.0494 (9)0.0022 (6)0.0202 (7)0.0034 (6)
O10.1041 (12)0.0577 (9)0.0781 (11)−0.0285 (9)0.0487 (10)0.0027 (8)
O20.0480 (7)0.0329 (7)0.0749 (9)−0.0048 (5)0.0318 (7)−0.0182 (6)
O30.0431 (6)0.0236 (6)0.0494 (7)−0.0037 (5)0.0176 (5)−0.0026 (5)
O40.0732 (9)0.0259 (6)0.0739 (9)0.0032 (6)0.0383 (7)0.0049 (6)
O50.0638 (9)0.0543 (8)0.0784 (10)0.0023 (7)0.0471 (8)0.0018 (7)

Geometric parameters (Å, °)

C1—O11.207 (2)C9—H9B0.9900
C1—C21.460 (2)C10—C111.499 (2)
C1—H10.9500C10—H10A0.9900
C2—C81.374 (2)C10—H10B0.9900
C2—C31.400 (2)C11—N11.468 (2)
C3—C51.371 (2)C11—H11A0.9900
C3—H30.9500C11—H11B0.9900
C4—O21.428 (2)C12—N21.315 (2)
C4—H4A0.9800C12—N11.371 (2)
C4—H4B0.9800C12—C131.483 (2)
C4—H4C0.9800C13—H13A0.9800
C5—O21.3615 (18)C13—H13B0.9800
C5—C61.412 (2)C13—H13C0.9800
C6—O31.3567 (18)C14—C151.355 (2)
C6—C71.376 (2)C14—N11.356 (2)
C7—C81.390 (2)C14—H140.9500
C7—H70.9500C15—N21.362 (2)
C8—H80.9500C15—N31.428 (2)
C9—O31.4304 (19)N3—O41.2235 (17)
C9—C101.514 (2)N3—O51.2339 (18)
C9—H9A0.9900
O1—C1—C2125.53 (19)C9—C10—H10A109.7
O1—C1—H1117.2C11—C10—H10B109.7
C2—C1—H1117.2C9—C10—H10B109.7
C8—C2—C3120.47 (14)H10A—C10—H10B108.2
C8—C2—C1118.55 (15)N1—C11—C10113.74 (14)
C3—C2—C1120.98 (16)N1—C11—H11A108.8
C5—C3—C2119.63 (15)C10—C11—H11A108.8
C5—C3—H3120.2N1—C11—H11B108.8
C2—C3—H3120.2C10—C11—H11B108.8
O2—C4—H4A109.5H11A—C11—H11B107.7
O2—C4—H4B109.5N2—C12—N1111.65 (15)
H4A—C4—H4B109.5N2—C12—C13125.48 (17)
O2—C4—H4C109.5N1—C12—C13122.86 (16)
H4A—C4—H4C109.5C12—C13—H13A109.5
H4B—C4—H4C109.5C12—C13—H13B109.5
O2—C5—C3125.59 (15)H13A—C13—H13B109.5
O2—C5—C6114.59 (14)C12—C13—H13C109.5
C3—C5—C6119.82 (14)H13A—C13—H13C109.5
O3—C6—C7125.37 (14)H13B—C13—H13C109.5
O3—C6—C5114.55 (13)C15—C14—N1104.31 (15)
C7—C6—C5120.08 (14)C15—C14—H14127.8
C6—C7—C8119.74 (14)N1—C14—H14127.8
C6—C7—H7120.1C14—C15—N2112.96 (14)
C8—C7—H7120.1C14—C15—N3125.07 (15)
C2—C8—C7120.23 (14)N2—C15—N3121.97 (13)
C2—C8—H8119.9C14—N1—C12107.49 (13)
C7—C8—H8119.9C14—N1—C11125.74 (17)
O3—C9—C10105.75 (12)C12—N1—C11126.73 (16)
O3—C9—H9A110.6C12—N2—C15103.59 (13)
C10—C9—H9A110.6O4—N3—O5123.37 (14)
O3—C9—H9B110.6O4—N3—C15119.10 (13)
C10—C9—H9B110.6O5—N3—C15117.52 (13)
H9A—C9—H9B108.7C5—O2—C4116.73 (14)
C11—C10—C9109.72 (14)C6—O3—C9118.76 (12)
C11—C10—H10A109.7

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C4—H4B···O4i0.982.583.415 (3)144
C8—H8···O4ii0.952.513.229 (2)133
C10—H10B···O2iii0.992.563.312 (2)133
C10—H10A···O1iv0.992.583.461 (2)148
C14—H14···O1iv0.952.293.166 (2)153

Symmetry codes: (i) x+1/2, −y+1/2, z−1/2; (ii) x, y+1, z; (iii) −x, −y+1, −z; (iv) x−1/2, −y+3/2, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2876).

References

  • Brandenburg, K. & Putz, H. (1999). DIADMOND. Crystal Impact GbR, Bonn, Germany.
  • Bruker (2000). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Demirayak, S., Karaburun, A. C. & Kiraz, N. (1999). Eur. J. Med. Chem.34, 275–278.
  • Huang, J. & Zhou, C. H. (2007). Chin. Clin. J. Tradit. Chin. West. Med.7, 538–542.
  • Khalafi-Nezhad, A., Soltani Rad, M. N., Mohabatkar, H., Asrari, Z. & Hemmateenejad, B. (2005). Bioorg. Med. Chem.13, 1931–1938. [PubMed]
  • Olender, D., Zwawiak, J., Lukianchuk, V., Lesyk, R., Kropacz, A., Fojutowski, A. & Zaprutko, L. (2009). Eur J Med Chem 44, 645–652. [PubMed]
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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