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Acta Crystallogr Sect E Struct Rep Online. 2008 June 1; 64(Pt 6): o1154.
Published online 2008 May 24. doi:  10.1107/S160053680801492X
PMCID: PMC2961447

3-[(E)-3,7-Dimethyl­octa-2,6-dien­yl]-5-methyl-N-nitro-1,3,5-oxadiazinan-4-imine

Abstract

The title compound, C14H24N4O3, was synthesized by the reaction of geranyl and 3-methyl-4-nitro­imino-1,3,5-oxadiazinane. In the crystal structure, mol­ecules are assembled by weak inter­molecular C—H(...)O hydrogen bonds. The nitryl and the long carbon chain are located on the same side of the C=N bond due to the two weak intra­molecular C—H(...)N hydrogen bonds; the configuration of the oxadiazinane is Z.

Related literature

For background literature, see: Bowers et al. (1972 [triangle]). For related literature, see: Yang et al. (2004 [triangle]); Van Oosten et al. (1990 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o1154-scheme1.jpg

Experimental

Crystal data

  • C14H24N4O3
  • M r = 296.37
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1154-efi5.jpg
  • a = 7.9318 (16) Å
  • b = 6.6423 (13) Å
  • c = 31.191 (7) Å
  • β = 99.55 (3)°
  • V = 1620.5 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 293 (2) K
  • 0.60 × 0.30 × 0.08 mm

Data collection

  • Rigaku R-AXIS RAPID IP diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 [triangle]) T min = 0.943, T max = 0.993
  • 7692 measured reflections
  • 2825 independent reflections
  • 1306 reflections with I > 2σ(I)
  • R int = 0.0508

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.152
  • S = 0.84
  • 2825 reflections
  • 194 parameters
  • H-atom parameters constrained
  • Δρmax = 0.28 e Å−3
  • Δρmin = −0.30 e Å−3

Data collection: RAPID-AUTO (Rigaku, 2000 [triangle]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2000 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680801492X/rk2083sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680801492X/rk2083Isup2.hkl

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

Acknowledgments

This work was supported by the National Basic Research Program of China (grant No. 2003CB 114400), the National High Technology Research and Development Program of China (grant No. 2006 A A10A209) and the ‘11th Five-Year Plan’ Scientific and Technological Support Project on Pesticide Development Engineering (grant No. 2006BAE01A01). The authors acknowledge Shi-Wei Zhang for carrying out the X-ray diffraction at the College of Chemistry and Molecular Engineering, Peking University, Beijing, People’s Republic of China.

supplementary crystallographic information

Comment

E-b-farnesene (EBF), the primary component of aphides alarm pheromone, not only stimulate the movement of aphid (Bowers et al., 1972), but also possess the acute activity to many economically aphid species at a dose of 100 ng/aphid (Van Oosten et al., 1990). However, EBF is limited in field application due to its high volatility, readily air oxidation and degradation under field conditions. In order to improve its chemical stability and biological efficacy, the pharmacophore of neonicotinoids was introduced to substitute the conjugated double bond of EBF (Yang et al., 2004). The title compound (I), in which 3-methyl-5-(E)-3,7-dimethylocta-2,6-dienyl connect to N-nitro-1,3,5-oxadiazinan-4-imine instead of the conjugated double bond, was synthesized as EBF analogue with potent insecticidal activity. To study the further structure-activity relationship, we reported here its molecular and crystal structure. The molecular structure showed Z-isomer by the interaction forces of weak intramolecular C5–H5b···N1 and C5–H5b···N2 hydrogen bonds (Fig. 1). The compound was assembled by four weak intermolecular hydrogen bonds (Fig. 2 and Table 1).

Experimental

To a solution of 3-methyl-N-nitro-1,3,5-oxadiazinan-4-imine (1.60 g, 10.0 mmol) dissolved in anhydrous acetonitrile (15 ml), geranyl (1.89 g, 10.1 mmol) was added. Then the reaction solution was slowly heated to reflux for 7h. After removing the solvent, the residue was purified by column chromatography on silica gel (200-300 mesh) with petroleum ether/ethylacetate (2.5:1v/v) as eluent to obtain the title compound I. Then, 50 mg I was dissolved in 20 ml me thanol. The solution was kept at room temperature for 20 d by natural evaporation to give colorless single crystals of I, suitable for X-Ray analysis.

1H NMR (CDCl3, 300 MHz) 1.60 (s, 3H, CH3–C═C), 1.68 [s, 6H, (CH3)2C═C], 2.07~2.10 (t, J = 5.27 Hz, 4H, -CH2–CH2-), 3.05 (s, 3H, N–CH3), 4.11 (d, J = 7.26, 2H,-CH2–N), 4.09 (s, 2H, N–CH2–O), 4.12 (s, 2H, O–CH2–N), 5.03~5.18 (m, 2H, 2CH═C); Calc. for C14H24N4O3: C 56.74, H 8.16, N 18.90; found C 56.69, H 8.19, N 18.80.

Refinement

The H atoms were fixed geometrically and allowed to ride on their parent atoms, with C–H = 0.93-0.97 Å, and with Uiso(H) = 1.2Ueq for (Caromatic and Cmethylene) or Uiso(H) = 1.5Ueq(Cmethyl). The intensities of equivalent reflections were merged (Rint = 0.000).

Figures

Fig. 1.
The molecular structure of I with the atom numbering scheme. The displacement ellipsoids are drawn at 50% probability level. H atoms are presented as a small spheres of arbitrary radius. Intramolecular hydrogen bonds are shown as dashed lines.
Fig. 2.
The crystal packing of I. Hydrogen bonds are shown as dashed lines. Symmetry codes: (i) x, y-1, z; (ii) -x-1, y-1/2, -z+3/2; (iii) -x, y-1/2, -z+3/2; (iv) x+1, y, z.

Crystal data

C14H24N4O3F000 = 640
Mr = 296.37Dx = 1.215 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 7693 reflections
a = 7.9318 (16) Åθ = 2.6–25.0º
b = 6.6423 (13) ŵ = 0.09 mm1
c = 31.191 (7) ÅT = 293 (2) K
β = 99.55 (3)ºBlock, colourless
V = 1620.5 (6) Å30.60 × 0.30 × 0.08 mm
Z = 4

Data collection

Rigaku R-AXIS RAPID IP diffractometer2825 independent reflections
Radiation source: Fine-focus sealed tube1306 reflections with I > 2σ(I)
Monochromator: GraphiteRint = 0.051
Detector resolution: 10.00 pixels mm-1θmax = 25.0º
T = 293(2) Kθmin = 1.3º
ω scansh = 0→9
Absorption correction: multi-scan(ABSCOR; Higashi, 1995)k = −7→0
Tmin = 0.943, Tmax = 0.993l = −37→35
2825 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.153  w = 1/[σ2(Fo2) + (0.0843P)2] where P = (Fo2 + 2Fc2)/3
S = 0.84(Δ/σ)max = 0.014
2825 reflectionsΔρmax = 0.28 e Å3
194 parametersΔρmin = −0.30 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: None

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
O1−0.0768 (3)0.9179 (3)0.82543 (8)0.0604 (7)
O2−0.2995 (3)1.0170 (4)0.85187 (8)0.0670 (7)
O3−0.1951 (2)0.2689 (3)0.74730 (7)0.0512 (6)
N1−0.2308 (3)0.9002 (4)0.82899 (8)0.0459 (7)
N2−0.3292 (3)0.7617 (4)0.80698 (8)0.0453 (7)
N3−0.1290 (3)0.4939 (4)0.80512 (8)0.0414 (6)
N4−0.3001 (3)0.6021 (4)0.74324 (8)0.0392 (6)
C1−0.2455 (3)0.6227 (4)0.78538 (9)0.0362 (7)
C2−0.0594 (4)0.3511 (5)0.77744 (10)0.0472 (8)
H2a0.02120.41830.76210.057*
H2b0.00040.24450.79500.057*
C3−0.2672 (4)0.4183 (5)0.71928 (10)0.0501 (9)
H3a−0.37390.36990.70270.060*
H3b−0.19070.45020.69900.060*
C4−0.4042 (4)0.7564 (5)0.71773 (10)0.0560 (9)
H4a−0.38820.74820.68790.084*
H4b−0.37000.88710.72910.084*
H4c−0.52250.73480.71950.084*
C5−0.0734 (3)0.4762 (5)0.85230 (9)0.0439 (8)
H5a−0.10160.34330.86190.053*
H5b−0.13320.57470.86720.053*
C60.1153 (4)0.5098 (5)0.86376 (10)0.0474 (8)
H60.15670.62750.85320.057*
C70.2293 (4)0.3932 (5)0.88694 (10)0.0499 (8)
C80.4169 (4)0.4518 (6)0.89472 (10)0.0608 (10)
H8a0.48350.34030.88640.073*
H8b0.43280.56540.87630.073*
C90.4840 (4)0.5072 (7)0.94162 (11)0.0740 (11)
H9a0.42400.62540.94940.089*
H9b0.46150.39760.96040.089*
C100.6736 (4)0.5496 (6)0.94863 (11)0.0624 (10)
H100.74440.43830.94830.075*
C110.7505 (4)0.7241 (6)0.95516 (10)0.0597 (9)
C120.9427 (5)0.7390 (6)0.96099 (13)0.0838 (13)
H12a0.97420.84050.94190.126*
H12b0.98920.61170.95420.126*
H12c0.98700.77440.99060.126*
C130.6634 (6)0.9221 (6)0.95783 (15)0.0974 (14)
H13a0.70910.98700.98480.146*
H13b0.54300.90070.95650.146*
H13c0.68241.00580.93400.146*
C140.1868 (5)0.2002 (6)0.90720 (13)0.0861 (14)
H14a0.26560.09750.90160.129*
H14b0.07250.16050.89500.129*
H14c0.19500.21830.93800.129*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0374 (12)0.0485 (14)0.0951 (18)−0.0067 (11)0.0103 (12)−0.0033 (13)
O20.0714 (16)0.0645 (16)0.0645 (15)0.0175 (13)0.0094 (12)−0.0191 (13)
O30.0433 (12)0.0422 (12)0.0677 (14)−0.0059 (11)0.0082 (11)−0.0098 (12)
N10.0461 (17)0.0434 (16)0.0465 (16)0.0077 (14)0.0025 (13)0.0017 (14)
N20.0296 (13)0.0510 (16)0.0534 (16)0.0058 (13)0.0011 (12)−0.0096 (14)
N30.0336 (13)0.0400 (14)0.0478 (15)0.0059 (12)−0.0012 (11)−0.0038 (13)
N40.0296 (12)0.0432 (15)0.0435 (15)−0.0001 (11)0.0027 (11)−0.0017 (13)
C10.0183 (14)0.0412 (18)0.0479 (19)−0.0034 (13)0.0021 (13)0.0002 (15)
C20.0379 (18)0.0395 (18)0.062 (2)0.0052 (15)0.0016 (15)−0.0042 (17)
C30.0330 (17)0.061 (2)0.056 (2)−0.0053 (16)0.0070 (15)−0.0113 (19)
C40.0399 (17)0.074 (2)0.0498 (19)0.0089 (18)−0.0048 (15)0.0077 (18)
C50.0368 (16)0.0465 (19)0.0465 (18)−0.0003 (15)0.0014 (14)0.0047 (16)
C60.0393 (17)0.0513 (19)0.0485 (18)−0.0036 (16)−0.0022 (14)0.0069 (17)
C70.0458 (18)0.056 (2)0.0440 (18)0.0006 (17)−0.0053 (14)−0.0021 (17)
C80.0424 (18)0.082 (3)0.053 (2)0.0028 (18)−0.0071 (16)0.0019 (19)
C90.053 (2)0.108 (3)0.056 (2)−0.015 (2)−0.0043 (17)−0.010 (2)
C100.046 (2)0.072 (3)0.065 (2)−0.0023 (19)−0.0049 (17)−0.008 (2)
C110.057 (2)0.066 (3)0.053 (2)0.000 (2)−0.0002 (17)−0.0038 (19)
C120.059 (2)0.097 (3)0.091 (3)−0.022 (2)0.002 (2)−0.011 (3)
C130.100 (3)0.084 (3)0.105 (4)0.010 (3)0.008 (3)−0.007 (3)
C140.078 (3)0.067 (3)0.097 (3)−0.005 (2)−0.032 (2)0.027 (2)

Geometric parameters (Å, °)

O1—N11.251 (3)C6—H60.9300
O2—N11.240 (3)C7—C141.493 (5)
O3—C31.382 (3)C7—C81.518 (4)
O3—C21.416 (3)C8—C91.517 (4)
N1—N21.323 (3)C8—H8a0.9700
N2—C11.376 (3)C8—H8b0.9700
N3—C11.333 (3)C9—C101.510 (4)
N3—C21.452 (4)C9—H9a0.9700
N3—C51.469 (4)C9—H9b0.9700
N4—C11.321 (3)C10—C111.310 (5)
N4—C41.465 (4)C10—H100.9300
N4—C31.477 (4)C11—C131.494 (5)
C2—H2a0.9700C11—C121.508 (5)
C2—H2b0.9700C12—H12a0.9600
C3—H3a0.9700C12—H12b0.9600
C3—H3b0.9700C12—H12c0.9600
C4—H4a0.9600C13—H13a0.9600
C4—H4b0.9600C13—H13b0.9600
C4—H4c0.9600C13—H13c0.9600
C5—C61.496 (4)C14—H14a0.9600
C5—H5a0.9700C14—H14b0.9600
C5—H5b0.9700C14—H14c0.9600
C6—C71.313 (4)
C3—O3—C2109.4 (2)C5—C6—H6116.1
O2—N1—O1121.4 (3)C6—C7—C14123.8 (3)
O2—N1—N2117.2 (3)C6—C7—C8120.3 (3)
O1—N1—N2121.3 (3)C14—C7—C8115.9 (3)
N1—N2—C1115.5 (2)C9—C8—C7113.2 (3)
C1—N3—C2116.6 (2)C9—C8—H8a108.9
C1—N3—C5125.7 (2)C7—C8—H8a108.9
C2—N3—C5117.6 (2)C9—C8—H8b108.9
C1—N4—C4122.0 (2)C7—C8—H8b108.9
C1—N4—C3122.2 (2)H8a—C8—H8b107.8
C4—N4—C3115.7 (2)C10—C9—C8111.5 (3)
N4—C1—N3118.7 (3)C10—C9—H9a109.3
N4—C1—N2116.8 (2)C8—C9—H9a109.3
N3—C1—N2123.9 (3)C10—C9—H9b109.3
O3—C2—N3108.9 (2)C8—C9—H9b109.3
O3—C2—H2a109.9H9a—C9—H9b108.0
N3—C2—H2a109.9C11—C10—C9127.9 (4)
O3—C2—H2b109.9C11—C10—H10116.0
N3—C2—H2b109.9C9—C10—H10116.0
H2a—C2—H2b108.3C10—C11—C13125.4 (3)
O3—C3—N4111.3 (2)C10—C11—C12120.8 (3)
O3—C3—H3a109.4C13—C11—C12113.7 (3)
N4—C3—H3a109.4C11—C12—H12a109.5
O3—C3—H3b109.4C11—C12—H12b109.5
N4—C3—H3b109.4H12a—C12—H12b109.5
H3a—C3—H3b108.0C11—C12—H12c109.5
N4—C4—H4a109.5H12a—C12—H12c109.5
N4—C4—H4b109.5H12b—C12—H12c109.5
H4a—C4—H4b109.5C11—C13—H13a109.5
N4—C4—H4c109.5C11—C13—H13b109.5
H4a—C4—H4c109.5H13a—C13—H13b109.5
H4b—C4—H4c109.5C11—C13—H13c109.5
N3—C5—C6110.5 (2)H13a—C13—H13c109.5
N3—C5—H5a109.6H13b—C13—H13c109.5
C6—C5—H5a109.6C7—C14—H14a109.5
N3—C5—H5b109.6C7—C14—H14b109.5
C6—C5—H5b109.6H14a—C14—H14b109.5
H5a—C5—H5b108.1C7—C14—H14c109.5
C7—C6—C5127.9 (3)H14a—C14—H14c109.5
C7—C6—H6116.1H14b—C14—H14c109.5

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C2—H2B···O1i0.972.483.257 (4)136
C3—H3A···N2ii0.972.433.336 (4)155
C3—H3B···O1iii0.972.383.264 (4)151
C5—H5B···N10.972.533.117 (4)119
C5—H5B···N20.972.552.960 (4)105
C13—H13C···O2iv0.962.593.425 (5)145

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RK2083).

References

  • Bowers, W. S., Nault, L. R., Webb, R. E. & Dutky, S. R. (1972). Science, 177, 1121–1122. [PubMed]
  • Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
  • Rigaku (2000). RAPID-AUTO Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC (2000). CrystalStructure Rigaku/MSC, The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Van Oosten, A. M., Gut, J., Harrewijn, P. & Piron, P. G. M. (1990). Acta Phytopathol. Entomol. Hung.25, 331–342.
  • Yang, X. L., Huang, W. Y., Ling, Y., Kan, W., Fang, Y. L. & Zhang, Z. N. (2004). Chem. J. Chin. Univ.25, 1657–1661.

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