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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2359.
Published online 2010 August 21. doi:  10.1107/S1600536810032691
PMCID: PMC3007992

(E)-1-[(1,3-Dioxan-4-yl)meth­yl]-2-(nitro­methyl­idene)imidazolidine

Abstract

In the title compound, C9H15N3O4, the 1,3-dioxane ring displays a chair conformation and the five-membered ring is close to planar (r.m.s. deviation = 0.054 Å). An intra­molecular N—H(...)O hydrogen bond to one of the nitro-group O atoms generates an S(6) ring. In the crystal, inter­molecular N—H(...)O hydrogen bonds link the mol­ecules into C(6) chains propagating in [010] and a C—H(...)O link also occurs.

Related literature

For a related structure, see Tian et al. (2009 [triangle]). For background to neonicotinoid insecticides, see Mori et al. (2001 [triangle]); Ohno et al. (2009 [triangle]); Jeschke & Nauen (2008 [triangle]); Kagabu (1997 [triangle]); Tian et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2359-scheme1.jpg

Experimental

Crystal data

  • C9H15N3O4
  • M r = 229.24
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2359-efi1.jpg
  • a = 5.0138 (4) Å
  • b = 9.8092 (9) Å
  • c = 21.7162 (18) Å
  • V = 1068.03 (16) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 296 K
  • 0.42 × 0.26 × 0.16 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.954, T max = 0.982
  • 5866 measured reflections
  • 1933 independent reflections
  • 1395 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.054
  • wR(F 2) = 0.174
  • S = 1.10
  • 1933 reflections
  • 145 parameters
  • H-atom parameters constrained
  • Δρmax = 0.35 e Å−3
  • Δρmin = −0.28 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810032691/hb5607sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810032691/hb5607Isup2.hkl

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

Acknowledgments

The authors thank the National Natural Science Foundation of China (grant No. 20902037), the Opening Fund of Shanghai Key Laboratory of Chemical Biology (grant No. SKLCB-2008–08) and Doctoral Foundation of University of Jinan (B0542) for financial support.

supplementary crystallographic information

Comment

By virtue of novel modes of action (targeting insect nicotinic acetylcholine receptors (nAChRs) (Ohno et al., 2009), low mammalian toxicity, broad insecticidal spectra, and good systemic properties (Jeschke et al., 2008), neonicotinoids has accounted for 18% of world insecticide sales in the past decades. Our interest was introducing oxygen atoms into the lead struture and synthesizing a series of new compounds, in which the title compound exhibited moderate insecticidal activities against pea aphids.

The structure of the title compound is shown in Fig. 1 with the atom-numbering scheme. The 1,3-dioxane ring displays an chair conformation with bond angles lying between 110.0 (2)° and 111.7 (2)°. The nitro moiety is in trans configuration relative to the 1,3-dioxane ring and coplanar with the olefin-amine plane [N3—C2—C1—N1 = -177.49 (18)°]. Around N2 and N3 atoms the sums of the angles are 360° and 359.72°, respectively, indicating that they are typical sp2 hybridized and leading to an essentially planar imidazole ring.

Experimental

A solution of N-((1,3-dioxan-4-yl)methyl)ethane-1,2-diamine (2 mmol), and 1,1-bis(thiomethyl)-2-nitroethylene (2 mmol) in 30 ml of ethanol was refluxed for 8 h and then cooled to room temperature. Evaporation under reduced pressure gave the title product after purifiction by flash chromatography. Colourless prisms of (I) were obtained by slow evaporation of a solution of the title compound in dichloromethane and ethyl acetate.

Refinement

All H atoms were placed in their calculated positions and then refined using riding model with C—H = 0.93–0.99 Å, Uiso(H) = 1.2 (1.5 for methyl groups) times Ueq(C).

Figures

Fig. 1.
The molecular structure of (I) with displacement ellipsoids drawn at the 40% probability level. The H atoms are shown as spheres of arbitrary size.

Crystal data

C9H15N3O4F(000) = 488
Mr = 229.24Dx = 1.426 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2831 reflections
a = 5.0138 (4) Åθ = 3.5–28.7°
b = 9.8092 (9) ŵ = 0.11 mm1
c = 21.7162 (18) ÅT = 296 K
β = 90°Prism, colourless
V = 1068.03 (16) Å30.42 × 0.26 × 0.16 mm
Z = 4

Data collection

Bruker APEXII CCD diffractometer1933 independent reflections
Radiation source: fine-focus sealed tube1395 reflections with I > 2σ(I)
graphiteRint = 0.022
[var phi] and ω scansθmax = 25.4°, θmin = 3.5°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −6→6
Tmin = 0.954, Tmax = 0.982k = −11→11
5866 measured reflectionsl = −26→26

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)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.174H-atom parameters constrained
S = 1.10w = 1/[σ2(Fo2) + (0.1126P)2] where P = (Fo2 + 2Fc2)/3
1933 reflections(Δ/σ)max < 0.001
145 parametersΔρmax = 0.35 e Å3
0 restraintsΔρmin = −0.28 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
O20.7955 (3)0.71286 (16)0.23056 (8)0.0532 (5)
N10.7422 (4)0.58813 (19)0.22961 (9)0.0420 (5)
C20.3945 (4)0.6124 (2)0.30617 (10)0.0343 (5)
O30.2691 (4)0.39753 (16)0.44986 (7)0.0536 (5)
N20.4042 (4)0.74655 (19)0.31417 (9)0.0435 (5)
H20.50380.80030.29300.052*
C10.5501 (4)0.5344 (2)0.26581 (10)0.0390 (6)
H10.51960.44090.26380.047*
N30.2104 (4)0.55718 (19)0.34370 (8)0.0421 (5)
O10.8720 (4)0.51016 (18)0.19406 (9)0.0640 (6)
C50.1287 (5)0.4153 (2)0.34624 (11)0.0432 (6)
H5A0.15140.37530.30570.052*
H5B−0.05970.41150.35630.052*
C60.2786 (5)0.3314 (2)0.39185 (10)0.0406 (6)
H60.46530.32680.37870.049*
O40.2921 (5)0.1954 (2)0.50513 (9)0.0741 (7)
C70.1743 (5)0.1882 (2)0.39737 (11)0.0453 (6)
H7A0.21090.13870.35960.054*
H7B−0.01750.19040.40320.054*
C40.0734 (5)0.6627 (3)0.37948 (11)0.0474 (6)
H4B0.08350.64380.42330.057*
H4A−0.11250.66990.36750.057*
C30.2257 (5)0.7920 (2)0.36326 (11)0.0507 (7)
H3A0.10610.86290.34880.061*
H3B0.32550.82580.39840.061*
C90.4109 (7)0.3220 (3)0.49462 (13)0.0653 (8)
H9A0.59300.30860.48080.078*
H9B0.41630.37310.53280.078*
C80.3037 (7)0.1152 (3)0.45115 (13)0.0651 (8)
H8B0.21320.02930.45830.078*
H8A0.48850.09560.44130.078*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O20.0554 (11)0.0286 (10)0.0756 (13)−0.0030 (7)0.0114 (9)0.0037 (8)
N10.0450 (11)0.0278 (11)0.0533 (12)0.0051 (8)0.0010 (9)0.0052 (9)
C20.0377 (11)0.0255 (12)0.0397 (12)0.0020 (9)−0.0111 (9)0.0038 (9)
O30.0719 (11)0.0445 (11)0.0443 (10)−0.0009 (9)−0.0041 (8)−0.0026 (8)
N20.0474 (11)0.0262 (10)0.0569 (12)0.0006 (8)0.0004 (9)0.0001 (9)
C10.0458 (13)0.0261 (12)0.0451 (13)−0.0020 (9)−0.0025 (10)0.0019 (10)
N30.0524 (12)0.0317 (11)0.0423 (11)−0.0025 (8)0.0010 (9)0.0015 (8)
O10.0772 (13)0.0398 (11)0.0750 (13)0.0116 (9)0.0302 (10)0.0017 (10)
C50.0450 (13)0.0410 (14)0.0437 (13)−0.0091 (11)−0.0063 (10)0.0035 (10)
C60.0441 (12)0.0376 (13)0.0399 (12)−0.0056 (10)−0.0015 (9)0.0002 (10)
O40.1233 (19)0.0549 (12)0.0441 (10)−0.0022 (12)0.0030 (11)0.0089 (9)
C70.0536 (14)0.0350 (13)0.0471 (14)−0.0038 (10)0.0041 (11)−0.0019 (10)
C40.0462 (13)0.0482 (15)0.0477 (13)0.0052 (11)−0.0027 (10)−0.0031 (12)
C30.0677 (17)0.0349 (14)0.0494 (14)0.0088 (12)−0.0027 (12)−0.0024 (11)
C90.095 (2)0.0565 (18)0.0446 (15)0.0001 (15)−0.0174 (14)0.0038 (13)
C80.096 (2)0.0411 (16)0.0584 (17)0.0051 (15)0.0003 (15)0.0049 (13)

Geometric parameters (Å, °)

O2—N11.253 (2)C6—H60.9800
N1—C11.350 (3)C6—C71.504 (3)
N1—O11.267 (2)O4—C91.396 (4)
C2—N21.329 (3)O4—C81.413 (3)
C2—C11.401 (3)C7—H7A0.9700
C2—N31.345 (3)C7—H7B0.9700
O3—C61.418 (3)C7—C81.516 (4)
O3—C91.414 (3)C4—H4B0.9700
N2—H20.8600C4—H4A0.9700
N2—C31.462 (3)C4—C31.522 (4)
C1—H10.9300C3—H3A0.9700
N3—C51.452 (3)C3—H3B0.9700
N3—C41.465 (3)C9—H9A0.9700
C5—H5A0.9700C9—H9B0.9700
C5—H5B0.9700C8—H8B0.9700
C5—C61.491 (3)C8—H8A0.9700
O2—N1—C1121.61 (19)H5A—C5—H5B107.6
O2—N1—O1119.35 (19)C6—C5—H5A108.7
N1—C1—C2123.2 (2)C6—C5—H5B108.7
N1—C1—H1118.4C6—C7—H7A109.5
C2—N2—H2124.0C6—C7—H7B109.5
C2—N2—C3112.0 (2)C6—C7—C8110.7 (2)
C2—C1—H1118.4O4—C9—O3111.3 (2)
C2—N3—C5127.03 (19)O4—C9—H9A109.4
C2—N3—C4111.03 (19)O4—C9—H9B109.4
O3—C6—C5108.72 (19)O4—C8—C7111.0 (2)
O3—C6—H6108.2O4—C8—H8B109.4
O3—C6—C7110.17 (18)O4—C8—H8A109.4
O3—C9—H9A109.4C7—C6—H6108.2
O3—C9—H9B109.4C7—C8—H8B109.4
N2—C2—C1127.1 (2)C7—C8—H8A109.4
N2—C2—N3110.1 (2)H7A—C7—H7B108.1
N2—C3—C4102.82 (18)C4—C3—H3A111.2
N2—C3—H3A111.2C4—C3—H3B111.2
N2—C3—H3B111.2H4B—C4—H4A109.1
N3—C2—C1122.80 (19)C3—N2—H2124.0
N3—C5—H5A108.7C3—C4—H4B111.1
N3—C5—H5B108.7C3—C4—H4A111.1
N3—C5—C6114.35 (18)H3A—C3—H3B109.1
N3—C4—H4B111.1C9—O3—C6110.8 (2)
N3—C4—H4A111.1C9—O4—C8110.0 (2)
N3—C4—C3103.34 (19)H9A—C9—H9B108.0
O1—N1—C1119.04 (19)C8—C7—H7A109.5
C5—N3—C4121.66 (19)C8—C7—H7B109.5
C5—C6—H6108.2H8B—C8—H8A108.0
C5—C6—C7113.16 (18)
O2—N1—C1—C20.9 (3)N3—C5—C6—O352.3 (3)
C2—N2—C3—C4−7.0 (2)N3—C5—C6—C7175.06 (19)
C2—N3—C5—C692.4 (3)N3—C4—C3—N27.6 (2)
C2—N3—C4—C3−6.3 (2)O1—N1—C1—C2−179.4 (2)
O3—C6—C7—C8−49.0 (3)C5—N3—C4—C3179.39 (19)
N2—C2—C1—N11.8 (3)C5—C6—C7—C8−170.9 (2)
N2—C2—N3—C5176.06 (19)C6—O3—C9—O4−64.4 (3)
N2—C2—N3—C42.1 (2)C6—C7—C8—O449.6 (3)
C1—C2—N2—C3−176.0 (2)C4—N3—C5—C6−94.3 (3)
C1—C2—N3—C5−4.5 (3)C9—O3—C6—C5−179.5 (2)
C1—C2—N3—C4−178.49 (19)C9—O3—C6—C756.0 (3)
N3—C2—N2—C33.4 (2)C9—O4—C8—C7−56.4 (3)
N3—C2—C1—N1−177.49 (18)C8—O4—C9—O364.1 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···O20.862.172.694 (3)119
N2—H2···O1i0.862.172.824 (3)133
C1—H1···O2ii0.932.423.249 (3)148

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5607).

References

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  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
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  • Jeschke, P. & Nauen, R. (2008). Pest Manag. Sci.64, 1084–1098. [PubMed]
  • Kagabu, S. (1997). Rev. Toxicol.1, 75–129.
  • Mori, K., Okumoto, T., Kawahara, N. & Ozoe, Y. (2001). Pest. Manag. Sci.46, 40–46.
  • Ohno, I., Tomizawa, M., Durkin, K. A., Naruse, Y., Casida, J. E. & Kagabu, S. (2009). Chem. Res. Toxicol.22, 476–482. [PubMed]
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