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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2416.
Published online 2010 August 28. doi:  10.1107/S1600536810033829
PMCID: PMC3008034

1-[(1,3-Dithio­lan-2-yl)meth­yl]-8-nitro-6-propyl-1,2,3,5,6,7-hexa­hydro­imidazo[1,2-c]pyrimidine

Abstract

In the title compound, C13H22N4O2S2, the six-membered ring displays a half-chair conformation. The olefin amine unit is close to being coplanar with the imidazolidine ring (r.m.s. deviation = 0.059 Å). The dithiol­ane ring adopts a twisted conformation. In the crystal, mol­ecules are linked by weak C—H(...)O inter­actions.

Related literature

For related structures, see Tian et al. (2010 [triangle]); Li et al. (2010 [triangle]). For background to neonicotinoid insecticides, see Mori et al. (2001 [triangle]); Ohno et al. (2009 [triangle]); Jeschke et al. (2008 [triangle]); Kagabu (1997 [triangle]); Tian et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2416-scheme1.jpg

Experimental

Crystal data

  • C13H22N4O2S2
  • M r = 330.47
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2416-efi1.jpg
  • a = 11.9680 (3) Å
  • b = 13.6304 (3) Å
  • c = 10.8866 (3) Å
  • β = 115.465 (3)°
  • V = 1603.38 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.34 mm−1
  • T = 293 K
  • 0.45 × 0.41 × 0.26 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.917, T max = 1.0
  • 13404 measured reflections
  • 3256 independent reflections
  • 2486 reflections with I > 2σ(I)
  • R int = 0.024

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.096
  • S = 1.04
  • 3256 reflections
  • 191 parameters
  • H-atom parameters constrained
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.16 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/S1600536810033829/hb5612sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810033829/hb5612Isup2.hkl

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

Acknowledgments

The authors thank the National Natural Science Foundation of China (grant 20902037) and the Doctoral Foundation of University of Jinan (B0542) for financial support.

supplementary crystallographic information

Comment

Neonicotinoid inseticides have become an important chemical class of insecticides (Ohno et al., 2009 and Jeschke et al., 2008). We have synthesized a series of new compounds by introducing sulfur atoms into the lead struture to improve the lipid solubility of neonicotinoids insecticides. 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 title compound is homolog of 1-[(1,3-Dithiolan-2-yl)methyl]-6-methyl- 8-nitro-1,2,3,5,6,7-hexahydroimidazo- [1,2-c]pyrimidine (Tian et al., 2010). The six-membered ring displays an half-chair conformation. The olefin-amine moity is close to being coplanar with imidazolidine ring. The dithiolane is in a twisted conformation [C9—C10—S1 = 110.31 (13)° and C9—S2—C8 = 94.61 (8)°]. The packing of the molecules is mainly stabilized by C—H···O interactions (Table 1).

Experimental

A mixture of 1-((1,3-dithiolan-2-yl)methyl)-2-(nitromethylene)imidazolidine (0.75 mmol), formaldehyde (1.6 mmol, in the form of 35% aqueous solution), and propylamine (0.83 mmol) in ethanol (5 ml) was stirred overnight. The solution thus obtained was concentrated under vacuum and further purified by flash chromatography to give the desired product. Colourless prisms of (I) were obtained by slow evaporation of a solution of dichloromethane and ethyl acetate of the title compound.

Refinement

All H atoms were placed in their calculated positions and then refined using riding model with C—H = 0.96–0.98 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 30% probability level. The H atoms are shown as spheres of arbitrary size.

Crystal data

C13H22N4O2S2F(000) = 704
Mr = 330.47Dx = 1.369 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.7107 Å
Hall symbol: -P 2ybcCell parameters from 7164 reflections
a = 11.9680 (3) Åθ = 3.3–28.9°
b = 13.6304 (3) ŵ = 0.34 mm1
c = 10.8866 (3) ÅT = 293 K
β = 115.465 (3)°Prism, colourless
V = 1603.38 (8) Å30.45 × 0.41 × 0.26 mm
Z = 4

Data collection

Bruker APEXII CCD diffractometer3256 independent reflections
Radiation source: fine-focus sealed tube2486 reflections with I > 2σ(I)
graphiteRint = 0.024
Detector resolution: 16.0355 pixels mm-1θmax = 26.4°, θmin = 3.5°
[var phi] and ω scansh = −14→14
Absorption correction: multi-scan (SADABS; Bruker, 2005)k = −17→17
Tmin = 0.917, Tmax = 1.0l = −13→13
13404 measured reflections

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)] = 0.033Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0605P)2] where P = (Fo2 + 2Fc2)/3
3256 reflections(Δ/σ)max < 0.001
191 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.16 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
C10.21596 (14)0.03042 (13)0.24992 (18)0.0490 (4)
H1A0.15840.01700.15650.059*
H1B0.1937−0.01100.30830.059*
C20.30273 (15)0.15638 (14)0.41120 (18)0.0527 (4)
H2A0.29600.11510.48030.063*
H2B0.29490.22420.43360.063*
C30.52500 (16)0.21274 (12)0.46180 (18)0.0488 (4)
H3B0.55170.22620.55780.059*
H3A0.50150.27370.41120.059*
C40.62423 (15)0.15974 (12)0.43666 (18)0.0489 (4)
H4A0.66090.20280.39310.059*
H4B0.68890.13600.52140.059*
C50.44343 (13)0.07042 (11)0.34006 (14)0.0358 (3)
C60.34568 (13)0.00437 (12)0.26942 (15)0.0392 (4)
C70.58540 (13)0.05456 (12)0.23001 (15)0.0389 (4)
H7B0.60830.11490.19930.047*
H7A0.51030.03030.15630.047*
C80.68837 (13)−0.02085 (12)0.25948 (15)0.0372 (3)
H80.6626−0.08270.28550.045*
C90.88413 (18)0.07980 (17)0.2809 (2)0.0653 (6)
H9A0.84000.14170.25520.078*
H9B0.97210.09360.32660.078*
C100.85620 (19)0.01841 (19)0.1568 (2)0.0737 (6)
H10B0.9206−0.03040.17650.088*
H10A0.85480.05970.08360.088*
C110.19972 (16)0.19983 (15)0.17239 (19)0.0577 (5)
H11A0.25780.17710.13820.069*
H11B0.22560.26470.21060.069*
C120.07252 (19)0.20656 (19)0.0556 (2)0.0789 (7)
H12B0.07850.2407−0.01950.095*
H12A0.04220.14090.02500.095*
C13−0.01760 (19)0.25861 (18)0.0930 (3)0.0896 (8)
H13B−0.09830.25610.01810.134*
H13C0.00730.32580.11400.134*
H13A−0.02000.22760.17090.134*
N10.55919 (10)0.07677 (9)0.34598 (13)0.0372 (3)
N20.42417 (11)0.14173 (10)0.41168 (13)0.0436 (3)
N30.20390 (12)0.13306 (11)0.28063 (14)0.0472 (4)
N40.36386 (12)−0.08788 (10)0.23411 (14)0.0439 (3)
O10.46924 (10)−0.12073 (8)0.25825 (12)0.0487 (3)
O20.26936 (11)−0.14243 (10)0.17994 (15)0.0678 (4)
S10.70823 (4)−0.04188 (4)0.10432 (4)0.05415 (16)
S20.83629 (3)0.01316 (4)0.39184 (4)0.04712 (15)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0408 (9)0.0547 (11)0.0542 (11)0.0003 (8)0.0230 (8)0.0050 (8)
C20.0557 (10)0.0621 (11)0.0483 (10)0.0097 (9)0.0299 (8)0.0015 (9)
C30.0617 (10)0.0354 (8)0.0463 (9)−0.0014 (8)0.0205 (8)−0.0012 (8)
C40.0462 (9)0.0384 (9)0.0531 (10)−0.0057 (7)0.0128 (8)−0.0025 (8)
C50.0377 (8)0.0368 (8)0.0319 (7)0.0036 (6)0.0140 (6)0.0059 (6)
C60.0372 (8)0.0417 (9)0.0399 (8)−0.0011 (7)0.0177 (7)−0.0014 (7)
C70.0335 (8)0.0478 (9)0.0336 (8)0.0014 (7)0.0128 (6)0.0087 (7)
C80.0336 (7)0.0456 (9)0.0331 (7)−0.0021 (7)0.0150 (6)0.0033 (7)
C90.0534 (11)0.0806 (14)0.0620 (12)−0.0236 (10)0.0249 (9)−0.0013 (11)
C100.0649 (13)0.1042 (17)0.0659 (13)−0.0218 (12)0.0414 (11)−0.0039 (12)
C110.0521 (10)0.0646 (12)0.0598 (11)0.0118 (9)0.0273 (9)0.0205 (10)
C120.0761 (14)0.0835 (16)0.0628 (13)0.0131 (12)0.0162 (11)0.0208 (12)
C130.0573 (12)0.0760 (16)0.122 (2)0.0094 (11)0.0252 (13)0.0350 (15)
N10.0340 (6)0.0366 (7)0.0393 (7)−0.0021 (5)0.0143 (5)−0.0013 (6)
N20.0453 (7)0.0432 (8)0.0427 (8)0.0025 (6)0.0194 (6)−0.0047 (6)
N30.0445 (7)0.0536 (9)0.0483 (8)0.0105 (6)0.0246 (6)0.0094 (7)
N40.0429 (7)0.0457 (8)0.0447 (8)−0.0073 (6)0.0203 (6)−0.0049 (6)
O10.0441 (6)0.0443 (6)0.0623 (8)−0.0003 (5)0.0273 (5)−0.0079 (6)
O20.0505 (7)0.0591 (8)0.0897 (10)−0.0204 (6)0.0263 (7)−0.0248 (7)
S10.0480 (3)0.0784 (4)0.0390 (2)−0.0091 (2)0.02147 (19)−0.0101 (2)
S20.0341 (2)0.0642 (3)0.0365 (2)0.00106 (18)0.00896 (16)0.00165 (19)

Geometric parameters (Å, °)

C1—H1A0.9700C8—H80.9800
C1—H1B0.9700C8—S11.8268 (15)
C1—C61.516 (2)C8—S21.7976 (15)
C1—N31.460 (2)C9—H9A0.9700
C2—H2A0.9700C9—H9B0.9700
C2—H2B0.9700C9—C101.499 (3)
C2—N21.465 (2)C9—S21.791 (2)
C2—N31.440 (2)C10—H10B0.9700
C3—H3B0.9700C10—H10A0.9700
C3—H3A0.9700C10—S11.8078 (19)
C3—C41.512 (2)C11—H11A0.9700
C3—N21.458 (2)C11—H11B0.9700
C4—H4A0.9700C11—C121.509 (3)
C4—H4B0.9700C11—N31.473 (2)
C4—N11.483 (2)C12—H12B0.9700
C5—C61.413 (2)C12—H12A0.9700
C5—N11.3617 (18)C12—C131.486 (3)
C5—N21.3269 (19)C13—H13B0.9600
C6—N41.359 (2)C13—H13C0.9600
C7—H7B0.9700C13—H13A0.9600
C7—H7A0.9700N4—O11.2550 (16)
C7—C81.529 (2)N4—O21.2674 (16)
C7—N11.4576 (19)
C1—N3—C11112.44 (14)C12—C13—H13A109.5
H1A—C1—H1B107.8H12B—C12—H12A107.8
C2—N3—C1108.50 (13)C13—C12—C11112.7 (2)
C2—N3—C11112.60 (14)C13—C12—H12B109.0
H2A—C2—H2B108.0C13—C12—H12A109.0
C3—C4—H4A110.8H13B—C13—H13C109.5
C3—C4—H4B110.8H13B—C13—H13A109.5
C3—N2—C2124.84 (14)H13C—C13—H13A109.5
H3B—C3—H3A109.3N1—C4—C3104.87 (12)
C4—C3—H3B111.4N1—C4—H4A110.8
C4—C3—H3A111.4N1—C4—H4B110.8
H4A—C4—H4B108.8N1—C5—C6130.82 (14)
C5—C6—C1119.04 (14)N1—C7—H7B108.7
C5—N1—C4108.19 (12)N1—C7—H7A108.7
C5—N1—C7122.63 (12)N1—C7—C8114.33 (12)
C5—N2—C2121.37 (13)N2—C2—H2A109.3
C5—N2—C3112.42 (13)N2—C2—H2B109.3
C6—C1—H1A109.0N2—C3—H3B111.4
C6—C1—H1B109.0N2—C3—H3A111.4
C7—C8—H8108.3N2—C3—C4101.72 (13)
C7—C8—S1108.97 (10)N2—C5—C6118.30 (13)
C7—C8—S2114.96 (11)N2—C5—N1110.84 (13)
C7—N1—C4119.23 (13)N3—C1—H1A109.0
H7B—C7—H7A107.6N3—C1—H1B109.0
C8—C7—H7B108.7N3—C1—C6112.87 (13)
C8—C7—H7A108.7N3—C2—H2A109.3
C9—C10—H10B109.6N3—C2—H2B109.3
C9—C10—H10A109.6N3—C2—N2111.46 (13)
C9—C10—S1110.31 (13)N3—C11—H11A109.0
C9—S2—C894.61 (8)N3—C11—H11B109.0
H9A—C9—H9B108.4N3—C11—C12112.74 (16)
C10—C9—H9A110.1N4—C6—C1117.12 (13)
C10—C9—H9B110.1N4—C6—C5123.19 (13)
C10—C9—S2108.21 (15)O1—N4—C6122.64 (13)
C10—S1—C897.79 (9)O1—N4—O2120.23 (13)
H10B—C10—H10A108.1O2—N4—C6117.06 (13)
C11—C12—H12B109.0S1—C8—H8108.3
C11—C12—H12A109.0S1—C10—H10B109.6
H11A—C11—H11B107.8S1—C10—H10A109.6
C12—C11—H11A109.0S2—C8—H8108.3
C12—C11—H11B109.0S2—C8—S1107.87 (8)
C12—C13—H13B109.5S2—C9—H9A110.1
C12—C13—H13C109.5S2—C9—H9B110.1
C1—C6—N4—O1−172.73 (14)N1—C5—C6—C1−163.47 (15)
C1—C6—N4—O24.3 (2)N1—C5—C6—N426.1 (3)
C3—C4—N1—C5−10.33 (17)N1—C5—N2—C2174.29 (13)
C3—C4—N1—C7136.21 (14)N1—C5—N2—C37.03 (18)
C4—C3—N2—C2−179.65 (14)N1—C7—C8—S1179.15 (10)
C4—C3—N2—C5−12.91 (17)N1—C7—C8—S2−59.67 (16)
C5—C6—N4—O1−2.1 (2)N2—C2—N3—C159.98 (18)
C5—C6—N4—O2174.92 (14)N2—C2—N3—C11−65.14 (19)
C6—C1—N3—C2−49.56 (18)N2—C3—C4—N113.31 (16)
C6—C1—N3—C1175.65 (17)N2—C5—C6—C114.4 (2)
C6—C5—N1—C4−179.54 (15)N2—C5—C6—N4−156.09 (15)
C6—C5—N1—C735.3 (2)N2—C5—N1—C42.50 (17)
C6—C5—N2—C2−4.0 (2)N2—C5—N1—C7−142.66 (14)
C6—C5—N2—C3−171.22 (13)N3—C1—C6—C513.5 (2)
C7—C8—S1—C10109.21 (13)N3—C1—C6—N4−175.50 (14)
C7—C8—S2—C9−86.58 (13)N3—C2—N2—C3131.22 (16)
C8—C7—N1—C491.93 (16)N3—C2—N2—C5−34.4 (2)
C8—C7—N1—C5−126.53 (15)N3—C11—C12—C1369.8 (2)
C9—C10—S1—C8−14.29 (18)S1—C8—S2—C935.20 (11)
C10—C9—S2—C8−46.45 (16)S2—C8—S1—C10−16.21 (11)
C12—C11—N3—C182.0 (2)S2—C9—C10—S140.3 (2)
C12—C11—N3—C2−155.08 (17)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C3—H3A···O1i0.972.483.322 (2)145
C3—H3B···O1ii0.972.563.269 (2)130
C4—H4A···O2i0.972.523.449 (2)160

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5612).

References

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