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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2330.
Published online 2010 August 18. doi:  10.1107/S160053681003206X
PMCID: PMC3007836

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

Abstract

In the title compound, C11H18N4O2S2, the dithiol­ane ring displays an envelope conformation, the tetra­hydro­pyrimidine ring has a conformation that is between half-chair and screw-boat, and the imidazole ring is essentially planar (r.m.s. deviation = 0.0017 Å). No significant directional inter­molecular inter­actions are present in the structure.

Related literature

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

An external file that holds a picture, illustration, etc.
Object name is e-66-o2330-scheme1.jpg

Experimental

Crystal data

  • C11H18N4O2S2
  • M r = 302.41
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2330-efi1.jpg
  • a = 8.0326 (7) Å
  • b = 9.3521 (8) Å
  • c = 10.1109 (9) Å
  • α = 80.461 (1)°
  • β = 83.497 (1)°
  • γ = 68.043 (1)°
  • V = 693.62 (10) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.39 mm−1
  • T = 293 K
  • 0.26 × 0.23 × 0.18 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.906, T max = 0.934
  • 7993 measured reflections
  • 3178 independent reflections
  • 2826 reflections with I > 2σ(I)
  • R int = 0.020

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.098
  • S = 1.06
  • 3178 reflections
  • 173 parameters
  • H-atom parameters constrained
  • Δρmax = 0.38 e Å−3
  • Δρmin = −0.34 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]).

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681003206X/zl2297sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681003206X/zl2297Isup2.hkl

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

Acknowledgments

The authors thank the National Natural Science Foundation of China (grant 20902037), the Opening Fund of Shanghai Key Laboratory of Chemical Biology (grant SKLCB-2008–08) and the Doctoral Foundation of the University of Jinan (B0542) for financial support.

supplementary crystallographic information

Comment

Imidacloprid, a commercially sold insecticide modeled after nicotine, gains its activity by acting on the nicotinic acetylcholine receptor (nAChR) of insect neuronal systems (Mori et al., 2001). Imidacloprid and other neonicotinoid insecticides have become a major insecticide class with high activities and are widely used for crop protection and veterinary pest control (Kagabu, 1997). Our interest was introducing sulfur 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 dithiolane ring displays a typical envelope conformation. The nitro group is almost coplanar with the olefin-amine plane [C7—C1—N1—O2 = 173.30 (14)°]. Around N3 and N4 the sums of the angles are 353.32° and 349.31°, respectively, indicating that they are nearly sp2 hybridized and leading to an essentially planar imidazole ring. The N2 atom exhibits a hybridization close to sp3 with C—N—C angles between 109.41 (13)° and 110.33 (14)°. The tetrahydropyrimidine ring has a conformation that is in between half-chair and screw-boat. No significant directional intermolecular interactions are present in the structure and the packing is dominated by van der Waals forces.

Experimental

The title compound was synthesized according to the literature (Tian et al., 2007). Single crystals suitable for X-ray analysis 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 a riding model with C—H = 0.95–0.99 Å, Uiso(H) = 1.2 (1.5 for methyl groups) times Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. The H atoms are shown as spheres of arbitrary size.

Crystal data

C11H18N4O2S2Z = 2
Mr = 302.41F(000) = 320
Triclinic, P1Dx = 1.448 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.0326 (7) ÅCell parameters from 4541 reflections
b = 9.3521 (8) Åθ = 2.4–27.7°
c = 10.1109 (9) ŵ = 0.39 mm1
α = 80.461 (1)°T = 293 K
β = 83.497 (1)°Prism, colourless
γ = 68.043 (1)°0.26 × 0.23 × 0.18 mm
V = 693.62 (10) Å3

Data collection

Bruker APEXII CCD area-detector diffractometer3178 independent reflections
Radiation source: fine-focus sealed tube2826 reflections with I > 2σ(I)
graphiteRint = 0.020
[var phi] and ω scansθmax = 27.7°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −10→10
Tmin = 0.906, Tmax = 0.934k = −12→11
7993 measured reflectionsl = −13→13

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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.098H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0447P)2 + 0.2729P] where P = (Fo2 + 2Fc2)/3
3178 reflections(Δ/σ)max < 0.001
173 parametersΔρmax = 0.38 e Å3
0 restraintsΔρmin = −0.34 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
C10.92947 (18)0.16249 (17)0.65277 (14)0.0319 (3)
C21.0078 (2)0.10338 (19)0.78875 (16)0.0375 (3)
H2A0.91890.15160.85700.045*
H2B1.0364−0.00810.80740.045*
C31.2634 (3)0.0458 (2)0.9163 (2)0.0549 (5)
H3A1.2903−0.06280.91370.082*
H3B1.18760.07700.99490.082*
H3C1.37310.06360.91890.082*
C41.2876 (2)0.0997 (2)0.67697 (17)0.0409 (4)
H4A1.39930.11410.68510.049*
H4B1.3154−0.00770.66500.049*
C51.2874 (2)0.2345 (2)0.43686 (17)0.0459 (4)
H5A1.35950.13930.40030.055*
H5B1.36350.29140.44660.055*
C61.1325 (2)0.3324 (3)0.35069 (19)0.0544 (5)
H6A1.11060.44220.34660.065*
H6B1.15540.30500.26020.065*
C71.02457 (19)0.22041 (17)0.54533 (14)0.0316 (3)
C80.7976 (2)0.40401 (18)0.38887 (15)0.0361 (3)
H8A0.80200.50740.36460.043*
H8B0.71820.40570.46880.043*
C90.7185 (2)0.36571 (18)0.27473 (15)0.0369 (3)
H90.71400.26140.30050.044*
C100.7343 (3)0.5774 (2)0.0715 (2)0.0580 (5)
H10A0.79050.62890.11790.070*
H10B0.75170.6059−0.02440.070*
C110.5376 (3)0.6301 (2)0.1105 (2)0.0553 (5)
H11A0.47230.63190.03490.066*
H11B0.49670.73500.13340.066*
N10.78451 (16)0.12503 (15)0.63650 (13)0.0351 (3)
N21.17052 (18)0.13662 (16)0.79623 (13)0.0379 (3)
N31.19480 (17)0.20279 (17)0.56373 (13)0.0392 (3)
N40.97815 (17)0.29393 (16)0.42032 (13)0.0371 (3)
O10.71913 (17)0.14805 (16)0.52435 (12)0.0489 (3)
O20.72085 (16)0.06008 (15)0.73842 (12)0.0468 (3)
S10.83905 (6)0.36969 (6)0.11346 (4)0.04884 (14)
S20.49010 (6)0.50283 (6)0.25217 (5)0.05506 (15)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0265 (6)0.0378 (7)0.0330 (7)−0.0138 (6)−0.0029 (5)−0.0035 (6)
C20.0335 (7)0.0431 (8)0.0374 (8)−0.0172 (6)−0.0063 (6)0.0011 (6)
C30.0567 (11)0.0614 (11)0.0527 (11)−0.0299 (9)−0.0264 (9)0.0123 (8)
C40.0278 (7)0.0460 (9)0.0500 (9)−0.0147 (6)−0.0088 (6)−0.0018 (7)
C50.0339 (8)0.0632 (11)0.0447 (9)−0.0253 (8)0.0054 (7)−0.0052 (8)
C60.0422 (9)0.0823 (13)0.0432 (9)−0.0350 (9)−0.0002 (7)0.0080 (9)
C70.0273 (6)0.0357 (7)0.0345 (7)−0.0137 (6)−0.0021 (5)−0.0063 (6)
C80.0357 (7)0.0391 (8)0.0330 (7)−0.0133 (6)−0.0027 (6)−0.0035 (6)
C90.0377 (8)0.0389 (8)0.0347 (7)−0.0155 (6)−0.0057 (6)−0.0001 (6)
C100.0654 (12)0.0611 (12)0.0487 (10)−0.0323 (10)−0.0003 (9)0.0097 (9)
C110.0624 (12)0.0449 (10)0.0529 (11)−0.0161 (9)−0.0072 (9)0.0039 (8)
N10.0296 (6)0.0421 (7)0.0368 (6)−0.0173 (5)−0.0016 (5)−0.0039 (5)
N20.0367 (7)0.0424 (7)0.0384 (7)−0.0187 (6)−0.0115 (5)0.0009 (5)
N30.0281 (6)0.0519 (8)0.0399 (7)−0.0200 (6)−0.0026 (5)0.0010 (6)
N40.0312 (6)0.0487 (7)0.0322 (6)−0.0179 (6)−0.0007 (5)−0.0005 (5)
O10.0481 (7)0.0701 (8)0.0408 (6)−0.0360 (6)−0.0129 (5)0.0011 (6)
O20.0402 (6)0.0648 (8)0.0420 (6)−0.0314 (6)0.0006 (5)0.0030 (5)
S10.0490 (3)0.0596 (3)0.0356 (2)−0.0154 (2)−0.00023 (17)−0.01182 (18)
S20.0342 (2)0.0736 (3)0.0498 (3)−0.0182 (2)−0.00542 (18)0.0116 (2)

Geometric parameters (Å, °)

C1—N11.3686 (18)C6—H6B0.9700
C1—C71.408 (2)C7—N31.3455 (18)
C1—C21.509 (2)C7—N41.3552 (19)
C2—N21.4642 (19)C8—N41.4640 (19)
C2—H2A0.9700C8—C91.529 (2)
C2—H2B0.9700C8—H8A0.9700
C3—N21.463 (2)C8—H8B0.9700
C3—H3A0.9600C9—S11.8019 (16)
C3—H3B0.9600C9—S21.8169 (16)
C3—H3C0.9600C9—H90.9800
C4—N31.444 (2)C10—C111.495 (3)
C4—N21.448 (2)C10—S11.802 (2)
C4—H4A0.9700C10—H10A0.9700
C4—H4B0.9700C10—H10B0.9700
C5—N31.452 (2)C11—S21.8068 (19)
C5—C61.508 (2)C11—H11A0.9700
C5—H5A0.9700C11—H11B0.9700
C5—H5B0.9700N1—O11.2559 (17)
C6—N41.488 (2)N1—O21.2641 (17)
C6—H6A0.9700
N1—C1—C7123.33 (13)N4—C8—H8A108.8
N1—C1—C2114.77 (12)C9—C8—H8A108.8
C7—C1—C2120.49 (12)N4—C8—H8B108.8
N2—C2—C1112.09 (12)C9—C8—H8B108.8
N2—C2—H2A109.2H8A—C8—H8B107.7
C1—C2—H2A109.2C8—C9—S1115.71 (11)
N2—C2—H2B109.2C8—C9—S2109.68 (11)
C1—C2—H2B109.2S1—C9—S2106.91 (8)
H2A—C2—H2B107.9C8—C9—H9108.1
N2—C3—H3A109.5S1—C9—H9108.1
N2—C3—H3B109.5S2—C9—H9108.1
H3A—C3—H3B109.5C11—C10—S1110.59 (13)
N2—C3—H3C109.5C11—C10—H10A109.5
H3A—C3—H3C109.5S1—C10—H10A109.5
H3B—C3—H3C109.5C11—C10—H10B109.5
N3—C4—N2107.66 (13)S1—C10—H10B109.5
N3—C4—H4A110.2H10A—C10—H10B108.1
N2—C4—H4A110.2C10—C11—S2111.27 (13)
N3—C4—H4B110.2C10—C11—H11A109.4
N2—C4—H4B110.2S2—C11—H11A109.4
H4A—C4—H4B108.5C10—C11—H11B109.4
N3—C5—C6101.87 (13)S2—C11—H11B109.4
N3—C5—H5A111.4H11A—C11—H11B108.0
C6—C5—H5A111.4O1—N1—O2120.14 (12)
N3—C5—H5B111.4O1—N1—C1122.24 (13)
C6—C5—H5B111.4O2—N1—C1117.56 (12)
H5A—C5—H5B109.3C4—N2—C3110.33 (14)
N4—C6—C5103.53 (13)C4—N2—C2110.28 (12)
N4—C6—H6A111.1C3—N2—C2109.41 (13)
C5—C6—H6A111.1C7—N3—C4120.45 (13)
N4—C6—H6B111.1C7—N3—C5110.88 (13)
C5—C6—H6B111.1C4—N3—C5122.79 (13)
H6A—C6—H6B109.0C7—N4—C8123.79 (12)
N3—C7—N4110.27 (13)C7—N4—C6108.50 (12)
N3—C7—C1117.58 (13)C8—N4—C6117.02 (13)
N4—C7—C1132.15 (13)C10—S1—C993.94 (8)
N4—C8—C9113.81 (13)C11—S2—C998.01 (8)
N1—C1—C2—N2175.52 (13)N4—C7—N3—C5−13.07 (19)
C7—C1—C2—N28.6 (2)C1—C7—N3—C5166.80 (14)
N3—C5—C6—N4−20.74 (19)N2—C4—N3—C7−49.50 (19)
N1—C1—C7—N3−157.53 (14)N2—C4—N3—C5159.98 (14)
C2—C1—C7—N38.2 (2)C6—C5—N3—C721.40 (19)
N1—C1—C7—N422.3 (3)C6—C5—N3—C4174.39 (16)
C2—C1—C7—N4−171.97 (15)N3—C7—N4—C8−144.85 (14)
N4—C8—C9—S1−62.50 (16)C1—C7—N4—C835.3 (2)
N4—C8—C9—S2176.50 (10)N3—C7—N4—C6−1.68 (19)
S1—C10—C11—S228.7 (2)C1—C7—N4—C6178.48 (17)
C7—C1—N1—O1−4.1 (2)C9—C8—N4—C7−127.28 (15)
C2—C1—N1—O1−170.58 (14)C9—C8—N4—C692.38 (18)
C7—C1—N1—O2173.30 (14)C5—C6—N4—C714.7 (2)
C2—C1—N1—O26.8 (2)C5—C6—N4—C8160.67 (14)
N3—C4—N2—C3−174.80 (13)C11—C10—S1—C9−42.36 (16)
N3—C4—N2—C264.22 (16)C8—C9—S1—C10−82.86 (13)
C1—C2—N2—C4−44.99 (17)S2—C9—S1—C1039.62 (10)
C1—C2—N2—C3−166.51 (14)C10—C11—S2—C9−0.91 (17)
N4—C7—N3—C4−166.78 (14)C8—C9—S2—C1199.63 (12)
C1—C7—N3—C413.1 (2)S1—C9—S2—C11−26.54 (10)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZL2297).

References

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  • Kagabu, S. (1997). Rev. Toxicol.1, 75–129.
  • Mori, K., Okumoto, T., Kawahara, N. & Ozoe, Y. (2001). Pest. Manage. Sci.46, 40–46.
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