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

Tian, Z.; Dong, H.; Li, D.; Wang, G.

doi:10.1107/S160053681003206X

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 66| Part 9| September 2010| Page o2330

https://doi.org/10.1107/S160053681003206X

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

Zhongzhen Tian,^a Haijun Dong,^b Dongmei Li ^a ^* and Gaolei Wang ^a

^aShandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, People's Republic of China, and ^bSchool of Sciences, University of Jinan, People's Republic of China
^*Correspondence e-mail: chm_lidm@ujn.edu.cn

(Received 1 August 2010; accepted 10 August 2010; online 18 August 2010)

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 ). For background to neonicotinoid insecticides, see Mori et al. (2001 ); Kagabu (1997 ); Tian et al. (2007 ).

Experimental

Crystal data

C₁₁H₁₈N₄O₂S₂
M_r = 302.41
Triclinic, $[P \overline 1]$
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 ) 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[F² > 2σ(F²)] = 0.037
wR(F²) = 0.098
S = 1.06
3178 reflections
173 parameters
H-atom parameters constrained
Δρ_max = 0.38 e Å⁻³
Δρ_min = −0.34 e Å⁻³

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

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053681003206X/zl2297Isup2.hkl

checkCIF report

Comment top

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.

Related literature top

For related structures, see: Tian et al. (2009). For background to neonicotinoid insecticides, see Mori et al. (2001); Kagabu (19977); Tian et al. (2007).

Experimental top

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.

Structure description top

For related structures, see: Tian et al. (2009). For background to neonicotinoid insecticides, see Mori et al. (2001); Kagabu (19977); Tian et al. (2007).

Computing details top

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

Figures top

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.

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

Crystal data top

C₁₁H₁₈N₄O₂S₂	Z = 2
M_r = 302.41	F(000) = 320
Triclinic, P1	D_x = 1.448 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.0326 (7) Å	Cell parameters from 4541 reflections
b = 9.3521 (8) Å	θ = 2.4–27.7°
c = 10.1109 (9) Å	µ = 0.39 mm⁻¹
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 top

Bruker APEXII CCD area-detector diffractometer	3178 independent reflections
Radiation source: fine-focus sealed tube	2826 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.020
φ and ω scans	θ_max = 27.7°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −10→10
T_min = 0.906, T_max = 0.934	k = −12→11
7993 measured reflections	l = −13→13

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.037	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.098	H-atom parameters constrained
S = 1.06	w = 1/[σ²(F_o²) + (0.0447P)² + 0.2729P] where P = (F_o² + 2F_c²)/3
3178 reflections	(Δ/σ)_max < 0.001
173 parameters	Δρ_max = 0.38 e Å⁻³
0 restraints	Δρ_min = −0.34 e Å⁻³

Crystal data top

C₁₁H₁₈N₄O₂S₂	γ = 68.043 (1)°
M_r = 302.41	V = 693.62 (10) Å³
Triclinic, P1	Z = 2
a = 8.0326 (7) Å	Mo Kα radiation
b = 9.3521 (8) Å	µ = 0.39 mm⁻¹
c = 10.1109 (9) Å	T = 293 K
α = 80.461 (1)°	0.26 × 0.23 × 0.18 mm
β = 83.497 (1)°

Data collection top

Bruker APEXII CCD area-detector diffractometer	3178 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	2826 reflections with I > 2σ(I)
T_min = 0.906, T_max = 0.934	R_int = 0.020
7993 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	0 restraints
wR(F²) = 0.098	H-atom parameters constrained
S = 1.06	Δρ_max = 0.38 e Å⁻³
3178 reflections	Δρ_min = −0.34 e Å⁻³
173 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
C1	0.92947 (18)	0.16249 (17)	0.65277 (14)	0.0319 (3)
C2	1.0078 (2)	0.10338 (19)	0.78875 (16)	0.0375 (3)
H2A	0.9189	0.1516	0.8570	0.045*
H2B	1.0364	−0.0081	0.8074	0.045*
C3	1.2634 (3)	0.0458 (2)	0.9163 (2)	0.0549 (5)
H3A	1.2903	−0.0628	0.9137	0.082*
H3B	1.1876	0.0770	0.9949	0.082*
H3C	1.3731	0.0636	0.9189	0.082*
C4	1.2876 (2)	0.0997 (2)	0.67697 (17)	0.0409 (4)
H4A	1.3993	0.1141	0.6851	0.049*
H4B	1.3154	−0.0077	0.6650	0.049*
C5	1.2874 (2)	0.2345 (2)	0.43686 (17)	0.0459 (4)
H5A	1.3595	0.1393	0.4003	0.055*
H5B	1.3635	0.2914	0.4466	0.055*
C6	1.1325 (2)	0.3324 (3)	0.35069 (19)	0.0544 (5)
H6A	1.1106	0.4422	0.3466	0.065*
H6B	1.1554	0.3050	0.2602	0.065*
C7	1.02457 (19)	0.22041 (17)	0.54533 (14)	0.0316 (3)
C8	0.7976 (2)	0.40401 (18)	0.38887 (15)	0.0361 (3)
H8A	0.8020	0.5074	0.3646	0.043*
H8B	0.7182	0.4057	0.4688	0.043*
C9	0.7185 (2)	0.36571 (18)	0.27473 (15)	0.0369 (3)
H9	0.7140	0.2614	0.3005	0.044*
C10	0.7343 (3)	0.5774 (2)	0.0715 (2)	0.0580 (5)
H10A	0.7905	0.6289	0.1179	0.070*
H10B	0.7517	0.6059	−0.0244	0.070*
C11	0.5376 (3)	0.6301 (2)	0.1105 (2)	0.0553 (5)
H11A	0.4723	0.6319	0.0349	0.066*
H11B	0.4967	0.7350	0.1334	0.066*
N1	0.78451 (16)	0.12503 (15)	0.63650 (13)	0.0351 (3)
N2	1.17052 (18)	0.13662 (16)	0.79623 (13)	0.0379 (3)
N3	1.19480 (17)	0.20279 (17)	0.56373 (13)	0.0392 (3)
N4	0.97815 (17)	0.29393 (16)	0.42032 (13)	0.0371 (3)
O1	0.71913 (17)	0.14805 (16)	0.52435 (12)	0.0489 (3)
O2	0.72085 (16)	0.06008 (15)	0.73842 (12)	0.0468 (3)
S1	0.83905 (6)	0.36969 (6)	0.11346 (4)	0.04884 (14)
S2	0.49010 (6)	0.50283 (6)	0.25217 (5)	0.05506 (15)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0265 (6)	0.0378 (7)	0.0330 (7)	−0.0138 (6)	−0.0029 (5)	−0.0035 (6)
C2	0.0335 (7)	0.0431 (8)	0.0374 (8)	−0.0172 (6)	−0.0063 (6)	0.0011 (6)
C3	0.0567 (11)	0.0614 (11)	0.0527 (11)	−0.0299 (9)	−0.0264 (9)	0.0123 (8)
C4	0.0278 (7)	0.0460 (9)	0.0500 (9)	−0.0147 (6)	−0.0088 (6)	−0.0018 (7)
C5	0.0339 (8)	0.0632 (11)	0.0447 (9)	−0.0253 (8)	0.0054 (7)	−0.0052 (8)
C6	0.0422 (9)	0.0823 (13)	0.0432 (9)	−0.0350 (9)	−0.0002 (7)	0.0080 (9)
C7	0.0273 (6)	0.0357 (7)	0.0345 (7)	−0.0137 (6)	−0.0021 (5)	−0.0063 (6)
C8	0.0357 (7)	0.0391 (8)	0.0330 (7)	−0.0133 (6)	−0.0027 (6)	−0.0035 (6)
C9	0.0377 (8)	0.0389 (8)	0.0347 (7)	−0.0155 (6)	−0.0057 (6)	−0.0001 (6)
C10	0.0654 (12)	0.0611 (12)	0.0487 (10)	−0.0323 (10)	−0.0003 (9)	0.0097 (9)
C11	0.0624 (12)	0.0449 (10)	0.0529 (11)	−0.0161 (9)	−0.0072 (9)	0.0039 (8)
N1	0.0296 (6)	0.0421 (7)	0.0368 (6)	−0.0173 (5)	−0.0016 (5)	−0.0039 (5)
N2	0.0367 (7)	0.0424 (7)	0.0384 (7)	−0.0187 (6)	−0.0115 (5)	0.0009 (5)
N3	0.0281 (6)	0.0519 (8)	0.0399 (7)	−0.0200 (6)	−0.0026 (5)	0.0010 (6)
N4	0.0312 (6)	0.0487 (7)	0.0322 (6)	−0.0179 (6)	−0.0007 (5)	−0.0005 (5)
O1	0.0481 (7)	0.0701 (8)	0.0408 (6)	−0.0360 (6)	−0.0129 (5)	0.0011 (6)
O2	0.0402 (6)	0.0648 (8)	0.0420 (6)	−0.0314 (6)	0.0006 (5)	0.0030 (5)
S1	0.0490 (3)	0.0596 (3)	0.0356 (2)	−0.0154 (2)	−0.00023 (17)	−0.01182 (18)
S2	0.0342 (2)	0.0736 (3)	0.0498 (3)	−0.0182 (2)	−0.00542 (18)	0.0116 (2)

Geometric parameters (Å, º) top

C1—N1	1.3686 (18)	C6—H6B	0.9700
C1—C7	1.408 (2)	C7—N3	1.3455 (18)
C1—C2	1.509 (2)	C7—N4	1.3552 (19)
C2—N2	1.4642 (19)	C8—N4	1.4640 (19)
C2—H2A	0.9700	C8—C9	1.529 (2)
C2—H2B	0.9700	C8—H8A	0.9700
C3—N2	1.463 (2)	C8—H8B	0.9700
C3—H3A	0.9600	C9—S1	1.8019 (16)
C3—H3B	0.9600	C9—S2	1.8169 (16)
C3—H3C	0.9600	C9—H9	0.9800
C4—N3	1.444 (2)	C10—C11	1.495 (3)
C4—N2	1.448 (2)	C10—S1	1.802 (2)
C4—H4A	0.9700	C10—H10A	0.9700
C4—H4B	0.9700	C10—H10B	0.9700
C5—N3	1.452 (2)	C11—S2	1.8068 (19)
C5—C6	1.508 (2)	C11—H11A	0.9700
C5—H5A	0.9700	C11—H11B	0.9700
C5—H5B	0.9700	N1—O1	1.2559 (17)
C6—N4	1.488 (2)	N1—O2	1.2641 (17)
C6—H6A	0.9700

N1—C1—C7	123.33 (13)	N4—C8—H8A	108.8
N1—C1—C2	114.77 (12)	C9—C8—H8A	108.8
C7—C1—C2	120.49 (12)	N4—C8—H8B	108.8
N2—C2—C1	112.09 (12)	C9—C8—H8B	108.8
N2—C2—H2A	109.2	H8A—C8—H8B	107.7
C1—C2—H2A	109.2	C8—C9—S1	115.71 (11)
N2—C2—H2B	109.2	C8—C9—S2	109.68 (11)
C1—C2—H2B	109.2	S1—C9—S2	106.91 (8)
H2A—C2—H2B	107.9	C8—C9—H9	108.1
N2—C3—H3A	109.5	S1—C9—H9	108.1
N2—C3—H3B	109.5	S2—C9—H9	108.1
H3A—C3—H3B	109.5	C11—C10—S1	110.59 (13)
N2—C3—H3C	109.5	C11—C10—H10A	109.5
H3A—C3—H3C	109.5	S1—C10—H10A	109.5
H3B—C3—H3C	109.5	C11—C10—H10B	109.5
N3—C4—N2	107.66 (13)	S1—C10—H10B	109.5
N3—C4—H4A	110.2	H10A—C10—H10B	108.1
N2—C4—H4A	110.2	C10—C11—S2	111.27 (13)
N3—C4—H4B	110.2	C10—C11—H11A	109.4
N2—C4—H4B	110.2	S2—C11—H11A	109.4
H4A—C4—H4B	108.5	C10—C11—H11B	109.4
N3—C5—C6	101.87 (13)	S2—C11—H11B	109.4
N3—C5—H5A	111.4	H11A—C11—H11B	108.0
C6—C5—H5A	111.4	O1—N1—O2	120.14 (12)
N3—C5—H5B	111.4	O1—N1—C1	122.24 (13)
C6—C5—H5B	111.4	O2—N1—C1	117.56 (12)
H5A—C5—H5B	109.3	C4—N2—C3	110.33 (14)
N4—C6—C5	103.53 (13)	C4—N2—C2	110.28 (12)
N4—C6—H6A	111.1	C3—N2—C2	109.41 (13)
C5—C6—H6A	111.1	C7—N3—C4	120.45 (13)
N4—C6—H6B	111.1	C7—N3—C5	110.88 (13)
C5—C6—H6B	111.1	C4—N3—C5	122.79 (13)
H6A—C6—H6B	109.0	C7—N4—C8	123.79 (12)
N3—C7—N4	110.27 (13)	C7—N4—C6	108.50 (12)
N3—C7—C1	117.58 (13)	C8—N4—C6	117.02 (13)
N4—C7—C1	132.15 (13)	C10—S1—C9	93.94 (8)
N4—C8—C9	113.81 (13)	C11—S2—C9	98.01 (8)

N1—C1—C2—N2	175.52 (13)	N4—C7—N3—C5	−13.07 (19)
C7—C1—C2—N2	8.6 (2)	C1—C7—N3—C5	166.80 (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—C5	159.98 (14)
C2—C1—C7—N3	8.2 (2)	C6—C5—N3—C7	21.40 (19)
N1—C1—C7—N4	22.3 (3)	C6—C5—N3—C4	174.39 (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—C8	35.3 (2)
N4—C8—C9—S2	176.50 (10)	N3—C7—N4—C6	−1.68 (19)
S1—C10—C11—S2	28.7 (2)	C1—C7—N4—C6	178.48 (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—C6	92.38 (18)
C7—C1—N1—O2	173.30 (14)	C5—C6—N4—C7	14.7 (2)
C2—C1—N1—O2	6.8 (2)	C5—C6—N4—C8	160.67 (14)
N3—C4—N2—C3	−174.80 (13)	C11—C10—S1—C9	−42.36 (16)
N3—C4—N2—C2	64.22 (16)	C8—C9—S1—C10	−82.86 (13)
C1—C2—N2—C4	−44.99 (17)	S2—C9—S1—C10	39.62 (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—C11	99.63 (12)
C1—C7—N3—C4	13.1 (2)	S1—C9—S2—C11	−26.54 (10)

Experimental details

Crystal data
Chemical formula	C₁₁H₁₈N₄O₂S₂
M_r	302.41
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	8.0326 (7), 9.3521 (8), 10.1109 (9)
α, β, γ (°)	80.461 (1), 83.497 (1), 68.043 (1)
V (Å³)	693.62 (10)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.39
Crystal size (mm)	0.26 × 0.23 × 0.18

Data collection
Diffractometer	Bruker APEXII CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.906, 0.934
No. of measured, independent and observed [I > 2σ(I)] reflections	7993, 3178, 2826
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.653

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.098, 1.06
No. of reflections	3178
No. of parameters	173
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.38, −0.34

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), WinGX (Farrugia, 1999).

Acknowledgements

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.

References

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