Literature DB >> 22259433

1-[(6-Chloro-pyridin-3-yl)meth-yl]imidazolidin-2-iminium chloride.

Rajni Kant, Vivek K Gupta, Kamini Kapoor, Madhukar B Deshmukh, Chetan S Shripanavar.

Abstract

The title compound, C(9)H(12)ClN(4) (+)·Cl(-), is a natural metabolic product of n class="Chemical">imidacloprid [systematic name: (E)-1-(6-chloro-3-pyridyl-meth-yl)-N-nitro-imidazolidin-2-yl-idene-amine] and was obtained by the reduction of the latter using Fe in HCl. The dihedral angle between the pyridine and imidazole rings is 62.09 (12)°. The crystal structure is stabilized by N-H⋯Cl and C-H⋯Cl inter-actions involving the chloride anion. The pyridine N and the chloride atoms are not involved in inter-molecular inter-actions.

Entities: Chemical Disease Gene

Year: 2011 PMID： 22259433 PMCID： PMC3254490 DOI： 10.1107/S1600536811053487

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For background to the insecticidal applications of imidacloprid, see: Kanne et al. (2005 ▶); Schulz-Jander et al. (2002 ▶); n class="Gene">Dai et al. (2010 ▶ ); Tanner (2010 ▶). For ring conformations, see: Duax & Norton (1975 ▶). For related structures, see: Kapoor et al. (2011 ▶).

Experimental

Crystal data

C9H12ClN4 +·Cl− M = 247.13 Triclinic, a = 6.4773 (3) Å b = 7.3091 (3) Å c = 12.4758 (4) Å α = 88.996 (3)° β = 77.214 (3)° γ = 79.925 (3)° V = 566.98 (4) Å3 Z = 2 Mo Kα radiation μ = 0.55 mm−1 T = 293 K 0.3 × 0.2 × 0.1 mm

Data collection

Oxford Diffraction Xcalibur Sapphire3 diffractometer Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010 ▶) T min = 0.742, T max = 1.000 14139 measured reflections 2468 independent reflections 2059 reflections with I > 2σ(I) R int = 0.035

Refinement

R[F 2 > 2σ(F 2)] = 0.041 wR(F 2) = 0.108 S = 1.03 2468 reflections 137 parameters H-atom parameters constrained Δρmax = 0.36 e Å−3 Δρmin = −0.34 e Å−3 Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis n class="Disease">RED (Oxford Diffraction, 2010 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶) and PARST (Nardelli, 1995 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811053487/gg2070sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811053487/gg2070Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811053487/gg2070Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₉H₁₂ClN₄⁺·Cl⁻	Z = 2
M_r = 247.13	F(000) = 256
Triclinic, P1	D_x = 1.448 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.4773 (3) Å	Cell parameters from 7015 reflections
b = 7.3091 (3) Å	θ = 3.9–29.1°
c = 12.4758 (4) Å	µ = 0.55 mm⁻¹
α = 88.996 (3)°	T = 293 K
β = 77.214 (3)°	Plate, yellow
γ = 79.925 (3)°	0.3 × 0.2 × 0.1 mm
V = 566.98 (4) Å³

Oxford Diffraction Xcalibur Sapphire3 diffractometer	2468 independent reflections
Radiation source: fine-focus sealed tube	2059 reflections with I > 2σ(I)
graphite	R_int = 0.035
Detector resolution: 16.1049 pixels mm^-1	θ_max = 27.0°, θ_min = 3.9°
ω scans	h = −8→8
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)	k = −9→9
T_min = 0.742, T_max = 1.000	l = −15→15
14139 measured reflections

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.041	H-atom parameters constrained
wR(F²) = 0.108	w = 1/[σ²(F_o²) + (0.0442P)² + 0.3165P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max = 0.001
2468 reflections	Δρ_max = 0.36 e Å⁻³
137 parameters	Δρ_min = −0.34 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.027 (4)

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.

	x	y	z	U_iso*/U_eq
Cl2	0.86358 (8)	0.30462 (7)	0.60008 (4)	0.04939 (19)
Cl1	0.23994 (12)	0.35819 (11)	1.17486 (5)	0.0720 (2)
N1	0.1057 (3)	0.2611 (3)	1.00679 (16)	0.0649 (6)
C2	0.1336 (3)	0.2148 (4)	0.89995 (19)	0.0587 (6)
H2	0.0126	0.2007	0.8745	0.070*
C3	0.3286 (3)	0.1868 (3)	0.82568 (15)	0.0365 (4)
C4	0.5059 (3)	0.2069 (3)	0.86513 (18)	0.0500 (5)
H4	0.6416	0.1874	0.8184	0.060*
C5	0.4824 (4)	0.2558 (4)	0.97404 (19)	0.0544 (6)
H5	0.6002	0.2700	1.0023	0.065*
C6	0.2785 (4)	0.2826 (3)	1.03902 (16)	0.0473 (5)
C7	0.3440 (3)	0.1424 (3)	0.70621 (15)	0.0380 (4)
H7A	0.2113	0.1987	0.6860	0.046*
H7B	0.4600	0.1959	0.6613	0.046*
N8	0.3828 (3)	−0.0570 (2)	0.68359 (13)	0.0392 (4)
C9	0.2100 (4)	−0.1652 (3)	0.7134 (2)	0.0510 (5)
H9A	0.0927	−0.1189	0.6779	0.061*
H9B	0.1550	−0.1632	0.7923	0.061*
C10	0.3206 (4)	−0.3597 (3)	0.6710 (2)	0.0566 (6)
H10A	0.3486	−0.4399	0.7308	0.068*
H10B	0.2345	−0.4152	0.6305	0.068*
N11	0.5199 (3)	−0.3268 (2)	0.59921 (15)	0.0503 (5)
H11	0.6049	−0.4064	0.5525	0.060*
C12	0.5523 (3)	−0.1553 (3)	0.61621 (15)	0.0388 (4)
N13	0.7288 (3)	−0.0930 (3)	0.57049 (15)	0.0512 (5)
H13A	0.7407	0.0194	0.5835	0.061*
H13B	0.8325	−0.1646	0.5276	0.061*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl2	0.0360 (3)	0.0522 (3)	0.0531 (3)	−0.0003 (2)	−0.0009 (2)	−0.0019 (2)
Cl1	0.0869 (5)	0.0993 (5)	0.0355 (3)	−0.0398 (4)	−0.0064 (3)	−0.0068 (3)
N1	0.0480 (11)	0.1002 (17)	0.0444 (11)	−0.0233 (11)	0.0042 (8)	−0.0210 (10)
C2	0.0351 (11)	0.0911 (18)	0.0490 (13)	−0.0136 (11)	−0.0034 (9)	−0.0215 (12)
C3	0.0359 (10)	0.0346 (9)	0.0362 (10)	−0.0034 (7)	−0.0042 (7)	−0.0012 (7)
C4	0.0356 (10)	0.0674 (14)	0.0445 (11)	−0.0099 (10)	−0.0025 (9)	−0.0040 (10)
C5	0.0448 (12)	0.0730 (15)	0.0499 (12)	−0.0173 (11)	−0.0145 (10)	−0.0023 (11)
C6	0.0590 (13)	0.0517 (12)	0.0330 (10)	−0.0199 (10)	−0.0059 (9)	−0.0001 (8)
C7	0.0378 (10)	0.0366 (10)	0.0361 (10)	−0.0015 (8)	−0.0045 (8)	−0.0021 (7)
N8	0.0363 (8)	0.0393 (9)	0.0390 (9)	−0.0055 (7)	−0.0023 (7)	−0.0044 (7)
C9	0.0455 (12)	0.0518 (12)	0.0554 (13)	−0.0158 (10)	−0.0048 (10)	0.0007 (10)
C10	0.0685 (15)	0.0456 (12)	0.0600 (14)	−0.0166 (11)	−0.0184 (12)	0.0011 (10)
N11	0.0540 (11)	0.0429 (10)	0.0514 (11)	0.0018 (8)	−0.0136 (8)	−0.0121 (8)
C12	0.0384 (10)	0.0437 (10)	0.0326 (9)	0.0016 (8)	−0.0106 (8)	−0.0033 (8)
N13	0.0386 (9)	0.0571 (11)	0.0497 (10)	−0.0015 (8)	0.0034 (8)	−0.0121 (8)

Cl1—C6	1.743 (2)	N8—C12	1.328 (2)
N1—C6	1.305 (3)	N8—C9	1.460 (3)
N1—C2	1.346 (3)	C9—C10	1.522 (3)
C2—C3	1.376 (3)	C9—H9A	0.9700
C2—H2	0.9300	C9—H9B	0.9700
C3—C4	1.377 (3)	C10—N11	1.455 (3)
C3—C7	1.509 (3)	C10—H10A	0.9700
C4—C5	1.380 (3)	C10—H10B	0.9700
C4—H4	0.9300	N11—C12	1.334 (3)
C5—C6	1.372 (3)	N11—H11	0.8600
C5—H5	0.9300	C12—N13	1.313 (3)
C7—N8	1.457 (2)	N13—H13A	0.8600
C7—H7A	0.9700	N13—H13B	0.8600
C7—H7B	0.9700

C6—N1—C2	115.96 (19)	C12—N8—C9	110.48 (17)
N1—C2—C3	124.6 (2)	C7—N8—C9	121.21 (16)
N1—C2—H2	117.7	N8—C9—C10	102.83 (18)
C3—C2—H2	117.7	N8—C9—H9A	111.2
C2—C3—C4	116.79 (19)	C10—C9—H9A	111.2
C2—C3—C7	121.09 (18)	N8—C9—H9B	111.2
C4—C3—C7	122.09 (17)	C10—C9—H9B	111.2
C3—C4—C5	120.0 (2)	H9A—C9—H9B	109.1
C3—C4—H4	120.0	N11—C10—C9	102.83 (18)
C5—C4—H4	120.0	N11—C10—H10A	111.2
C6—C5—C4	117.4 (2)	C9—C10—H10A	111.2
C6—C5—H5	121.3	N11—C10—H10B	111.2
C4—C5—H5	121.3	C9—C10—H10B	111.2
N1—C6—C5	125.2 (2)	H10A—C10—H10B	109.1
N1—C6—Cl1	115.99 (17)	C12—N11—C10	110.36 (17)
C5—C6—Cl1	118.74 (17)	C12—N11—H11	124.8
N8—C7—C3	112.18 (15)	C10—N11—H11	124.8
N8—C7—H7A	109.2	N13—C12—N8	125.00 (19)
C3—C7—H7A	109.2	N13—C12—N11	123.74 (18)
N8—C7—H7B	109.2	N8—C12—N11	111.26 (18)
C3—C7—H7B	109.2	C12—N13—H13A	120.0
H7A—C7—H7B	107.9	C12—N13—H13B	120.0
C12—N8—C7	126.77 (17)	H13A—N13—H13B	120.0

C6—N1—C2—C3	1.1 (4)	C3—C7—N8—C12	−118.6 (2)
N1—C2—C3—C4	0.5 (4)	C3—C7—N8—C9	76.9 (2)
N1—C2—C3—C7	−177.6 (2)	C12—N8—C9—C10	11.1 (2)
C2—C3—C4—C5	−1.0 (3)	C7—N8—C9—C10	177.87 (18)
C7—C3—C4—C5	177.1 (2)	N8—C9—C10—N11	−14.3 (2)
C3—C4—C5—C6	0.0 (4)	C9—C10—N11—C12	13.7 (2)
C2—N1—C6—C5	−2.3 (4)	C7—N8—C12—N13	10.4 (3)
C2—N1—C6—Cl1	175.7 (2)	C9—N8—C12—N13	176.29 (19)
C4—C5—C6—N1	1.8 (4)	C7—N8—C12—N11	−168.74 (18)
C4—C5—C6—Cl1	−176.16 (18)	C9—N8—C12—N11	−2.9 (2)
C2—C3—C7—N8	−91.8 (2)	C10—N11—C12—N13	173.4 (2)
C4—C3—C7—N8	90.2 (2)	C10—N11—C12—N8	−7.4 (2)

D—H···A	D—H	H···A	D···A	D—H···A
N13—H13A···Cl2	0.86	2.39	3.227 (2)	166
N13—H13B···Cl2ⁱ	0.86	2.33	3.177 (2)	169
N11—H11···Cl2ⁱⁱ	0.86	2.60	3.182 (2)	126
C7—H7A···Cl2ⁱⁱⁱ	0.97	2.69	3.650 (2)	169
C7—H7B···Cl2	0.97	2.80	3.722 (2)	158

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N13—H13A⋯Cl2	0.86	2.39	3.227 (2)	166
N13—H13B⋯Cl2ⁱ	0.86	2.33	3.177 (2)	169
N11—H11⋯Cl2ⁱⁱ	0.86	2.60	3.182 (2)	126
C7—H7A⋯Cl2ⁱⁱⁱ	0.97	2.69	3.650 (2)	169
C7—H7B⋯Cl2	0.97	2.80	3.722 (2)	158

Symmetry codes: (i) ; (ii) ; (iii) .

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1. A short history of SHELX.

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5. Structure validation in chemical crystallography.

Authors: Anthony L Spek
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