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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 6| June 2012| Page o1939
doi:10.1107/S1600536812023537

1-[(6-Chloro­pyridin-3-yl)meth­yl]­imidazolidin-2-one

Rajni Kant,a* Vivek K. Gupta,a Kamini Kapoor,a Chetan S. Shripanavarb and Kaushik Banerjeec

aX-ray Crystallography Laboratory, Post-Graduate Department of Physics and Electronics, University of Jammu, Jammu Tawi 180 006, India, bDepartment of Chemistry, Shivaji University, Kolhapur 416 004, India, and cNational Research Centre for Grapes, Pune 412 307, India
*Correspondence e-mail: rkvk.paper11@gmail.com

(Received 14 May 2012; accepted 23 May 2012; online 31 May 2012)

In the title mol­ecule, C9H10ClN3O, the dihedral angle between the pyridine ring and imidazoline ring mean plane [maximum deviation = 0.031–(3) Å] is 76.2 (1)°. In the crystal, N—H⋯O hydrogen bonds link pairs of mol­ecules to form inversion dimers. In addition, weak C—H⋯N hydrogen bonds and π–π stacking inter­actions between pyridine rings [centroid–centroid distance = 3.977 (2) Å] are observed.

Related literature

For the background to the insecticidal applications of imidacloprid (N-{1-[(6-chloro-3-pyrid­yl)meth­yl]-4,5-dihydro­imidazol-2-yl}nitramide), see: Samaritoni et al. (2003[Samaritoni, J. G., Demeter, D. A., Gifford, J. M., Watson, G. B., Kempe, M. S. & Bruce, T. J. (2003). J. Agric. Food Chem. 51, 3035-3042.]); Suchail et al. (2001[Suchail, S., Guez, D. & Belzunces, L. P. (2001). Environ. Toxicol. Chem. 20, 2482-2486.], 2004[Suchail, S., De Sousa, G., Rahmani, R. & Belzunces, L. P. (2004). Pest Manage. Sci. 60, 1956-1062.]); Schulz-Jander & Casida (2002[Schulz-Jander, D. A. & Casida, J. E. (2002). Toxicol. Lett. 132, 65-70.]); Kagabu et al. (2007[Kagabu, S., Ishihara, R., Hieda, Y., Nishimura, K. & Naruse, Y. (2007). J. Agric. Food Chem. 55, 812-818.]); Pandey et al. (2009[Pandey, G., Dorrian, S. J., Russel, R. J. & Oakeshott, J. G. (2009). Biochem. Biophys. Res. Commun. 380, 710-714.]). For related structures, see: Kapoor et al. (2011[Kapoor, K., Gupta, V. K., Kant, R., Deshmukh, M. B. & Shripanavar, C. S. (2011). X-ray Struct. Anal. Online, 27, 55-56.], 2012[Kapoor, K., Gupta, V. K., Deshmukh, M. B., Shripanavar, C. S. & Kant, R. (2012). Acta Cryst. E68, o469.]); Kant et al. (2012[Kant, R., Gupta, V. K., Kapoor, K., Deshmukh, M. B. & Shripanavar, C. S. (2012). Acta Cryst. E68, o147.]).

[Scheme 1]

Experimental

Crystal data

  • C9H10ClN3O

  • Mr = 211.65

  • Triclinic, [P \overline 1]

  • a = 5.9864 (3) Å

  • b = 7.4724 (5) Å

  • c = 11.0235 (8) Å

  • α = 83.103 (6)°

  • β = 80.040 (5)°

  • γ = 80.020 (5)°

  • V = 476.26 (5) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.37 mm−1

  • T = 293 K

  • 0.3 × 0.2 × 0.1 mm
Data collection

  • Oxford Diffraction Xcalibur Sapphire3 diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]) Tmin = 0.835, Tmax = 1.000

  • 6991 measured reflections

  • 1876 independent reflections

  • 1127 reflections with I > 2σ(I)

  • Rint = 0.053
Refinement

  • R[F2 > 2σ(F2)] = 0.068

  • wR(F2) = 0.205

  • S = 0.98

  • 1876 reflections

  • 131 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.60 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N11—H11⋯O12i 0.85 (5) 2.08 (5) 2.924 (4) 174 (5)
C4—H4⋯N1ii 0.93 2.55 3.369 (5) 147
Symmetry codes: (i) -x-1, -y, -z+1; (ii) x-1, y, z.

Data collection: CrysAlis PRO (Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812023537/lh5478sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812023537/lh5478Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812023537/lh5478Isup3.cml

checkCIF report


Comment top

Imidacloprid is an insecticide which acts as an agonist of the acetylcholine receptor of insect nervous system. Oral, acute and chronic toxicity of imidacloprid and its main metabolite 1-[(6-chloropyridin-3-yl)methyl] imidazolidin-2-one (urea derivative) in mid-gut and rectum were investigated in Apis mellifera (Suchail et al., 2001; Suchail et al., 2004). Acute intoxication by imidacloprid or its metabolites results in rapid appearance of neurotoxicity symptoms, such as hyper-responsiveness and, hyperactivity (Suchail et al., 2001). Many metabolites of imidacloprid have been identified, but the enzymatic basis for their formation has not been reported in many cases (Schulz-Jander & Casida, 2002). Imidacloprid is degraded by liver enzymes to other nitroimines such as the corresponding guanidine and urea derivatives. The fate of imidacloprid in soil environment in terms of the metabolites toxic to vertebrates has been reported by Pandey et al. (2009). The supreme biological profile of imidacloprid is giving impulse to the development of new products by modifying the structural features of the prototype (Kagabu et al., 2007). Therefore, in a search for new neonicotinoid insecticides with improved profiles, some neonicotinoid derivatives have been designed and synthesized. The crystal structure of the title compound (I) is shown in Fig. 1.

The bond lengths and angles in (I) show normal values and are comparable with related structures (Kapoor et al., 2011,2012; Kant et al., 2012). The plane through the pyridine ring forms dihedral angle of 76.2 (1)Å with the imidazoline ring plane. In the crystal, N—H···O hydrogen bonds link pairs of molecules to form inversion dimers (Fig. 2). These dimers are linked by weak C—H···N interactions. The crystal structure is further stabilized by π–π interactions between the pyridine ring of the molecule at (x, y, z) and the pyridine ring of an inversion related molecule at (1 - x, -y, -z)[centroid separation = 3.977 (2) Å, interplanar spacing = 3.267 Å and centroid shift = 2.267 Å].

Related literature top

For the background to the insecticidal applications of imidacloprid (N-{1-[(6-chloro-3-pyridyl)methyl]-4,5-dihydroimidazol-2-yl}nitramide), see: Samaritoni et al. (2003); Suchail et al. (2001, 2004); Schulz-Jander & Casida (2002); Kagabu et al. (2007); Pandey et al. (2009). For related structures, see: Kapoor et al. (2011, 2012); Kant et al. (2012).

Experimental top

Imidacloprid (0.256 g, 0.001 mol) was dissolved in 5 ml methanol and to it 5 ml of 1 N NaOH solution was added. The reaction mixture was refluxed for about 10 hrs on a water bath at 343K and then cooled. The reaction mixture was neutralized with 1 N HCl solution. The neutralized solution was kept standing for slow evaporation until a white transparent crystalline separated out (m.p. 416 K). LC—MS/MS: 212[M+H+], 195, 169, 159, 128, 126, 99, 92 m/z.

Refinement top

Hydrogen atom H11 was found in a difference map and refined isotropically. All other H atoms were positioned geometrically and were treated as riding on their parent C atoms, with C—H distances of 0.93–0.97 Å and with Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (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).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) with thermal ellipsoids drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. The packing of (I) with broken lines to show N—H···O hydrogen bonds.
1-[(6-Chloropyridin-3-yl)methyl]imidazolidin-2-one top
Crystal data top
C9H10ClN3OZ = 2
Mr = 211.65F(000) = 220
Triclinic, P1Dx = 1.476 Mg m−3
Hall symbol: -P 1Melting point: 416 K
a = 5.9864 (3) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.4724 (5) ÅCell parameters from 2653 reflections
c = 11.0235 (8) Åθ = 3.5–28.9°
α = 83.103 (6)°µ = 0.37 mm−1
β = 80.040 (5)°T = 293 K
γ = 80.020 (5)°Block, white
V = 476.26 (5) Å30.3 × 0.2 × 0.1 mm
Data collection top
Oxford Diffraction Xcalibur Sapphire3
diffractometer		1876 independent reflections
Radiation source: fine-focus sealed tube1127 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.053
Detector resolution: 16.1049 pixels mm-1θmax = 26.0°, θmin = 3.5°
ω scansh = −7→7
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)		k = −9→9
Tmin = 0.835, Tmax = 1.000l = −13→13
6991 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.068Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.205H atoms treated by a mixture of independent and constrained refinement
S = 0.98 w = 1/[σ2(Fo2) + (0.1095P)2]
where P = (Fo2 + 2Fc2)/3
1876 reflections(Δ/σ)max = 0.001
131 parametersΔρmax = 0.60 e Å−3
0 restraintsΔρmin = −0.26 e Å−3
Crystal data top
C9H10ClN3Oγ = 80.020 (5)°
Mr = 211.65V = 476.26 (5) Å3
Triclinic, P1Z = 2
a = 5.9864 (3) ÅMo Kα radiation
b = 7.4724 (5) ŵ = 0.37 mm−1
c = 11.0235 (8) ÅT = 293 K
α = 83.103 (6)°0.3 × 0.2 × 0.1 mm
β = 80.040 (5)°
Data collection top
Oxford Diffraction Xcalibur Sapphire3
diffractometer		1876 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)		1127 reflections with I > 2σ(I)
Tmin = 0.835, Tmax = 1.000Rint = 0.053
6991 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0680 restraints
wR(F2) = 0.205H atoms treated by a mixture of independent and constrained refinement
S = 0.98Δρmax = 0.60 e Å−3
1876 reflectionsΔρmin = −0.26 e Å−3
131 parameters
Special details top

Experimental. CrysAlis PRO, Oxford Diffraction Ltd., Version 1.171.34.40 (release 27–08-2010 CrysAlis171. NET) (compiled Aug 27 2010,11:50:40) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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
xyzUiso*/Ueq
Cl10.4849 (2)0.45046 (14)−0.23011 (9)0.0729 (5)
N10.5214 (5)0.2659 (4)−0.0175 (3)0.0489 (8)
C40.0675 (6)0.2139 (5)0.0355 (4)0.0542 (10)
H4−0.08580.19790.05280.065*
C30.2141 (5)0.1420 (4)0.1179 (3)0.0410 (8)
C20.4371 (5)0.1719 (5)0.0871 (3)0.0432 (8)
H20.53740.12370.14270.052*
C50.1490 (6)0.3105 (5)−0.0738 (3)0.0496 (9)
H50.05350.3601−0.13160.059*
C60.3766 (6)0.3299 (4)−0.0931 (3)0.0436 (8)
C70.1389 (6)0.0288 (5)0.2357 (4)0.0528 (9)
H7A0.0729−0.07170.21580.063*
H7B0.2721−0.02240.27470.063*
N8−0.0276 (5)0.1334 (4)0.3217 (3)0.0539 (8)
C90.0273 (6)0.2816 (5)0.3778 (3)0.0489 (9)
H9A0.04010.38770.31850.059*
H9B0.17030.24600.41080.059*
C10−0.1757 (6)0.3212 (5)0.4818 (4)0.0556 (10)
H10A−0.12500.30540.56190.067*
H10B−0.25750.44420.46880.067*
N11−0.3167 (6)0.1876 (5)0.4724 (3)0.0645 (10)
C12−0.2227 (6)0.0748 (5)0.3831 (3)0.0456 (9)
O12−0.2977 (4)−0.0596 (4)0.3591 (2)0.0627 (8)
H11−0.435 (8)0.156 (6)0.518 (4)0.091 (15)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0942 (9)0.0714 (8)0.0479 (7)−0.0244 (6)0.0061 (6)0.0070 (5)
N10.0365 (16)0.0625 (18)0.0457 (19)−0.0145 (13)0.0013 (14)0.0024 (15)
C40.0285 (17)0.068 (2)0.068 (3)−0.0144 (16)−0.0060 (17)−0.005 (2)
C30.0331 (17)0.0449 (17)0.044 (2)−0.0102 (14)0.0038 (15)−0.0095 (15)
C20.0330 (17)0.056 (2)0.040 (2)−0.0110 (14)−0.0023 (15)−0.0025 (16)
C50.043 (2)0.058 (2)0.048 (2)−0.0045 (16)−0.0123 (17)−0.0026 (18)
C60.048 (2)0.0440 (18)0.036 (2)−0.0116 (15)0.0023 (16)−0.0025 (15)
C70.048 (2)0.052 (2)0.053 (2)−0.0131 (16)0.0096 (18)−0.0017 (18)
N80.0459 (16)0.0637 (19)0.051 (2)−0.0266 (14)0.0192 (14)−0.0135 (16)
C90.051 (2)0.052 (2)0.043 (2)−0.0176 (16)0.0032 (17)−0.0041 (17)
C100.060 (2)0.063 (2)0.040 (2)−0.0163 (18)0.0084 (18)−0.0049 (18)
N110.054 (2)0.090 (2)0.052 (2)−0.0363 (19)0.0183 (17)−0.0188 (19)
C120.0399 (18)0.064 (2)0.034 (2)−0.0194 (16)−0.0016 (15)0.0038 (17)
O120.0553 (16)0.0826 (19)0.0558 (18)−0.0392 (14)0.0077 (13)−0.0107 (15)
Geometric parameters (Å, º) top
Cl1—C61.746 (3)C7—H7B0.9700
N1—C61.298 (4)N8—C121.359 (4)
N1—C21.344 (4)N8—C91.442 (4)
C4—C31.371 (5)C9—C101.534 (5)
C4—C51.386 (5)C9—H9A0.9700
C4—H40.9300C9—H9B0.9700
C3—C21.370 (4)C10—N111.437 (5)
C3—C71.507 (5)C10—H10A0.9700
C2—H20.9300C10—H10B0.9700
C5—C61.373 (5)N11—C121.357 (5)
C5—H50.9300N11—H110.85 (4)
C7—N81.444 (5)C12—O121.241 (4)
C7—H7A0.9700
C6—N1—C2115.8 (3)C12—N8—C9111.8 (3)
C3—C4—C5119.6 (3)C12—N8—C7123.6 (3)
C3—C4—H4120.2C9—N8—C7122.2 (3)
C5—C4—H4120.2N8—C9—C10103.9 (3)
C2—C3—C4117.2 (3)N8—C9—H9A111.0
C2—C3—C7120.5 (3)C10—C9—H9A111.0
C4—C3—C7122.3 (3)N8—C9—H9B111.0
N1—C2—C3124.7 (3)C10—C9—H9B111.0
N1—C2—H2117.6H9A—C9—H9B109.0
C3—C2—H2117.6N11—C10—C9102.9 (3)
C6—C5—C4117.1 (3)N11—C10—H10A111.2
C6—C5—H5121.4C9—C10—H10A111.2
C4—C5—H5121.4N11—C10—H10B111.2
N1—C6—C5125.5 (3)C9—C10—H10B111.2
N1—C6—Cl1116.2 (3)H10A—C10—H10B109.1
C5—C6—Cl1118.3 (3)C12—N11—C10112.8 (3)
N8—C7—C3112.5 (3)C12—N11—H11114 (3)
N8—C7—H7A109.1C10—N11—H11133 (3)
C3—C7—H7A109.1O12—C12—N11127.2 (3)
N8—C7—H7B109.1O12—C12—N8124.5 (3)
C3—C7—H7B109.1N11—C12—N8108.3 (3)
H7A—C7—H7B107.8
C5—C4—C3—C20.6 (5)C3—C7—N8—C12134.0 (3)
C5—C4—C3—C7−177.3 (3)C3—C7—N8—C9−64.8 (4)
C6—N1—C2—C3−0.5 (5)C12—N8—C9—C10−4.1 (4)
C4—C3—C2—N1−0.1 (5)C7—N8—C9—C10−167.3 (3)
C7—C3—C2—N1177.8 (3)N8—C9—C10—N111.1 (4)
C3—C4—C5—C6−0.4 (5)C9—C10—N11—C122.2 (4)
C2—N1—C6—C50.6 (5)C10—N11—C12—O12175.2 (4)
C2—N1—C6—Cl1−179.4 (2)C10—N11—C12—N8−4.9 (4)
C4—C5—C6—N1−0.2 (5)C9—N8—C12—O12−174.4 (3)
C4—C5—C6—Cl1179.8 (3)C7—N8—C12—O12−11.5 (6)
C2—C3—C7—N8115.6 (3)C9—N8—C12—N115.7 (4)
C4—C3—C7—N8−66.6 (4)C7—N8—C12—N11168.6 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N11—H11···O12i0.85 (5)2.08 (5)2.924 (4)174 (5)
C4—H4···N1ii0.932.553.369 (5)147
Symmetry codes: (i) −x−1, −y, −z+1; (ii) x−1, y, z.

Experimental details

Crystal data
Chemical formulaC9H10ClN3O
Mr211.65
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)5.9864 (3), 7.4724 (5), 11.0235 (8)
α, β, γ (°)83.103 (6), 80.040 (5), 80.020 (5)
V (Å3)476.26 (5)
Z2
Radiation typeMo Kα
µ (mm−1)0.37
Crystal size (mm)0.3 × 0.2 × 0.1
Data collection
DiffractometerOxford Diffraction Xcalibur Sapphire3
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
Tmin, Tmax0.835, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections		6991, 1876, 1127
Rint0.053
(sin θ/λ)max (Å−1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.068, 0.205, 0.98
No. of reflections1876
No. of parameters131
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.60, −0.26

Computer programs: CrysAlis PRO (Oxford Diffraction, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N11—H11···O12i0.85 (5)2.08 (5)2.924 (4)174 (5)
C4—H4···N1ii0.932.553.369 (5)147
Symmetry codes: (i) −x−1, −y, −z+1; (ii) x−1, y, z.
 

Acknowledgements

RK acknowledges the Department of Science and Technology for access to the single-crystal X-ray diffractometer sanctioned as a National Facility under project No. SR/S2/CMP-47/2003 and the University of Jammu, India, for financial support.

References

First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
 First citationKagabu, S., Ishihara, R., Hieda, Y., Nishimura, K. & Naruse, Y. (2007). J. Agric. Food Chem. 55, 812–818.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationKant, R., Gupta, V. K., Kapoor, K., Deshmukh, M. B. & Shripanavar, C. S. (2012). Acta Cryst. E68, o147.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationKapoor, K., Gupta, V. K., Deshmukh, M. B., Shripanavar, C. S. & Kant, R. (2012). Acta Cryst. E68, o469.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationKapoor, K., Gupta, V. K., Kant, R., Deshmukh, M. B. & Shripanavar, C. S. (2011). X-ray Struct. Anal. Online, 27, 55–56.  CrossRef CAS Google Scholar
 First citationOxford Diffraction (2010). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.  Google Scholar
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ISSN: 2056-9890
Volume 68| Part 6| June 2012| Page o1939
doi:10.1107/S1600536812023537
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