Home The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2
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The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2

  • Zhen Chen ORCID logo , Kang Guo , Yanwen Sun EMAIL logo , Chang Liu and Sijun Li
Published/Copyright: March 27, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 3

Abstract

C10H11ClN4O2, monoclinic, P21/c (no. 14), a = 12.7802(17) Å, b = 7.6211(12) Å, c = 12.0486(17) Å, β = 95.551(4)°, V = 1168.0(3) Å3, Z = 4, R gt (F) = 0.0562, wR ref (F 2) = 0.1172, T = 273(2) K.

CCDC no.: 2326833

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.20 × 0.10 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.32 mm−1
Diffractometer, scan mode: Bruker Smart Apex II, φ and ω
θ max, completeness: 25.0°, >99 %
N(hkl)measured, N(hkl)unique, R int: 17,187, 2047, 0.071
Criterion for I obs, N(hkl)gt: I obs > 2σ (I obs), 1242
N(param)refined: 154
Programs: Bruker [1], Olex2 [2], Shelx [3, 4], Diamond [5]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
Cl1 −0.05579 (8) −0.73366 (15) 0.85293 (8) 0.0838 (4)
O1 0.53016 (17) −0.8124 (3) 0.28131 (19) 0.0634 (7)
O2 0.5971 (2) −0.5955 (3) 0.3834 (2) 0.0741 (8)
N1 0.1315 (2) −0.8538 (4) 0.8340 (2) 0.0520 (7)
N2 0.31630 (19) −0.9053 (3) 0.5092 (2) 0.0477 (7)
N3 0.3704 (2) −0.9947 (4) 0.3525 (2) 0.0540 (7)
H3 0.407054 −0.999009 0.296406 0.065*
N4 0.5304 (2) −0.7188 (4) 0.3678 (2) 0.0533 (7)
C1 0.0537 (3) −0.7680 (5) 0.7795 (3) 0.0518 (9)
C2 0.0527 (3) −0.7055 (5) 0.6729 (3) 0.0618 (10)
H2 −0.006112 −0.649300 0.637910 0.074*
C3 0.1421 (3) −0.7291 (4) 0.6195 (3) 0.0560 (9)
H3A 0.145117 −0.686529 0.547542 0.067*
C4 0.2275 (2) −0.8162 (4) 0.6730 (2) 0.0425 (8)
C5 0.2170 (2) −0.8778 (4) 0.7788 (2) 0.0463 (8)
H5 0.272945 −0.940372 0.814573 0.056*
C6 0.3296 (2) −0.8386 (5) 0.6230 (2) 0.0533 (9)
H6A 0.365395 −0.726346 0.623439 0.064*
H6B 0.373882 −0.919001 0.668914 0.064*
C7 0.2547 (3) −1.0645 (4) 0.4823 (3) 0.0552 (9)
H7A 0.179953 −1.041521 0.480825 0.066*
H7B 0.273775 −1.157219 0.535618 0.066*
C8 0.2846 (3) −1.1123 (5) 0.3672 (3) 0.0741 (12)
H8A 0.306815 −1.233801 0.364420 0.089*
H8B 0.226358 −1.093064 0.310714 0.089*
C9 0.3868 (2) −0.8800 (4) 0.4345 (2) 0.0419 (8)
C10 0.4627 (2) −0.7474 (4) 0.4453 (3) 0.0488 (8)
H10 0.466792 −0.676188 0.508198 0.059*

1 Source of materials

We started the synthesis of 2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine from 1,1-dimethylthio-2-nitroethylene and N-2(chloro-5-pyridylmethyl)ethylenediamine according to the literature reported by Li [6]. A mixture of 1,1-dimethylthio-2-nitroethylene (662 mg 4.0 mmol) prepared from nitromethane and carbon disulfide and N-2(chloro-5-pyridylmethyl)ethylenediamine (754 mg 4.1 mmol) in anhydrous ethanol (9 mL) was refluxed for 8 h affording a clear yellow solution. The solvent was removed in vacuo after cooling to ambient temperature. The crude product was purified by silica gel chromatography using dichloromethane:acetone (4:1, v/v) as eluant to give a white power. Then a certain amount of white powder was dissolved in ethyl acetate. After solvent slowly evaporated at room temperature, the crystals were obtained.

2 Experimental details

The structure was solved by Direct Methods with the SHELX program system [3]. All H-atoms were positioned geometrically and refined using a riding model with d(N–H) = 0.86 Å, d(C–H) = 0.93 Å (aromatic and olefin CH), 0.97 Å (methylene CH2). For all H atoms, isotropic displacement parameters were assigned as U iso (H) = 1.2 U eq (N, C).

3 Comment

Nitrogen-containing heterocyclic insecticide has successful established its place in the field of insecticides research and development [7]. Especially, the neonicotinic insecticides are widely concerned and studied in the field of crop protection [8]. In addition, how to construct nitrogen heterocyclic ring and polycyclic compounds is also a classical subject in the field of synthesis. Title compound (I) is a key intermediate in the synthesis of complicated neonicotinic insecticides [8], [9], [10], [11]. It is not only a nitrogen-containing heterocyclic compound in itself, but also a precursor to construct polycyclic compounds through cyclization with unsaturated aldehydes. In view of the excellent potential of this compound, it is worth studying its synthesis optimization and structural characteristics.

The asymmetric unit of (I) is shown in the figure. The C=C bond length is 1.398(4) Å and the C=C double bond in compound (I) will lead to geometrical isomerism. Single crystal X-ray diffraction confirmed that the title compound is the (E)-diastereomer. The C–Cl bond is 1.747(3) Å. The C–N bond lengths are between 1.312(4) and 1.466(4) Å. The N–O bond lengths are between 1.262(3) and 1.270(3) Å. The O–N–O bond angle is 119.2(3)°. All these values are in the normal range [12, 13]. The dihedral angle between the mean planes passing through the pyridine ring and the imidazoline ring is 81.79(3). The C4–C6–N2 bond angle 113.024(6)° is smaller than the value for this bond angle in the similar structure (E)-2-[1-[(6–chloropyridin-3-yl)methyl]-2-imidazolidinylidene]-2-nitroacetonitrile [14]. The torsion angle of C4–C6–N2–C7 is −52.253(9)° which is obviously different with the value 88.1° observed in similar structure 2(E)-2-[1-[(6–chloropyridin-3-yl)methyl]-2-imidazolidinylidene]-2-nitroacetonitrile, which may be due to the space effect and interaction of cyano group in comparative structure. There exist intramolecular interactions [N3⋯O1 = 2.684(4) Å and N3–H3⋯O1 = 120.147(7)°] and intermolecular interactions [N3⋯O2 i  = 3.012(3) Å and N3–H3⋯O2 i  = 142.543(8)° (i = 1 − X, −1/2 + Y, 1/2 − Z)] between N–H donors from imidazoline ring and the oxygen atoms from nitro group. The presence of intermolecular hydrogen bonds results in the formation of one-dimensional chain-like structure along the (010) direction. There are four non-classical hydrogen bonds between C–H donors and the oxygen atoms from nitro group. The intermolecular interactions [C6⋯O2 ii  = 3.441(4) Å and C6–H6A⋯O2 ii  = 162.998(6)° (ii = 1 − X, −1 − Y, 1 − Z)] and [C6⋯O1 iii  = 3.349(4) Å and C6–H6B⋯O1 iii  = 157.636(6)° (iii = 1 − X, −2 − Y, 1 − Z)] lead the extension of one-dimensional chain structure along the (001) direction to two-dimensional (2D) supramolecular layer. The existence of intermolecular interactions [C10⋯O2 ii  = 3.462(4) Å and C10–H10⋯O2 ii  = 150.724(6)° and C7⋯O2 iii  = 3.511(4) Å and C7–H7B⋯O2 iii  = 151.176(6)°] enhanced the stability of this structure.

Corresponding author: Yanwen Sun, School of Chemistry and Chemical Engineering, Hebei Normal University for Nationalities, Higher Education Park, Chengde 067000, P.R. China, E-mail:

Funding source: Scientific and Technological Research Project of Institutions of Higher Education in Hebei Province

Award Identifier / Grant number: ZC2024070

Funding source: S&T Program of Chengde

Award Identifier / Grant number: 202205B090, HZLC2024020

  1. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

  2. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  3. Research funding: The work was supported by Scientific and Technological Research Project of Institutions of Higher Education in Hebei Province (ZC2024070) and S&T Program of Chengde (No. 202205B090, No. HZLC2024020).

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Received: 2024-01-27
Accepted: 2024-03-01
Published Online: 2024-03-27
Published in Print: 2024-06-25

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/ncrs-2024-0045
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of tris((Z)-2-hydroxy-N-((E)-pyridin-2-ylmethylene)benzohydrazonato-k2O,N)europium(III), C39H30N9O6Eu
  4. Crystal structure of (E)-3-(benzylideneamino)-2-phenylthiazolidin-4-one, C16H14N2OS
  5. The crystal structure of (E)-4-fluoro-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H15FN2O
  6. Crystal structure of (6-chloropyridin-3-yl)methyl 2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  7. Crystal structure of methyl 3-methoxy-4-(2-methoxy-2-oxoethoxy)benzoate, C12H14O6
  8. The crystal structure of bis[(4-methoxyphenyl)(picolinoyl)amido-κ2 N:N′]copper(II), C26H22CuN4O4
  9. The crystal structure of poly[di(μ2-aqua)-diaqua-bis(3-aminopyridine-4-carboxylate-κ2 O: O′)-tetra(μ2-3-aminopyridine-4-carboxylate-κ2 O: O′)-dineodymium(III), [Nd2(C6H5N2O2)6(H2O)4] n
  10. The crystal structure of t-butyl 7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoate, C28H34FNO4
  11. Crystal structure of catena-poly[(benzylamine-κ1 N)-(sorbato-κ1 O)-(μ2-sorbato-κ2 O,O′)-copper(II), C19H23CuNO4
  12. Crystal structure of (4-(2-chlorophenyl)-1H-pyrrol-3-yl)(ferrocenyl) methanone, C21H16ClFeNO
  13. The crystal structure of N-[4-(4-bromophenyl)-1,3-thiazol-2-yl]-3-(2-methylphenyl)-2-sulfanylprop-2-enamide hydrate, C19H17BrN2O2S2
  14. The crystal structure of N′-{5-[2-(2,6-dimethylphenoxy) acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide hydrate
  15. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C26H24O3
  16. Crystal structure of naphthalen-1-ylmethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C25H22O3
  17. Crystal structure of poly[diaqua- (μ4-5-(1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ5N:O,O’:O’’:O’’’)calcium(II), C10H9CaN3O6
  18. Crystal structure of (E)-N′-(4-((E)-3-(dimethylamino)acryloyl)-3-hydroxyphenyl)-N, N-dimethylformimidamide, C14H19N3O2
  19. Crystal structure of (E)-3-(dimethylamino)-1-(2-hydroxy-4,6-dimethoxyphenyl)prop-2-en-1-one, C13H17NO4
  20. Crystal structure of (2-chloropyridin-3-yl)methyl-2-(6-methoxynaphthalen-2-yl)propanoate, C20H18ClNO3
  21. The crystal structure of diethyl 4-(3,4-dimethylphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate, C21H27NO4
  22. Crystal structure of (8R,9S,10R,13S,14S,17S)-17-hydroxy-10,13-dimethyl-17-((4-(2-phenylpropyl)phenyl)ethynyl)-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H42O2
  23. Synthesis and crystal structure of 4-(4-cyclopropylnaphthalen-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C15H13N3S
  24. Crystal structure of catena-poly[aqua-(2,6-di-(2-pyridyl)-pyridine-κ3 N,N′, N″)(μ2-1,4-naphthalene dicarboxylato-κ2 O,O′)nickel(II)], C27H19NiN3O5
  25. Crystal structure of 3-(diphenylphosphoryl)-3-hydroxy-1-phenylpropan-1-one, C21H19O3P
  26. The crystal structure of R,S-{N-[(2-oxidonaphthalen-1-yl)methylidene]phenylglycinato}divinylsilicon, C23H19NO3Si
  27. The crystal structure of 1,2,4-tris(bromomethyl)benzene, C9H9Br3
  28. Crystal structure of chlorido-[4-(pyridin-2-yl)benzaldehyde-κ2 N,C]-(diethylamine-κ1 N)platinum(II), C16H18ClN2OPt
  29. Crystal structure of 3-(methoxycarbonyl)-1-(4-methoxyphenyl)-2,3,4,9- tetrahydro-1H-pyrido[3,4-b]indol-2-ium chloride hydrate, C40H48Cl2N4O9
  30. The crystal structure of 1-(2-chlorobenzyl)-3-(3-chlorophenyl)urea, C14H12Cl2N2O
  31. Hydrothermal synthesis and crystal structure of aqua-tris(4-acetamidobenzoato-κ2 O,O′)-(1,10-phenanthroline-κ2 N,N′)terbium(III) hydrate C39H36N5O11Tb
  32. The crystal structure of zwitterionic 3-aminoisonicotinic acid, C6H6N2O2
  33. The crystal structure of bis{[monoaqua-μ2-4-[(pyridine-4-carbonyl)-amino]-phthalato-κ3 N:O,O′-(2,2′-bipyridine κ2 N,N′)copper(II)]}decahydrate, C48H56N8O22Cu2
  34. Crystal structure of poly[μ10-4,4′-methylene-bis(oxy)benzoatodipotassium], C15H10K2O6
  35. The crystal structure of catena-poly[[tetraaqua[(μ2-1,4-di(4-methyl-1-imidazolyl)benzene] cobalt(II)]bis(formate)], C16H24CoN4O8
  36. The crystal structure of (E)-2-chloro-5-((2-(nitromethylene)imidazolidin-1-yl)methyl)pyridine, C10H11ClN4O2
  37. The crystal structure of (E)-1-(((2-amino-4,5-dimethylphenyl)iminio)methyl)naphthalen-2-olate, C19H18N2O
  38. Crystal structure of N-(acridin-9-yl)-2-(4-methylpiperidin-1-yl) acetamide monohydrate, C21H25N3O2
  39. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2 O,O′)-zinc(II), C14H20Cl2N4O4Zn
  40. The crystal structure of 2,8-diethyl-1,3,7,9-tetramethyl-4λ4,5λ4-spiro[dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinine-5,2′-naphtho[1,8-de][1,3,2]dioxaborinine], C25H29BN2O2
  41. The crystal structure of 5-tert-butyl-2-(5-tert-butyl-3-iodo-benzofuran-2-yl)-3-iodobenzofuran, C24H24I2O2
  42. Synthesis and crystal structure of methyl 2-{[4-(4-cyclopropyl-1-naphthyl)-4H-1,2,4-triazole-3-yl]thio} acetate, C18H17N3O2S
  43. The crystal structure of n-propylammonium bis(2,3-dimethylbutane-2,3-diolato)borate-boric acid (1/1), [C3H10N][C12H24BO4]·B(OH)3
  44. Crystal structure of methyl 1-(2-bromophenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C19H17BrN2O2
  45. Crystal structure of (4-bromobenzyl)triphenylphosphonium bromide ethanol solvate, C52H48Br4OP2
  46. The crystal structure of unsymmetrical BOPHY C26H27BN4
  47. The crystal structure of Tb3B5O11(OH)2
  48. The crystal structure of (Z)-4-ethyl-2-((4-ethyl-3,5-dimethyl-1H-pyrrol-2-yl)methylene)-3,5-dimethyl-2H-pyrrol-1-ium 2,2'-spirobi[naphtho[1,8-de][1,3,2]dioxaborinin]-2-uide, C37H37BN2O4
  49. Crystal structure of bis(methylammonium) hexadecaselenidopalladate(II), (CH3NH3)2PdSe16
  50. The crystal structure of (2-diphenylphosphanylphenyl) 2-[7-(dimethylamino)-2-oxochromen-4-yl]acetate, C31H26NO4P
  51. Crystal structure of (E)-6-(4-ethylpiperazin-1-yl)-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C23H25FN2O
  52. The structure of RUB-56, (C6H16N)8 [Si32O64(OH)8]·32 H2O, a hydrous layer silicate (2D-zeolite) that contains microporous levyne-type silicate layers
  53. Crystal structure of 4-amino-3,5-dibromobenzonitrile, C7H4Br2N2
  54. Crystal structure of 2-(naphthalen-1-yl)ethyl 2-acetoxybenzoate, C21H18O4
  55. Single-crystal structure determination of Tm3B12O19(OH)7
  56. Crystal structure determination of NdB3.6O7
  57. The crystal structure of NdB6O8(OH)5·H3BO3
  58. Crystal structure of 2-(5-ethylpyridin-2-yl)ethyl 2-(6-methoxynaphthalen-2-yl)propanoate, C23H25NO3
  59. Crystal structure of N-(1-(3,4-dimethoxyphenyl)-2-methylpropyl)aniline, C18H23NO2
  60. Crystal structure of Ba6Cd12Mn4SiF48
  61. Synthesis and crystal structure of 5-fluoro-1-methyl-2-oxo-3-(2-oxochroman-4-yl)indolin-3-yl acetate, C20H16FNO5
  62. The crystal structure of 6-methacryloylbenzo[d][1,3]dioxol-5-yl 4-nitrobenzenesulfonate, C17H13NO8S
  63. Crystal structure of ethyl 2-(3-benzyl-4-oxo-3,4-dihydrophthalazin-1-yl)- 2,2-difluoroacetate, C19H16F2N2O3
  64. The crystal structure of tetrakis(μ 2-(1H-benzimidazole-2-methoxo-κ2 N,O:O:O)-(n-butanol-κO)-chlorido)-tetranickel(II), C48H68Cl4N8O8Ni4
  65. Synthesis and crystal structure of trans-tetraaqua-bis((1-((7-hydroxy-3-(4-methoxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carbonyl)oxy-κO)zinc(II)hexahydrate, C46H64N2O28S2Zn
  66. The crystal structure of 1-(4-carboxybutyl)-3-methyl-1H-imidazol-3-ium hexafluoridophosphate, C9H15F6N2O2P
  67. Crystal structure of 1-(4-chlorophenyl)-4-(2-furoyl)-3-phenyl-1H-pyrazol-5-ol, C20H13ClN2O3
  68. Crystal structure of dimethyl (R)-2-(3-(1-phenylethyl)thioureido)-[1,1′-biphenyl]-4,4′-dicarboxylate, C25H24N2O4S
  69. The crystal structure of 1-(3-carboxypropyl)-1H-imidazole-3-oxide, C7H10N2O3
  70. Synthesis and crystal structure of dimethyl 4,4′-(propane-1,3-diylbis(oxy))dibenzoate, C19H20O6
  71. Crystal structure of methyl-1-(p-tolyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, C20H20N2O2
  72. The crystal structure of 1-(1-adamantan-1-yl)ethyl-3-(3-methoxyphenyl)thiourea, C20H28N2OS
  73. The crystal structure of N,N′-carbonylbis(2,6-difluorobenzamide), C15H8F4N2O3
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