Startseite Naturwissenschaften The crystal structure of 4,9-bis(4-chlorophenyl)-1,6-bis(2-cyanobenzyl)-2,4a,5,6,7,7a-hexahydro-1H-2,7,5-(epiprop[2]ene[1,1,3]triyl)pyrrolo[3,4-b]pyridine-3,10-dicarbonitrile, C40H26Cl2N6
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The crystal structure of 4,9-bis(4-chlorophenyl)-1,6-bis(2-cyanobenzyl)-2,4a,5,6,7,7a-hexahydro-1H-2,7,5-(epiprop[2]ene[1,1,3]triyl)pyrrolo[3,4-b]pyridine-3,10-dicarbonitrile, C40H26Cl2N6

  • Ruotong Li ORCID logo EMAIL logo
Veröffentlicht/Copyright: 23. Oktober 2025

Abstract

C40H26Cl2N6, triclinic, P 1 (no. 2), a = 9.6327(10) Å, b = 11.4675(10) Å, c = 15.4576(15) Å, α = 88.213(4)°, β = 80.719(4)°, γ = 79.438(4)°, V = 1,656.6(3) Å3, Z = 2, Rgt(F) = 0.0759, wRref(F2) = 0.2355, T = 297 K.

CCDC no.: 2491833

The molecular structure is shown in the figure. Table 1 contains the crystallographic data and the list of the atoms including atomic coordinates and displacement parameters can be found in the cif-file attached to this article.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.23 × 0.20 × 0.18 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.24 mm−1
Diffractometer, scan mode: Bruker Apex-II, φ and ω scans
θmax, completeness: 25.0°, 100 %
N(hkl)measured, N(hkl)unique, Rint: 28,687, 5,838, 0.080
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 4,358
N(param)refined: 433
Programs: Bruker, 1 Olex2, 2 Shelx 3 , 4

1 Source of materials

The 2-cyanobenzyl bromide (7.84 g; 40 mmol) was added to the acetonitrile (40 mL) solution of 3-cyanopyridine (4.16 g; 40 mmol) to allow the mixture to react for 6–7 h. After the reaction is finished and cooled, dichloromethane is added to precipitate the product, the product is filtered and rinsed three times with dichloromethane (10 mL*3) to obtain 1-(2-cyanobenzyl)-3-cyano-1,4-dihydropyridine bromide, which is a white powder. The resulting 1-(2-cyanobenzyl)-3-cyano-1,4-dihydropyridine bromide (3.00 g; 10 mmol) is suspended in anhydrous THF (70 mL). After the addition of CuI (0.10 g; 0.5 mmol), a solution of 4-chlorophenylmagnesium bromide (1 M) in THF (10 mL, 10 mmol) was added dropwise to the suspension. After 1–1.5 h, the reaction solution was treated with a saturated aqueous solution of ammonium chloride (60 mL), then extracted with dichloromethane (50 mL*3) and water (150 mL), and distilled under reduced pressure to obtain the crude product. The 1-(2-cyanobenzyl)-3-cyano-4-(4-chlorophenyl)-1,4-dihydropyridine was obtained by methanol recrystallization. The 1-(2-cyanobenzyl)-3-cyano-4-(4-chlorophenyl)-1,4-dihydropyridine (1.23 g; 3.7 mmol) was dissolved in ethanol (30 mL) under stirring. Under room temperature and nitrogen protection, irradiation was performed with a blue LED light (10 W, 410 nm), and the reaction ended after 10 h. The solvent was removed by reduced pressure concentration and separated and purified by rapid chromatography (petroleum ether/ethyl acetate rations of 10:1 to 8:1) to obtain the title product (total yield of 41 %). Single crystals of the title compound were obtained by crystallization from a mixture of dichloromethane (1 mL) and n-hexane (2 mL).

2 Experimental details

Using Olex2, 2 the structure was solved with the SHELXT 3 structure solution program and refined with the SHELXL 4 refinement package. All hydrogen atoms were placed in the calculated positions.

3 Comment

Cage compounds are a unique molecular structure with significant applications in the medical field, serving various functions such as anti–HIV, 5 anticancer, 6 and acting as drug linkers. 7 The synthesized title compound is a 3,12-diazatetracyclododecane-diene derivative, which is a novel cage compound. 8 Based on the original compound, 3-cyanopyridine, we synthesized the structure of the new compound described in this paper with moderate yields. The reaction route adopted in this paper has good substrate applicability and functional group compatibility.

The title compound has a unique open-ended cage structure, with two dihydropyridine planes located in different planes, separated by a dihedral angle of 160.8°. In the crystal structure, the bond lengths of C–N are in the range of 1.137(4) Å–1.470(4) Å, and the bond lengths of C–Cl are 1.727(3) Å and 1.736(3) Å, respectively. The molecule is assembled by intermolecular interactions between benzene rings. 9


Corresponding author: Ruotong Li, College of Pharmacy, North China University of Science and Technology, Tangshan, Hebei 063210, P.R. China, E-mail:

  1. Author contributions: Author has accepted responsibility for the entire content of this submitted manuscript and approved submission.

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

References

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7. Vujcic, B.; Wyllie, J.; Tania, B. J.; White, K. F.; Cromwell, S.; Lupton, D. W.; Dutton, J. L.; Soares da Costa, T. P.; Houston, S. D. Cage Hydrocarbons as Linkers in Dimeric Drug Design: Case Studies with Trimethoprim and Tedizolid. Bioorg. Med. Chem. Lett. 2023, 80, 129086; https://doi.org/10.1016/j.bmcl.2022.129086.Suche in Google Scholar PubMed

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Received: 2025-07-05
Accepted: 2025-09-27
Published Online: 2025-10-23
Published in Print: 2025-12-17

© 2025 the author(s), published by De Gruyter, Berlin/Boston

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

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of (1Z, 2Z)-3-phenyl-2-propenal 2-(4-bromo-2-fluorophenyl)hydrazone, C15H12BrFN2
  4. Refinement of crystal structure of 2-(2,3-dihydro-3-oxo-1 H -inden-1-ylidene)-1 H -indene-1,3(2 H )-dione C18H10O3
  5. The crystal structure of 3-(1-fluoro-2-(naphthalen-2-yl)-2-oxoethyl)-2-methoxy-3,4-dihydroisoquinolin-1(2H)-one, C22H18FNO3
  6. Crystal structure of the dinuclear copper(II) complex bis(μ2-2,2′ -{[1,3-phenylenebis-(methylene)]bis(oxy)}dibenzoaot-κ4O,O′:O′′,O′′′)-bis(dimethylformamide-κ1O)dicopper(II), C50H44Cu2N2O14
  7. Crystal structure of poly[triaqua-(μ9-biphenyl-3,3′,5,5′-tetracarboxylic-κ8 O,O:O,O′: O,O″:O,O‴)samarium(III)sodium(I)], C16H12NaSmO11
  8. The crystal structure of 5-benzyl-1-(4-fluorobenzyl)-4-((4-fluorobenzyl)oxy)-1,5-dihydro-2H-pyrrol-2-one, C25H21F2NO2
  9. The crystal structure of diammonium 2,5-dihydroxyterephthalate, C8H12N2O6
  10. Crystal structure of (E)-4-(4-(1H-1,2,4-triazol-1-yl)benzylidene)-6,8-dimethoxy-3,4-dihydrobenzo[b]oxepin-5(2H)-one, C21H19N3O4
  11. Crystal structure of poly[oktakis(μ2-oxido-κ2O:O)-tetrakis(oxido-κ1O)-bis(μ2-1,1′-[1,4-phenylenebis(methylene)]di(1H-imidazole-κ2N:N′))-tetravanadium(V)-dizinc(II)] monohydrate, C28H30Zn2N8O13V4
  12. Crystal structure of acotiamide hydrochloride dimethylacetamide solvate (1/1), C25H40ClN5O6S
  13. Crystal structure of catena-poly[monoaqua (u2-(3-(3,5-dicarboxyphenyl)pyridine-2,6-dicarboxylic-k4O:O′:O″:N)zinc(II))] monohydrate, C15H11NO10Zn
  14. Crystal structure of dichlorido{2,6-bis(3,5-diisopropyl-N-pyrazolyl)pyridine}zinc(II), C23H33Cl2N5Zn
  15. Crystal structure of nitrato-κ2O,O′-[hydridotris(3,5-diethylpyrazol-1-yl)borato-κ3N,N′,N″]copper(II), C21H34BCuN7O3
  16. Crystal structure of 2,7-bis(3,5-diethyl-1H-pyrazol-4-yl)-benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone, C28H26N6O4
  17. Crystal structure of 2-(4-chlorophenyl)benzothiazole, C13H8ClNS
  18. Synthesis and crystal structure (3R,4′S)-4′-(3,5-dibromophenyl)-1′-methyl-2H-dispiro [benzofuran-3,3′-pyrrolidine-2′,2″-indene]-1″,2,3″-trione, C26H17Br2NO4
  19. Crystal structure of bis(((3a,7a-dihydro-1H-benzo[d][1,2,3]triazol-1-yl)methyl) triphenylphosphonium) tetrachloridomanganate(II), C50H42Cl4MnN6P2
  20. The crystal structure of 4,9-bis(4-chlorophenyl)-1,6-bis(2-cyanobenzyl)-2,4a,5,6,7,7a-hexahydro-1H-2,7,5-(epiprop[2]ene[1,1,3]triyl)pyrrolo[3,4-b]pyridine-3,10-dicarbonitrile, C40H26Cl2N6
  21. The crystal structure of poly((μ2-3-(3-nitro-4-carboxylphenyl)benzoate-κ3O, O′:O″)-μ2-1,4-bis(1-imidazolyl)benzene-κ2N:N′-cadmium(II)), C26H17N5O6Cd
  22. The crystal structure of 6-hydroxy-5H-pyrrolo[3,4-b]pyridine-5,7(6H)-dione monohydrate, C7H6N2O4
  23. Crystal structure of 4-((cyclohexylsulfonyl)methyl)-1,2,3,4-tetrahydrobenzo [4,5]imidazo[1,2-a]pyridine, C18H24N2O2S
  24. Crystal structure of 4,7-diphenyl-1,10-phenanthroline-κ2N,N′)-bis(2,4-di(fluorine)-1-phenylpyridine-κ2C,N)-iridium(III) hexafluorophosphate–dichloromethane (1/1), C47H30Cl2F10IrN4P
  25. Crystal structure of (4-(1-phenyl-1H-benzo[d]imidazol-2-yl)phenyl)boronic acid, C19H15BN2O2
  26. The crystal structure of (E)-(2-((pyridin-2-ylmethylene)amino)phenyl)arsonic acid, C12H11AsN2O3
  27. The crystal structure of N(benzyl(phenyl)carbomothioyl)benzamide, C21H18N2OS
  28. The crystal structure of bis(2-picolinium) hexachlorostannate dichloromethane monosolvate, C13H18Cl8N2Sn
  29. Crystal structure of poly[tetraaqua-bis(μ4-3–1-(carboxylatomethyl)-1H-1,2,4-triazole-3-carboxylato)-κ4O:O′,O″,N)zinc(II)], C5H7N3O6Zn
  30. The crystal structure of the co-crystal isonicotinamide – 2-(nitrophenyl)methanol (1/1), C6H6N2O·C7H7NO3
  31. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 2-fluorobenzoate hydrate, C23H25F2N3O6
  32. Crystal structure of [diaqua-{1H-benzo[d]imidazol-3-ium-5,6-dicarboxylato-κ2O,O′}magnesium(II)] C18H14MgN4O10
  33. Crystal structure of (3-(dimethoxymethyl)-5-methoxy-1H-indol-1-yl) (2-iodo-5-methoxyphenyl)methanone, C20H20INO5
  34. The crystal structure of 3,7,11-trimethylbenzo[5,6][1,4]thiazino[2,3,4-kl]phenothiazine 5,5,9,9-tetraoxide, C21H17NO4S2
  35. Crystal structure of tris(piperazine-1,4-diium)bis(2-hydroxy-1,2,3-propane-tricarboxylate) pentahydrate, C24H56N6O19
  36. Crystal structure of 2-chloro-5-((5-isopropyl-2-methylphenoxy)methyl)pyridine, C16H18ClNO
  37. Crystal structure of (E)-4-(4-(1H-pyrrol-1-yl)benzylidene)-6,8-dimethoxy-3,4-dihydrobenzo[(b)]oxepin-5(2H)-one, C23H21NO4
  38. Crystal structure of (E)-N′-(3,4-dichlorobenzylidene)-3,4,5-trimethoxybenzohydrazide, C17H16Cl2N2O4
  39. The crystal structure of 2-(2-hydroxyphenyl)-3-(pyridin-2-yl)-2,3- dihydroquinazolin-4(1H)-one, C19H15N3O2
  40. Crystal structure of 5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-8-methylchroman-4-one, C17H16O5
  41. Crystal structure of bis[(3,4-dimethoxybenzyl)triphenylphosphonium]di-μ2-bromido-dibromidodicopper(I)
  42. Crystal structure of bis [(1,3-dioxolan-2-ylmethyl)triphenylphosphonium] tetrabromidodicopper(I), C22H22Br2CuO2P
  43. Crystal structure of [1-(4-carboxyphenyl)-4-oxo-1,4-dihydropyridazine-3-carboxylic acid], C12H8N2O5
  44. The crystal structure of one-dimensional cooridnation polymer bis(thiocyanato)-bis((1E,2E)-1,2-bis(1-(pyridin-3-yl)ethylidene)-hydrazine κ2N:N)iron(II), (C30H28N10S2Fe)n
  45. Crystal structure of ((4-acetamidophenyl)sulfonyl)-l-alanine, C11H14N2O5S
  46. Crystal structure of [(1-naphthalen-1-yl-methyl)triphenylphosphonium] dichloridocopper(I), [C29H24P]+[CuCl2]
  47. RbTm3S5: the first rubidium lanthanoid(III) sulfide with CsEr3Se5-type crystal structure
  48. Crystal structure of 2,2′-((ethane-1,2-diylbis(methylammoniumdiyl))bis(methylene))bis(pyridin-1-ium) diiodido-tris(μ2-iodido-κ2I:I)dicopper(II) chloride dihydrate, C16H30Cu2I6N4O2
  49. The crystal structure of 4-(trifluoromethyl)pyridine-2-carboxylic acid, C7H4F3NO2
  50. The crystal structure of (E)-2-ethoxy-1-methoxy-4-(2-(methylsulfonyl)vinyl)benzene, C12H16O4S
  51. Crystal structure of potassium 1H,1H,2H,2H-perfluorooctanesulfonate, C8H4O3F13SK
  52. Crystal structure of 4-(4-(quinolin-8-yloxy)-1,2,5-thiadiazol-3-yl)morpholine, C15H14O2N4S
  53. The crystal structure of 1,4-bis(bromomethyl)-2,5-dimethylbenzene, C10H12Br2
  54. The crystal structure of imidazo[4,5-e][1,3]diazepine-4,6,8-triamine methanol solvate, C7H11N7O
  55. The crystal structure of chlorido-bis(1,10-phenantroline-κ2N,N′)-(2-formylphenoxyacetato-κ2O,O) lead(II), C33H23N4O4ClPb
  56. Crystal structure of pyridinium tetrakis(1,1,1-trifluoro-2,4-pentadionato-κ2O,O′)yttrium(III) C20F12H16YO8C5H6N
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