Home Crystal structure of 5-(2,2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a]isoquinoline-3-carbonitrile, C20H15F2N3O
Article Open Access

Crystal structure of 5-(2,2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a]isoquinoline-3-carbonitrile, C20H15F2N3O

  • Hongqian Liu , Hongmei Liu , Shaoyan Fu and Wenqiang Tang ORCID logo EMAIL logo
Published/Copyright: April 24, 2025

Abstract

C20H15F2N3O, monoclinic, P21/c (no. 14), a = 7.2737(2) Å, b = 9.5461(3) Å, c = 24.0298(8) Å, β = 91.5320(10)°, V = 1,667.92(9) Å3, Z = 4, R gt (F) = 0.0459, wR ref (F2) = 0.1164, T = 150 K.

CCDC no.: 2442661

The molecular structure is shown in the figure. Table 1 contains the crystallographic data. 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: 0.15 × 0.09 × 0.05 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: Rigaku SuperNova, ω scans
θmax, completeness: 26.4°, 99 %
N(hkl)measured, N(hkl)unique, Rint: 16209, 3363, 0.072
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 2,631
N(param)refined: 237
Programs: Rigaku 1 , SHELX 2 , 3 , Olex2 4

1 Source of materials

A 20 mL test tube equipped with a magnetic stir bar was charged with 4-(1-methacryloyl-1H-benzo[d]imidazol-2-yl)benzonitrile (1 equiv., 0.2 mmol), NaSO2CF2Me (3 equiv., 0.6 mmol), LiClO4 (0.3 M in MeCN/H2O), and a mixed solvent system of MeCN (4.5 mL) and H2O (1.5 mL) under an inert atmosphere. A carbon plate served as the anode, while a platinum plate functioned as the cathode. The reaction mixture was electrolyzed in an undivided cell at room temperature using a constant voltage of 2.1 V for 3 h. Post-electrolysis, the crude product was extracted thrice with EtOAc (10 mL each). The combined organic layers were dried over anhydrous Na2SO4, concentrated under reduced pressure, and purified via silica gel column chromatography (eluent: gradient of hexanes/EtOAc) to yield the final products.

2 Experimental details

Initial phase determination was achieved via the ShelXT algorithm, 2 followed by iterative refinement and constrained least-squares optimization using ShelXL 3 within the Olex2 platform. 4

3 Comment

Isoquinoline derivatives constitute a structurally diverse and biologically significant class of heterocyclic compounds, serving as fundamental building blocks in numerous alkaloids and pharmaceutical agents. 5 Despite extensive studies on their synthetic pathways and biological applications, the precise structural elucidation of complex isoquinoline derivatives-particularly those incorporating multiple stereocenters, fluorine-containing substituents, or fused ring systems-remains challenging yet critical for understanding molecular recognition mechanisms and reactivity patterns. 6 , 7 , 8 , 9 The present study focuses on the crystallographic characterization of 5-(2, 2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a] isoquinoline-3-carbonitrile, a multifunctional heterocycle exhibiting intriguing features.

The molecular architecture exhibits a central fused bicyclic framework comprising a benzimidazole ring and an isoquinoline ring. This fused system establishes a planar, electron-rich heterocyclic core. 10 , 11 , 12 , 13 , 14 A carbonyl double bond (C7=O) with a bond length of 1.208 Å is present at the 6-oxo substituent located at position C7.

The nitrile group at C11 resides in the same plane as the fused rings, maintaining coplanarity with the central heterocyclic system. Attaching to the fused ring junction are two substituents: a methyl group (–CH3) and a 2-difluoropropyl group (–CH2CF2CH3) at position C8. Notably, the fluorine atoms (F1/F2) exhibit significant electron-withdrawing effects, which destabilize ground-state conformations and exert substantial influence on intermolecular interactions.

Crystal structure analysis reveals the absence of pronounced hydrogen bonding networks. The molecules aggregate through ππ stacking interactions between adjacent aromatic rings, with interplanar distances between stacked layers measuring approximately 3.6 Å. These ππ interactions, combined with van der Waals forces, constitute the primary stabilizing mechanisms for the crystal lattice.


Corresponding author: Wenqiang Tang, Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang, Shaanxi, China, E-mail:

Acknowledgments

This work was financially supported by the projects of Social Development in Shaanxi Province Science and Technology Department (2023-YBSF-036), the 2024 Key Scientific Research Program Projects of the Shaanxi Provincial Department of Education (Key Laboratory Projects, 24JS004), the 2023 research and development project of the Xianyang Science and Technology Bureau (L2023-ZDYF-SF-030), Key Laboratory of Molecular Imaging and Drug Synthesis of Xianyang city (2021QXNL-PT-0008), School-level Scientific and Technological Innovation Team for Design, Synthesis and Structural Modification of Drug Molecules (2024KCTD04).

References

1. Rigaku, O. D. CrysAlisPRO; Rigaku Oxford Diffraction Ltd: Yarnton, Oxfordshire, England, 2017.Search in Google Scholar

2. Sheldrick, G. M. SHELXT-Integrated Space-Group and Crystal-Structure Determination. Acta Crystallogr., Sect. A: Found. Adv. 2015, 71, 3–8. https://doi.org/10.1107/s2053273314026370.Search in Google Scholar PubMed PubMed Central

3. Sheldrick, G. M. Crystal Structure Refinement with SHELXL. Acta Crystallogr. Sect. C: Struct. Chem. 2015, 71, 3–8. https://doi.org/10.1107/s2053229614024218.Search in Google Scholar

4. Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A.; Puschmann, H. OLEX2: A Complete Structure Solution, Refinement and Analysis Program. J. Appl. Crystallogr. 2009, 42, 339–341. https://doi.org/10.1107/s0021889808042726.Search in Google Scholar

5. Kraus, G. A.; Gupta, V.; Kohut, M.; Singh, N. A Direct Synthesis of 5,6-Dihydroindolo[2,1-a]isoquinolines that Exhibit Immunosuppressive Activity. Bioorg. Med. Chem. Lett. 2009, 19, 5539–5542. https://doi.org/10.1016/j.bmcl.2009.08.057.Search in Google Scholar PubMed

6. Kilcigil, G. A.; Kuş, C.; Altanlar, N.; Özbey, S. Synthesis and Antimicrobial Evaluation of Some New 2-(2-(p-Chlorophenyl) benzimidazol-1-yl methyl)-5-substituted amino-[1, 3, 4]-thiadiazoles. Turk. J. Chem. 2005, 29, 153–162.Search in Google Scholar

7. Özbey, S.; Kaynak, F. B.; Göker, H.; Kuş, C. Synthesis and Crystal Structure Elucidation of 1-(4-Fluorobenzyl)-2-(4-cyanophenyl)-1H-benzimidazole-5-carbonitrile. J. Chem. Crystallogr. 2004, 34, 851–858. https://doi.org/10.1007/s10870-004-7718-0.Search in Google Scholar

8. Chang, M.-Y.; Wu, M.-H.; Chen, Y.-L. Synthesis of Dihydrobenzoimidazo[2,1-a]isoquinolines. Tetrahedron Lett. 2012, 53, 4156–4160. https://doi.org/10.1016/j.tetlet.2012.05.132.Search in Google Scholar

9. Nandi, S.; Samanta, S.; Jana, S.; Ray, J. K. Synthesis of Substituted Benzimidazo[2,1-a]isoquinolines and its Condensed Analogues Using Pd(0)-Catalyzed Cyclization/C–H Activation. Tetrahedron Lett. 2010, 51, 5294–5297. https://doi.org/10.1016/j.tetlet.2010.07.162.Search in Google Scholar

10. Kazak, C.; Yilmaz, V. T.; Goker, H.; Kus, C. 1-n-Butyl-2-(4′-fluorophenyl)-1H-benzimidazole-6-carbonitrile. Acta Crystallogr. E 2004, 60, m819–m821. https://doi.org/10.1107/s1600536804011468.Search in Google Scholar

11. Low, J. N.; Insuasty, B.; Torres, H.; Cobo, J. 6-(4-Fluorophenyl)-5, 6-dihydrobenzimidazo[1,2-c]quinazoline. Acta Crystallogr. E 2003, 59, o1801–o1803. https://doi.org/10.1107/s1600536803023663.Search in Google Scholar

12. Zheng, L.; Hua, R. Modular Assembly of Ring-Fused and π-Extended Phenanthroimidazoles via C–H Activation and Alkyne Annulation. J. Org. Chem. 2014, 79, 3930–3936. https://doi.org/10.1021/jo500401n.Search in Google Scholar PubMed

13. Gilbert, J. G.; Addison, A. W.; Prabakaran, P.; Butcher, R. J.; Bocelli, G. A Novel Paradigm for Metal-Induced Ring Flipping in the Copper(II) Complex of 1, 2-Bis(N-methylbenzimidazol-2′-yl)benzene triflate. Inorg. Chem. Commun. 2004, 7, 701–704. https://doi.org/10.1016/j.inoche.2004.03.019.Search in Google Scholar

14. Ramesh, V.; Gangadhar, M.; Babu Nanubolu, J.; Reddy Adiyala, P. Visible-Light-Induced Deaminative Alkylation/Cyclization of Alkyl Amines with N-Methacryloyl-2-phenylbenzoimidazoles in Continuous-Flow Organo-Photocatalysis. J. Org. Chem. 2021, 86, 12908. https://doi.org/10.1021/acs.joc.1c01555.Search in Google Scholar PubMed

Received: 2025-03-11
Accepted: 2025-04-10
Published Online: 2025-04-24
Published in Print: 2025-06-26

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

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

Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of 5,5′-bis(2,4,6-trinitrophenyl)-2,2′-bi(1,3,4-oxadiazole), C16H4N10O14
  4. Crystal structure of catena-poly[(μ3-4,4′-oxydibenzoato- κ5 O,O: O,O:O)-bis(2,4,6-tri(3-pyridine)-1,3,5-triazine-κ1 N)cadmium(II)], C50H32CdN12O5
  5. The crystal structure of 1,4-diazepane-1,4-diium potassium trinitrate, C5H14KN5O9
  6. The crystal structure of benzyl 2,2,5,5-tetramethylthiazolidine-4-carboxylate, C15H21NO2S
  7. Crystal structure of 2-hydroxyethyl-triphenylphosphonium tetracyanidoborate, C24H20BN4OP
  8. The crystal structure of 1-methyl-3-(N-methylnitrous amide–N-methylene) imidazolidine-2,4,5-trione
  9. Crystal structure of N-((3-cyano-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-(2,2,2-trifluoroacetyl)-1H-pyrazol-5-yl)carbamoyl)-2,6-difluorobenzamide, C20H7Cl2F8N5O3S
  10. Crystal structure of 5-(2,2-difluoropropyl)-5-methylbenzo[4,5]imidazo[2,1-a] isoquinolin-6(5H)-one, C20H18F2N2O
  11. The crystal structure of N′,N″-[1,2-bis(4-chlorophenyl)ethane-1,2-diylidene]bis(furan-2- carbohydrazide), C24H16Cl2N4O4
  12. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromoantimony(III), [C25H21BrP]+[SbBr4]
  13. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromidoindium(III), [C25H21BrP]+[InBr4]
  14. The crystal structure of 4-carboxy-2-oxobutan-1-aminium chloride, C5H10ClNO3
  15. Crystal structure of (4-(4-chlorophenyl)-1H-pyrrole-3-carbonyl)ferrocene, C21H16ClFeNO
  16. The crystal structure of dichlorido(η6-p-cymene)(triphenylarsine)ruthenium(II), C28H29AsCl2Ru
  17. Crystal structure of (Z)-2-hydroxy-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H16N2O2
  18. The crystal structure of 10-(1-bromoethyl)-14-(bromomethyl)dibenzo[a, c]acridine, C24H17NBr2
  19. Synthesis and crystal structure of 6-methoxy-7-[(4-methoxyphenyl)methoxy]-2H-1-benzopyran-2-one, C18H16O5
  20. Synthesis and crystal structure of ethyl 4-((4-trifluoromethylbenzyl)amino)benzo, C17H16F3NO2
  21. The crystal structure of (Z)-2-(tert-butyl)-6-(7-(tert-butyl)-5-methylbenzo[d][1,3]oxathiol-2-ylidene)-4-methylcyclohexa-2,4-dien-1-one, C23H28O2S
  22. The crystal structure of (R)-2-aminobutanamide hydrochloride, C4H11ClN2O
  23. Crystal structure of bromido[hydridotris(3-tert-butyl-5-isopropylpyrazolyl)borato-κ3 N,N′,N″]copper(II), C30H52BBrCuN6
  24. Crystal structure of chlorido{hydridotris[3-mesityl-5-methyl-1H-pyrazol-1-yl-κN3]borato}-copper(II) dichloromethane monosolvate
  25. Crystal structure of 4-[3,5-bis(propan-2-yl)-1H-pyrazol-4-yl]pyridine, C14H19N3
  26. Crystal structure of ((4-(4-bromophenyl)-1H-pyrrol-3-yl)methyl)ferrocene, C21H16BrFeNO
  27. Crystal structure of [(4-chlorobenzyl)triphenylphosphonium] dichloridocopper(I), {[C25H21ClP]+[CuCl2]}n
  28. The crystal structure of {Cu(2,9-diisopropyl-4,7-diphenyl-1,10-phenanthroline)[4,5-bis(diphenylphosphino)-9,9-dimethylxanthene]}+ PF6·1.5(EtOAC)
  29. Crystal structure of 3,5-bis(t-butyl)-1H-pyrazol-4-amine, C11H21N3
  30. Crystal structure of [(2,4-dichlorobenzyl)triphenylphosphonium] trichloridocopper(II), [C25H20Cl2P]+[CuCl3]
  31. The crystal structure of dipotassium sulfide, K2S
  32. Crystal structure of (4-(4-methoxyphenyl)-1H-pyrrole-3-carbonyl)ferrocene, C22H19FeNO2
  33. Crystal structure of (E)-6-(4-methylpiperazin-1-yl)-2-(4-(trifluoromethyl)benzylidene)-3, 4-dihydronaphthalen-1(2H)-one, C23H23F3N2O
  34. Crystal structure of (E)-6-morpholino-2-(4-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C22H20F3NO2
  35. Crystal structure of Ce9Ir37Ge25
  36. The crystal structure of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate, C14H11N3O4S
  37. Crystal structure of (4-(4-isopropylphenyl)-1H-pyrrol-3-yl)(ferrocenyl)methanone, C24H23FeNO
  38. Crystal structure of bis(methylammonium) tetrathiotungstate(VI), (CH3NH3)2[WS4]
  39. Crystal structure of 6,11-dihydro-12H-benzo[e]indeno[1,2-b]oxepin-12-one, C17H12O2
  40. Crystal structure of 3-[(4-phenylpiperidin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4- oxadiazole-2-thione, C18H19N3OS2
  41. Crystal structure of N-isopropyl-1,8-naphthalimide C15H13NO2
  42. TiNiSi-type EuPdBi
  43. Crystal structure of 1-(p-tolylphenyl)-4-(2-thienoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O2S
  44. The crystal structure of 3-(3-carboxypropyl)-2-nitro-1H-pyrrole 1-oxide, C7H9N3O5
  45. The crystal structure of tetraaqua-bis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k2O:N)-tetrakis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k1N)trizinc(II) hexahydrate C36H52N18O32Zn3
  46. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 4-hydroxy-3,5-dimethoxybenzoate monohydrate, C25H30FN3O9
  47. Crystal structure of bis(DL-1-carboxy-2-(1H-indol-3-yl)ethan-1-aminium) oxalate — acetic acid (1/2)
  48. Crystal structure of methyl (E)-4-((4-methylphenyl)sulfonamido)but-2-enoate, C12H15NO4S
  49. The crystal structure of actarit, C10H11NO3
  50. The crystal structure of bicyclol, C19H18O9
  51. The crystal structure of topiroxostat, C13H8N6
  52. Crystal structure of 2,2-dichloro-N-methyl-N-(4-p-tolylthiazol-2-yl)acetamide, C13H12Cl2N2OS
  53. Crystal structure of 4-(trifluoromethyl)-7-coumarinyl trifluoromethanesulfonate C11H4F6O5S
  54. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ6O6)-((Z)-N,N′-bis(2-(dimethylamino)phenyl)carbamimidato-κ1N)potassium(I)
  55. Crystal structure of (Z)-2-(5-((4-(dimethylamino)naphthalen-1-yl)methylene)-4-oxo-2-thioxothiazolidin-3-yl)acetic acid, C18H16N2O3S2
  56. Crystal structure of (4-fluorobenzyl)triphenylphosphonium bromide, C25H21BrFP
  57. The crystal structure of dichlorido-[6-(pyridin-2-yl)phenanthridine-κ2N, N′]zinc(II)-chloroform (1/1), C19H13N2ZnCl5
  58. Crystal structure of (E)-(3-(2,4-dichlorophenyl)acryloyl)ferrocene, C19H14Cl2FeO
  59. The crystal structure of (E)-7-chloro-1-cyclopropyl-6-fluoro-3-((2-hydroxybenzylidene)amino)quinolin-4(1H)-one, C19H14ClFN2O2
  60. Crystal structure of 2-bromo-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13BrFNO4S2
  61. Crystal structure of 2-chloro-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13ClFNO4S2
  62. Crystal structure of 5-(2,2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a]isoquinoline-3-carbonitrile, C20H15F2N3O
Downloaded on 14.10.2025 from https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2025-0128/html?recommended=sidebar&srsltid=AfmBOooXFxe-1jFTeGO7GxrwSM0-YORRoFrDixvXyr2ZRdXeDHz806lU
Scroll to top button