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Synthesis, Crystal Structure, Hirshfeld Surface Analysis, Molecular Docking, IR Spectroscopy and DFT Calculations of a Novel 2D Layered Hybrid Compound (C6H10N3O)2Cu2Cl6

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Abstract

The 2D hybrid compound bis(2-amino-4-methoxy-6-methylpyrimidinium) bis(μ2-chloro)-tetrachloro-di-copper(II), (C6H10N3O)2Cu2Cl6, is successfully synthesized by slow solvent evaporation at room temperature. Structural properties have been investigated through single-crystal X-ray diffraction and reveal that the structure contains a centrosymmetric hexachlorodicuprate group where each Cu atom is coordinated to four Cl atoms in a slightly distorted square planar geometry. There are short contacts between neighboring [Cu2Cl6]2− dimer units. The crystalline building stability is ensured by N–H⋯Cl and C–H⋯O hydrogen bonding as well as weak C–H···π intermolecular interactions. From the infrared spectroscopy analysis, the functional groups were identified. Simultaneously, the electrical properties and Hirshfeld surface analyses were also elucidated. Furthermore, the molecular docking study of 2D hybrid compound bis(2-amino-4-methoxy-6-methylpyrimidinium) bis(2-chloro)-tetrachloro-di-copper(II) ligand with an HSP90/PDB: 5LRZ was performed by Autodock Vina. Additionally, drug-likeness and ADME properties and evaluations of the newly synthesized molecule were performed in detail. FT-IR was used to explore the modes of vibration of the different functional groups present in the studied compound.

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Acknowledgements

The authors especially thanks to Prof. Dr. Fatih UCUN from the Suleyman Demirel University for his helpful contribution for Gaussian calculations.

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Authors and Affiliations

  1. Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna, Tunisia

    Chaima Gharbi & Chérif Ben Nasr

  2. Science and Art Faculty-Department of Physics, Sorgun Vocational School, Yozgat Bozok University, Yozgat, Turkey

    Yusuf Sert

  3. Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayis University, 55200, Samsun, Turkey

    Emine Berrin Çınar & Necmi Dege

  4. Institut für Anorganische Chemie, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany

    Uwe Böhme

  5. Laboratoire des Matériaux Utiles, Institut National de Recherche et d’Analyse physico-chimique (INRAP), Technopole Sidi Thabet, 2020, Ariana, Tunisia

    Lamia Khedhiri

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  1. Chaima Gharbi
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Contributions

CBN and LK: Conceptualization, design, resources, editing and supervision. CG: Synthesis, Analysis, writing and manuscript draft. UB: X-ray data collections and structure resolution. YS, EBÇ and ND: DFT calculations, writing and proofreading.

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Correspondence to Lamia Khedhiri.

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Gharbi, C., Sert, Y., Çınar, E.B. et al. Synthesis, Crystal Structure, Hirshfeld Surface Analysis, Molecular Docking, IR Spectroscopy and DFT Calculations of a Novel 2D Layered Hybrid Compound (C6H10N3O)2Cu2Cl6. J Clust Sci 34, 1423–1435 (2023). https://doi.org/10.1007/s10876-022-02314-6

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