European Journal of Chemistry

Rationalization of supramolecular interactions of a newly synthesized binuclear Cu(II) complex derived from 4,4′,6,6′-tetramethyl 2,2′-bipyrimidine ligand through Hirshfeld surface analysis

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Samit Pramanik
Subrata Mukhopadhyay
Kinsuk Das

Abstract

A new binuclear copper (II) complex [Cu2L2Cl4(H2O)2] (1) derived from 4,4',6,6'-tetramethyl-2,2'-bipyrimidine (L) has been synthesized and characterized by the single crystal X-ray diffraction method. Single crystal analysis of complex 1 reveals that it crystallizes in the space group P21/n under a monoclinic system (β = 97.995(2)°, a = 7.6483(2), b = 7.2158(3) and c = 17.8477(6) Å). The ligand acts as a bis-bidentate one and each copper (II) center bears a square pyramidal geometry exploiting N2Cl2O chromophore. In the solid state, the complex is stabilized through classical O-H···Cl intermolecular hydrogen bonding incorporating coordinated water (as a solvent) and chloride ions and lone pair···π interactions. The Hirshfeld surface analysis demonstrates H···H/H···H, H···Cl/Cl···H, H···C/C···H, and C···Cl/Cl···C intermolecular interactions as the major contributor interactions in the solid-state packing of the molecular crystal. Interaction energy calculations carried out employing the wavefunction generated via B3LYP/6-31G(d,p) highlight the dominance of electrostatic energy and the contribution of polarization and dispersion energy towards the total energy of complex 1 in the solid state.


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Pramanik, S.; Mukhopadhyay, S.; Das, K. Rationalization of Supramolecular Interactions of a Newly Synthesized Binuclear Cu(II) Complex Derived from 4,4′,6,6′-Tetramethyl 2,2′-Bipyrimidine Ligand through Hirshfeld Surface Analysis. Eur. J. Chem. 2022, 13, 393-401.

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References

[1]. Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. Estimates of the ab initio limit for π−π interactions: The benzene dimer. J. Am. Chem. Soc. 2002, 124, 10887-10893.
https://doi.org/10.1021/ja025896h

[2]. Alkorta, I.; Elguero, J.; Frontera, A. Not only hydrogen bonds: Other noncovalent interactions. Crystals (Basel) 2020, 10, 180.
https://doi.org/10.3390/cryst10030180

[3]. Noncovalent Forces; Scheiner, S., Ed.; Springer International Publishing: Cham, Switzerland, 2016.

[4]. Mahadevi, A. S.; Sastry, G. N. Cooperativity in noncovalent interactions. Chem. Rev. 2016, 116, 2775-2825.
https://doi.org/10.1021/cr500344e

[5]. Alkorta, I.; Blanco, F.; Deyà, P. M.; Elguero, J.; Estarellas, C.; Frontera, A.; Quiñonero, D. Cooperativity in multiple unusual weak bonds. Theor. Chem. Acc. 2010, 126, 1-14.
https://doi.org/10.1007/s00214-009-0690-1

[6]. Bauzá, A.; Mooibroek, T. J.; Frontera, A. Small cycloalkane (CN)2CC(CN)2structures are highly directional non-covalent carbon-bond donors. Chemistry 2014, 20, 10245-10248.
https://doi.org/10.1002/chem.201403680

[7]. Mitra, M.; Manna, P.; Bauzá, A.; Ballester, P.; Seth, S. K.; Ray Choudhury, S.; Frontera, A.; Mukhopadhyay, S. 3-picoline mediated self-assembly of M(II)-malonate complexes (M = Ni/co/Mn/mg/Zn/cu) assisted by various weak forces involving lone pair−π, π-π, and anion···π-hole interactions. J. Phys. Chem. B 2014, 118, 14713-14726.
https://doi.org/10.1021/jp510075m

[8]. Bauzá, A.; Mooibroek, T. J.; Frontera, A. Directionality of π-holes in nitro compounds. Chem. Commun. (Camb.) 2015, 51, 1491-1493.
https://doi.org/10.1039/C4CC09132A

[9]. Non-covalent interactions in the synthesis and design of new compounds: Maharramov/non-covalent interactions in the synthesis and design of new compounds; Maharramov, A. M.; Mahmudov, K. T.; Kopylovich, M. N.; Pombeiro, A. J. L., Eds.; John Wiley & Sons: Nashville, TN, 2016.

[10]. Pal, P.; Das, K.; Hossain, A.; Frontera, A.; Mukhopadhyay, S. Supramolecular and theoretical perspectives of 2,2′:6′,2′′-terpyridine based Ni(ii) and Cu(ii) complexes: on the importance of C-H⋯Cl and π⋯π interactions. New J Chem 2020, 44, 7310-7318.
https://doi.org/10.1039/D0NJ00094A

[11]. Das, K.; Dolai, M.; Chatterjee, S.; Konar, S. Synthesis, X-ray crystal structure and BVS calculation of Co(II) complex of pyrimidine derived Schiff base ligand: Approached by Hirshfeld surface analysis and TDDFT calculation. J. Mol. Struct. 2021, 1236, 130269.
https://doi.org/10.1016/j.molstruc.2021.130269

[12]. Pal, P.; Das, K.; Hossain, A.; Gomila, R. M.; Frontera, A.; Mukhopadhyay, S. Synthesis and crystal structure of the simultaneous binding of Ni(ii) cation and chloride by the protonated 2,4,6 tris-(2-pyridyl)-1,3,5 triazine ligand: theoretical investigations of anion⋯π, π⋯π and hydrogen bonding interactions. New J Chem 2021, 45, 11689-11696.
https://doi.org/10.1039/D1NJ01880A

[13]. Kitagawa, S.; Matsuda, R. Chemistry of coordination space of porous coordination polymers. Coord. Chem. Rev. 2007, 251, 2490-2509.
https://doi.org/10.1016/j.ccr.2007.07.009

[14]. Perry, J. J., IV; Perman, J. A.; Zaworotko, M. J. Design and synthesis of metal-organic frameworks using metal-organic polyhedra as supermolecular building blocks. Chem. Soc. Rev. 2009, 38, 1400-1417.
https://doi.org/10.1039/b807086p

[15]. Biswas, C.; Drew, M. G. B.; Escudero, D.; Frontera, A.; Ghosh, A. Anion-π, lone‐pair-π, π-π and hydrogen‐bonding interactions in a cu II complex of 2‐picolinate and protonated 4,4′‐bipyridine: Crystal structure and theoretical studies. Eur. J. Inorg. Chem. 2009, 2009, 2238-2246.
https://doi.org/10.1002/ejic.200900110

[16]. Andruh, M. Oligonuclear complexes as tectons in crystal engineering: structural diversity and magnetic properties. Chem. Commun. (Camb.) 2007, 2565-2577.
https://doi.org/10.1039/b616972d

[17]. Pointillart, F.; Herson, P.; Boubekeur, K.; Train, C. Square-planar and trigonal prismatic silver(I) in bipyrimidine and oxalate bridged tetranuclear complexes and one-dimensional compounds: Synthesis and crystal structures. Inorganica Chim. Acta 2008, 361, 373-379.
https://doi.org/10.1016/j.ica.2007.06.023

[18]. Ma, N.; Wang, Y. Crystal structure of tetraaqua dinitrato-κ2O,O'-4,4',6,6'-tetramethyl-2,2'- bipyrimidine-κ4N,N':N'',N''' dinickel(II) dinitrate, C6H11N4NiO8. Z. Krist. - New Cryst. Struct. 2014, 229, 109-110.
https://doi.org/10.1515/ncrs-2014-0057

[19]. Naiya, S.; Biswas, C.; Drew, M. G. B.; Gómez-García, C. J.; Clemente-Juan, J. M.; Ghosh, A. A unique example of structural and magnetic diversity in four interconvertible copper(II)−Azide complexes with the same Schiff base ligand: A monomer, a dimer, a chain, and a layer. Inorg. Chem. 2010, 49, 6616-6627.
https://doi.org/10.1021/ic1005456

[20]. Das, K.; Mandal, T. N.; Roy, S.; Jana, A.; Konar, S.; Liu, C.-M.; Barik, A. K.; Kar, S. K. Syntheses, crystal structures and magnetic properties of two dicopper(II) complexes and a zigzag 1-D Cu(II) complex of a bidentate pyridyl-pyrazole ligand. Polyhedron 2011, 30, 715-724.
https://doi.org/10.1016/j.poly.2010.12.010

[21]. Luo, J.; Zhang, X.-R.; Gao, E.-Q.; Dai, W.-Q.; Cui, L.-L.; Liu, B.-S. Syntheses, structures and magnetic properties of two copper(II) tricyano methanide complexes with 2,2′-bipyrimidine as bridging ligands. Inorganica Chim. Acta 2009, 362, 1749-1754.
https://doi.org/10.1016/j.ica.2008.08.017

[22]. Marino, N.; Armentano, D.; De Munno, G.; Cano, J.; Lloret, F.; Julve, M. Synthesis, Structure, and Magnetic Properties of Regular Alternating μ-bpm/di-μ-X Copper(II) Chains (bpm = 2,2′-bipyrimidine; X = OH, F). Inorg. Chem. 2012, 51, 4323-4334.
https://doi.org/10.1021/ic202740b

[23]. Ma, N.; Wang, Y.; Miao, S.-B. Crystal structure of tetraaqua diacetato-κ2O,O'-4,4',6,6'-tetramethyl-2,2'- bipyrimidine-κ4N,N':N'',N''' dicobalt (II) diacetate dihydrate, C10H19CoN2O7. Z. Krist. - New Cryst. Struct. 2014, 229, 107-108.
https://doi.org/10.1515/ncrs-2014-0056

[24]. Williams, R. M.; Cola, L. D.; Hartl, F.; Lagref, J.-J.; Planeix, J.-M.; Cian, A. D.; Hosseini, M. W. Photophysical, electrochemical and electrochromic properties of copper-bis(4,4′-dimethyl-6,6′-diphenyl-2,2′-bipyridine) complexes. Coord. Chem. Rev. 2002, 230, 253-261.
https://doi.org/10.1016/S0010-8545(02)00046-2

[25]. Chandrasekaran, R.; Murugavel, S.; Guin, M.; Silambarasan, T. Crystal structure, Hirshfeld, computational biomolecular investigations, and MTT assay studies of amino pyrimidine derivative as EGFR kinase domain inhibitor. J. Mol. Struct. 2022, 1254, 132416.
https://doi.org/10.1016/j.molstruc.2022.132416

[26]. Rajni Swamy, V.; Krishnakumar, R. V.; Srinivasan, N.; Sivakumar, S.; Kumar, R. R. Coordinated compliance of chloro-methyl and bromo-methyl exchange rule in two dihydrofuran carbonitrile derivatives. J. Mol. Struct. 2021, 1228, 129741.
https://doi.org/10.1016/j.molstruc.2020.129741

[27]. Pramanik, S.; Pathak, S.; Frontera, A.; Mukhopadhyay, S. Syntheses, crystal structures and supramolecular assemblies of two Cu(ii) complexes based on a new heterocyclic ligand: insights into C-H⋯Cl and π⋯π interactions. CrystEngComm 2022, 24, 1598-1611.
https://doi.org/10.1039/D1CE01402A

[28]. Vlád, G.; Horváth, I. T. Improved synthesis of 2,2'-bipyrimidine. J. Org. Chem. 2002, 67, 6550-6552.
https://doi.org/10.1021/jo0255781

[29]. Bruker (2001). SMART. Bruker AXS Inc., Madison, Wisconsin, USA.

[30]. Sheldrick, G. M. (1997). SHELXS-97 and SHELXL-97. University of Göttingen, Germany.

[31]. Spackman, M. A.; Jayatilaka, D. Hirshfeld surface analysis. CrystEngComm 2009, 11, 19-32.
https://doi.org/10.1039/B818330A

[32]. Hirshfeld, F. L. Bonded-atom fragments for describing molecular charge densities. Theoret. Chim. Acta 1977, 44, 129-138.
https://doi.org/10.1007/BF00549096

[33]. Clausen, H. F.; Chevallier, M. S.; Spackman, M. A.; Iversen, B. B. Three new co-crystals of hydroquinone: crystal structures and Hirshfeld surface analysis of intermolecular interactions. New J Chem 2010, 34, 193-199.
https://doi.org/10.1039/B9NJ00463G

[34]. Rohl, A. L.; Moret, M.; Kaminsky, W.; Claborn, K.; McKinnon, J. J.; Kahr, B. Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: Pentamorphic 1,8-dihydroxyanthraquinone. Cryst. Growth Des. 2008, 8, 4517-4525.
https://doi.org/10.1021/cg8005212

[35]. Parkin, A.; Barr, G.; Dong, W.; Gilmore, C. J.; Jayatilaka, D.; McKinnon, J. J.; Spackman, M. A.; Wilson, C. C. Comparing entire crystal structures: structural genetic fingerprinting. CrystEngComm 2007, 9, 648-652.
https://doi.org/10.1039/b704177b

[36]. Spackman, M. A.; McKinnon, J. J. Fingerprinting intermolecular interactions in molecular crystals. CrystEngComm 2002, 4, 378-392.
https://doi.org/10.1039/B203191B

[37]. Spackman, P. R.; Turner, M. J.; McKinnon, J. J.; Wolff, S. K.; Grimwood, D. J.; Jayatilaka, D.; Spackman, M. A. CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. J. Appl. Crystallogr. 2021, 54, 1006-1011.
https://doi.org/10.1107/S1600576721002910

[38]. McKinnon, J. J.; Spackman, M. A.; Mitchell, A. S. Novel tools for visualizing and exploring intermolecular interactions in molecular crystals. Acta Crystallogr. B 2004, 60, 627-668.
https://doi.org/10.1107/S0108768104020300

[39]. Addison, A. W.; Rao, T. N.; Reedijk, J.; van Rijn, J.; Verschoor, G. C. Synthesis, structure, and spectroscopic properties of copper(II) compounds containing nitrogen-sulphur donor ligands; the crystal and molecular structure of aqua[1,7-bis(N-methylbenzimidazol-2′-yl)-2,6-dithiaheptane]copper(II) perchlorate. J. Chem. Soc., Dalton Trans. 1984, 1349-1356.
https://doi.org/10.1039/DT9840001349

[40]. Swamy, R.; Ravikumar Crystal structure determination, hirshfeld surface analysis and quantum computational studies of (3E,5E)-1-ethyl-3,5-bis (naphthalen-1-yl-methylidene) piperidin-4-one: A novel RORc inhibitor. J. Mol. Struct. 2021, 1225, 129313.
https://doi.org/10.1016/j.molstruc.2020.129313

[41]. Turner, M. J.; Thomas, S. P.; Shi, M. W.; Jayatilaka, D.; Spackman, M. A. Energy frameworks: insights into interaction anisotropy and the mechanical properties of molecular crystals. Chem. Commun. (Camb.) 2015, 51, 3735-3738.
https://doi.org/10.1039/C4CC09074H

[42]. Mackenzie, C. F.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCrJ 2017, 4, 575-587.
https://doi.org/10.1107/S205225251700848X

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The Council of Scientific and Industrial Research (CSIR, File no. 09/096(0947)/2018-EMR-I), New Delhi, India.
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