European Journal of Chemistry 2022, 13(4), 393-401 | doi: https://doi.org/10.5155/eurjchem.13.4.393-401.2318 | Get rights and content

Issue cover




Crossmark

  Open Access OPEN ACCESS | Open Access PEER-REVIEWED | RESEARCH ARTICLE | DOWNLOAD PDF | VIEW FULL-TEXT PDF | TOTAL VIEWS

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


Samit Pramanik (1) orcid , Subrata Mukhopadhyay (2) orcid , Kinsuk Das (3,*) orcid

(1) Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
(2) Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
(3) Department of Chemistry, Chandernagore College, Hooghly, West Bengal 712136, India
(*) Corresponding Author

Received: 10 Aug 2022 | Revised: 12 Sep 2022 | Accepted: 19 Sep 2022 | Published: 31 Dec 2022 | Issue Date: December 2022

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.


Announcements


One of our sponsors will cover the article processing fee for all submissions made between May 17, 2023 and May 31, 2023 (Voucher code: SPONSOR2023).

Editor-in-Chief
European Journal of Chemistry

Keywords


Hirshfeld surface; Bipyrimidine derivative; Lone pair···π interactions; Supramolecular architectures; Hydrogen bonding interactions; Single crystal X-ray crystallography

Full Text:

PDF
PDF    Open Access

DOI: 10.5155/eurjchem.13.4.393-401.2318

Links for Article


| | | | | | |

| | | | | | |

| | | |

Related Articles




Article Metrics

icon graph This Abstract was viewed 301 times | icon graph PDF Article downloaded 51 times

Funding information


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

Citations

/


[1]. Xinyue Shang, Mingwei Fu, Zhuoer Cai, Lai Wei, Shuwang Ge, Min Ge, Yihong Wang
Novel pharmaceutical salt and solvates of rebamipide: Preparations, structural analysis and properties
Journal of Molecular Structure  1288, 135786, 2023
DOI: 10.1016/j.molstruc.2023.135786
/

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


Supporting information


The Supplementary Material for this article can be found online at: Supplementary files

How to cite


Pramanik, S.; Mukhopadhyay, S.; Das, K. Eur. J. Chem. 2022, 13(4), 393-401. doi:10.5155/eurjchem.13.4.393-401.2318
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(4), 393-401. doi:10.5155/eurjchem.13.4.393-401.2318
Pramanik, S., Mukhopadhyay, S., & Das, K. (2022). 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. European Journal of Chemistry, 13(4), 393-401. doi:10.5155/eurjchem.13.4.393-401.2318
Pramanik, Samit, Subrata Mukhopadhyay, & Kinsuk Das. "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." European Journal of Chemistry [Online], 13.4 (2022): 393-401. Web. 29 May. 2023
Pramanik, Samit, Mukhopadhyay, Subrata, AND Das, Kinsuk. "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" European Journal of Chemistry [Online], Volume 13 Number 4 (31 December 2022)

The other citation formats (EndNote | Reference Manager | ProCite | BibTeX | RefWorks) for this article can be found online at: How to cite item



DOI Link: https://doi.org/10.5155/eurjchem.13.4.393-401.2318


CrossRef | Scilit | GrowKudos | Researchgate | Publons | ScienceGate | Scite | Lens | OUCI

WorldCat Paperbuzz | LibKey Citeas | Dimensions | Semanticscholar | Plumx | Kopernio | Zotero | Mendeley

ZoteroSave to Zotero MendeleySave to Mendeley



European Journal of Chemistry 2022, 13(4), 393-401 | doi: https://doi.org/10.5155/eurjchem.13.4.393-401.2318 | Get rights and content

Refbacks

  • There are currently no refbacks.


Bookmark and Share


Copyright (c) 2022 Authors

Creative Commons License
This work is published and licensed by Atlanta Publishing House LLC, Atlanta, GA, USA. The full terms of this license are available at http://www.eurjchem.com/index.php/eurjchem/pages/view/terms and incorporate the Creative Commons Attribution-Non Commercial (CC BY NC) (International, v4.0) License (http://creativecommons.org/licenses/by-nc/4.0). By accessing the work, you hereby accept the Terms. This is an open access article distributed under the terms and conditions of the CC BY NC License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited without any further permission from Atlanta Publishing House LLC (European Journal of Chemistry). No use, distribution or reproduction is permitted which does not comply with these terms. Permissions for commercial use of this work beyond the scope of the License (http://www.eurjchem.com/index.php/eurjchem/pages/view/terms) are administered by Atlanta Publishing House LLC (European Journal of Chemistry).


© Copyright 2010 - 2023 • Atlanta Publishing House LLC • All Right Reserved.

The opinions expressed in all articles published in European Journal of Chemistry are those of the specific author(s), and do not necessarily reflect the views of Atlanta Publishing House LLC, or European Journal of Chemistry, or any of its employees.

Copyright 2010-2023 Atlanta Publishing House LLC. All rights reserved. This site is owned and operated by Atlanta Publishing House LLC whose registered office is 2850 Smith Ridge Trce Peachtree Cor GA 30071-2636, USA. Registered in USA.