Abstract
The synthesis, spectra, electrochemical studies, single crystal structures and DFT studies of two new mixed ligand copper(II) malonates viz. [Cu(H2O)(bpy(OH)2)(mal)]·H2O 1 and [Cu(H2O)(dmp)(mal)]·2H2O 2 (bpy(OH)2) = 2,2′-bipyridine-6,6′-diol; dmp = 6,6′-dimethyl-1,10-phenanthroline; H2mal = malonic acid) are reported. The malonate, bpy(OH)2 (in 1), dmp (in 2) function as bidentate ligands in the distorted square pyramidal Cu(II) compounds while the aqua ligand occupies the axial site in 1. In contrast, one N of dmp occupies the axial site in 2. ESR studies reveal the distorted coordination geometry of Cu(II) in 1 and 2. Extensive hydrogen bonding (O−H⋅⋅⋅O and C−H⋅⋅⋅O) is observed between the malonate oxygens, oxygens of water and the monomeric Cu(II) species resulting in the formation of hydrogen bonded network structure in 1 and 2. The neutral monomeric Cu(II) species and lattice water molecules in 2 are linked via O−H⋅⋅⋅O hydrogen bond forming a water dimer. Both compounds exhibit π⋅⋅⋅π stacking and carbonyl(lp)⋅⋅⋅π interactions (in 2) stabilize the structure. DFT studies reveal stronger hydrogen bond energy for 2 compared to 1, while π⋅⋅⋅π stacking energy is larger in 1 than in 2 and carbonyl(lp)⋅⋅⋅π interactions in 2 are found to be moderate. In a series of five coordinated mixed ligand Cu(II) malonates, compound 2 exhibits maximum deviation of the {CuN2O3} polyhedron from square pyramidal towards trigonal bipyramidal geometry.
Graphic abstract
The supramolecular network structures of [Cu(H2O)(bpy(OH)2)(mal)]·H2O 1 and [Cu(H2O)(dmp)(mal)]·2H2O 2 are directed by O–H⋅⋅⋅O and C–H⋅⋅⋅O interactions. Additionally π⋅⋅⋅π stacking in 1 and π⋅⋅⋅π /carbonyl(lp)⋅⋅⋅π interactions in 2 contribute to the structure stabilization. 2 is an unique example showing severe distortion of the {CuN2O3} polyhedron.
Similar content being viewed by others
References
Seo J S, Whang D, Lee H, Jun S I, Oh J, Jeon Y J and Kim K 2000 A homochiral metal-organic porous material for enantioselective separation and catalysis Nature 404 982
Lee J, Farha O K, Roberts J, Scheidt K A, Nguyen S T and Hupp J T 2009 Metal-organic framework materials as catalysts Chem. Soc. Rev. 38 1450
Düren T, Sarkisov L, Yaghi O M and Snurr R Q 2004 Design of new materials for methane storage Langmuir 20 2683
Chae H K, Siberio-Pérez D Y, Kim J, Go Y, Eddaoudi M, Matzger A J, et al. 2004 A route to high surface area, porosity and inclusion of large molecules in crystals Nature 427 523
Kreno L E, Leong K, Farha O K, Allendorf M, Van Duyne R P and Hupp J T 2004 Metal-organic framework materials as chemical sensors Chem. Rev. 112 1105
Ariga K, Mori T, Kitao T and Uemura T 2020 Supramolecular chiral nanoarchitectonics Adv. Mater. 32 1905657
Tashiro S and Shionoya M 2020 Novel porous crystals with macrocycle-based well-defined molecular recognition sites Acc. Chem. Res. 53 632
Desiraju G R, Vittal J J and Ramanan A 2011 Crystal engineering, A Textbook(World Scientific: Singapore)
Desiraju G R 1995 Supramolecular synthons in crystal engineering-a new organic synthesis Angew. Chem. Int. Ed. Engl. 34 2311
Braga D, Grepioni F and Desiraju G R 1998 Crystal engineering and organometallic architecture Chem. Rev. 98 1375
Desiraju G R 2007 Crystal engineering: a holistic view Angew. Chem. Int. Ed. Engl. 46 8342
Desiraju G R 1997 Designer crystals: intermolecular interactions, network structures and supramolecular synthons Chem. Commun. 21 1475
Deshpande M S, Kumbhar A S and Näther C 2010 Stabilization of acyclic water tetramer in a copper(II) malonate framework Structure Dalton Trans. 39 9146
Mitra M, Manna P, Seth S K, Das A, Meredith J, Helliwell M, et al. 2013 Salt-bridge–π (sb–π) interactions at work: associative interactions of sb–π, π–π and anion–π in Cu(ii)-malonate-2-aminopyridine-hexafluoridophosphate ternary system CrystEngComm. 15 686
Mitra M, Manna P, Bauza A, Ballester P, Seth S K, Choudhury S R, et al. 2014 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 118 14713
Manna P, Seth S K, Bauzá M, Mitra M, Choudhury S R, Frontera A and Mukhopadhyay S 2014 pH dependent formation of unprecedented water-bromide cluster in the bromide salts of PTP assisted by anion−π interactions: synthesis, structure, and DFT study Cryst. Growth Des. 14 747
Stephenson M D and Hardie M J 2005 Extended structures of transition metal complexes of 6,7-dicyanodipyridoquinoxaline: π-stacking, weak hydrogen bonding, and CN···π interactions Cryst. Growth Des. 6 423
Janiak C 2000 A critical account on π–π stacking in metal complexes with aromatic nitrogen-containing ligands Dalton Trans. 13 3885
Sinnokrot M O and Sherrill C D 2004 Highly accurate coupled cluster potential energy curves for the benzene dimer: sandwich, T-shaped, and parallel-displaced configurations J. Phys. Chem. A 108 10200
Deshmukh M M and Sakaki S 2012 Two-step evaluation of binding energy and potential energy surface of van der Waals complexes J. Comput. Chem. 33 617
Deshmukh M M and Sakaki S 2011 Binding energy of gas molecule with two pyrazine molecules as organic linker in metal-organic framework: its theoretical evaluation and understanding of determining factors Theor. Chem. Acc. 130 475
Gadre S R, Yeole S and Sahu N 2014 Quantum chemical investigations on molecular clusters Chem. Rev. 114 12132
Egli M and Sarkhel S 2007 Lone pair-aromatic interactions: To stabilize or not to stabilize Acc. Chem. Res. 40 197
Lu Z, Gamez P, Mutikainen I, Turpeinen U and Reedijk J 2007 Supramolecular assemblies generated from both lone-pair···π and C−H···π binding interactions Cryst. Growth Des. 7 1669
Mooibroek T J, Gamez P and Reedijk J 2008 Lone pair–π interactions: a new supramolecular bond CrystEngComm. 10 1501
Singh S K and Das A 2015 The n → π* interaction: a rapidly emerging non-covalent interaction Phys. Chem. Chem. Phys. 17 9596
Sarkhel S, Rich A and Egli M 2003 Water−Nucleobase “Stacking”: H−π and lone pair−π interactions in the atomic resolution crystal structure of an RNA pseudoknot J. Am. Chem. Soc. 125 8998
Eddaoudi M, Moler D B, Li H, Chen B, Reineke T M, O’Keeffe M and Yaghi O M 2001 Modular chemistry: secondary building units as a basis for the design of highly porous and robust metal-organic carboxylate frameworks Acc. Chem. Res. 34 319
Pachfule P, Das R, Poddar P and Banerjee R 2010 Structural, magnetic, and gas adsorption study of a two-dimensional tetrazole-pyrimidine based metal-organic framework Cryst. Growth Des. 10 2475
Chen B, Eddaoudi M, Reineke T M, Kampf J W, O’Keeffe M and Yaghi O M 2000 Cu2(ATC)·6H2O: Design of open metal sites in porous metal-organic crystals (ATC: 1,3,5,7-adamantane tetracarboxylate) J. Am. Chem. Soc. 122 11559
Suresh E and Bhadbhade M M 1997 Metal–α, ω-dicarboxylate complexes. I. Aqua (2,2’-bipyridyl-N, N’)(malonato-O, O’) copper (II) monohydrate Acta Crystallogr. C53 193
Choudhury S R, Lee H M, Hsiao T-H, Colacio E, Jana A D and Mukhopadhyay S 2010 Co-operation of π⋯π, Cu(II)⋯π, carbonyl⋯π and hydrogen-bonding forces leading to the formation of water cluster mimics observed in the reassessed crystal structure of [Cu(mal)(phen)(H2O)]2·3H2O (H2mal = malonic acid, phen = 1,10-phenanthroline) J. Mol. Struct. 967 131
Diallo M, Dieng M, Gaye M, Sall A S, Barry A H and Chahrazed B 2007 Aquamalonato(1,10-phenanthroline)-copper(II) sesquihydrate Acta Crystallogr. E63 m1810
Kwik W-L, Ang K-P, Chan H S-O, Chebolu V and Koch S A 1986 Thermal, spectroscopic, and structural properties of aqua(malonato-O, O’)(l, l′-phenanthroline)copper(II) hydrate (1/1.5) J. Chem. Soc. Dalton Trans. 13 2519
Youngme S, Phatchimkun J and Chaichit N 2006 Aqua(di-2-pyridylamine-k2N,N′)(malonato-k2O,O′)copper(II) monohydrate Acta Crystallogr. C62 m602
Gasque L, Moreno-Eaparza R, Mollins E, Brianso-Penalva J L, Ruis-Ramirez L and Medina-Dickinson G 1999 Aqua(5,6-dimethyl-l,10-phenanthroline-N,N’)(malonato-O,O’) copper(II) hydrate Acta Crystallogr. C55 158
Delgado F S, Lahoz F, Lloret F, Julve M and Ruiz-Pérez C 2008 Supramolecular networks in copper(II) malonate complexes Cryst. Growth Des. 8 3219
Santini C, Pellei M, Gandin V, Porchia M, Tisato F and Marzano C 2013 Advances in copper complexes as anticancer agents Chem. Rev. 114 815
Chikira M, Tomizawa Y, Fukita D, Sugizaki T, Sugawara N, Yamazaki T, et al. 2002 DNA-fiber EPR study of the orientation of Cu(II) complexes of 1,10-phenanthroline and its derivatives bound to DNA: mono(phenanthroline)-copper(II) and its ternary complexes with amino acids J. Inorg. Biochem. 89 163
Selvakumar B, Rajendiran V, Uma Maheswari P, Stoeckli-Evans H M and Palaniandavar M 2006 Structures, spectra, and DNA-binding properties of mixed ligand copper(II) complexes of iminodiacetic acid: the novel role of diimine co-ligands on DNA conformation and hydrolytic and oxidative double strand DNA cleavage J. Inorg. Biochem. 100 316
Barve A, Kumbhar A, Bhat M, Joshi B, Butcher R, Sonawane U and Joshi R 2009 Mixed-ligand copper(II) maltolate complexes: synthesis, characterization, DNA binding and cleavage, and cytotoxicity Inorg. Chem. 48 9120
Rodríguez-Martín Y, Hernández-Molina M, Delgado F S, Pasan J, Ruiz-Pérez C, Sanchiz J, et al. 2002 Structural versatility of the malonate ligand as a tool for crystal engineering in the design of molecular magnets CrystEngComm 4 522
Delgado F S, Sanchiz J, Ruiz-Pérez C, Lloret F and Julve M 2003 Design of high-dimensional copper(II) malonate complexes with exo-polydentate N-donor ligands Inorg. Chem. 42 5938
Rodríguez-Martín Y, Sanchiz J, Ruiz-Pérez C, Lloret F and Julve M 2002 Alternating cationic–anionic layers in the [Mii(H2O)6][Cuii(mal)2(H2O)] complexes linked through hydrogen bonds (M = Mn, Co, Ni, Cu and Zn; H2mal = malonic acid) CrystEngComm 4 631
Delgado F S, Ruiz-Pérez C, Sanchiz J, Lloret F and Julve M 2006 Versatile supramolecular self-assembly, Part II. Network formation and magnetic behaviour of copper(ii) malonate anions in ammonium derivatives CrystEngComm 8 530
Kurth D G, Fromm K M and Lehn J-M 2001 Hydrogen-bonding and metal-ion-mediated self-assembly of a nanoporous crystal lattice Eur. J. Inorg. Chem. 26 1523
Aakeroy C B, Champness N R and Janiak C 2010 Recent advances in crystal engineering CrystEngComm 12 22
Desiraju G R 2005 C-H⋯O and other weak hydrogen bonds. From crystal engineering to virtual screening Chem. Commun. 26 2995
Kumbhar A S, Deshpande M S and Butcher R J 2008 Hydrogen bond directed open-framework of bis(bipyridine-glycoluril) phosphatocobalt(III) with solvent accessible void space CrystEngComm 10 1520
Deshpande M S, Kumbhar A S and Puranik V G 2008 Hydrogen bonding-directed metallosupramolecular structural motifs based on a peripheral urea fused bipyridine tecton Cryst. Growth Des. 8 1952
Deshpande M S, Kumbhar A S, Puranik V G and Selvaraj K 2006 Supramolecular self-assembled ruthenium-polypyridyl framework encapsulating discrete water cluster Cryst. Growth Des. 6 743
Sheldrick G M 2015 Crystal structure refinement with SHELXL Acta Crystallogr. C71 3
Becke A D 1988 Density-functional exchange-energy approximation with correct asymptotic behaviour Phys. Rev. A: At. Mol. Opt. Phys. 38 3098
Becke A D 1993 Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 98 5648
Hariharan P C and Pople J A 1973 The influence of polarization functions on molecular orbital hydrogenation energies Theor. Chim. Acta. 28 213
Francl M M, Pietro W J, Hehre W J, Binkley J S, Gordon M S, DeFrees D J and Pople J A 1982 Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements J. Chem. Phys. 77 3654
Hay P J and Wadt W R 1985 Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg J. Chem. Phys. 82 270
Wadt W R and Hay P J 1985 Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi J. Chem. Phys. 82 284
Hay P J and Wadt W R 1985 Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals J. Chem. Phys. 82 299
Bergner A, Dolg M, Kuechle W, Stoll H and Preuss H 1993 Ab initio energy-adjusted pseudopotentials for elements of groups 13–17 Mol. Phys. 80 1431
Dolg M, Stoll H, Preuss H and Pitzer R M 1993 Relativistic and correlation effects for element 105 (hahnium, Ha): a comparative study of M and MO (M = Nb, Ta, Ha) using energy-adjusted ab initio pseudopotentials J. Phys. Chem. 97 5852
M. J. Frisch et al. Gaussian 09, revision E.01; Gaussian, Inc.: Wallingford, CT, (2009) (for detail author list see SI).
Deshmukh M M, Bartolotti L J and Gadre S R 2008 Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach J. Phys. Chem. A 112 312
Deshmukh M M and Gadre S R 2009 Estimation of N–H···O=C Intramolecular hydrogen bond energy in polypeptides J. Phys. Chem. A 113 7927
Deshmukh M M, Bartolotti L J and Gadre S R 2011 Intramolecular hydrogen bond energy and cooperative interactions in α-, β-, and γ-cyclodextrin conformers J. Comput. Chem. 32 2996
Ganesh V, Dongare R K, Balanarayan P and Gadre S R 2006 Molecular tailoring approach for geometry optimization of large molecules: Energy evaluation and parallelization strategies J. Chem. Phys. 125 104109
Eisenberg D and Kauzmann W 1969 The structure and properties of water (Oxford University Press: Oxford)
Liu K, Brown M G, Carter C, Saykally R J, Gregory J K and Clary D C 1996 Characterization of a cage form of the water hexamer Nature 381 501
Lever A B P 1984 Inorganic electronic spectroscopy (Elsevier: Amsterdam) 33
Subramanian P S, Suresh E and Srinivas D 2000 Synthesis, X-ray structure, single-crystal EPR and 1H-NMR studies of a distorted square planar Cu(salEen)2(ClO4)2 complex in a novel bilayered architecture:salEen) N, N-Diethylethylenesalicylidenamine Inorg. Chem. 39 2053
Hathaway B J, Billing D E, Dudley R J, Fereday R J and Tomlinson A A G 1970 Electronic and electron spin resonance spectra of diamminocopper(II) trithiocyanato argentate (I) and iodo bis-(2,2’- bipyridyl )copper(II) iodide J. Chem. Soc. A 11 806
Bencini A and Gatteschi D 1977 Single-crystal polarized electronic and electron spin resonance spectra of the trigonal-bipyramidal complex aquobis(1, l0-phenanthroline)copper(II) nitrate Inorg. Chem. 16 1994
Bencini A, Bertini I, Gatteschi D and Scozzafava A 1978 Single-crystal ESR spectra of copper(II) complexes with geometries intermediate between a square pyramid and a trigonal bipyramid Inorg. Chem. 17 3195
Wayland B B and Kapur V K 1974 Electron paramagnetic resonance and electronic spectral evidence for isomers resulting from basal and axial ligation of bis (hexafluoroacetylacetonato) copper(II) by triphenylphosphine Inorg. Chem. 13 2517
Ritterskamp N, Sharples K, Richards E, Folli A, Chiesa M, Platts J A and Murphy D M 2017 Understanding the coordination modes of [Cu(acac)2(imidazole)n=1,2] adducts by EPR, ENDOR, HYSCORE, and DFT analysis Inorg. Chem. 56 11862
Attanasio D, Collamati I and Ercolani C 1974 Ligand arrangement and tetragonal distortion in CuO4N2 chromophores studied by electronic and electron spin resonance spectroscopy J. Chem. Soc. Dalton Trans. 11 1319
Hirohama T, Kuranuki Y, Ebina E, Sugizaki T, Arii H, Chikira M, et al. 2005 Copper(II) complexes of 1,10-phenanthroline-derived ligands: studies on DNA binding properties and nuclease activity J. Inorg. Biochem. 99 1205
Spek A L 2009 Structure validation in chemical crystallography Acta Crystallogr. D65 148
Spek A L 2003 Single-crystal structure validation with the program PLATON J. Appl. Crystallogr. 36 7
Addison A W, Rao T N, Reedijk J, Rijn J V and Verschoor G C 1984 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. 7 1349
Manikumari S, Shivaiah V and Das S K 2002 Identification of a Near-linear supramolecular water dimer, (H2O)2, in the channel of an inorganic framework material Inorg. Chem. 41 6953
Schmidt R, Oh J H, Sun Y S, Deppisch M, Krause A M, Radacki K, et al. 2009 High-performance air-stable n-channel organic thin film transistors based on halogenated perylene bisimide semiconductors J. Am. Chem. Soc. 131 6215
Anthony J E, Brooks J S, Eaton D L and Parkin S R 2001 Functionalized pentacene: improved electronic properties from control of solid-state order J. Am. Chem. Soc. 123 9482
Yang J, Yan D and Jones T S 2015 Molecular template growth and its applications in organic electronics and optoelectronics Chem. Rev. 115 5570
Ahirwar M B, Gadre S R and Deshmukh M M 2020 Direct and reliable method for estimating the hydrogen bond energies and cooperativity in water clusters, Wn, n = 3 to 8 J. Phys. Chem. A 124 6699
Deshmukh M M, Gadre S R and Bartolotti L J 2006 Estimation of intramolecular hydrogen bond energy via molecular tailoring approach J. Phys. Chem. A 110 12519
Deshmukh M M, Suresh C H and Gadre S R 2007 Intramolecular hydrogen bond energy in polyhydroxy systems: a critical comparison of molecular tailoring and isodesmic approaches J. Phys. Chem. A 111 6472
Acknowledgments
The authors thank the Sophisticated Analytical Instrument Facility (SAIF), Indian Institute of Technology (IIT) Madras for the ESR spectral data of the compounds. MSD acknowledges funding from the University Grants Commission (UGC), New Delhi for the D. S. Kothari Postdoctoral Fellowship (No. F.4-2/2006(BSR)/CH/17-18/ 0105). MMD is thankful to the UGC for the initial Start-up Grant (No. F.30-56/2014/BSR). MBA is thankful to Dr. Harisingh Gour Vishwavidyalaya, Sagar, for a Research Fellowship.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Deshpande, M.S., Morajkar, S.M., Ahirwar, M.B. et al. Synthesis, structural, and DFT studies of mixed ligand copper(II) malonates. J Chem Sci 133, 99 (2021). https://doi.org/10.1007/s12039-021-01947-w
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12039-021-01947-w