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Synthesis, crystal structures and supramolecular architectures of square pyramidal Cu(II) complexes containing aromatic chelating N,N’-donor ligands



Design of new metal complexes is an interesting field for development of new functional molecular-based materials. In this process by the usage of mixed functional ligands one can precisely tune the physical and chemical properties of those metal complexes. However, it is difficult to obtain the desired complex in many cases for factors like different coordination abilities of the ligands and the types of anions have a great influence on the structure.


A series of five copper(II) complexes [Cu(Bipy) (5-TPC) 2(H2O)] (1), [Cu(Phen) (5-TPC) 2(H2O)] (2), [Cu(NO3) (4,7-Phen) (5-TPC) (H2O)].H2O (3), [Cu(Bipy) 2(5-TPC)]2.(ClO4)2 (4), and [Cu2(Bipy)4(H2PO4)] (5) (where Bipy = 2,2'-bipyridine, Phen = 1,10-phenanthroline, 4,7-Phen = 4,7-hydroxy-1,10-phenanthroline, 5-TPC = 5-chloro-2- thiophene carboxylate) has been synthesized and characterised using single crystal X-ray diffraction studies. In all the compounds, the N,N’ ligand coordinates in a bidentate chelating manner and the copper has a square pyramidal geometry.


Complexes (1,2) are expected to be isostructural due to similarity of the N.N’-chelating ligands used, but due to the difference in supramolecular architectures no similar unit cells were observed. This is important in crystal engineering point of view. Complexes (1–4) possess the neutral mononuclear and complex (5) possesses a dinuclear entity. These entities are connected by intermolecular interactions like X∙∙∙π, H∙∙∙X, (X = Cl) generating supramolecular architectures.


Bipyridines and its analogues such as phenanthroline as well as substituted phenanthrolines are widely used in the formation of metal complexes [13] for their potential applications in electrochemistry, catalysis, analytical chemistry, biochemistry and also in the mimic chemistry as a substitute for amino acid side group [419]. These ligands due to their chelating nature in metal complexes effectively control the aggregation behavior by effectively chelating around the metal centre. In this regard some of the substituted bipyridine and phenanthroline like ligands have been studied [2023]. The substitution of a methyl or hydroxy group in the bipyridine has a steric influence which alters the structural behavior of these compounds. Due to the presence of an extended π-system, various non covalent π-interactions which mimic various biological processes, the study of these complexes have gained importance [24]. The coordination geometry of the copper(II) complexes depends on on the ligands, co-ligands, and counter ions [2538]. Numerous Cu in different coordination environments have been developed to study the supramolecular Cu networks [3942]. The five coordinated copper(II) complexes which containing N,N’ chelating ligands and monodentate co-ligands have diverse stereo and physicochemical properties [2537]. Recently in addition to investigations of the copper(II) complexes of these ligands with simple anions such as Cl-, Br- there are also reports of their mixed ligand complexes and tris chelate mixed ligand complexes. 5-TPC (5-TPC = 5-chloro-2- thiophene carboxylate) not only shows versatile coordination modes but also exhibit non covalent interactions like Cl…π and C-H…Cl [4348].


Materials and methods

Commercial starting materials were used without further purification.5-chloro thiophene 2- carboxylic acid (Hoechst Aktiengesellschaft), Cu(NO3)2.3H2O, Cu(ClO4).6H2O Aldrich, Methanol (Qualigens) and other organic ligands (Aldrich) were used. Single crystal diffraction studies were done on a BRUKER SMART APEXII CCD area-detector diffractometer(Scheme 1).

Scheme 1

Monodentate and bidentate chelating modes of the 5-TPC ligand

Monodentate and bidentate chelating modes of the 5-TPC ligand.

Synthesis of [Cu(Bipy) (5-TPC)2(H2O)] (1), [Cu(Phen) (5-TPC)2(H2O)] (2), and [Cu(NO3) (4,7-Phen) (5-TPC) (H2O)].H2O (3)

A solution of Cu(NO3)2.3H2O (g) in 10 ml of (1:1) CH3OH/H2O mixture was stirred over a hot plate magnetic stirrer for half an hour and 5-chloro thiophene 2-Carboxylic acid (0.0833g) dissolved in 10 ml of CH3OH was added to it. The mixture was stirred for an additional of 2 hours. A green colored solution was formed. About (0.0442g) of (2-2′-bipyridine) was dissolved in 10ml of hot water and added to the reaction mixture. The mixture was stirred for 3 hours. The precipitate was filtered off and the resulting solution was kept for slow evaporation. Green block-shape single crystals of (1) suitable for X-ray analysis were obtained after few days. The synthesis procedures of (2, 3) were the same as that of (1) except PHEN and 4,7-PHEN were used in the place of BIPY. The crystals were filtered and washed with small portions of methanol and were dried in air (yield 75% based on Cu).

Synthesis of [Cu(Bipy)2(5-TPC)]2.(ClO4)2(4)

Complex (4) was obtained by same reaction procedures as that of (1) except Cu(ClO4)2.6H2O was used in the place of Cu(NO3)2.3H2O. The crystals were filtered and washed with small portions of methanol and were dried in air (yield 69% based on Cu).

Synthesis of [Cu2(Bipy)4(H2PO4)] (5)

The complex (5) was synthesized by the same procedure as that of (1). To the resulting green solution 2ml of H3PO4 was added. The mixture was stirred for 3 hours. The resulting solution was kept for slow evaporation. Blue block-shape single crystals of (5) suitable for X-ray analysis were obtained after a few days.

X-ray crystallography

Intensity data sets were collected at room temperature, on a BRUKER SMART APEXII CCD [49] area-detector diffractometer equipped with graphite monochromated Mo Kα radiation (λ = 0.71073 Å). The data were reduced by using the program SAINT [49] and empirical absorption corrections were done by using the SADABS[49]. The structures were solved by direct methods using SHELXS-97[50] and subsequent Fourier analyses, refined anisotropically by full-matrix least-squares method using SHELXL-97 [50] within the WINGX suite of software, based on F2 with all reflections. All carbon hydrogens were positioned geometrically and refined by a riding model with Uiso 1.2 times that of attached atoms. All non H atoms were refined anisotropically. The molecular structures were drawn using the ORTEP-III [51], POV-ray [52] and MERCURY [53]. Crystal data and the selected parameters for complexes (1–5) were summarized in (Tables 1 and 2) respectively. The crystals remained stable throughout the data collection. The H atoms of the water molecules in the structure of (1) were located from the difference map and refined with no positional constraints. The water H atoms of (2 and 3) were located in a difference Fourier map and refined as riding on the O atom in these positions with Uiso(H) = 1.2Ueq(O). Comparisons of various coordination modes of carboxylates are given (Table 3), Additional file 1.

Table 1 Crystal data and structure refinement information for complexes (1–5)
Table 2 Hydrogen bond metrics for complexes (1–5)
Table 3 Comparison of coordination modes of various carboxylates and some structural parameters around the copper(II) ion

Results and discussion

Geometry around Cu(II) atoms

The coordination environment of metal center in both complexes (1) and (2) is square pyramidal in which two equatorial sites are occupied by the nitrogen atoms of the BIPY and the PHEN rings (respectively in 1 and 2) and the remaining two sites are occupied by two oxygen atoms of which one is from a coordinated water molecule and the other is from monodentate 5-TPC anion and the apical site is occupied by another monodentate 5-TPC anion (Figure 1). Complex (3) has a similar geometry around the central Cu(II) atom, but unlike those two complexes the NO3 group in (3) mimics the role of one of the carboxylate. The square pyramidal geometry of each Cu(II) ion is furnished by the two nitrogen atoms from the 4,7-PHEN and two oxygen atoms (O1W, O1) from coordinated water molecule and monodentate 5-TPC anion respectively in the basal plane and one oxygen (O5) of the NO3 anion in the apical position. Apart from the coordinated water molecule, there is one more water molecule (O2W) at the lattice. (4) has two monodentate Cu(II) atoms with the an identical square pyramidal environment. The same square pyramidal geometry like that of (1–3) is observed in (4). The equatorial positions are occupied by three nitrogen atoms of BIPY molecules and oxygen of the monodentate carboxylate molecules. The axial position is occupied by one of the nitrogens of a BIPY molecule. There are two perchlorate anions in the lattice. Complex (5) is a discrete Cu(II) dimer. The molecular structure consists of two square pyramidal copper(II) ions bridged by two oxygens (O1,O4) from two dihydrogen phosphate ions (H2PO4)- in the basal plane to form a dimer; the rest of the coordination sites of each copper ion in the basal plane are occupied by two nitrogen atoms from the BIPY molecule. The apical position of each copper is accommodated by one oxygen from the dihydrogen phosphate. The distance between two copper metal centers in the dimer is 5.100Å. The assignment of P = O, P - O-, and P - OH bonds are consistent with the literature [54]. The largest angle around the Cu(II) center (β) is considerably different from the second largest one(α). The distortion of the coordination polyhedron from the square-pyramidal geometry in (1–5) is rather small as reflected in the structural index τ (where τ = (β-α)/60) (Table 3) [55]. The deviation of the Cu atoms above the basal plane of the square pyramid as well as the axial bond lengths are given in (Table 3).

Figure 1

Comparison of coordination environment around the Cu(II) ions (a-e) Coordination environment around the Cu(II) ions in complexes 1-5 respectively.

Crystal structure description of [Cu(Bipy) (5-TPC)2(H2O)] (1), [Cu(Phen) (5-TPC)2(H2O)] (2)

The ORTEP drawings of the asymmetric units of (1) and (2) with the atom-numbering schemes are illustrated in (Figure 2a, b) and, respectively. Complexes (1) and (2) crystallize in two different space groups (C2/c and P21/c respectively) but contain both the same neutral mononuclear unit with general formula [Cu(L) (5-TPC)2(H2O)] where L = BIPY in (1) and PHEN in (2). The copper(II) ion in the complex [Cu(L) (5-TPC)2(H2O)] unit displays a square-pyramidal coordination with the same CuN2O2O' chromophore.

Figure 2

Molecular structures of (1) and (2). (a,b) Crystallographic numbering scheme with displacement ellipsoids drawn at the 50% probability level. The hydrogen atoms are included as spheres of arbitrary radii. (c,d) Hydrogen bonding in between two Cu(II) monomeric units in 1 and 2 respectively.

The most characteristic feature of both the complexes is the involvement of both the water hydrogens (apical water) in O-H…O hydrogen bonding with the monodentate carboxylate leading to two a graph set motifs with graph set notation of S(6) (Figure 2c,d) [5658]. Although the first order coordination of both complexes is same they differ in their supramolecular architectures. In (1) each monomer is linked to another monomer in the crystallographic c axis through the π-π stacking interactions inbetween the BIPY rings. The stacked molecules further extend into a chain by a C-H…O interaction. Further this chain is still stabilized by a Cl-π interaction inbetween Cl2 → Cg5iii and π-π stacking interactions [59]. Each of this chain is linked to the adjacent chain by a Cl-π interaction inbetween Cl1 → Cg2iii (Figure 3).

Figure 3

π-π stacking and C-H…O interactions. (a) Formation of chain by π-π stacking and C-H…O interactions. (b) Two of these chains linked by Cl-π interactions.

In (2) two of the monomeric units linked by C-H∙∙∙O interactions are linked into a chain by a pair of C-H∙∙∙Cl interactions inbetween the hydrogen of a 5-TPC ring and Cl of the adjacent 5-TPC (C9iv-H9 iv∙∙∙Cl1). Also this chain is stabilized by π-π stacking interactions in between the thiophene rings Cg1 → Cg1iii (where Cg1 = S1, C2-C5). As in the case of (1), here each of this chain is linked to the adjacent chain by Cl-π interaction inbetween Cl1 → Cg2iii (Figure 4).

Figure 4

Formation of a chain in 2 by C-H…O and C-H…Cl interactions.

Crystal structure description of [Cu(NO3) (4,7-Phen) (5-TPC) (H2O)].H2O (3)

In complex (3) one of the water hydrogens (apical water) is involved in O-H…O hydrogen bonding with the monodentate carboxylate leading to a S(6) graph set motif as in (1) and (2) (Figure 5a). The presence of coordinated water molecule, carboxylate and nitrate groups, together with the molecule of solvation (H2O) causes extensive hydrogen bonding interactions in complex (3). The H-bonds to a charged carboxylate group or nitrate anion can be termed “charge-assisted H-bonds”, here the carboxylate or nitrate groups as hydrogen bond acceptors carry negative ionic charges. Such charge-assisted H-bonds are much stronger than hydrogen bonds between neutral atoms [6067]. Each of the monomer is connected to each other by (O1W-H2W…O6X (symmetry code x = -x,–y,1–z hydrogen bonds) inbetween the coordinated apical nitrate anions and coordinated water molecules (Figure 5b). Also the presence of hydroxyl groups in the ligand (4,7-PHEN) introduces a steric influence in the structural behavior of the (3). This hydroxyl group (O4) of a 4,7-PHEN is involved in C17-H17…O4 hydrogen bonding with another 4,7-PHEN in the same plane giving rise to a hydrogen-bonding motif with the graph-set descriptor R22(10). One of the hydrogen atoms of the uncoordinated water molecule (H3W) and hydrogen of another 4,7-PHEN lying in the same plane are connected by two O-H…O hydrogen bonds (O2W-H3W…O2, O3-H3A…O2W). Consequently, the layer like pattern is formed by C-H…O and O-H∙∙∙O hydrogen bonds (Figure 6).As depicted in (Figure 6), two of these layers are linked to each other by four sets of O-H…O hydrogen bonds inbetween the coordinated nitrate, carboxylate and uncoordinated water molecules. Also there is a Cl…π interaction observed inbetween the Cl1 and Cg5 [where Cg5 = C9, C10,C11,C12,C17,C16].

Figure 5

Molecular structure of 3 displaying the crystallographic numbering scheme. a) Displacement ellipsoids are drawn at the 50% probability level. The hydrogen atoms are included as spheres of arbitrary radii. b) Two of the Cu(II) monomers linked by O-H…O interactions.

Figure 6

Formation of layers (yellow and green) by C-H∙∙∙O and O-H∙∙∙O hydrogen bonds and layers connected by uncoordinated water molecules.

In general, the coordination bond lengths in complexes (1–3) are in good agreement with those found for the corresponding bonds in similar five-coordinate copper(II) complexes which posses axial water molecules [Cu(BIPY) (OXL) (H2O)].2H2O, [Cu(OXL) (H2O) (NPHEN)].2H2O, [Cu(OXL) (H2O) (PHEN)].H2O, [Cu(BIPY) (OXL) (H2O)].H2O, [Cu(BIPY) (OXL) (H2O)]. HOXL (NPHEN = 5-nitro-1,10-phenanthroline, HOXL = oxalic acid and OXL = oxalate) [6871].

Crystal structure description of [Cu(Bipy)2(5-TPC)]2.(ClO4)2(4)

In (4), two crystallographically independent Cu(II) monomeric units are found. In each unit a monodentate carboxylate as well as two BIPY ligands chelate the Cu(II) ion to form a square pyramidal environment; there are two perchlorate anions to make the charge balance (Figure 7). Each of the monomeric unit is connected to adjacent monomeric unit by the C-H…O hydrogen bonds inbetween the BIPY and the monodentate carboxylate oxygen (C4-H4…O2i, C7-H7…O2i symmetry code i = 1-x,1-y,1-z). Also these monomeric units are held together by a pair of C-H…O hydrogen bonds inbetween the BIPY and the ClO4- anion (C1i-H1 i…O11, C8-H8…O12 symmetry code i = 1-x,1-y,1-z). These monomeric units are linked to the next pair of monomeric units by a pair of C-H…Cl interactions inbetween 5TPC and BIPY molecules. Thus these monomeric units are bridged by this C-H…Cl interactions which extend into a chain (Figure 8). The bridging thiophene rings are linked to another ClO4- anion by C-H…O interactions inbetween the hydrogen of the thiophene ring and the perchlorate oxygen (C24-H24…O7). These perchlorate anions play a major role in extending these supramolecular architectures.

Figure 7

Molecular structure of 4 displaying the crystallographic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. The hydrogen atoms are included as spheres of arbitrary radii.

Figure 8

Formation of chain by C-H∙∙∙Cl interaction and a chain connected to uncoordinated perchlorate molecules (white and red).

Crystal structure description of [Cu2(Bipy)4(H2PO4)] (5)

The complex (5) is a discrete copper dimer that crystallizes in monoclinic space group C2/c. The complex was obtained by serendipity and is totally different from the rest of the complexes. The dihydrogen phosphate anions show two type of coordination such as bidentate bridging and monodentate (Figure 9). In the crystal structure each of the dimer is linked to the next dimer by a pair of O-H∙∙∙O hydrogen bonds. These interactions are found inbetween the axially coordinated H2PO4 anions. This results in the formation of R22(8) motif (Figure 10a).

Figure 9

Molecular structure of 5 displaying the crystallographic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. The hydrogen atoms are included as spheres of arbitrary radii.

Figure 10

O-H∙∙∙O interactions in 5. (a) A view of the complex showing the R22(8) motif inbetween two dinuclear units and the chain by O-H∙∙∙O interactions extending along the crystallographic c axis. (b) O-H∙∙∙O hydrogen bonds in between the bridging H2PO4 anions of one chain and axial H2PO4 anions

This R22(8) motif is frequently observed in carboxylic acid dimers. This leads to a chain of O-H∙∙∙O hydrogen bonds extending along the crystallographic c axis. This chain is linked to the next chain by two O-H∙∙∙O hydrogen bonds in between the bridging H2PO4 anions of one chain and axial H2PO4 anions of the next chain (Figure 10b). These chains extend along the crystallographic a axis perpendicular to the direction of previous chain.

Conformations of 2,2′-bipy in complexes 1,4,5

Conformations of 2-2′-bipy in the complexes (1, 4–5) are different depending on the anion. The dihedral angles between two pyridyl rings of 2-2′-bipy are listed in (Table 4). The above complexes show different structures with different coordination modes of carboxylate, different numbers of 2-2′-bipy coordinated to the Cu2+ ion.

Table 4 The dihedral angles (°) between two pyridyl rings of 2-2’-bipy in complexes 1,4 and 5


We have presented a systematic investigation of one dinuclear and four mononuclear Cu(II) complexes. Their structures show various coordination modes depending on the anions. Since different anions provide different coordination environment around the Cu2+, it is clear that selection of appropriate anion can control the coordination geometry of the Cu2+ ion. Also comparing structures (1–5) we can find the role of anion in controlling the supramolecular architectures. In structures (1) and (2) the primary coordination of the Cu(II) ion is unchanged, even in presence of different chelating N,N-ligands. In (3) the NO3 anion mimics the role of a carboxylate when compared to (1) and (2). The observation of structures (1–5) reveals the structural changes made just by the replacement of the anion alone. In addition to noncovalent interaction like C-H∙∙∙O, which is the reason for assembly of primary motifs, various other interactions like X∙∙∙π, H∙∙∙X, (X = Cl) add additional support in organizing these supermolecules in to extended architectures.


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SJJ thank the UGC-SAP for the award of RFSMS. PTM thanks U.G.C. for onetime B.S.R-grant. The authors thank the DST India (FIST programme) for the use of the diffractometer and EPR facilities at the School of Chemistry, Bharathidasan University, Tiruchirappalli, Tamilnadu, India.

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Correspondence to Packianathan Thomas Muthiah.

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The authors declare that they have no competing interests.

Authors’ contributions

This work was prepared in the research group of PTM. He proposed the work and drafted the manuscript. SJJ participated in the design and presided over the experiments, collected the X-ray data and drafted the manuscript. Both authors read and approved the final manuscript.

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Supplementary crystallographic data for the complexes 1–5 respectively and can be obtained free of charge via

Additional file 1:, or from the Cambridge Crystallographic Data Center, 12 Union Road, Cambridge CB2 IEZ, UK; fax:(+44)1223-336-033; or e-mail: 28 KB)

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Jennifer, S.J., Muthiah, P.T. Synthesis, crystal structures and supramolecular architectures of square pyramidal Cu(II) complexes containing aromatic chelating N,N’-donor ligands. Chemistry Central Journal 8, 42 (2014).

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  • Copper(II) complexes
  • 2,2'-bipyridine
  • 1,10-phenanthroline
  • 4,7-hydroxy-1,10-phenanthroline
  • Single crystal X-ray diffraction