Synthesis and characterization of square planar and square pyramidal copper(II) compounds with tridentate Schiff bases: Formation of a molecular zipper via H-bonding interaction

Article abstract of DOI:10.1016/j.ica.2012.04.004

Three copper(II) compounds, [Cu(L¹)(H₂O) ₂]NO₃ (1), [Cu(L¹)(N₃)] ·2H₂O (2), and [Cu(L²)Cl₂] (3), where HL¹ = 2-[(pyridine-2-ylmethylene)-amino]-p

Full text of DOI:10.1016/j.ica.2012.04.004

Inorganica Chimica Acta 390 (2012) 167–177
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Inorganica Chimica Acta
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Synthesis and characterization of square planar and square pyramidal
copper(II) compounds with tridentate Schiff bases: Formation of a molecular
zipper via H-bonding interaction
⇑
Prasanta Kumar Bhaumik, Subrata Jana, Shouvik Chattopadhyay
Department of Chemistry, Inorganic Section, Jadavpur University, Kolkata 700 032, India
a r t i c l e i n f o
a b s t r a c t
Three copper(II) compounds, [Cu(L1)(H2O)2]NO3 (1), [Cu(L1)(N3)]ꢀ2H2O (2), and [Cu(L2)Cl2] (3), where
HL1 = 2-[(pyridine-2-ylmethylene)-amino]-phenol and L2 = (2-methoxy-phenyl)-pyridin-2-ylmethylene-
amine are tridentate Schiff-base ligands, have been prepared and characterized by elemental analysis,
IR and UV–Vis spectroscopy, Thermo-gravimetric study and single-crystal X-ray diffraction. Compound
Article history:
Received 9 November 2011
Received in revised form 27 March 2012
Accepted 1 April 2012
Available online 19 April 2012
ꢀ
1 crystallizes in triclinic space group P1 with cell dimensions a = 7.725(5), b = 9.140(5), c = 11.162(5),
a
= 102.229(5), b = 104.330(5) and c = 104.710(5), whereas compounds 2 and 3 crystallize in monoclinic
Keywords:
Copper(II)
Schiff base
Crystal structure
Molecular zipper
space groups P21/c and P21/n respectively with cell dimensions of a = 10.2111(3), b = 6.6366(2),
c = 20.8098(5), b = 101.851(2) (for 2) and a = 7.9914(1), b = 18.2591(3), c = 9.5695(2), b = 91.384(1) (for
3). In compound 1, copper(II) center exhibits a distorted square pyramidal geometry while in case of com-
pound 2, copper(II) acquires square planar geometry. The geometry of copper(II) in compound 3 is inter-
mediate between square pyramid and a structure, which is known as ‘inverse square pyramid’. A zipper
like infinite chain was formed in compound 2 via hydrogen bonding network between the complex moi-
ety, azide and enclathrated water molecules.
Ó 2012 Elsevier B.V. All rights reserved.
1. Introduction
co-ligands and also would like to investigate the diversity in the
H-bonding assembly with varying counter anions.
The synthesis and characterization of copper(II) compounds
have already attracted tremendous attention over the past decades
due to the interest in investigating the structure and role of poly-
nuclear copper active sites in several catalytic biological processes,
in understanding the magneto-structural correlations arising from
the electronic exchange coupling among copper(II) centers, and in
developing new molecular-based functional materials [1–7]. In this
context, a variety of copper(II) compounds ranging from discrete
assemblies to multi-dimensional coordination polymers have been
synthesized [8–15]. Octahedral copper(II) prefers tetragonally elon-
gated conformations [16]. Tetrahedral copper(II) tends toward
tetragonally compressed conformations and a square-planar coor-
dination as extreme case [17–18]. Five-coordinate copper(II) is
characterized by a ground state potential surface, which possesses
three equivalent minima at the positions of tetragonally elongated
square pyramids, whose dynamical average is an elongated trigonal
bipyramid [19–20]. We would like to investigate if any change in
geometry around copper(II) would occur on changing the anionic
On the other hand, non-covalent multiple strand arrays fre-
quently occur in biological macromolecules such as nucleic acid
helices and are topical targets for various bio-mimetic studies
[21–23]. DNA stores genetic information as a sequence of cova-
lently-linked nucleotides, and its ability to reproduce this informa-
tion is based on the self-assembly of two complementary linear
strands into double-stranded compounds. H-bonding interactions
between the bases permit one strand to ‘read’ the sequence of an-
other strand, and this property is liable for the high specificity ob-
served in the self assembly and self-replication of double-stranded
nucleic acids [24]. In recent years, chemists have also devoted con-
siderable effort to the formation of supra-molecular architectures
by self-assembly of comparatively lower strands into multi-
stranded structural motifs, of which the ladder like and zipper like
topologies (Scheme 1) are of particular interest. Among these, the
zipper motif is of fundamental importance for processes such as
self-replication, the behavior of biological fibers such as muscle
and for the formation of multi-component compounds with func-
tional properties [25–28]. However, these studies have usually
been focused on the design and synthesis of polymeric zipper motif
mediated by oligomeric nucleic acid derivatives [29], steroid deriv-
atives [30], polypeptides or amides [31] and metalloporphyrins
⇑
Corresponding author. Tel.: +91 9903756480.
E-mail address: shouvik.chem@gmail.com (S. Chattopadhyay).
0020-1693/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.ica.2012.04.004

168
P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
2.2. Synthesis
2.2.1. Synthesis of 2-[(pyridine-2-ylmethylene)-amino]-phenol (HL1)
The deep red solution of ligand, HL1, was synthesized by refluxing
a methanol solution (40 ml) of pyridine-2-carboxaldehyde (0.19 ml,
2 mmol) and 2-aminophenol (218 mg, 2 mmol) in 1:1 ratio for 1 hr.
It was then used directly for the preparation of compounds 1 and 2.
2.2.2. Synthesis of (2-methoxy-phenyl)-pyridin-2-ylmethylene-amine
(L2)
Zipper
Ladder
The deep red solution of ligand, L2, was synthesized by refluxing a
methanol solution (40 ml) of pyridine-2-carboxaldehyde (0.19 ml,
2 mmol) and o-anisidine (246 mg, 2 mmol) in 1:1 ratio for 1 h. It
was then used directly for the preparation of compound 3.
2.2.3. Synthesis of [Cu(L1)(H2O)2]NO3 (1)
Methanol solution (20 ml) containing Cu(NO3)2.3H2O (483 mg,
2 mmol) was added to a methanol solution (40 ml) of the ligand,
HL1 (ꢁ2 mmol) and refluxed. Within 1 h a deep reddish brown pre-
cipitate formed was collected by filtration and air dried. Single
crystals of the compound suitable for X-ray crystallography were
obtained from acetonitrile.
+
Scheme 1. Schematic illustration of building block assembly into supramolecular
zipper and ladder structures.
Yield: 528 mg (1.47 mmol). Anal. Calc. for C12H13CuN3O6: C,
40.17; H, 3.65; N, 11.71%. Found: C, 40.1; H, 3.6; N, 11.7%. UV–
Vis (acetonitrile): kmax
(
e
max, dm3 molꢂ1 cmꢂ1) = 509 (2.74 ꢃ 103),
[32]. Metal coordination compounds containing 2,20-bipyridine,
1,10-phenanthroline, and terpyridine as ligands are also well-
known to form zipper structures [33–34]. But the extended zipper
structures of non-oligomeric components with non-coordinating
backbones are scanty in the literature. Such supra-molecular zip-
pers are undoubtedly harder to design than the oligomeric ones.
The use of the tridentate ligand (HL1), viz. 2-[(pyridine-2-ylmethyl-
ene)-amino]-phenol, has already been proved to be an effective
tool in preparing molecular zipper via H-bonding interaction
[35]. However, in the work reported in reference [35], the halide
ions have been used as the auxiliary ligands which could not in-
volve in the H-bond interaction. Keeping this observation in mind,
we have tried to use azide as the auxiliary ligand, capable of form-
ing strong H-bonds.
In addition, it has been shown that the lattice of a crystal host
may offer an alternative environment for stabilizing various topol-
ogies of water clusters [36–37]. Identification of water clusters in
diverse environments can provide the key to understand the
behavior of water molecules. Among all of the water clusters,
one-dimensional (1D) water tape draws considerable interest be-
cause of its important roles in several biological processes [38–
40]. In the present work, we have observed that a T9(2) tape [41]
is formed involving four water molecules, azide N atoms, copper
atom and one phenoxo oxygen atom. Herein, we report the synthe-
sis, characterizations and X-ray crystal structures of three new
copper(II)) compounds with two tridentate ligands derived from
pyridine-2-carboxaldehyde and o-aminophenol/o-anisidine.
302 (1.03 ꢃ 104) nm. Magnetic moment is 1.73 BM.
2.2.4. Synthesis of [Cu(L1)N3]ꢀ2H2O (2)
Methanol solution (20 ml) containing Cu(ClO4)2ꢀ6H2O (741 mg,
2 mmol) and NaN3 (130 mg, 2.00 mmol) was added to a methanol
solution (40 ml) of the ligand, HL1 (ꢁ2 mmol) and refluxed. Within
1 h a deep reddish brown precipitate formed was collected by filtra-
tion and air dried. Single crystals of the compound suitable for X-
ray crystallography were obtained from N,N-dimethyl formamide.
Yield: 459 mg (1.35 mmol). Anal. Calc. for C12H13CuN5O3: C,
42.54; H, 3.87; N, 20.67%. Found: C, 42.5; H, 3.8; N, 20.6%. UV–
Vis (acetonitrile): kmax
(
e
max, dm3 molꢂ1 cmꢂ1) = 509 (6.78 ꢃ 103),
343 (8.53 ꢃ 103) nm. Magnetic moment is 1.73 BM.
2.2.5. Synthesis of [Cu(L2)Cl2] (3)
Methanol solution (20 ml) containing CuCl2.2H2O (341 mg,
2 mmol) was added to a methanol solution (40 ml) of the ligand,
L2 (ꢁ2 mmol) and refluxed for 1 h to give a deep reddish brown
solution. Single crystals of the compound suitable for X-ray crystal-
lography were obtained from mother liquor.
Yield: 540 mg (1.56 mmol). Anal. Calc. for C13H12Cl2CuN2O: C,
45.04; H, 3.49; N, 8.08%. Found: C, 45.0; H, 3.4; N, 8.0%. UV–Vis
(acetonitrile): kmax
(emax
,
dm3 molꢂ1 cmꢂ1) = 369 (7.97 ꢃ 103),
302 (1.03 ꢃ 104) nm. Magnetic moment is 1.73 BM.
2.3. Physical measurements
Elemental analysis (carbon, hydrogen and nitrogen) was per-
formed using a Perkin–Elmer 240C elemental analyzer. IR spectra
in KBr (4500–500 cmꢂ1) were recorded using a Perkin–Elmer RXI
FT-IR spectrophotometer. Electronic spectra in acetonitrile (900–
200 nm) were recorded in a Hitachi U-3501 spectrophotometer.
The magnetic susceptibility measurements were done with an EG
& PAR vibrating sample magnetometer, model 155 at room temper-
ature and diamagnetic corrections were made using Pascal’s con-
stants. The thermal behavior of the compounds was studied in a
dynamic nitrogen atmosphere (150 mL minꢂ1) at a heating rate of
10 °C minꢂ1 using thermo-gravimetric (TG) and derivative ther-
mo-gravimetric (DTG) techniques in a Perkin Elmer (SINGAPORE)
2. Experimental
2.1. Materials
All chemicals were of reagent grade and used without further
purification.
Caution! The azide compounds are potentially explosive.
Although no problem was encountered in the present study, small
amounts of the materials should be prepared and must be handled
with care.

P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
169
The parameter dnorm displays a surface with a red–white–blue color
scheme, where bright red spots highlight shorter contacts, white
areas represent contacts around the van der Waals separation,
and blue regions are devoid of close contacts. For a given crystal
structure and set of spherical atomic electron densities, the Hirsh-
feld surface is unique [51] and it is this property that suggests the
possibility of gaining additional insight into the intermolecular
interaction of molecular crystals.
Pyris Diamond TG/DTA instrument. Electrochemical behavior of all
the three copper compounds (1, 2 and 3) were studied in acetoni-
trile solution by cyclic voltammetry (CV), using a platinum disc
working electrode, Pt auxiliary electrode and Ag/AgCl reference
electrode under dry nitrogen atmosphere with TBAP (tetrabutyl
ammonium perchlorate) as supporting electrolyte in the potential
range from -2 to 2 V. The value for the Ferrocenium–Ferrocene cou-
ple under our conditions was 0.39 V.
2.4. X-ray crystallography
3. Results and discussion
Single crystals having suitable dimensions were used for data
collection by means of a ‘Bruker SMART APEX II’ diffractometer
3.1. Synthesis
equipped with graphite-monochromated Mo
Ka radiation
(k = 0.71073 Å) at 293 K. The structure was solved by direct
methods and refined by full-matrix least squares on F2, using the
SHELX-97 package [42]. Non-hydrogen atoms were refined with
anisotropic thermal parameters. The H atoms of the water mole-
cules were located by difference Fourier maps and were kept at
fixed positions. Other hydrogen atoms were placed in their geo-
metrically idealized positions and constrained to ride on the atoms
to which they are attached. Empirical absorption corrections were
carried out with the ABSPACK program [43]. The crystallographic and
refinement data are summarized in Table 1.
The condensation of pyridine-2-carboxaldehyde in 1:1 molar
ratio with o-aminophenol or o-anisidine afforded the Schiff bases,
HL1 and L2, respectively. HL1 on reaction with copper(II) nitrate in
1:1 molar ratios yielded compound 1. Use of copper perchlorate in-
stead of copper nitrate increased the yield. [Cu(L1)Cl] was pro-
duced by refluxing the ligand HL1 with copper(II) chloride. The
structure of this compound was reported elsewhere [35]. [Cu(L1)Cl]
could easily be converted to compound 2 by treating with sodium
azide. When [Cu(L1)Cl] was made to react with aqueous sodium ni-
trate solution, [Cu(L1)(H2O)2]NO3 (1) was produced, the less steric
effect of smaller water molecules facilitated the conversion of tet-
ra-coordinated copper into penta-coordinated one. However, when
compound 1 was treated with excess sodium azide, compound 2
was regenerated; the increase in CFSE on going from square pyra-
midal to square planar might be the driving force of this reaction.
Compound 3 was produced on treating L2 with copper(II) chloride;
L2 being a neutral ligand, the copper center accommodates two
chloride ions to compensate its charge whereas it needs only one
chloride in case of HL1 (L1 is mono negative). Hence the charge dif-
ference between the two ligands might play a key role to acquire
square pyramidal geometry for the former one rather allowing
square planar one. The formation of all the compounds is shown
in Scheme 2.
2.5. Hirshfeld surface analysis
Hirshfeld surfaces [44–46] and the associated 2D-fingerprint
[47–49] plots were calculated using Crystal Explorer, [50] which
accepts a structure input file in CIF format. Bond lengths to hydro-
gen atoms were set to standard values. For each point on the Hirsh-
feld isosurface, two distances de, the distance from the point to the
nearest nucleus external to the surface and di, the distance to the
nearest nucleus internal to the surface, are defined. The normalized
contact distance (dnorm) based on de and di is given by
di ꢂ rvi dW de ꢂ rvedW
dnorm
¼
þ
rvedw
rvi dw
where rvi dW and revdW are the van der Waals radii of the atoms. The
value of dnorm is negative or positive depending on intermolecular
contacts being shorter or longer than the van der Waals separations.
3.2. Description of the structures
3.2.1. Compound 1
ꢀ
The compound 1 crystallizes in the space group P1. An ORTEP
Table 1
view of discrete mononuclear unit of compound 1 with the
atom-labeling scheme is shown in Fig. 1. The tridentate ligand
coordinates to the copper ion via the phenolate O, the imine N,
and the pyridine N atom forming two five membered chelate rings.
The chelate bite angles for the five-membered rings formed by
Schiff base ligand are in the range 80.85–83.73°. The two water
molecules coordinate with the copper ion forming a square pyra-
midal structure which is confirmed by the Addison structural in-
Crystal data and refinement details of compounds 1–3.
1
2
3
Formula
C
12H13CuN3O6 C12H13CuN5O3 C13H12Cl2CuN2O
Formula weight
Temperature (K)
Crystal system
Space group
a (Å)
358.80
293
triclinic
338.82
293
monoclinic
P21/c
10.2111(3)
6.6366(2)
20.8098(5)
90
101.851(2)
90
346.70
293
monoclinic
P21/n
7.9914(1)
18.2591(3)
9.5695(2)
90
91.384(1)
90
ꢀ
P1
7.725(5)
9.140(5)
11.162(5)
102.229(5)
104.330(5)
104.710(5)
2
1.688
1.580
366
7266
dex,
s
= 0.015 (
s
= (a
ꢂ b)/60°, where
a and b are the bond angles
b (Å)
c (Å)
of the trans donor atoms in the basal plane) [52]. The basal plane
of the said geometrical structure is formed by two N donor sites
{N(1), N(2)} and one oxygen donor, O(1) from tridentate Schiff base
ligand and another oxygen atom, O(200) of one of the coordinated
water molecules and the apical position is occupied by another
oxygen donor, O(100) of a second water molecule. Deviations of
the coordinating atoms O(1), N(1), N(2) and O(200) from the
least-square basal plane are 0.083, ꢂ0.094, 0.083 and ꢂ0.071 Å
respectively and that of copper atom from the same plane is
0.166 Å. Sum of the different angles around the metal center in
the equatorial plane is ꢁ358.79°. The axial bond {Cu(1)–O(100)}
length is of 2.261(5) Å and the equatorial bond length of Cu(1)–
N(1), Cu(1)–N(2), Cu(1)–O(1) and Cu(1)–O(200) are 1.947(4),
2.016(4), 1.947(3) and 1.963(4) Å, respectively. The bond lengths
a
(°)
b (°)
c
(°)
Z
4
4
dcalc (g cmꢂ3
)
1.631
1.600
692
20508
3224
1.650
1.938
700
19489
3184
l
(mmꢂ1
F(000)
)
Total reflections
Unique reflections
Observed
data[I > 2r(I)]
Number of parameters
R(int)
R1, wR2 (all data)
R1, wR2 [I > 2r(I)]
1628
1471
2589
2605
215
0.025
221
0.034
172
0.028
0.0400, 0.0974 0.0412, 0.0791 0.0379, 0.0797
0.0360, 0.0945 0.0307, 0.0746 0.0279, 0.0744

170
P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
Scheme 2. Formation of the compounds 1, 2 and 3.
Fig. 1. ORTEP3 diagram of the compound 1 with 30% ellipsoid probability.
and angles are comparable with those for the related copper(II)
compounds [53].
Electrostatic calculations [54] for ML5 compounds give evidence
that a trigonal bipyramid (TBP) with larger axial than equatorial
M–L bond lengths is energetically slightly preferred with respect
to a square pyramid (SP) in which the equatorial M–L bonds are
longer than the apical bond distance. This result is supported by
the available experimental data, if one restricts to examples where

P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
171
Table 2
additional electronic effects are absent. In most cases trigonal
Selected bond lengths and bond angles of compound 1.
bipyramids are found, but some coordination polyhedra with inter-
mediate geometries are also known. The influence of electronic ef-
fects is obvious, if a lone pair of electrons is present. In general a
square-pyramidal geometry is stabilized in those cases [55–56].
It is also worthwhile, however, to consider the effect of d electrons
on the interplay between the two coordination alternatives [19]. It
has been shown that d9-configured cations in a chemical environ-
ment of five equal ligands tend to stabilize either a compressed tri-
gonal bipyramid or an apically elongated square pyramid with
obviously an energetic preference for the latter coordination [19].
Calculation of the ground-state potential surface [57] showed the
presence of three rather flat minima which correspond to the three
square-pyramidal conformations, inter-convertible via a trigonal
bipyramid intermediate as depicted in Scheme 3. The strain by
the rigid tridentate ligand has stabilized one of the three possible
square-pyramidal conformations in case of compound 1. The axial
Cu–O-bond is ꢁ0.3 Å longer than the equatorial Cu–O-bond length,
as observed in similar systems [53]. The details of bond lengths and
bond angles are given in Table 2.
1
Cu(1)–O(1)
Cu(1)–N(1)
Cu(1)–N(2)
Cu(1)–O(100)
1.947(3)
1.947(4)
2.016(4)
2.261(5)
1.963(4)
96.39(16)
97.78(14)
83.73(13)
164.33(14)
91.30(18)
103.18(17)
89.85(17)
165.22(17)
96.43(15)
80.85(14)
111.5(3)
Cu(1)–O(200)
O(1)–Cu(1)–O(100)
O(1)–Cu(1)–O(200)
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(2)
O(100)–Cu(1)–O(200)
O(100)–Cu(1)–N(1)
O(100)–Cu(1)–N(2)
O(200)–Cu(1)–N(1)
O(200)–Cu(1)–N(2)
N(1)–Cu(1)–N(2)
Cu(1)–O(1)–C(1)
Cu(1)–N(1)–C(7)
Cu(1)–N(1)–C(6)
Cu(1)–N(2)–C(8)
Cu(1)–N(2)–C(12)
116.4(3)
113.1(3)
112.6(3)
128.6(3)
It is interesting to note that the crystal packing shows a one-
dimensional architecture through H-bonding interactions (Fig. 2).
The H atom, H(201), attached with O(200) is involved in strong
H-bonding with O(1)⁄ of a symmetry related (1 ꢂ x, 1 ꢂ y, 1 ꢂ z)
unit to form a H-bonded dimer. The uncoordinated nitrate anion
also plays a significant role in the H-bonding and functions as a
bridge connecting two neighboring H-bonded dimeric units. Both
hydrogen atoms, H(100) and H(101) on the water oxygen (O100)
form H-bonds to oxygen atoms of the counter nitrate anion. How-
ever, while H(100) is directed towards O(31) at x, y, z; H(101) is di-
rected towards O(32)# at symmetry element ꢂx, 1 ꢂ y, 1 ꢂ z thus
leading to the formation of a 1-D zigzag H-bonded structure. The
details of the H-bond are given in Table 3.
via the phenolate O, the imine N, and the pyridine N atoms forming
two five membered chelate rings. The chelate bite angles for the
five-membered rings formed by HL1 are in the range 81.07–
83.83°. The azide ion occupies the fourth coordination site and
completes an ON3 square plane around the metal center. Sum of
the different angles around the copper atom is ꢁ360.06° indicating
almost undistorted square-planar geometry around copper ion. The
trans angles are found to be 164.83(7) {O(1)–Cu(1)–N(2)} and
176.53(7) {N(1)–Cu(1)–N(3)}. Deviations of the coordinating atoms
O(1), N(1), N(2) and N(3) from the least-square mean planes
through them are 0.036(1), ꢂ0.040(1), 0.035(1) and ꢂ0.031(2) Å
respectively and that of copper atom from the same plane is
0.02 Å. The bond lengths and angles are comparable with those
for the related copper(II) compounds [58]. The details of bond
lengths and bond angles are given in Table 4.
3.2.2. Compound 2
The dihydrated species 2 crystallizes in the space group P21/c.
An ORTEP view of compound 2 together with the atom-numbering
scheme is shown in Fig. 3. The structure consists of discrete mono-
nuclear units. The tridentate ligand coordinates to the copper ion
There are strong H bonds between two enclathrated water mol-
ecules, W1 and W2, the corresponding oxygen atoms of which are
Scheme 3. Interconversion of three square-pyramidal conformations of ML5 via a trigonal bipyramid intermediate.

172
P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
Fig. 2. H bonding network in compound 1.
Table 3
Table 4
Hydrogen bond distances (Å) and angles (°) of compound 1.
Selected bond lengths and bond angles of compound 2.
D–Hꢀ ꢀ ꢀA
D–H
Dꢀ ꢀ ꢀA
Hꢀ ꢀ ꢀA
\D–Hꢀ ꢀ ꢀA
2
O(100)–H(100)ꢀ ꢀ ꢀO(31)
O(100)–H(100)ꢀ ꢀ ꢀO(32)
O(100)–H(101)ꢀ ꢀ ꢀO(32)#
O(200)–H(201)ꢀ ꢀ ꢀO(1)⁄
0.72(5)
0.72(5)
0.79(7)
0.82(7)
3.137(9)
3.138(7)
2.767(8)
2.627(5)
2.44(5)
2.53(6)
1.99(7)
1.82(7)
165(6)
144(6)
169(8)
168(6)
Cu(1)–O(1)
Cu(1)–N(1)
Cu(1)–N(2)
Cu(1)–N(3)
1.9311(15)
1.9431(16)
2.0029(16)
1.924(2)
83.83(6)
164.84(7)
97.34(7)
81.07(7)
176.53(7)
97.82(7)
112.12(12)
116.89(14)
113.17(13)
112.75(13)
128.20(14)
119.10(16)
Symmetry elements # = ꢂx, 1 ꢂ y, 1 ꢂ z; ⁄ = 1 ꢂ x, 1 ꢂ y, 1 ꢂ z.
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(2)
O(1)–Cu(1)–N(3)
N(1)–Cu(1)–N(2)
N(1)–Cu(1)–N(3)
N(2)–Cu(1)–N(3)
Cu(1)–O(1)–C(1)
Cu(1)–N(1)–C(7)
Cu(1)–N(1)–C(6)
Cu(1)–N(2)–C(8)
Cu(1)–N(2)–C(12)
Cu(1)–N(3)–N(4)
molecular beam resonance experiments [60] and also through
vibration–rotation tunneling (VRT) spectroscopy [61]. The mea-
sured bond length of 2.976 Å is significantly larger compared to
the value observed in liquid and ice water that is attributable to
the cooperative nature of H-bonding in a larger set of water mole-
cules. The relative orientation of the two water molecules in the
present system is quite similar to that found in the gas phase,
although the Oꢀ ꢀ ꢀO distance is shortened to 2.84 Å. This shortening
is due to H-bonding interactions of the dimer with the framework.
Both oxygen atoms of the water dimer have a formal coordination
number of three (two hydrogen atoms attached to each oxygen of
the dimer act as acceptor and one of the two lone pairs as donor).
Although the free water dimers in the channel are not at all in-
volved in covalent interaction with the host molecule, it is con-
nected to the host framework through O–H–O, hydrogen bonding
via phenolate oxygen and N–H–O hydrogen bonding via azide
nitrogen atom (Fig. 5). Thus a T9(2) tape is formed.
Fig. 3. ORTEP3 diagram of the compound
Hydrogen atoms and lattice water molecules are not shown for clarity.
2 with 30% ellipsoid probability.
represented by O(100) and O(200) respectively to form a dimeric
water cluster. This is again connected to a symmetry-related water
dimer and so on to form an infinite tape (Fig. 4). The O. . .O distance
in the (H2O)2 dimer (present study) is 2.84 Å. For comparison, the
corresponding values in regular ice, in liquid water, and in the va-
por phase are 2.74, 2.85, and 2.98 Å, respectively [59].
The compound has near-perfect square-planar geometry. Such
species with sufficient
p-electrons are expected to form stacked
supra-molecular structures [62]. Presence of other functionalities
on such a molecule which can participate in additional intermo-
lecular non-covalent interactions with themselves or with the
Water dimer is the smallest cluster found in several MOF cavi-
ties. The water dimer in the vapor phase can be identified by

P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
173
Fig. 4. Hydrogen-bonding motif of the self-assembled chain of water molecules in compound 2.
Fig. 5. The hydrogen bonds (O–H–O and N–H–O) between the host compound and guest water molecules in compound 2.
incorporated solvent molecules can lead to interesting architec-
tural motifs. The molecules of [Cu(L1)N3] possess the H-bond
acceptor sites phenolate O and azide N which can be involved in
H-bonding interactions if some donor groups (in this work, water
of crystallization) are available in close proximity. Water mole-
cules are utilized in forming three H-bonds. The self-assembly
pattern and the resulting supra-molecular architecture of 2 are
guided by p-stacking as well as the number of H-bonds formed
by the solvent molecule.
One of the two lattice water molecules, W1 {the corresponding
oxygen atoms of which is represented by O(100)} is connected
through strong H-bonds to the phenolate oxygen, O(1), of the
molecule via H(100) and to another symmetry-related water
molecule W2 [40] via H(101). On the other hand, the other lattice

174
P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
water (W2) is H-bonded to N(5) of the azide group via H(200) and
to another symmetry-related water molecule via H(201). The
phenolate O and azide N of each molecule is serving as a H-
bond acceptor for two water molecules on both sides. Conse-
quently, a water dimer is trapped between two molecules. All of
the H-bonding parameters are given in Table 5. Thus, the alternat-
ing water dimer and the planar molecule form a single-strand
zipper structure, where the distance between the parallel teeth is
6.566 Å. Due to the dimeric water spacer, there is enough space
between the teeth for self recognition of a similar strand through
p-stacking of the perfectly planar molecules. As a result, an infinite
zipper structure has been formed along the crystallographic b axis
(Fig. 6). The copper–copper distance in this linear arrangement is
6.637 Å. The parallel zippers are again connected by H-bonds
involving the water molecules. Finally, a two-dimensional sheet
structure is formed which is parallel to the crystallographic ab
plane (Fig. 7).
3.2.3. Compound 3
The compound 3 crystallizes in the space group P21/n. Perspec-
tive view of discrete mononuclear unit of compound 3 together with
atom-labeling scheme is displayed in Fig. 8. The tridentate Schiff
base, L2 coordinates to the copper ion via the phenolate O, the imine
N, and the pyridine N atoms forming two five membered chelate
rings. The chelate bite angles for the five-membered rings formed
by L2 are in the range 74.74–80.53°. The basal plane of the said geo-
metrical structure is formed by two N atoms {N(1), N(2)} and one
oxygen atom, O(1) from tridentate Schiff base and one chlorine
atom, Cl(2). The apical site is occupied by another chlorine atom,
Cl(1). The penta-coordinated copper(II) is in a distorted square pyra-
midal geometry with trigonality index
s (Addison parame-
ter) = 0.055 [52]. More rigorously, here a conformation is realized,
which is near to intermediate between a square pyramid and a
structure, which is termed an ‘inverse square pyramid’ [63]. The lat-
ter is the static average between two square pyramids and contains
two long (here Cu(1)–O(1) 2.2352(15) Å and Cu(1)–Cl(1))
2.3455(6) Å and three, in comparison, shorter bonds (Cu(1)–N(1),
1.9793(16) Å; Cu(1)–N(2), 2.0240(18) Å; Cu(1)–Cl(2), 2.2115(8)
Å); it is characterized by bond angles (here O(1)–Cu(1)–N(2)
150.71(6) and Cl(1)–Cu(1)–N(2) 108.22(5)). Ideally, the angles
should be equal to 165° in a square pyramid, and should be equal
to 187.5° and 97.5° in ‘reverse square pyramid’ or intermediate
geometry [57]. The latter angle is the one observed for compound
3, while former is fixed by the rigidity of the L2 ligand and is larger
than expected. The strain, introduced by the weakening of the Cu–
O(1) bond due to the presence of a methyl-group on O(1), may be
the reason for the shift of the minimum in the ground state potential
surface towards an intermediate-type position.
Deviations of the coordinating atoms O(1), N(1), N(2) and Cl(2)
from the least-square basal plane are 0.037, ꢂ0.046, 0.037 and
ꢂ0.028 Å, respectively and that of copper atom from the same plane
is 0.422 Å. Sum of the different angles around the metal center in
the basal plane is ꢁ350.83° indicating distorted square pyramidal
geometry around copper ion. The bond lengths and angles are com-
parable with those for the related copper(II) compounds [64]. The
details of bond lengths and bond angles are given in Table 6.
Fig. 6. Zipper motif of compound 2 (double strand).
3.3. Thermo-gravimetric study
Table 5
In the thermo-gravimetric analysis of compound 1, a weight
loss of 10.1% took place in the temperature range 80–115 °C, corre-
sponding to the loss of two water molecules (calc. 10%). Similarly,
in case of compound 2, a weight loss of 10% took place in the tem-
perature range 40–80 °C, corresponding to the loss of two water
molecules (calc. 10.6%). Endothermic peaks were also observed in
the corresponding DTA curves as expected. The dehydrated species
Hydrogen bond distances (Å) and angles (°) of compound 2.
D–Hꢀ ꢀ ꢀA
D–H
Dꢀ ꢀ ꢀA
Hꢀ ꢀ ꢀA
\D–Hꢀ ꢀ ꢀA
O(200)–H(201)ꢀ ꢀ ꢀO(100)
O(100)–H(100)ꢀ ꢀ ꢀO(1)
O(100)–H(101)ꢀ ꢀ ꢀO(200)
O(200)–H(200)ꢀ ꢀ ꢀN(5)
0.83(4)
0.81(4)
0.74(4)
0.68(3)
2.713(5)
2.784(4)
2.791(5)
2.988(4)
1.91(4)
2.01(4)
2.13(4)
2.32(3)
164(5)
162(4)
150(3)
173(3)

P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
175
Fig. 7. Two-dimensional sheet structure from the parallel zippers.
Fig. 8. ORTEP3 diagram of the compound 3 with 30% ellipsoid probability.
did not absorb any water molecules on exposure to open atmo-
sphere. In the IR spectra of the compounds 1 and 2, the broad
bands at ca. 3377 and 3400 cmꢂ1 respectively due to an OH
stretching vibration were missing in the dehydrated species, con-
firming the elimination of the water molecule on heating.
azide [66]. The infrared spectrum of the compound 1 displayed an
intense band at 1384 cmꢂ1 assigned to
mNO3. A broad band at
3377 cmꢂ1 was observed due to OH stretching vibration. The elec-
tronic spectra of compounds 1 and 2 consisted of a broad band at
ꢁ509 nm of lower intensity (
e
= 2.74 ꢃ 103 and 6.78 ꢃ 103 dm3
molꢂ1 cmꢂ1, respectively). Compound 3 did not have any absorp-
tion peak in the visible region, the peak appeared in the near-UV
3.4. IR and electronic spectra and magnetic moments
at 343 nm (
e
= 8.53 ꢃ 103 dm3 molꢂ1 cmꢂ1), but the tail of this band
fell in the visible region and was responsible for its color. The high-
energy, very intense (1.03 ꢃ 104 dm3 molꢂ1 cmꢂ1) bands in the UV
region were associated with a charge-transfer transition.
Copper(II) ions in five-coordination generally stabilize an elon-
gated square pyramid, which is slightly preferred to a compressed
trigonal bipyramid. This stereochemical behavior can be under-
In the IR spectra of all three compounds, the distinct bands due
to azomethine (C@N) group within 1649–1573 cmꢂ1 were rou-
tinely noticed. The lowering of the positions of the bands due to
C@N stretching vibration indicated their coordination to the metal
centers [65]. In the IR spectrum of compound 2, the appearance of
strong band at 2055 cmꢂ1 indicated the presence of monodentate

176
P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
Table 6
and Fig. S3 for compound 2. There is no Oꢀ ꢀ ꢀH/Hꢀ ꢀ ꢀO intermolecular
Selected bond lengths and bond angles of compound 3.
interactions in compound 3. The major intermolecular interactions
in compound 3 is Clꢀ ꢀ ꢀH/Hꢀ ꢀ ꢀCl interaction which comprises 32.1%
of Hirshfeld surfaces for each molecule of compound 3. This Clꢀ ꢀ ꢀH/
Hꢀ ꢀ ꢀCl interaction appears as two distinct spikes in the 2D finger-
print plot. The upper spike corresponding to the donor spike repre-
sents the Oꢀ ꢀ ꢀH interactions (di = 0.961, de = 1.573 Å) and the lower
spike being an acceptor spike represents the Hꢀ ꢀ ꢀO interactions
(de = 0.961, di = 1.573 Å) in the Fingerprint plot, Fig. S4.
3
Cu(1)–O(1)
Cu(1)–N(1)
Cu(1)–N(2)
Cu(1)–Cl(1)
2.2352(15)
1.9793(16)
2.0240(18)
2.3455(6)
2.2115(8)
Cu(1)–Cl(2)
Cl(1)–Cu(1)–Cl(2)
Cl(1)–Cu(1)–O(1)
Cl(1)–Cu(1)–N(1)
Cl(1)–Cu(1)–N(2)
Cl(2)–Cu(1)–O(1)
Cl(2)–Cu(1)–N(1)
Cl(2)–Cu(1)–N(2)
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(2)
N(1)–Cu(1)–N(2)
Cu(1)–O(1)–C(1)
Cu(1)–O(1)–C(2)
Cu(1)–N(1)–C(7)
Cu(1)–N(1)–C(8)
Cu(1)–N(2)–C(9)
Cu(1)–N(2)–C(13)
103.67(3)
91.82(4)
100.81(5)
108.22(5)
95.80(4)
The relative contributions to the Hirshfeld surface area due to
Hꢀ ꢀ ꢀH, Cꢀ ꢀ ꢀH, Cꢀ ꢀ ꢀO, Nꢀ ꢀ ꢀH and Oꢀ ꢀ ꢀH interactions for compounds
1, 2 and 3 as well as some similar compounds available in the
CSD are shown in Fig. S5.
154.02(5)
99.76(5)
74.74(6)
150.71(6)
80.53(7)
3.6. Cyclic voltammetry
123.87(14)
113.23(12)
120.71(12)
115.25(13)
112.35(13)
128.55(16)
In the positive range, from 0 to +2 V, the oxidation and reduction
processes due to ligand were observed. Cyclic scanning between 0
and ꢂ2 V permitted the study of the copper centered reduction pro-
cesses. Electrochemical response in the total range studied for com-
pounds 1–3 showed a similar pattern. The cyclic voltammograms of
these compounds, registered at 100 mV sꢂ1 towards the cathodic
zone, presented a reduction peak (Ic) at about the potential
ꢂ625 mV. This can be assigned as CuII/CuI reduction process. Other
peaks at more negative potential may be due to the reduction to fur-
ther lower oxidation states of copper. A representative example of
this behavior is shown in Fig. 9 for compound 1. The Figure shows
a poorly defined wave (Ia) at ꢂ410 mV during the reverse scan.
The occurrence of a relatively slow electron transfer, quasi-revers-
ible in electrochemical terms, is indicative of important stereo-
chemical reorganization. All the redox signals were similar under
different scan rates at ambient temperature (300 K). Electrochemi-
cal data for the oxidation and reduction of the copper(II) centers of
the compounds 1, 2 and 3 are given in Table 7.
0
stood by considering the vibronic interaction between the A1
ground state and the first excited E’ state via the e0 vibrations in
D3h symmetry (pseudo-Jahn-Teller coupling), in combination with
Jahn-Teller coupling in the excited state, leading into the lower
symmetries [20]. Although the details study of vibronic coupling
is beyond the scope of the present work, it may be helpful to ratio-
nalize the structural features more clearly.
Room temperature magnetic susceptibility measurements
showed that all have magnetic moments close to 1.73 BM as ex-
pected for discrete magnetically non-coupled spin-only value for
copper(II) ion, as was observed in similar systems [58,66,67].
3.5. Hirshfeld surfaces
The Hirshfeld surfaces of the compounds are illustrated in
Fig. S1, showing surfaces that have been mapped over a dnorm
(range of ꢂ0.5 to 1.5 Å), shape index and curvedness. The surfaces
are shown as transparent to allow visualization of the molecular
moiety, in a similar orientation for all structures, around which
they are calculated.
The dominant interactions between Oꢀ ꢀ ꢀH, Nꢀ ꢀ ꢀH and Clꢀ ꢀ ꢀH
atoms in the compounds 1, 2 and 3 can be seen in the Hirshfeld
surface as the red areas in Figure S1. Other visible spots in the
Hirshfeld surfaces correspond to Hꢀ ꢀ ꢀH contacts. The small extent
of area and light color on the surface indicate weaker and longer
contact other than H-bonds. The Oꢀ ꢀ ꢀH/Hꢀ ꢀ ꢀO intermolecular inter-
actions between water molecules appear as distinct spikes in the
2D fingerprint plot of compounds 1 and 2 in Figs. S2 and S3, respec-
tively. Complementary regions are visible in the fingerprint plots
where one molecule act as donor (de > di) and the other as an
acceptor (de < di). The fingerprint plots can be decomposed to high-
light particular atom pairs close contacts [68]. This decomposition
enables separation of contributions from different interaction
types, which overlap in the full fingerprint. The Oꢀ ꢀ ꢀH/Hꢀ ꢀ ꢀO inter-
molecular interactions appear as two distinct spikes in the 2D
fingerprint plots, labeled correspondingly. The proportion of
Oꢀ ꢀ ꢀH/Hꢀ ꢀ ꢀO interactions comprising 40.2% of the Hirshfeld sur-
faces for each molecule of 1, whereas that in 2 is 12.4%. The upper
spike corresponding to the donor spike represents the Oꢀ ꢀ ꢀH inter-
actions (di = 0.646, de = 1.016 Å in 1 and di = 0.741, de = 1.097 Å in
2) and the lower spike being an acceptor spike represents the
Hꢀ ꢀ ꢀO interactions (de = 0.646, di = 1.016 Å in 1 and de = 0.741,
di = 1.097 Å in 2) in the Fingerprint plot, Fig. S2 for compound 1
Fig. 9. Cyclic voltammogram for compound 1 in acetonitrile.
Table 7
Electrochemical data for the oxidation and reduction of the copper(II) center of the
compounds 1, 2 and 3.
Compound
Epa (V)
Epc (V)
E1/2 (V)
DEP (mV)
1
2
3
ꢂ0.6252
ꢂ0.5386
ꢂ0.6497
ꢂ0.4098
ꢂ0.3698
ꢂ0.4098
ꢂ0.5175
ꢂ0.4542
ꢂ0.5297
215
169
240
E1/2 is calculated as the average of anodic (Epa) and cathodic (Epc) peak potentials;
Ep = (Epa ꢂ Epc).
D

P.K. Bhaumik et al. / Inorganica Chimica Acta 390 (2012) 167–177
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