Synthesis and structural studies of some copper-benzoate complexes

Article abstract of DOI:10.1007/s11243-013-9725-5

The reaction of CuCl₂·2H₂O with 3,5-diisopropylpyrazole (Pz^iPr2H) in the presence of sodium parafluorobenzoate (Na-p-FBz) resulted in the formation of an oxo-chloro-bridged tetranuclear complex [Cu₄(Pz^iPr2<

Full text of DOI:10.1007/s11243-013-9725-5

Transition Met Chem (2013) 38:573–585
DOI 10.1007/s11243-013-9725-5
Synthesis and structural studies of some copper-benzoate
complexes
•
Sujata Kashyap Udai P. Singh A. K. Singh
•
•
•
Pravindra Kumar Shivendra Pratap Singh
Received: 6 February 2013 / Accepted: 23 April 2013 / Published online: 5 May 2013
Ó Springer Science+Business Media Dordrecht 2013
Abstract The reaction of CuCl2ꢀ2H2O with 3,5-dii-
sopropylpyrazole (PziPr2H) in the presence of sodium par-
afluorobenzoate (Na-p-FBz) resulted in the formation of an
oxo-chloro-bridged tetranuclear complex [Cu4(PziPr2H)4-
(l-O)(l-Cl)6] 1, whereas the reaction of Cu(NO3)2ꢀ3H2O
with PziPr2H in the presence of different benzoates gave
[Cu(PziPr2H)2(l-OCH3)]2(NO3)2 2, [Cu(PziPr2H)3(NO3)(p-ClBz)]ꢀ
CH3CN 3, [Cu(p-CH3Bz)2(PziPr2H)]2ꢀ2CH3CN 4, [Cu(p-OCH3-
Bz)2(CH3CN)]2ꢀ4CH3CN 5 and [Cu(p-CNBz)(CH3CN)]2 6.
Single-crystal X-ray diffraction studies confirmed these
formulations. DNA binding studies for these complexes
were performed by means of UV-visible absorption titration
and viscosity measurements. Gel electrophoresis studies
showed that hydroxyl radicals are involved in DNA cleav-
age in the presence of the complexes.
been reported as possible models for the active sites of such
proteins. Copper complexes also play an important role in
the endogenous oxidative DNA damage associated with
aging and cancer. Some of these complexes have efficient
oxidative cleavage activity and specificity for DNA [8].
As artificial nucleases, multinuclear complexes have
attracted much attention because similar metal centers are
often found in natural nucleases, and they may demonstrate
synergistic effects in O2 activation and DNA recognition
[9]. Also, these complexes are often cationic species that
encourage the electrostatic attraction to the anionic phos-
phate backbone of DNA. The ditopic pyrazole ligand with
various substituents on the 3- or 5-positions is an excellent
candidate for the engineering of structures, being an isomer
of imidazole as well as a common motif biochemical
structures [10, 11].
To the best of our knowledge, no literature is currently
available for the interactions of DNA with copper-pyra-
zole-benzoate complexes, except for a recently reported
DNA cleavage studies with copper-benzoate complexes
having other ligands [12–14]. In this work, we have pre-
pared copper complexes for DNA binding studies. Gel
electrophoresis experiments suggested that in the presence
of hydrogen peroxide, these copper complexes can cleave
pUC19 DNA effectively.
Introduction
Copper complexes have been used to mimic the active sites
of many copper metalloproteins, including cytochrome c
oxidase, azurin, plastocyanin, hemocyanin, superoxide
dismutase and nitrite reductase [1, 2]. A variety of copper
complexes [3–7] with synthetic and natural ligands have
Electronic supplementary material The online version of this
article (doi:10.1007/s11243-013-9725-5) contains supplementary
material, which is available to authorized users.
Experimental
S. Kashyap ꢀ U. P. Singh (&) ꢀ A. K. Singh
Department of Chemistry, Indian Institute of Technology
Roorkee, Roorkee 247 667, India
All manipulations were performed in air using commercial
grade solvents. The solvents were dried with appropriate
drying agents by the literature methods [15]. 3,5-Dii-
sopropylpyrazole (PziPr2H) was prepared as reported
earlier [16]. Calf thymus DNA (CT-DNA, activated and
lyophilized), agarose (molecular biology grade) and
e-mail: udaipfcy@iitr.ernet.in
P. Kumar ꢀ S. P. Singh
Department of Biotechnology, Indian Institute of Technology
Roorkee, Roorkee 247 667, India
123

574
Transition Met Chem (2013) 38:573–585
ethidium bromide (EB) were purchased from Aldrich.
Supercoiled pUC19 DNA (cesium chloride purified) was
purchased from Bangalore Genie (India). Copper(II) chlo-
ride dihydrate and copper(II) nitrate trihydrate (reagent
grade) were purchased from Merck. Tris(hydroxymethyl)-
aminomethane-HCl (Tris–HCl) buffer solution (pH 7.4)
was prepared using doubly distilled miliQ water. Samples
of the crystalline complexes were carefully dried under
vacuum for several hours prior to elemental analysis on an
Elementar Vario EL III analyzer. IR spectra were obtained
on a Thermo Nicolet Nexus FTIR spectrometer using KBr
pellets. Absorption spectra were recorded on a PerkinElmer
UV-visible Spectrophotometer (Lambda 35), equipped
with a thermostatic bath (Julabo). Mass spectra were
obtained with a Bruker MICROTOF-II mass spectrometer.
X-ray data collections were performed on a Bruker Kappa
Apex four circle-CCD diffractometer using graphite-
blue powder. The compound was redissolved in acetoni-
trile, and blue crystals suitable for X-ray data collection
were obtained by slow cooling at -20 °C. Yield: 0.28 g,
61 %. Anal. Calcd for C19H35N5O4Cu: C, 49.5; H, 7.7; N,
15.2. Found: C, 49.4; H, 7.8; N, 15.3 %. IR (KBr, cm-1):
3,452, 2,966, 1,634, 1,567.
Synthesis of complex 3
Compound 3 was prepared and crystallized by the method
described for the preparation of complex 2 using sodium
parachlorobenzoate (Na-p-ClBz). Yield: 0.45 g, 59 %.
Anal. Calcd for C36H52N8O5ClCu: C, 55.7; H, 6.8; N, 14.4.
Found: C, 55.2; H, 6.9; N, 14.2 %. IR (KBr, cm-1): 3,625,
3,449, 2,916, 1,630, 1,520, 1,210.
Synthesis of complex 4
˚
monochromated MoKa radiation (k = 0.71070 A) at
100 K. In the reduction of data Lorentz and polarization
corrections and empirical absorption corrections were
made [17]. Crystal structures were solved by direct or
Patterson methods. Structure solution, refinement and data
output were carried out with the SHELXTL program [18,
19]. Non-hydrogen atoms were refined anisotropically.
Hydrogen atoms were placed in geometrically calculated
positions using a riding model. Images and hydrogen-
bonding interactions were created in the crystal lattice with
DIAMOND and MERCURY software [20, 21].
Compound 4 was prepared and crystallized by the method
described for the preparation of complex 2 using sodium
paramethylbenzoate (Na-p-CH3Bz). Yield: 0.71 g, 68 %.
Anal. Calcd for C54H66N6O8Cu2: C, 61.5; H, 6.3; N, 7.9.
Found: C, 61.3; H, 6.2; N, 7.5 %. IR (KBr, cm-1): 3,623,
3,452, 2,966, 1,634, 1,523, 1,452.
Synthesis of complex 5
Compound 5 was prepared and crystallized by the method
described for the preparation of complex 2 using sodium
paramethoxybenzoate (Na-p-OCH3Bz). Yield: 0.70 g,
72 %. Anal. Calcd for C44H46N6O12Cu2: C, 54.0; H, 4.7; N,
8.6. Found: C, 54.4; H, 4.6; N, 8.4 %. IR (KBr, cm-1):
3,653, 3,138, 2,968, 1,616, 1,564, 1,339, 628.
Synthesis of complex 1
A methanolic (10 mL) solution of CuCl2.2H2O (0.17 g,
1.0 mmol) and a solution of PziPr2H (0.15 g, 1.0 mmol) in
dichloromethane (10 mL) were added to a methanolic
solution (5 mL) of sodium parafluorobenzoate (Na-p-FBz)
(0.16 g, 1.0 mmol). The resultant mixture was stirred at
room temperature for 4 h and then filtered. The filtrate was
concentrated under vacuum to afford a brown-green pow-
der. Brown crystals suitable for X-ray data collection were
obtained at -20 °C from acetonitrile solution. Yield:
0.73 g, 67 %. Anal. Calcd for C36H64N8OCl6Cu4: C, 39.6;
H, 5.9; N, 10.3. Found: C, 39.4; H, 5.6; N, 10.1 %. IR
(KBr, cm-1): 3,260, 2,930, 1,573, 1,495, 1,386, 643.
Synthesis of complex 6
Compound 6 was prepared and crystallized by the method
described for the preparation of complex 2 using sodium
paracyanobenzoate (Na-p-CNBz). Yield: 0.48 g, 61 %.
Anal. Calcd for C36H22N6O8Cu2: C, 54.5; H, 2.8; N, 10.6.
Found: C, 54.2; H, 2.5; N, 10.8 %. IR (KBr, cm-1): 3,452,
2,966, 1,634, 1,567, 1,346.
DNA binding and cleavage studies
Synthesis of complex 2
The CT-DNA solution gave a UV absorbance ratio at 260
and 280 nm in the range of 1.85–1.87, indicating that the
DNA was sufficiently free from protein and RNA. The
absorption titrations were performed at a fixed concentra-
tion of the complex (50 lM) by varying the concentration
of DNA (10 lL of 10 lM in each addition). In order to
eliminate the interferences due to DNA absorption, the data
were obtained while keeping the same concentration of
To a solution of Cu(NO3)2ꢀ3H2O (0.23 g, 1.0 mmol) and
sodium parafluorobenzoate (Na-p-FBz) (0.16 g, 1.0 mmol)
in methanol (10 mL), a solution of PziPr2H (0.15 g,
1.0 mmol) in dichloromethane (10 mL) was added. The
mixture was stirred at room temperature for 4 h and fil-
tered. The filtrate was concentrated under vacuum to afford
123

Transition Met Chem (2013) 38:573–585
575
COONa
X
DNA in the reference cuvette. DNA was added until no
further change in absorbance was observed in the absorp-
tion spectrum. The binding constants (Kb) for the interac-
tion of the complexes with DNA were calculated by the
literature methods [22].
PzR1,R2
H
CuCl2
X=F, Cl, CH3, OCH3, CN
Viscosity measurements were taken using an Ostwald
viscometer which was immersed in a thermostatic water
bath at 27.0 0.1 °C. A digital stopwatch was used to
measure the flow time. In order to minimize the com-
plexities arising from the flexibility of DNA, samples were
prepared by sonication.
NH
N
N
N
Cl
H
Cu
Cu
Cl
O
Cl
Cl
DNA cleavage study
Cl
Cu
Cu
H
Cleavage of plasmid DNA was monitored by agarose gel
electrophoresis, performed with a reaction mixture having
pUC19 plasmid DNA (300 ng) and varied concentrations
of the complex (30–100 lM) in the presence of H2O2 in
Tris–HCl buffer (pH 7.4). The samples were incubated for
60 min at 37.0 °C, and the loading buffer (25 % bromo-
phenol blue and 30 % glycerol) was then added. The
electrophoresis of the DNA cleavage products was per-
formed at 60 V for 30 min in TBE buffer on freshly pre-
pared agarose gel (0.8 %) containing 0.4 lg/mL of EB.
The different fragments were identified under UV light and
photographed with a gel documentation system (Bio-Rad).
For comparison, reactions were also carried out with the
respective copper salts, since it is known that copper(II)
ions in the presence of hydrogen peroxide cause extensive
DNA cleavage.
N
Cl
N
N
HN
Scheme 1 Synthesis of complex 1
[Cu(PziPr2H)(l-Cl)Cl]2 [24]. However, the same reaction in
the presence of sodium parafluorobenzoate (Na-p-FBz)
(Scheme 1) resulted in the formation of an oxo- and
chloro-bridged tetranuclear complex 1 with the formula
[Cu4(PziPr2H)4(l-O)(l-Cl)6]. The above reaction in the
presence of other para-substituted sodiumbenzoates (Na-p-
XBz, where X = Cl, CH3, OCH3 or CN) always gave the
same product, irrespective of the nature of the para-sub-
stituent of the benzoate. On the other hand, the reaction of
Cu(NO3)2 with PziPr2H in the presence of the above ben-
zoates (Scheme 2) gave compounds 2–6, with different
formulations specifically [Cu(PziPr2H)2(l-OCH3)]2(NO3)2
2, [Cu(PziPr2H)3(NO3)(p-ClBz)]ꢀCH3CN 3, [Cu(p-CH3Bz)2
Antibacterial study
The synthesized ligand and its copper(II) complexes were
screened in vitro for their antimicrobial activity against
Escherichia coli (Gram negative), Salmonella typhimurium
(Gram negative), Listeria monocytogenes (Gram positive)
and Staphylococcus aureus (Gram positive) through the
disk diffusion method [23]. The complexes were stored dry
at room temperature and dissolved in DMF (10 mg mL-1).
Each bacterium was suspended and diluted to ca
106 cfu mL-1. They were flood inoculated onto the surface
of Luria–Bertani agar (LBA). The plates were then incu-
bated at 37 °C for 24 h. The inhibitory activity of DMF
was also tested in the same way. The antimicrobial activ-
ities of the complexes were evaluated by measuring one
diameter of the inhibition zone.
(PziPr2H)]2ꢀ2CH3CN
4,
[Cu(p-OCH3Bz)2(CH3CN)]2ꢀ
4CH3CN 5 and [Cu(p-CNBz)(CH3CN)]2 6. Their IR
spectra show differences of masym (COO-) and msym
(COO-) in the range of 221–229, suggesting bidentate
coordination of the benzoate ligand in complexes 4–6
rather than monodentate behavior as in complex 3 [25].
Crystal structure descriptions
The crystallographic data for complexes 1–6 are presented
in Table 1, and the important bond lengths and angles are
given in Table 2. Non-covalent interactions are summa-
rized in Table 3.
Tetranuclear complex 1 crystallizes in the monoclinic
C2/c space group (Fig. 1). The polyhedral structure lies on
an inversion center and contains a non-planar, tetranuclear
copper(II) core. Each metal center is bridged to the other
three metal centers through one central oxygen atom and
Results and discussion
The reaction of CuCl2 with PziPr2H resulted in the forma-
tion of a dinuclear chloro-bridged complex formulated as
123

576
Transition Met Chem (2013) 38:573–585
Scheme 2 Synthesis of
complexes 2–6
O
N
H
N
N
H
O
N
O
O
O
N
H
N
N
N
H
N
N
Cu
N
O
Cu
O
H
N
CH3
O
O
O
H
N
CH3CN
C
H3C
3
O
Cu
N
N
H
N
O
N
O
p-Cl-Bz
p-F-Bz
Cl
H3C
2
Cu(NO3)2 + PziPr2
H
CN
NC
N
NH
p-CN-Bz
O
p-CH3-Bz
O
CH3
O
O
p-OCH3-Bz
O
O
O
H3C
O
O
O
O
Cu
O
OCH3
NCCH3
H3CCN
H3CO
Cu
O
N
HN
O
O
O
CH3
2CH3CN
4
O
O
O
O
CN
NCCH3
NC
H3CCN
Cu
O
O
O
O
6
4CH3CN
OCH3
H3CO
5
˚
six chlorine atoms. Each copper atom is coordinated by a
terminal PziPr2H, three bridged chloride and one oxygen
atom, giving a square-pyramidal geometry (Fig. S1). The
tetranuclear unit has a symmetrical-bridging l4-O group at
its center, pointing to the opposite sides of the copper plane
a Cu1–Cu1A distance of 2.978(2) A, and the Cu1–O1–
Cu1A angles are 124.3(18) and 124.4(18), similar to the
respective average values in a series of di-l-alkoxo-
bridged copper(II) complexes [28, 29]. The copper-bridg-
˚
ing methoxy bond distance is 1.920(16) A. The methyl C–
˚
where the O atom is 0.024 A above the Cu4-plane (Fig.
H of the isopropyl group and the pyrazole-1-yl N–H form
C–HꢀꢀꢀO and N–HꢀꢀꢀO interactions (Fig. S4) with the nitrate
oxygen on their respective side, leading to a one-dimen-
sional packing (Fig. 4).
S2). The Cu–O bond distances are in the range of
˚
1.901–1.907 A. Various other oxo-bridged tetranuclear
copper complexes with different ligands have been repor-
ted in the literature [26, 27]. During the refinement, the
occupancy was found to be half for chlorine (Cl1). The
different non-covalent interactions (C–HꢀꢀꢀCl and N–HꢀꢀꢀCl
(Fig. S3) formed by the involvement of isopropyl C–H and
pyrazole-1yl N–H with chloride) lead to a one-dimensional
chain in complex 1 (Fig. 2).
Complex 3 is mononuclear in nature, with penta-coor-
dinated metal centers. The coordination sphere is close to
a distorted square pyramid, which is achieved by means of
three N atoms (N1, N3, and N5) from three PziPr2
H
ligands, one oxygen atom (O3) from the nitrate and
another oxygen atom (O1) from parachlorobenzoate
(Fig. 5). Both Cu–N and Cu–O bond distances are in the
The dinuclear complex 2 crystallizes in the monoclinic
space group P21/n (Fig. 3), where each copper center is in
a slightly distorted square-planar coordination geometry.
The complex is present at the symmetry axis. The basal
plane consists of two bridging methoxy oxygens (O1 and
O1A) and two nitrogen atoms from two neutral pyrazole
ligands. The two nitrate anions lie on opposite sides of the
Cu2O2 plane. The molecule has a center of symmetry with
˚
˚
range of 1.995(3)–2.006(3) A and 1.956(2)–2.379(3) A,
respectively. The Cu–O1 bond distance is smaller than
Cu–O3, due to the higher electronegativity of chlorine in
parachlorobenzoate which decreases the Cu–O1 bond
distance. The methyl C–H of the isopropyl group present
on the pyrazole ring forms a C–Hꢀꢀꢀp interaction with the
p electrons of the pyrazole from a neighboring copper
123

Transition Met Chem (2013) 38:573–585
577
Table 1 Crystallographic data for complexes 1–6
1
2
3
4
5
6
Empirical
formula
C36H64Cl6Cu4N8O C19H35CuN5O4
C36H52ClCuN8O5 C54H66Cu2N6O8
C44H46Cu2N6O12
C36H22Cu2N6O8
Formula weight 1,091.81
461.07
775.86
1,054.23
0.7107
Triclinic
P-1
977.97
793.68
0.7107
Hexagonal
R-3
˚
Wavelength (A) 0.7107
0.7107
0.7107
0.7107
Crystal system
Space group
Monoclinic
Monoclinic
P 21/n
Monoclinic
P 21/c
Monoclinic
C 2/c
C2/c
˚
Unit-cell dimensions (A, °)
˚
a (A)
21.550(4)
9.3720(19)
23.850(5)
90.00
9.5559(11)
18.209(2)
14.8572(17)
90.00
12.2114(13)
5.7576(16)
23.033(3)
90.00
12.0764(10)
12.1133(11)
18.7008(17)
82.311(4)
81.331(3)
89.870(3)
2,679.6(4)
2
25.0233(19)
10.0386(6)
23.0117(17)
90.00
28.9406(7)
28.9406(7)
16.0198(5)
90.00
˚
b(A)
˚
c(A)
a (°)
b (°)
c (°)
102.57(3)
90.00
104.995(5)
90.00
104.681(7)
90.00
119.448(7)
90.00
90.00
120.00
3
˚
Volume (A )
4,701.4(16)
4
2,497.2(5)
4
4,287.4(8)
4
5,033.7(6)
4
11,619.9(5)
9
Z
Q (Calcd.)
1.543
1.226
1.202
1.307
1.291
1.021
(mg cm-3
)
F (000)
2,248
980.0
1,640.0
1,108.0
2,024.0
3,618
h range for data 1.75–27.59
collection
2.24–26.00
1.58–28.38
1.11–28.66
1.87–21.86
1.51–28.30
Absorption
correction
Multi-scan
Multi-scan
Multi-scan
Multi-scan
Multi-scan
Multi-scan
6,439/3,868
Reflections
collected/
unique
5,410/4,279
4,898/3,773
10,751/5,178
13,805/10,680
3,037/2,340
Refinement
method
Full-matrix least
squares on F2
Full-matrix least
squares on F2
Full-matrix least
squares on F2
Full-matrix least
squares on F2
Full-matrix least
squares on F2
Full-matrix least
squares on F2
Data/restraints/
Parameters
5,410/0/267
4898/24/262
1.045
10,678/133/389
1.262
13,602/176/609
1.296
3,034/0/295
1.297
6,439/0/234
0.979
Goodness-of-fit
on F2
1.051
Final R indices
[I [ 2r(I)]
R1 = 0.0303;
wR2 = 0.0727
R1 = 0.0465;
wR2 = 0.0779
R1 = 0.0463;
wR2 = 0.1422
R1 = 0.0632;
wR2 = 0.1541
R1 = 0.0725;
wR2 = 0.2031
R1 = 0.1629;
wR2 = 0.2450
R1 = 0.0525;
wR2 = 0.1620
R1 = 0.0733;
wR2 = 0.1840
R1 = 0.0559;
wR2 = 0.1312
R1 = 0.0848;
wR2 = 0.1780
R1 = 0.0589;
wR2 = 0.1830
R1 = 0.0989;
wR2 = 0.1940
R indices (all
data)
complex (Fig. S5), giving a one-dimensional chain-like
structure (Fig. 6).
benzoate oxygen of a neighboring molecule, resulting in a
one-dimensional rail-like structure (Fig. 8).
The paddle-wheel dinuclear copper complex 4 crystal-
ꢀ
lizes in the triclinic P1 space group having two acetonitrile
Complexes 5 and 6 also have paddle-wheel structure and
crystallize in the monoclinic C2/c group and rhombohedral
space group R-3, respectively. The molecular structures of
5 and 6 are shown in Figs. 9 and 10. Each metal center is
five coordinated with four bridging benzoates and a ter-
minal acetonitrile occupying the axial position, giving an
approximate square-pyramidal geometry with the formula
[Cu2(p-XBz)4(CH3CN)2] (X = OCH3 for 5 and X = CN
for 6). Complex 5 has two additional acetonitriles in the
lattice, which are present on the symmetry axis. The
molecules in the lattice (Fig. 7). The X-ray structure shows
that each metal center is five coordinated with four bridg-
ing benzoates and one terminal Pzipr2H ligand giving a
square-pyramidal arrangement with Cu–Cu bond distance
˚
2.654(5) A. The Cu-O bond lengths are in the range of
˚
1.960(15)–1.981(15) A, falling in the reported range of
˚
1.96–1.98 A [30]. The pyrazole-1-yl N–H forms a N–HꢀꢀꢀN
interaction with the nitrogen of acetonitrile, and the C–H of
˚
Cu–Cu bond length of 2.624(12) A in 5 is almost the same
acetonitrile forms a C–HꢀꢀꢀO interaction (Fig. S6) with the
123

578
Transition Met Chem (2013) 38:573–585
Table 2 Selected bond lengths and angles in for 1–6
Table 2 continued
˚
Bond lengths/A
˚
Bond lengths/A
Bond angles/°
Bond angles/°
1
4
Cu(1)–N(1)
Cu(1)–O(1)
Cu(1)–Cl(1)
Cu(1)–Cl(2)
Cu(1)–Cl(3)
Cu(2)–N(3)
Cu(2)–O(1)
Cu(2)–Cl(2)
Cu(2)–Cl(3)
Cu(2)–Cl(4)
Cl(1)–Cu(1)
Cl(2)–Cu(1)
Cl(4)–Cu(2)
O(1)–Cu(1)
O(1)–Cu(2)
1.960(18)
1.904(12)
2.408(13)
2.374(9)
2.376(7)
1.969(19)
1.905(11)
2.340(8)
2.368(10)
2.522(8)
2.459(13)
2.374(9)
2.522(8)
1.904(12)
1.905(11)
N(1)–Cu(1)–Cl(1)
N(1)–Cu(1)–Cl(2)
N(1)–Cu(1)–Cl(3)
N(3)–Cu(2)–Cl(2)
N(3)–Cu(2)–Cl(3)
Cl(2– Cu(1)–Cl(1)
O(1)–Cu(1)–N(1)
O(1)–Cu(2)–N(3)
O(1)–Cu(2)–Cl(2)
O(1)–Cu(2)–Cl(3)
O(1)–Cu(1)–Cl(1)
O(1)–Cu(1)–Cl(1)
O(1)–Cu(1)–Cl(2)
O(1)–Cu(1)–Cl(3)
O(1)–Cu(2)–Cl(4)
Cl(1)–Cu(1)–Cl(1)
Cl(2)–Cu(1)–Cl(3)
Cl(2)–Cu(1)–Cl(1)
Cl(2)–Cu(2)–Cl(3)
Cl(2)–Cu(2)–Cl(4)
Cl(3)–Cu(1)–Cl(1)
Cl(3)–Cu(1)–Cl(1)
90.3(7)
99.8(6)
97.0(6)
94.7(6)
99.9(6)
102.0(5)
173.8(7)
173.6(7)
85.3(4)
85.1(3)
84.3(6)
82.9(6)
84.4(3)
85.0(4)
83.7(5)
27.7(7)
115.4(3)
129.1(4)
126.3(3)
120.3(3)
139.6(4)
112.1(5)
Cu(1)–N(1)
Cu(1)–O(1)
Cu(1)–O(2)
Cu(1)-O(3)
Cu(1)–O(4)
Cu(1)–Cu(1)
2.152(17)
1.981(15)
1.963(14)
1.968(14)
1.960(15)
2.654(5)
O(1)–Cu(1)–N(1)
O(2)–Cu(1)–N(1)
O(3)–Cu(1)–N(1)
O(4)–Cu(1)–N(1)
O(2)–Cu(1)–O(1)
O(2)–Cu(1)–O(3)
O(3)–Cu(1)–O(1)
O(4)–Cu(1)–O(1)
O(4)–Cu(1)–O(3)
O(4)–Cu(1)–O(2)
N(1)–Cu(1)–Cu(1)
O(1)–Cu(1)–Cu(1)
O(2)–Cu(1)–Cu(1)
O(3)–Cu(1)–Cu(1)
O(4)–Cu(1)–Cu(1)
93.9(7)
93.0(6)
99.0(6)
98.1(7)
88.3(6)
167.6(6)
88.6(6)
167.9(6)
90.0(6)
90.4(6)
175.1(5)
87.9(5)
82.5(5)
85.4(5)
80.0(5)
5
Cu(1)–N(1)
Cu(1)–O(1)
Cu(1)–O(2)
Cu(1)–O(3)
Cu(1)–O(4)
Cu(1)–Cu(1)
2.200(5)
1.963(4)
1.947(3)
1.957(4)
1.952(4)
2.624(12)
N(1)–Cu(1) Cu(1)
O(1)–Cu(1) N(1)
O(1)–Cu(1) Cu(1)
O(2)–Cu(1) N(1)
O(2)–Cu(1) O(1)
O(2)–Cu(1) O(3)
O(2)–Cu(1) O(4)
O(2)–Cu(1) Cu(1)
O(3)–Cu(1) N(1)
O(3)–Cu(1) O(1)
O(3)–Cu(1) Cu(1)
O(4)–Cu(1) N(1)
O(4)–Cu(1) O(1)
O(4)–Cu(1) O(3)
O(4)–Cu(1) Cu(1)
177.9(14)
94.7(17)
83.8(12)
96.7(17)
168.5(15)
89.7(16)
88.7(16)
84.6(11)
96.6(17)
89.5(18)
84.9(12)
94.9(18)
89.7(17)
168.4(15)
83.4(12)
2
Cu(1)–N(1)
Cu(1)–N(3)
Cu(1)–Cu(1a)
Cu(1)–O(1)
O(1)–C(19)
1.965(3)
1.980(2)
2.978(7)
1.9219(18)
1.399(3)
N(1)–Cu(1)–N(3)
N(1)–Cu(1)–Cu(1)
N(3)–Cu(1)–Cu(1)
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(3)
O(1)–Cu(1)–N(3)
O(1)–Cu(1)–O(1)
O(1)–Cu(1)–Cu(1)
O(1)–Cu(1)–Cu(1)
Cu(1– O(1)–Cu(1)
C(19)–O(1)–Cu(1)
C(19)–O(1)-Cu(1)
96.6(9)
131.9(6)
131.4(6)
168.6(8)
93.2(8)
92.7(8)
167.7(8)
78.3(7)
39.1(5)
6
39.1(5)
Cu(1)–N(1)
Cu(1)–O(1)
Cu(1)–O(2)
Cu(1)–O(3)
Cu(1)–O(4)
Cu(1)–Cu(1)
2.168(3)
1.964(2)
1.977(2)
1.958(2)
1.969(2)
2.655(8)
N(1)–Cu(1)-Cu1)
O(1)-Cu(1)–N(1)
O(1)–Cu(1)–O(2)
O(1)–Cu(1)–O(4)
O(1)–Cu(1)–Cu(1)
O(2)–Cu(1)–N(1)
O(2)–Cu(1)–Cu(1)
O(3)–Cu(1)–N(1)
O(3)–Cu(1)–O(1)
O(3)–Cu(1)–O(2)
O(3)–Cu(1)–O(4)
O(3)–Cu(1)–Cu(1)
O(4)–Cu(1)–N(1)
O(4)–Cu(1)–O(2)
O(4)–Cu(1)–Cu(1)
178.7(8)
95.4(10)
168.1(9)
88.1(9)
85.7(7)
96.4(9)
82.4(7)
95.4(10)
89.3(10)
89.5(10)
168.0(9)
85.0(7)
96.4(10)
90.4(9)
83.1(7)
101.6(7)
124.4(18)
124.3(18)
3
Cu(1)–N(1)
Cu(1)–N(3)
Cu(1)–N(5)
Cu(1)–O(1)
Cu(1)–O(3)
1.995(3)
2.006(3)
2.004(3)
1.956(2)
2.379(3)
N(1)–Cu(1)–N(3)
N(1)–Cu(1)–N(5)
N(1)–Cu(1)–O(3)
N(3)–Cu(1)–O(3)
N(5)–Cu(1)–N(3)
N(5)–Cu(1)–O(3)
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(3)
O(1)–Cu(1)–N(5)
O(1)–Cu(1)–O(3)
91.2(11)
168.9(13)
98.0(11)
95.7(10)
90.8(12)
92.5(12)
91.2(11)
176.2(11)
86.1(12)
86.6(10)
123

Transition Met Chem (2013) 38:573–585
579
Table 3 Non-covalent interactions in complexes 1–6
D–HꢀꢀꢀA
d(D–H)
d(H–A)
d(D–A)
\(DHA)[
1
N2–H19ꢀꢀꢀCl1
N2–H19ꢀꢀꢀCl4
N4–H20ꢀꢀꢀCl4
C16–H16ꢀꢀꢀCl1
2
0.861(10) 2.377(24) 2.983(36) 127.8
0.861(10) 3.141(24) 3.916(35) 150.9
0.860(2)
0.981(4)
2.468(27) 3.048(35) 125.3
3.156(37) 3.924(44) 136.2
N2–H2ꢀꢀꢀO2
N2–H2ꢀꢀꢀO3
N4–H4ꢀꢀꢀO2
N4–H4ꢀꢀꢀO4
C12–H12ꢀꢀꢀO3
0.860(3)
0.860(3)
0.861(3)
0.861(3)
0.980(3)
2.163(3)
2.356(3)
2.546(3)
2.199(6)
2.761(3)
2.884(7)
2.733(4)
2.990(4)
2.983(4)
3.337(5)
2.898(9)
3.581(4)
3.436(9)
3.624(8)
161.2
130.1
153.2
138.1
141.5
117.5
154.5
C17–H17AꢀꢀꢀO3 0.960(9)
C18–H18BꢀꢀꢀO2 0.960(6)
3
4
C25H25ꢀꢀꢀp
C18–H28ꢀꢀꢀp
0.961(7)
0.960(7)
3.136(10) 3.776(12) 125.4
3.454(11) 4.170(17) 133.1
C16–H16CꢀꢀꢀO3 0.960(3)
C51–H15CꢀꢀꢀO1 0.959(4)
C51–H15BꢀꢀꢀO3 0.960(4)
2.794(4)
2.899(5)
2.564(4)
3.648(6)
3.323(7)
3.467(7)
148.6
156.6
107.9
5
C11–H11ꢀꢀꢀN2
C16–H16ꢀꢀꢀN3
C6–H6ꢀꢀꢀO6
0.930(6)
0.961(9)
0.929(8)
0.930(6)
2.790(27) 3.507(27) 134.6
2.890(2)
2.713(3)
2.818(7)
2.580(5)
2.906(5)
3.830(22) 166.2
3.542(12) 149.0
3.383(10) 120.3
3.486(10) 157.5
Fig. 1 Crystal structure of complex 1. Color code: C gray; N blue; O
red; Cl green; Cu cyan. (Color figure online)
C14–H14ꢀꢀꢀO5
C18–H18BꢀꢀꢀO1 0.960(7)
C18–H18BꢀꢀꢀO3 0.960(7)
C19–H19BꢀꢀꢀO4 0.961(22) 2.600(4)
C21–H21AꢀꢀꢀO2 0.961(20) 2.657(6)
C21-H21AꢀꢀꢀO3 0.961(20) 2.772(7)
C19–H19CꢀꢀꢀO1 0.960(16) 2.923(11) 3.615(23) 129.9
C21–H21BꢀꢀꢀN2 0.961(10) 2.915(33) 3.829(36) 159.4
3.507(9)
121.7
assembly with cuboidal cavities for the guest acetonitrile
molecule (Fig. S8).
3.413(21) 142.4
3.466(18) 142.0
3.675(22) 156.7
The phenyl C–H groups of benzoate in complex 6 are
involved in C–HꢀꢀꢀN interactions with the cyano nitrogen
present in the coordinated benzoates of other molecules
while the methyl C–H of coordinated acetonitrile shows C–
HꢀꢀꢀN interactions with the cyano nitrogens (Fig. S9). Due
to the presence of different intermolecular interactions, the
packing of complex 6 shows a three-dimensional structure
6
C14–H14ꢀꢀꢀN2
C18–H18ꢀꢀꢀN3
0.930(3)
0.962(3)
3.149(5)
2.631(5)
3.750(5)
3.302(4)
124.0
127.2
˚
with star-shaped cavities of 4.2 A radius (Figs. 11 and
S10).
˚
Mass spectrometry
as in 6, at 2.657(8) A. The Cu–N bond distances in 5 and 6
are also very similar but larger than complex 4. The Cu–O
and Cu–Cu bond distances for 4–6 are in the ranges
reported earlier [31].
The mass spectra of the complexes exhibited the molecular
ion peaks [M ? H]?, m/z at 1,087, 922, 775, 1,054, 980
and 793 a.m.u corresponding to their molecular formulae
[Cu4C36H64N8OCl6] 1, [CuC19H35N5O4] 2, [CuC34H52-
N7O5Cl] 3, [Cu2C50H60N4O8] 4, [Cu2C36H34N2O12] 5 and
[Cu2C36H22N6O8] 6, respectively (Fig S11). The mass
spectrum of the tetranuclear Cu(II) complex (1) shows a
molecular ion peak at m/z 1,087, which corresponds to
[C36H64N8Cu4OCl6] ? [H]?, the calculated m/z being
In complex 5, the methyl C–H of coordinated acetoni-
trile forms a C–HꢀꢀꢀO interaction with the methoxy oxygen
of the neighboring molecule, and the CH3 group of unco-
ordinated acetonitrile forms a C–HꢀꢀꢀO interaction with the
bridged benzoate oxygen (Fig. S7). The presence of dif-
ferent non-covalent interactions can be viewed as a host–
guest structure, where the complex molecules form the host
123

580
Transition Met Chem (2013) 38:573–585
Fig. 2 One-dimensional
packing of complex 1. Color
code: C gray; N blue; O red; Cl
green; Cu cyan. (Color figure
online)
concentrations. The hypochromism (H %) values are listed
in Table S3.
H % ¼ 100 %:ðAfree ꢁ AboundÞ=Afree
The intrinsic binding constants were calculated with the
help of the following equation: [22].
½DNAꢂ=ðeA ꢁ efÞ ¼ ½DNAꢂ=ðeB ꢁ efÞ þ 1=KbðeB ꢁ efÞ
where eA, ef, and eB correspond to Aobs/[complex], and the
extinction coefficients of the complex in the free and fully
bound forms, respectively. Graphs of [DNA]/(eA - ef)
versus [DNA] were plotted, and the values of Kb (binding
constant) were obtained from the ratio of the slope to the
intercept. The binding constants are summarized in
Table 4; complex 1 has highest binding constant, while the
other complexes 2–6 have very similar binding constants.
The results suggest that none of these complexes are
intercalating, but rather grove binders (Table 4), since the
binding constants are smaller than those for typical inter-
calators (EB-DNA = 106) [34].
Viscosity measurements were taken in order to clarify
the nature of interaction of DNA with these complexes.
Viscosity measurements are considered to provide least
ambiguous test for the binding mode in the absence of
crystallographic data, as they are highly sensitive to
changes in length of the DNA. A classical intercalative
mode causes a significant increase in viscosity of the DNA
solution due to increased separation of the base pairs at the
intercalation sites and hence an increase in overall DNA
length [35–37]. In contrast, groove or electrostatic inter-
actions make little or no change in the viscosity of DNA
solution, as they produce kinks in the DNA that reduce its
effective length and concomitantly its viscosity.
Fig. 3 Crystal structure of 2. Color code: C gray; N blue; O red; Cu
cyan. (Color figure online)
1,086. The mass spectra of complexes 1–6 are summarized
in Table S1.
DNA binding studies
The UV-visible absorption titration is an effective method
of investigation for the binding mode of DNA with metal
complexes [32, 33]. The absorption spectra of the com-
plexes were recorded in 10.0 mM Tris–HCl buffer (pH 7.4)
in the absence and presence of DNA (Fig. 12). This figure
shows that the titration of these complexes with CT-DNA
gives rise to isobestic points (Table S2). Complexes 1–6 all
showed hypochromism and red shift with increasing DNA
Values of (g/g0)1/3 were plotted against [comp/DNA] in
the absence and presence of the complex, where g and g0
are the viscosity of DNA in the presence and absence of the
complex (Fig. 13). The decrease in viscosity with
123

Transition Met Chem (2013) 38:573–585
581
Fig. 4 One-dimensional packing of complex 2. Color code: C gray; N blue; O red; Cu cyan. (Color figure online)
with DNA in the presence of H2O2. When the circular
DNA plasmid is subjected to electrophoresis, the fastest
migration will be observed for the supercoiled (SC) form
having minimal surface area (Form I). If one of the strands
is cleaved, the supercoiled form will relax to produce a
slower moving open circular form (Form II). If both the
strand cleave, a linear form (Form III) will be generated
that migrates in between.
Figure 14 shows that, with increasing concentrations of
complex 1 (lanes 4–7), the intensity of the circular super-
coiled DNA (Form I) decreases, while that of the nicked
(Form II) and linear (Form III) bands increases. In lane
8–9, Form I completely disappeared at 90–100 lM con-
centration. The time-dependent experiment at 60 lM
concentration of complex 1, shown in Fig. 15, lanes, 4
(45 min), 5 (50 min), 6 (55 min), 7 (60 min), 8 (70 min), 9
(80 min) and 10 (90 min), implies that more DNA cleav-
age products are produced as the reaction time increases
and smearing starts after 90 min. Under identical experi-
mental conditions, the efficiency of dinuclear complexes 2,
4–6 was lower than that of tetranuclear complex 1
(Fig. 16). The binuclear copper (II) complexes were found
to be more active in cleaving DNA in the presence of
hydrogen peroxide than the mononuclear copper (II)
complex. This may be explained on the basis that the
copper ions in the complexes react with H2O2 to form
peroxo-dicopper species.
Fig. 5 Crystal structure of 3. Color code: C gray; N blue; O red; Cu
cyan. (Color figure online)
increasing concentration of complexes (1–6) clearly shows
that all the complexes are groove binders. Hence, the vis-
cosity experiments are in good agreement with the above
UV-visible absorption titration experiments.
DNA cleavage studies
These experiments were repeated in the presence of
hydroxyl radical and singlet oxygen scavengers in order to
identify one reactive oxygen species which are responsible
for DNA cleavage [38–40]. DMSO, D-mannitol and tert-
butyl alcohol inhibit the cleavage reactions completely,
demonstrating the involvement of hydroxyl radicals
The cleavage of DNA by metal complexes can occur by
production of oxygen or hydroxyl radicals by the complex
after interacting with DNA. In order to ascertain the
nuclease activity of these complexes, they were incubated
123

582
Transition Met Chem (2013) 38:573–585
Fig. 6 One-dimensional packing of complex 3. Color code: C gray; N blue; O red; Cu cyan. (Color figure online)
(Fig. 17). On the other hand, no inhibition occurs in the
presence of the singlet oxygen quencher, sodium azide.
The antibacterial activities against two Gram-positive
and two Gram-negative bacteria were screened for the free
ligand as well as the copper complexes. The antibacterial
activity of the ligand was lower than that of its copper
complexes, indicating that chelation with copper enhances
the antibacterial activity (Table S4).
Conclusions
The reactions of copper chloride and 3,5-diisopropylpy-
razole (PziPr2H) in the presence of different benzoates
resulted in the formation of tetranuclear species, whereas
the reaction of the same ligands with copper nitrate gave
mono- and dinuclear complexes. These complexes showed
different crystal structures and efficiencies for DNA
cleavage. The complexes show good hydrolytic cleavage
activity of supercoiled plasmid DNA under physiological
conditions in the presence of H2O2 and act as effective
Fig. 7 Crystal structure of 4. Color code: C gray; N blue; O red; Cl
green; Cu cyan. (Color figure online)
Fig. 8 One-dimensional packing of complex 4 Color code: C gray; N blue; O red; Cu cyan. (Color figure online)
123

Transition Met Chem (2013) 38:573–585
583
Fig. 11 Three-dimensional packing (space-fill model) due to non-
covalent interactions present in complex 6. Star-shaped cavities were
formed. Color code: C gray; N blue; O red; Cucyan. (Colorfigure online)
2.51
2.01
1.51
Fig. 9 Crystal structure of 5. Color code: C gray; N blue; O red; Cl
green; Cu cyan. (Color figure online)
1.01
vs
al1
2
3
0.51
4
0.01
200
250
300
350
400
450
Wavelength
Fig. 12 UV-visible absorption titration of complex 1
Table 4 DNA binding constants of complexes 1–6
Complexes
Binding constant (Kb, M-1
)
(1)
(2)
(3)
(4)
(5)
(6)
5.0 9 103
2.3 9 103
2.7 9 103
2.4 9 103
2.5 9 103
2.4 9 103
Fig. 10 Crystal structure of 6. Color code: C gray; N blue; O red; Cl
green; Cu cyan. (Color figure online)
123

584
Transition Met Chem (2013) 38:573–585
Fig. 17 Effect of different scavengers on the cleavage of pUC19
plasmid by 50 lM complex 1. Agarose gel electrophoresis of pUC19
plasmid DNA treated with complexes 1 in the presence H2O2 for
30 min of incubations time, Lane
1 Control DNA; Lane 2
DNA ? H2O2; Lane 3 DNA ? 50 lM of 1 ? 20 lM DMSO; Lane
4 DNA ? 50 lM of 1 ? 50 lM DMSO; Lane 5 DNA ? 50 lM of
1 ? 20 lM tert-butyl alcohol; Lane 6 DNA ? 50 lM of 1 ? 50 lM
tert-butyl alcohol; Lane 7 DNA ? 50 lM of 1 ? 20 lM NaN3; Lane
8 DNA ? 50 lM of 1 ? 40 lM NaN3; Lane 9 DNA ? 50 lM of
1 ? 60 lM NaN3
[Comp]/[DNA]
Fig. 13 Viscosity graph for complexes 1–6
inorganic nucleases. Among all the complexes, the best
cleavage activity was shown by tetranuclear complex 1.
Dinuclear complexes 2 and 4–6 show better nuclease
activities as compared to 3; however, their efficiency was
found to be lower than that of the tetranuclear complex. All
of the complexes show antibacterial activity.
Fig. 14 Concentration-dependent DNA cleavage (Agarose gel elec-
trophoresis of pUC19 plasmid DNA treated with complex 1 in the
presence of the H2O2 (10 lM) for different concentration). Lane 1
Supplementary data
Control DNA; lane
2 DNA ? H2O2; lane 3 DNA ? 60 lM
CuCl2 ? H2O2; lane 4, DNA ? 30 lM of 1 ? H2O2; lane
5
DNA ? 40 lM of 1 ? H2O2; lane 6 DNA ? 60 lM of 1 ? H2O2;
lane 7 DNA ? 80 lM of 1 ? H2O2; lane 8 DNA ? 90 lM of
1 ? H2O2; lane 9 DNA ? 100 lM of 1 ? H2O2
CIF files for the X-ray crystal structures have been
deposited with the Cambridge Crystallographic Data Cen-
ter (CCDC number 798646–798651). Copies of this
information may be obtained free of charge from the
Director, CCDC, 12 Union Road, Cambridge, CB2 1EZ,
UK (fax: ?44 1223 336033; e-mail: deposit@ccdc.cam.
ac.uk or http://www.ccdc.cam.ac.uk).
Acknowledgments The authors gratefully acknowledge CSIR, New
Delhi, India for financial assistance in form of SRF to SK.
Fig. 15 Time-dependent DNA cleavage (Agarose gel electrophoresis
of pUC19 plasmid DNA treated with complex 1 in the presence of the
H2O2 for different incubation period). Lane 1 Control DNA; lane 2
DNA ? H2O2, 20 min.; lane 3 DNA ? 60 lM CuCl2 ? H2O2,
30 min.; lane 4 DNA ? 60 lM of 1 ? H2O2, 45 min.; lane 5
DNA ? 60 lM of 1 ? H2O2, 50 min.; lane 6 DNA ? 60 lM of
1 ? H2O2, 55 min.; lane 7 DNA ? 60 lM of 1 ? H2O2, 60 min.;
lane 8 DNA ? 60 lM of 1 ? H2O2, 70 min.; lane 9 DNA ? 60 lM
of 1 ? H2O2, 80 min.; lane 10 DNA ? 60 lM of 1 ? H2O2, 90 min
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