Treatment of cadmium(II) and zinc(II) with N2-donor linkages in presence of β-diketone ligand; supported by structural, spectral, theoretical and docking studies

Article abstract of DOI:10.1016/j.ica.2018.07.014

Five compounds, {(μ-OAc)(DPPD)Cd(μ-PYZ)Cd(DPPD)(μ-OAc)}_n (1); HDPPD: 1,3-diphenylpropane-1,3-dione; PYZ: pyrazine, {Cd(μ-4,4′-Bipy)(DPPD)₂}_n (2) Bipy: bipyridine [(DPPD)₂Zn(μ-4,4′-Bipy)Zn(DPPD)₂] (3), {Cd(μ-DPP)(DPPD)₂}_n (4); DPP: 1,3-di(pyridin-4-yl)propane and (Z)-3-hydroxy-1,3-bis(4-methoxyphenyl)prop-2-en-1-one (Z-HMPP), were prepared and identified by elemental analysis, FT-IR, ¹H NMR spectroscopy and single-crystal X-ray diffraction. 1,2 and 4 form 1D coordination polymers whereas 3 adopts a binuclear structure with the zinc atom in a distorted square-pyramidal geometry. In addition to these complexes, the enolic structure of the Z-HMPP is reported. The ability of compounds to interact with the nine biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) is investigated by the Docking calculations (for 3 and its ligands). The charge distribution pattern of the optimized structure of 3 was studied by NBO analysis. The Polymer Stability Slope for pentameric chain (PSS⁵, new parameter which is proposed in this paper) of the coordination polymers of 1, 2 and 4 were calculated to investigate the variation of energy level during the growing the polymeric chain in the solid phase.

Full text of DOI:10.1016/j.ica.2018.07.014

Inorganica Chimica Acta 482 (2018) 717–725
Contents lists available at ScienceDirect
Inorganica Chimica Acta
journal homepage: www.elsevier.com/locate/ica
Research paper
Treatment of cadmium(II) and zinc(II) with N -donor linkages in presence of
2
β-diketone ligand; supported by structural, spectral, theoretical and docking
studies
a,⁎
a,⁎
a
b
c
Farzin Marandi , Keyvan Moeini , Fereshteh Alizadeh , Zahra Mardani , Ching Kheng Quah ,
Wan-Sin Loh , J. Derek Woollins
c
d
a
Chemistry Department, Payame Noor University, 19395-4697 Tehran, Islamic Republic of Iran
b
c
Inorganic Chemistry Department, Faculty of Chemistry, Urmia University, 57561-51818 Urmia, Islamic Republic of Iran
X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
EaStCHEM School of Chemistry, University of St Andrews, St Andrews Fife UK, KY16 9ST, United Kingdom
d
A R T I C L E I N F O
A B S T R A C T
Keywords:
Cadmium(II)
Nitrogen donor linker
DFT study
Docking study
Coordination polymer
n
Five compounds, {(μ-OAc)(DPPD)Cd(μ-PYZ)Cd(DPPD)(μ-OAc)} (1); HDPPD: 1,3-diphenylpropane-1,3-dione;
PYZ: pyrazine, {Cd(μ-4,4′-Bipy)(DPPD) } (2) Bipy: bipyridine [(DPPD) Zn(μ-4,4′-Bipy)Zn(DPPD) ] (3), {Cd(μ-
2
n
2
2
2 n
DPP)(DPPD) } (4); DPP: 1,3-di(pyridin-4-yl)propane and (Z)-3-hydroxy-1,3-bis(4-methoxyphenyl)prop-2-en-1-
1
one (Z-HMPP), were prepared and identified by elemental analysis, FT-IR, H NMR spectroscopy and single-
crystal X-ray diffraction. 1,2 and 4 form 1D coordination polymers whereas 3 adopts a binuclear structure with
the zinc atom in a distorted square-pyramidal geometry. In addition to these complexes, the enolic structure of
the Z-HMPP is reported. The ability of compounds to interact with the nine biomacromolecules (BRAF kinase,
CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) is investigated by the Docking calculations (for 3 and
its ligands). The charge distribution pattern of the optimized structure of 3 was studied by NBO analysis. The
5
Polymer Stability Slope for pentameric chain (PSS , new parameter which is proposed in this paper) of the
coordination polymers of 1, 2 and 4 were calculated to investigate the variation of energy level during the
growing the polymeric chain in the solid phase.
1. Introduction
luminescence (ML) [38] and room-temperature phosphorescence
properties [39–41]. Some 1D-, 2D- and 3D-coordination polymers
Coordination polymers are interesting metal-organic hybrid mate-
containing β-diketone derivatives have been reported [42,43].
In order to extend the chemistry of these coordination polymers, in
this work, the synthesis of compounds including, {(μ-OAc)(DPPD)Cd(μ-
rials in which metal ions or metal-containing clusters act as nodes and
organic ligands act as spacers; both units are linked via coordination
bonds to form one-, two- or three-dimensional extended structures [1].
This class of compounds has been used as electrodes in supercapacitors
PYZ)Cd(DPPD)(μ-OAc)}
(Scheme 1); PYZ: pyrazine (Scheme 1), {Cd(μ-4,4′-Bipy)(DPPD)
Bipy: bipyridine (Scheme 1), [(DPPD) Zn(μ-4,4′-Bipy)Zn(DPPD)
{Cd(μ-DPP)(DPPD) (4); DPP: 1,3-di(pyridin-4-yl)propane (Scheme
n
(1); HDPPD: 1,3-diphenylpropane-1,3-dione
(2);
] (3),
2 n
}
[
2], gas storage/separation and ion exchange [3–8], biological and
2
2
material science [9,10], sensing [11–15], precursors for the preparation
of nano-materials [16], magnetism [17–21], luminescent materials
nonlinear optics [22–25], catalysis [26–29],.
Aromatic β-diketones are frequently used as chelating ligands for
Lewis acids and to produce complexes used in many applications such
as catalysis [30], vapour deposition [31], luminescent compounds
32,33], near infrared organic light emitting devices [34,35] and op-
toelectronics [36]. For example, difluoroboron diketonates [37] have
lately received tremendous attention due to their mechanochromic
2 n
}
1) and (Z)-3-hydroxy-1,3-bis(4-methoxyphenyl)prop-2-en-1-one (Z-
HMPP), are described, along with the characterization and theoretical
study of the compounds.
In addition to the expected biological properties of compounds
containing β-diketons [44,45] and pyridine derivatives [46–49],
binding of the zinc(II) ion to this unit make these complexes as a good
choice for biologically active compounds [50–52], thus docking cal-
culations were run to investigate the possibility of interaction between
[
⁎
Corresponding authors.
E-mail addresses: f.marandi@gmail.com (F. Marandi), k1_moeini@yahoo.com (K. Moeini).
https://doi.org/10.1016/j.ica.2018.07.014
Received 25 April 2018; Received in revised form 6 July 2018; Accepted 6 July 2018
Available online 11 July 2018
0020-1693/ © 2018 Elsevier B.V. All rights reserved.

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
−
1
ar
Found: C, 67.32; H, 4.28; N, 4.01%. IR (KBr, cm ): 3091 w (ν CH) ,
β-diketone
β-diketone
3
056 w (ν CH)
, 1597 s (ν C]C + ν C]O)
, 1552 m (ν
β-diketone
ar
C]O + ν C]C)
, 1513 m (ν C]N), 1477 m (ν C]C) , 1454 s (δ
, ppm, Hz): δ]
.69–8.71)d, 4 H, 4,4′-bipy), 7.90–8.17)m, 8 H, DPPD), 7.79–7.81)d,
H, 4,4′-bipy), 7.33–7.66)m, 12H, DPPD), 6.54)s, 2 H, β-diketone).
CH + ν C]C)β-diketone. 1H NMR (250 MHz, DMSO‑d
6
8
4
2
.1.3. Synthesis of [(DPPD)
The procedure for synthesis of 3 was similar to 2 except that Cd
OAc) ·2H O was replaced by Zn(OAc) ·2H O (0.066 g, 0.3 mmol) using
2
Zn(μ-4,4′-Bipy)Zn(DPPD)
2
] (3)
(
2
2
2
2
the MeOH/EtOH in a ratio of 3:1. Yellowish crystals were formed after a
few days in the cooler arm and filtered. Yield: 0.026 g, 15%; m. p.
2
4
52 2 8 2
37–238 °C. Anal. Calcd for C70H N O Zn (1179.87): C, 71.25; H,
−1
.44; N, 2.37. Found: C, 71.51; H, 4.53; N, 2.35%. IR (KBr, cm ): 3102
ar
β-diketone
β-diketone
β-diketone
w (ν CH) , 3066 w (ν CH)
, 1606 m (ν C]C + ν C]O)
,
Scheme 1. Structures of the 1,3-diphenylpropane-1,3-dione (HDPPD), pyrazine
ar
1
1
555 m (ν C]O + ν C]C)
, 1544 m (ν C]N), 1474 s (ν C]C) ,
(PYZ), 4,4′-bipyridine (4,4′-Bipy) and 1,3-di(pyridin-4-yl)propane (DPP) li-
458 s (δ CH + ν C]C)β-diketone. 1H NMR (250 MHz, DMSO-d
6
, ppm,
gands.
Hz): δ = 8.73)d, 2H, 4,4′-bipy), 8.02–8.05)d, 8 H, DPPD), 7.80–7.82)d,
2
H, 4,4′-bipy), 7.46–7.48)m, 12 H, DPPD), 6.76)s, 2 H, β-diketone).
3
and its ligands (4,4′-bipyridine and DPPD) with the nine protein
targets, including: BRAF kinase, Cathepsin B (CatB), DNA gyrase, His-
tone deacetylase (HDAC7), recombinant Human albumin (rHA), Ribo-
nucleotide reductases (RNR), Thioredoxin reductase (TrxR), Thymidy-
late synthase (TS), Topoisomerase II (Top II). These proteins are used in
this project either due to their reported roles in the cancer growth or as
transport agents that affect drug pharmacokinetic properties (e.g.,
rHA). Also, DNA gyrase was included to study the possibility of the
compounds also acting as antimalarial agents [53].
2.1.4. Synthesis of {Cd(μ-DPP)(DPPD) } (4)
2
n
The procedure for synthesis of 4 was similar to 1 except that pyr-
azine was replaced by DPP (0.178 g, 0.9 mmol) using the MeOH/EtOH
in a ratio of 1:3. After one week, the reaction mixture was filtered and
then colorless crystals suitable for X-ray diffraction studies were ob-
tained by slow evaporation after a few days. Yield: 0.017 g, 8%; m. p.
215 °C. Anal. Calcd for C43H36CdN O4 (757.14): C, 68.21; H, 4.79; N,
2
−
1
3.70. Found: C, 67.94; H, 4.77; N, 3.71%. IR (KBr, cm ): 3087 w (ν
ar
β-diketone
CH) , 3060 w (ν CH)
2
, 2945 w (ν CH ), 1594 s (ν C]C + ν C]
β-diketone
β-diketone
2. Experimental
O)
1
, 1547 m (ν C]O + ν C]C)
, 1515 m (ν C]N),
ar
β-diketone
478 m (ν C]C) , 1455 s (δ CH + ν C]C)
, 1406 s (δas CH
NMR (250 MHz, DMSO-d6, ppm, Hz): δ
8.43–8.45)d, 4H, DPP), 7.89–7.91)d, 8H, DPPD), 7.41)m, 12 H,
2
),
1
2.1. Materials and instrumentation
1301
w
(δ CH ).
H
s
2
=
All starting chemicals and solvents were reagent or analytical grade
and used as received. Infrared spectra in the range 4000–400 cm
DPPD), 7.22–7.24)m, 4 H, DPP), 6.53)s, 2 H, β-diketone), 2.56–2.63 (t,
4 H, DPP), 1.87–1.93 (m, 2 H, DPP).
−1
were recorded on KBr pellets with a FT-IR 8400-Shimadzu spectro-
1
meter. H NMR spectra were recorded on a Bruker spectrometer at
2
2.1.5. Preperation of (Z)-3-hydroxy-1,3-bis(4-methoxyphenyl)prop-2-en-
1-one (Z-HMPP)
50 MHz; chemical shifts δ are given in parts per million, relative to
TMS as an internal standard. The carbon, hydrogen and nitrogen con-
tents were determined in a Thermo Finnigan Flash Elemental Analyzer
112 EA. Melting points were determined with
Electrothermal 9200 electrically heated apparatus.
The procedure for synthesis of Z-HMPP was similar to 3 except that
HDPPD and pyrazine was replaced by 1,3-bis(4-methoxyphenyl)pro-
pane-1,3-dione, HMPP (0.171 g, 0.6 mmol), and 1,2-di(pyridin-4-yl)
ethane, DPE (0.164 g, 0.9 mmol), using the MeOH. After a few days,
yellow crystals that were deposited in the cooler arm were filtered off
1
a
Barnsted
2
.1.1. Synthesis of {(μ-OAc)(DPPD)Cd(μ-PYZ)Cd(DPPD)(μ-OAc)}
HDPPD (0.135 g, 0.6 mmol), pyrazine (0.072 g, 0.9 mmol) and Cd
OAc) ·2H O (0.080 g, 0.3 mmol) were placed in the large arms of a
n
(1)
16 4
and dried in air. Yield: 0.050 g; m. p. 222 °C. Anal. Calcd for C17H O
−1
(284.30): C, 71.82; H, 5.67. Found: C, 71.96; H, 5.66%. IR (KBr, cm ):
ar
enol
(
2
2
3
3060 w (ν CH) , 2962 w (ν CH ), 1604 s (ν C]O) , 1545 w (ν
enol
ar
branched tube (see ref [54]). Ethanol was carefully added to fill both
arms. The tube was then sealed and the ligand-containing arm was
immersed in a bath at 60 °C while the other arm was maintained at
ambient temperature [55]. After a few days, the colorless crystals de-
posited in the cooler arm were filtered off and dried in air. Yield:
C]C) , 1491 m and 1458 w (ν C]C) , 1438 m (δ CH ), 1303 m (ν
as
3
enol 1
CeO
and/or δ CH ). H NMR (250 MHz, DMSO‑d , ppm, Hz): δ
s
3
6
= 8.10–8.13)d, 4 H, Ph), 7.51)s, 1 H, β-diketone), 7.17)s, 1 H, OH),
7.05–7.08)d, 4 H, Ph), 3.82–3.84 (s, 6 H, methoxy).
0
.058 g, 45%; m. p. 212–217 °C. Anal. Calcd for C19
H
16CdNO
4
(434.73):
2.2. Crystal structure determination
C, 52.49; H, 3.71; N, 3.22. Found: C, 52.62; H, 3.75; N, 3.19%. IR (KBr,
−
1
ar
β-diketone
cm ): 3105 w (ν CH) , 3063 w (ν CH)
(
, 2997 w (ν CH), 1592 s
Suitable crystals of 1–4 and Z-HMPP were chosen and their X-ray
analysis were done using Apex-II Duo CCDC diffractometer with fine-
focus sealed tube graphite-monochromated Mo-Kα radiation
(λ = 0.71073 Å) at room temperature. The data was processed with
SAINT and corrected for absorption using SADABS [56]. The structures
were solved by direct method using the program SHELXTL [57] and
were refined by full-matrix least squares technique on F2 using aniso-
tropic displacement parameters for all non-hydrogen atoms. Diagrams
of the molecular structure and unit cell were created using Ortep-III
[58,59] and Diamond [60] softwares. Details of crystal data, data col-
lection, structure solutions and refinements are given in Table 1. Se-
lected bond lengths and angles of complexes are listed in Table 2 and
hydrogen bond geometries in Table S2 (Supplementary Materials).
β-diketone
OAc
ν C]C + ν C]O)
, 1580 m (ν C]N), 1543 m (νas COO)
,
ar
1
522 m (ν C]O + ν C]C), 1456 w (ν C]C and/or δas CH
3
), 1434 m
), 674 (δ
, ppm, Hz): δ = 8.64)s, 2 H,
Oac
β-diketone
(
ν
s
COO
and/or δ CH + ν C]C
s 2
), 1343 w (δ CH
OCO) . 1H NMR (250 MHz, DMSO-d
OAc
6
pyrazine), 7.40–7.91)m, 10 H, phenyl-DPPD), 6.54)s, 1 H, β-diketone),
.82)s, 3H, OAc).
1
2
2 n
.1.2. Synthesis of {Cd(μ-4,4′-Bipy)(DPPD) } (2)
The procedure for synthesis of 2 was similar to 1 except that pyr-
azine was replaced by 4,4′-bipyridine (0.141 g, 0.9 mmol) using the
MeOH/H O in a ratio of 3:1. Yield: 0.028 g, 13%; m. p. 204–214 °C.
Anal. Calcd for C40 30CdN (715.06): C, 67.18; H, 4.23; N, 3.92.
2
H
2 4
O
718

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
Table 1
Crystal data and structure refinement for complexes of 1–4 and Z-HMPP.
Z-HMPP
Complex 1
Complex 2
Complex 3
Complex 4
Empirical formula
Formula weight, g
C
17
H
16
O
4
C
19
H
16CdNO
4
C
40
H
30CdN
2
O
4
C
70
H
52
N
2
O
8
Zn
2
C
43
H
36CdN
2 4
O
284.30
434.73
715.06
1179.87
757.14
−
1
mol
Crystal size, mm3
Temperature, K
Crystal system
0.78 × 0.26 × 0.14
296
monoclinic
0.35 × 0.18 × 0.03
296
triclinic
P
1¯
0.69 × 0.37 × 0.08
296
Orthorhombic
Aba2
0.66 × 0.12 × 0.05
296
monoclinic
0.40 × 0.35 × 0.16
296
monoclinic
C2/c
Space group
Unit cell dimensions
P2
1
/n
1
P2 /c
(Å, °)
a
b
c
α
β
γ
4.1858(6)
10.2691(16)
32.589(5)
6.5640(19)
9.733(3)
15.095(4)
94.274(6)
102.239
109.674(4)
876.2(4)
2
10.9938(9)
25.63a5(3)
11.8497(10)
10.8018(14)
28.923(4)
18.183(2)
13.1149(11)
30.534(3)
10.8920(9)
90.758(3)
93.739(2)
125.236(1)
Volume, Å3
1400.7(4)
4
3339.5(5)
4
5668.6(13)
4
3562.5(5)
4
Z
Calculated density, g
1.348
1.648
1.422
1.383
1.412
−
3
cm
Absorption coefficient,
0.10
1.27
0.70
0.91
0.66
−
1
mm
F(0 0 0), e
600
434
1456
2440
1552
2
θ range for data
4.6–44.8
5.0–50.8
4.8–58.2
4.4–33.6
5.4–49.4
collection (°)
h, k, l ranges
−5 ≤ h ≤ 5,
−8 ≤ h ≤ 7,
−11 ≤ k ≤ 11,
−18 ≤ l ≤ 18
3296/3296/
−14 ≤ h ≤ 15,
−35 ≤ k ≤ 35,
−16 ≤ l ≤ 16
−13 ≤ h ≤ 13,
−36 ≤ k ≤ 36,
−23 ≤ l ≤ 23
117,745/12,379/0.142
−17 ≤ h ≤ 17,
−41 ≤ k ≤ 41,
−14 ≤ l ≤ 14
−
−
13 ≤ k ≤ 13,
44 ≤ l ≤ 44
Reflections collected/
independent/Rint
28,663/3717/0.036
33,979/4496/0.034
42,213/4791/0.031
Data/ref. parameters
Goodness-of-fit on F2
Final R indexes
3717/196
1.04
3296/229
1.11
4496/215
1.05
12,379/739
1.00
4791/252
1.03
R
1
= 0.047, wR
2
2
= 0.127
= 0.150
R
1
= 0.040, wR
2
2
= 0.092
= 0.095
R
1
= 0.027, wR
2
2
= 0.063
= 0.069
R
1
= 0.054, wR
2
2
= 0.094
= 0.131
R
1
= 0.050, wR
2
2
= 0.141
= 0.154
[
I > = 2σ (I)]
Final R indexes [all
R
1
= 0.087, wR
R
1
= 0.045, wR
R
1
= 0.037, wR
R
1
= 0.148, wR
R
1
= 0.063, wR
data]
Largest diff. peak/hole, 0.12/−0.14
1.21/–0.56
0.41/–0.26
0.29/–0.23
0.62/–0.66
−3
e Å
2
.3. Computational details
Histone deacetylase (HDAC7), recombinant Human albumin (rHA),
Ribonucleotide reductases (RNR), Thioredoxin reductase (TrxR),
Thymidylate synthase (TS), Topoisomerase II (Top II), respectively,
used in this research were obtained from the Protein Data Bank (pdb)
[59]. The obtained full version of Genetic Optimisation for Ligand
Docking (GOLD) 5.5 [63] was used for the docking. The Hermes vi-
sualizer in the GOLD Suite was used to further prepare the metal
complexes and the receptors for docking. The optimized DPPD and 4,4′-
bipyridine ligands and also cif file of the complex 3 were used for
docking studies. The region of interest used for Gold docking was de-
fined as all the protein residues within the 6 Å of the reference ligand
All structures were optimized with the Gaussian 09 software [61]
and calculated for an isolated molecule using Density Functional
Theory (DFT) [62] at the B3LYP/LanL2DZ level of theory for complex 3
as well as for NBO analysis and B3LYP/6-31+G for Z-HMPP and
HDPPD isomers. Cif files of complex 3 and Z-HMPP were used as input
file for theoretical calculations.
2.4. Docking details
“
A” that accompanied the downloaded protein. All free water molecules
The pdb files 4r5y, 3ai8, 5cdn, 3c0z, 2bx8, 1peo, 3qfa, 1njb, 4gfh for
the nine receptors, BRAF kinase, Cathepsin B (CatB), DNA gyrase,
in the structure of the proteins were deleted before docking. Default
Table 2
Selected bond length (Å) and angles (°) for complexes 1–4 and Z-HMPP with standard deviations in parentheses.
Z-HMPP
1
2
3
4
Distances
Angles
C7 − O1
C9 − O2
C3 − O3
C13 − O4
C6 − 7
1.287(2)
1.295(2)
1.352(2)
1.361(2)
1.465(2)
1.463(2)
Cd1 − O1
Cd1 − O2
Cd1 − O3
Cd1 − O4
Cd1 − O4
Cd1 − N1
2.241(5)
2.193(4)
2.264(4)
2.569(5)
2.310(5)
2.302(5)
Cd1 − O1
Cd1 − O2
Cd1 − N1
Cd1 − N2
2.241
2.240
2.35
Zn1A − O1A
Zn1A − O2A
Zn1A − O3A
Zn1A –O4A
Zn1A –N1A
2.002(2)
2.036(3)
2.012(3)
1.972(3)
2.058(3)
Cd1 − O1
Cd1 − O2
Cd1 − N1
2.241
2.240
2.370
2.43
C9 − C10
C4 − C3 − O3
C6 − C7 − O1
C8 − C9 − O2
C12 − C13 − O4
116.2(1)
116.5(1)
119.4(1)
124.9(2)
O1 − Cd1 − O2
O2 − Cd1 − O3
O3 − Cd1 − O4
O4 − Cd1 − O4
O4 − Cd1 − N1
N1 − Cd1 − O1
82.5(2)
141.5(2)
52.8(2)
73.5(2)
89.5(2)
88.3(2)
O1 − Cd1 − O2
O2 − Cd1 − N2
N2 − Cd1 − N1
N1 − Cd1 − O1
83.2
82.1
180.0
87.3
O1A − Zn1A − O2A
O2A − Zn1A − O3A
O3A − Zn1A–O4A
O4A − Zn1A − N1A
N1A − Zn1A − O2A
87.2(1)
165.5(1)
89.4(1)
100.9(1)
94.9(1)
O1 − Cd1 − O2
O2 − Cd1 − O2
O1 − Cd1 − N1
N1 − Cd1 − N1
81.1
95.9
96.3
94.2
719

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
−
1
acetate salt [68,69]. The Δ value for 1 is 109 cm
sponding to the bidentate acetate ligand.
which is corre-
1
The H NMR spectrum of the complex 1 (Supplementary Materials)
revealed that aromatic (7.40–8.64 ppm), aliphatic (1.82) and alkene
(
6.54 ppm) moieties of this structure. The hydrogen atoms of the
acetato and pyrazine ligands are observed at the highest and lowest
magnetic field, respectively. A singlet at the 6.54 ppm with integral of 1
is characteristic peak of the anionic β-diketone unit of the DPPD. By
comparing the intensity of this signal with acetato and pyrazine ligands,
the structure of the complex can be determined. Based on the intensity
ratio of 3:1:2 respectively for acetate, β-diketone unit and pyrazine li-
gand, we can conclude that the stoicometery of 1 mol acetate,1 mol
DPPD and 0.5 mol pyrazine per each cadmium atom in the structure of
the complex 1 which is confirmed by the X-ray analysis.
1
The H NMR spectrum of 2 revealed that a mixed ligands structure.
The sum of the integral numbers of all signals related to the DPPD is 22
(
each DPPD has 11 hydrogen atoms) and 4,4′-bipyridine is 8 (each 4,4′-
bipyridine has 8 hydrogen atoms), confirming the stoicometery of 2:1
for DPPD:4,4′-bipy. Two doublet signals for 4,4′-bipyridine ligand re-
veal a symmetrical bridging coordination mode. The integral numbers
1
in the H NMR spectrum of 3 supports a different stoicometery to 2. In
this complex, the stoicometery of DPPD:4,4′-bipy is 2:0.5 which can be
adopt only with the binuclear structure in which the 4,4′- bipyridine
coordinates as symmetrical bridged ligand between two zinc atoms.
1
Fig. 1. ORTEP diagram of the excerpt from coordination polymer structure of 1.
In the H NMR spectrum of the complex 4, eight hydrogen atoms of
The ellipsoids are drawn at the 35% probability level.
the two pyridinic rings of the DPP ligand appear as two sets of dublet
signals which support the symmetrical bridging behaviour of this li-
gand. Also sum of the integral numbers of the DPPD and DPP ligands
confirms the ratio of 2:1, respectively, thus a polymeric structure is
anticipated for the complex 4.
values of all other parameters were used and the complexes were
submitted to 10 genetic algorithm runs using the GOLDScore fitness
function.
The FT-IR and 1H NMR spectra of Z-HMPP reveal a β-diketone li-
gand in its enolic form. In the FT-IR spectrum of this compound, the
3. Results and discussion
−1
frequencies at 1604, 1545 and 1303 cm correspond to the ν (C]C), ν
(
C]O) and ν (CeO) which are characteristics of the enolic form [70].
Reaction between cadmium(II) acetate with HDPPD/pyrazine,
1
Also singlet signals of the 7.51 and 7.17 ppm in the H NMR spectrum
were assigned to the hydrogen atoms methylene and alcoholic groups of
the β-diketone moiety in agree with its enolic structure.
HDPPD/4,4′-bipyridine and HDPPD/DPP mixtures in branched tubes
provide 1D coordination polymers 1, 2 and 4, respectively. In similar
reaction, the zinc(II) acetate was reacted with HDPPD/4,4′-bipyridine
mixture and observed that the zinc atom preferred a binuclear structure
respect to the polymeric backbone. The complexes are air-stable and
soluble in DMSO.
3
.2. Description of the crystal structures
3
.2.1. Crystal structures of {(μ-OAc)(DPPD)Cd(μ-PYZ)Cd(DPPD)(μ-
n
OAc)} (1)
3
.1. Spectroscopic characterization
In the crystal structure of 1 (Fig. 1), the cadmium atom is co-
ordinated by three oxygen atoms of two acetato ligands, two oxygen
atoms of one DPPD and one nitrogen atom of a pyrazine ligand with
distorted octahedral geometry. Among the five CdeO bond lengths, the
bond lengths of DPPD ligand are shorter than the others. The complex
In the IR spectra of the complexes 1–4, the relatively weak ab-
−1
sorption bands at about 3100 and 3050 cm
modes of the aromatic rings and β-diketone unit, respectively. For
complexes 1 and 4, frequencies near the 2950 cm
are due to the CeH
−
1
are related to the
i
has one center of inversion on the center of pyrazine ring and C sym-
aliphatic moieties (acetate in 1 and propane in 4) in their structures. In
metry. This structure is a 1D asymmetric zigzag-coordination polymer
(Figs. S1 and S5, Supplementary Materials) [71] of cadmium containing
two types of bridges, one Cd-pyrazine-Cd bridge and two Cd-acetato-Cd
bridges. The DPPD ligand does not participate in the polymeric back-
bone but completes the octahedral geometry around the cadmium atom
(Fig. S5, Supplementary Materials). To compare the coordination mode
of the acetato ligand in 1 with published analogues, a structural survey
was carried out and results are presented in Table S3 (Supplementary
Materials). These data revealed that seven different coordination modes
have been reported for cadmium complexes containing the acetato li-
gand. Among these coordination modes, the “(O,O)” mode (Fig. 2) is
all the spectra of complexes, there are three bands corresponding to the
−1
anionic β-diketone unit of the DPPD including 1550–1600 cm due to
the ν (C]C) coupled with ν (C]O), 1500–1550 to the ν (C]O) coupled
−
1
with ν (C]C) and near 1450 cm
(
to the δ (CeH) coupled with ν
−1
C]C) [64]. The neutral free HDPPD has a band 1655 cm
corre-
sponding to the carbonyl unit of the keto form [65] which is shifted to
lower frequencies upon coordination due to the deprotonation of the β-
diketone unit. The pyridine and pyrazine rings of the linkage ligands
are noted in the FT-IR spectra of complexes in the region of
−
1
1
500–1600 cm
In the FT-IR spectrum of 1, three bands at 1543, 1434 and 674 cm
were assigned to the νas (COO), ν (COO) and δ (OCO) respectively [67],
confirming the presence of the acetate unit in this complex. The dif-
ferences between asymmetric (νas) and symmetric (ν ) stretching of the
acetate group (Δ) can reveal its coordination type. In monodentate
owing to the ν (C]N)ar [66].
−
1
2
the most observed ones (54%) in which the acetato unit acts as O -
s
donor and forms one four-membered chelate ring. The observed mode
in 1 is “(O, μ-O)” which is the second most common in the CSD ana-
logues (24%). In another comparison, the percentage of bridged and
non-bridged structures was calculated. These data revealed that the
acetato unit commonly forms a non-bridged structure (71%). In mostly
cases this ligand forms a chelate ring with cadmium atom (81%).
s
−
1
complexes, Δ values are much greater than the acetate salt (164 cm
while in bidentate complexes these values are significantly less than the
)
720

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
In this structure, the six-membered chelate ring formed by DPPD is
not planar (with r.m.s value of 0.265 Å for O2 atom). The average of
bending angles of two phenyl groups from the chelate ring is 41.85°
which is higher than that of the complex 1. These observations (non-
planar chelate ring and increasing the bending angle of phenyl groups)
can be attributed to the increasing the CeCeC bond angle of the β-
diketone moiety about 0.73° respect to the 1.
The two pyridine rings of the 4,4′-bipyridine ligand are not coplanar
and dihedral angle between their planes is 41.39° which is higher than
the CSD average for bridged 4,4′-bipyridine between two cadmium
atom (17.07°). This angle in the free ligand [73] is 26.69° (this value is
the average of dihedral angles for two independent structures [73]).
3
.2.3. Crystal structure of [(DPPD)
In the crystal structure of the complex 3 (Fig. 4), there are two in-
2
Zn(μ-4,4′-Bipy)Zn(DPPD)
2
] (3)
dependent binuclear zinc complexes with slightly difference in geo-
metrical parameters. The zinc atom is coordinated by one nitrogen
atom of a 4,4′-bipyridine ligand and four oxygen atoms of two DPPD
ligand with coordination number of five. A penta-coordinate geometry
of 3, may adopt either a square pyramidal or a trigonal bipyramidal
structure which is determined by applying the formula of Addison et al.
Fig. 2. Pie chart, the percentage of different coordination modes of the acetato
ligand among the complexes of cadmium.
Each DPPD ligand acts as bidentate and forms a six-membered
planar chelate ring (with r.m.s value of 0.075 Å for O1 atom). Two
phenyl groups are not coplanar with the chelate ring and are bended
from this plane with the average bending angles of 39.07°. For study of
the bond lengths and angles variation of the HDPPD after coordination
to the cadmium atom, the geometrical parameters of free ligand
[
74,75]. The angular structural parameter, τ (τ = (β – α)/60, where α
and β are the two largest angles at the zinc atom with β ≥ α), was
calculated to be 0.31 and 0.30, respectively for Zn1A and Zn1B
indicating
a
distorted square-pyramidal geometry (Fig. S7,
(
Scheme S2, Supplementary Materials) [72] were compared with the 1.
After coordination, the CeCeC bond angle of the β-diketone moiety
127.20°) is increased about 6.78° and the bending angle of the phenyl
Supplementary Materials). Studying the CSD database for the base
presented in Scheme S3(b), Supplementary Materials, revealed that the
coordinated bond lengths of 3 are comparable with the CSD average
(
groups respect to the plane through the β-diketone moiety (39.07°) is
increased about 28.2° (these values for free ligand are 120.42° and
(
ZneN, 2.057; ZneO, 2.006) and in all complexes the average of all
ZneO bond lengths is shorter than the ZneN bond lengths.
10.86°, respectively).
The coordinated DPPD ligand forms a non-planar six-membered
chelate ring around the zinc atom. The average of dihedral angles be-
tween phenyl groups and chelate ring plane is 14.57° which is lower
than in1 and 2 which can be related to the lowest value of the CeCeC
bond angle in 3 (126.00°) respect to the 1 and 2.
The pyrazine ligand in the complex of 1 connects two cadmium
atoms. These atoms are not lie on the mean plane through the pyrazine
ring; one cadmium atom places above this plane and another under it
with distance of 0.229 Å.
The dihedral angle between two pyridine rings of the 4,4′-bipyridine
ligand is 0.00°, showing that the planar coordination behavior of this
ligand toward zinc atom. This value for the CSD analogues is 14.94°
which is lower than that of the cadmium analogues (17.07°).
3
2 n
.2.2. Crystal structure of {Cd(μ-4,4′-Bipy)(DPPD) } (2)
In the crystal structure of 2 (Fig. 3), the cadmium atom is co-
ordinated by two O-donor DPPD and two 4,4′-bipyridine with
slightly distorted octahedral geometry (Fig. S6, Supplementary
Materials). The 4,4′-bipyridine ligand connects two cadmium atoms
to form 1D linear-coordination polymer [71]. The CdeO bond
lengths are shorter than the CdeN bond lengths (Table 2) and these
two bond lengths are comparable with the CSD average for com-
plexes containing the unit (Scheme S3(a), Supplementary
Materials).
3
.2.4. Crystal structure of {Cd(μ-DPP)(DPPD)
2 n
} (4)
X-ray analysis of the complex 4 reveals (Fig. 5) 1D symmetric linear-
coordination polymer; extending by bridging 1,3-di(pyridin-4-yl)pro-
pane between cadmium atoms. In this structure, the cadmium atom by
coordination of four oxygen atoms of two O -donor DPPD and two ni-
2
trogen atoms of two 1,3-di(pyridin-4-yl)propane has a octahedral geo-
metry (Fig. S8, Supplementary Materials). The CdeO bond lengths
(
2.241 Å) are shorter than the CdeN (2.370 Å) and theses two bond
lengths are comparable with the CSD average (Scheme S3(a),
Supplementary Materials).
The dihedral angles average between phenyl groups with the planar
chelate ring of DPPD (with r.m.s value of 0.029 Å for C7 atom) is 19.89°
which is higher than that of the free ligand and can be attributed to the
increasing the CeCeC bond angle of coordinated DPPD (Table 3). The
dihedral angle between two pyridine rings of the 1,3-di(pyridin-4-yl)
propane ligand is 79.87°.
3.2.5. Crystal structure of (Z)-3-hydroxy-1,3-bis(4-methoxyphenyl)prop-2-
en-1-one (Z-HMPP)
X-ray analysis of the (Z)-3-hydroxy-1,3-bis(4-methoxyphenyl)prop-
2-en-1-one revealed a Z conformation and enolic form of this ligand
(
Fig. 6). These types of the compounds have two tautomeric forms in-
cluding enol and keto. Study of the all CSD structures containing β-
diketone unit (the structures in which the β-diketone unit is fused to a
ring were omitted) revealed that the enol form (292 hits, 88%) is more
common than the keto form (41 hits, 12%) as observed in the Z-HMPP.
Fig. 3. ORTEP diagram of the excerpt from coordination polymer structure of 2.
The ellipsoids are drawn at the 35% probability level.
721

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
Fig. 4. ORTEP diagram of the molecular structure of 3. The ellipsoids are drawn at the 25% probability level.
The bond lengths average of the β-diketone unit were extracted and
presented in Scheme S4, Supplementary Materials. The data revealed
that the C]O bond length is the shortest bond in this unit. The hy-
drogen atom of the hydroxyl group along with the oxygen atom of the
side carbonyl group form a planar six-membered hydrogen bonding
ring (with r.m.s value of 0.039 Å for H1 atom). The phenyl groups of the
ligand are almost coplanar with this ring with the dihedral angle
average of 3.87°.
Table 3
Differences (Δ) of the CeC and CeO bond lengths and central CeCeC bond
angle of the β-diketone unit and dihedral angles average between phenyl groups
with the mean plan through the chelate ring of the coordinated DPPD in the
complexes 1–4 and HDPPD.
Δ (CeC)
Δ (CeO)
CeCeC
Dihedral Angle
HDPPD
0.027
0.005
0.018
0.005
0.000
0.025
0.008
0.000
0.006
0.007
120.42°
127.20
127.93
126.00
127.03
10.86°
39.07
41.85°
14.57°
19.89
1
2
3
4
3.2.6. Crystal network interactions
In the crystal network of compounds (Figs. S5–S9, Supplementary
Materials) intermolecular CeH···O, and CeH···C (except in 1 and Z-
HMPP) also intramolecular OeH···O (Z-HMPP) hydrogen bonds appear
between adjacent complexes. In this way the carbon and oxygen atoms
participate in hydrogen bonding as proton donors and acceptors at the
same time. In addition to the hydrogen bonds, the crystal networks of
the compounds are further stabilized by π–π stacking interactions be-
tween aromatic rings [76,77] of the adjacent ligands (Figs. S5–S9,
Supplementary Materials). In the crystal network of 1 (Fig. S5,
Supplementary Materials), there are π–π stacking interaction between
the pyrazine and phenyl group of the DPPD which has the shortest
centroid-centroid distance among the all compounds and strongest ones
(
Table S1, Supplementary Materials). Similar interaction is appeared
Fig. 6. ORTEP diagram of the molecular structure of Z-HMPP. The ellipsoids
between phenyl ring of the DPPD and pyridine ring of the 4,4′-bipyr-
idine ligands. Although the complexes 2 and 3 have similar ligands but
are drawn at the 35% probability level.
Fig. 5. ORTEP diagram of the excerpt from coordination polymer structure of 4. The ellipsoids are drawn at the 35% probability level.
722

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
have different π–π stacking pattern (Figs. S6 and S7, Supplementary
Materials). In this pattern, in addition of π–π stacking interaction be-
tween two 4,4′-bipyridine ligands, two DPPD ligands which are not
exactly on top of each other, form two different types of interactions
including Ph∙∙∙β-diketone and Ph∙∙∙Ph (Table S1, Supplementary
Materials). The centroid-centroid distance of the Ph∙∙∙β-diketone
stacking is shorter than the Ph∙∙∙Ph and thus is stronger than it. In the
crystal network of 4 (Fig. S8, Supplementary Materials), the pyridine
rings of the DPP ligand do not participate in the π–π stacking interac-
tions while phenyl and β-diketone units of the DPPD have important
role in this way.
Total intermolecular interaction energy1 for one molecule of com-
plex 3 and Z-HMPP were calculated using Mercury [78] and its CSD-
materials tool [79,80]. For this, the sum of the intermolecular inter-
actions energy in a molecular packing shell containing 100 molecules
[
−
81] around the one molecule of 3 and Z-HMPP were calculated to be
997.12 (complex 3 containing Zn1B), −969.762 (complex 3 con-
Fig. 7. Variation diagram of total intermolecular interactions energy (E) for
complex 3 and Z-HMPP with increasing the number of surrounding molecules.
taining Zn1A) and −339.548 kJ/mol (Fig. 7), respectively, confirming
that one molecule of complex 3 is more stabilized in the solid state by
its network interactions than Z-HMPP [81]. Also the interactions of the
enantiomer containing Zn1B, in complex 3, are stronger than its Zn1A
enantiomer. In complex 3, 50% (Zn1B enantiomer) and 52% (Zn1A
enantiomer) of the total energy is corresponding to the interactions
with its four closest neighboring molecules in ranges of 5.401–10.802 Å
distances (Fig. 7). This value for the same condition in Z-HMPP is 61%
within the distances range of 4.186–7.992 Å.
3.3. Theoretical studies
For investigation the variation of energy level with growing the
polymeric chain in the solid phase (without considering the inter-
molecular interactions) in complexes 1, 2 and 4, a DFT calculation was
performed and results are presented in Fig. 8. For this aim, a mono-
Fig. 8. Variation of the energy level with growing the polymeric chain in the
solid phase of complexes 1, 2 and 4.
meric species as a core ([Cd
2
(μ-OAc)
2 2 2
(PYZ) (DPPD) ], [Cd(4,4′-Bi-
py) (DPPD) ], [Cd(DPP) (DPPD)
2
2
2
2
], respectively for 1, 2 and 4) was
extracted from the corresponding cif and then the energy variations
were studied upon growing the chain by adding the monomers of
[
Cd
2
(μ-OAc)
2 2 2
(PYZ)(DPPD) ], [Cd(4,4′-Bipy)(DPPD) ] and [Cd(DPP)
], respectively for 1, 2 and 4, to form a pentameric structure.
(
DPPD)
2
With increasing the chain length the total energy for all complexes is
increased but with different slopes. The Polymer Stability Slope for
5
pentameric chain (PSS , new parameter which is proposed in this
paper) for three complexes has the general trend 1 > 4 > 2 (−2274,
−
2118 and −2000, respectively for 1, 2 and 4), showing that the rate
of increasing the thermodynamic stability in 1 is higher than the others.
It seems that the bridging ligands have significant effect on the PSS5
index of the complexes (DPPD ligand is same in three complexes).Fig. 9.
To study the charge distribution before and after complexation, an
NBO analysis was done on the free 4,4′-bipyridine, anionic DPPD and
opt
complex 3 (Table S4, Supplementary Materials). For this study two
opt
free ligands and their complex with zinc (3 ) were optimized before
NBO analysis. The results reveal that the calculated charge on the zinc
atom is about +1.41 and lower than the formal charge (+2) owing to
the electron donation of ligand during the complexation. Based on the
calculated total charge values, the charge of the carbon and hydrogen
atoms belonging to the coordinated 4,4′-bipyridine and DPPD are more
positive than that of the free ligands, whilst the total charge of nitrogen
Fig. 9. Docking study results, showing the interaction between complex 3 and
TS protein.
bipyramidal geometry (τ = 0.97) while in the solid state phase the
coordinated ligands create a distorted square-pyramidal geometry
around the zinc atom to enable the best direction to interact with ad-
jacent complexes. Similarly to the solid phase, all ZneO (with average
of 2.047 Å) bond lengths are shorter than the ZneN (2.155 Å). The
(
coordinated 4,4′-bipyridine) and oxygen (coordinated DPPD) atoms is
more negative than respect to the free 4,4′-bipyridine and DPPD li-
gands. This observation reveals that the hydrogen and carbon atoms
play an important role in electron donation toward metal atom, thus
decreasing the charge of the zinc atom.
average of dihedral angles between phenyl groups and chelate ring
opt
plane and also the CeCeC bond angle of β-diketone unit in 3
are
1
3.12 and 124.48° which are lower than those of complex 3. The di-
In the binuclear complex 3opt, the zinc atom has a trigonal
hedral angle between two pyridine rings of the 4,4′-bipyridine ligand
opt
is 0.00°, confirming that the planarity of this ligand in 3 as observed
1
in 3.
This parameter can be calculated only for non-polymeric structures
723

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
Table 4
The calculated fitness values for the complex 3, 4,4′-bipyridine and DPPD.
Top II
TS
TrxR
RNR
rHA
HDAC7
DNA-Gyrase
CatB
BRAF-Kinase
32.44
41.77
0.00
32.93
39.88
81.66
36.76
45.58
63.56
32.75
36.98
79.60
33.95
43.64
−185.66
38.16
45.11
0.00
36.27
39.68
0.00
24.02
28.70
0.00
33.85
42.73
0.00
4,4′-Bipyridine
DPPD
Complex 3
3.4. Docking studies
fitness values of titled compounds, we suggest that studying anticancer
activities of these compounds could be interesting. The PSS parameter
5
For predicting and comparison the biological activates of the com-
for three complexes 1, 2 and 4 were calculated to be −2274, −2118
and −2000, confirming that by growing the chain of complex 1 the
thermodynamic stability of it is increased higher than the others. The
NBO analysis of the optimized complex 3 revealed that the hydrogen
and carbon atoms of two coordinated ligands act as electron donor and
decrease the charge of the zinc atom.
2
plex 3 and its ligands (4,4′-bipyridine and DPPD), interactions of these
compounds with nine macromolecule receptors using Gold [63]
docking software were studied. The Gold docking results are reported in
terms of the values of fitness which means the higher the fitness the
better the docked interaction of the compounds [53]. The results of the
docking presented in this work is the best binding results out of the
favorably ten predicted by Gold.
Appendix A. Supplementary data
The general features from the Gold docking prediction (Table 4)
show that all studied structures can be consider as biologically active
compounds (Fig. S9 and S10, S11 Supplementary). The best predicted
targets for the 4,4′-bipyridine and DPPD ligands is HDAC7 and TrxR,
respectively, while for the studied complex 3 is TS. The GOLDScore
fitness values of the complex 3 revealed that this complex can interact
selectively with three biomacromolecules of RNR, TrxR and TS among
the nine biomacromolecules. Also complex 3 can interacted with the
mentioned proteins better than the free ligands of 4,4′-bipyridine and
DPPD. In other cases (other biomacromolecules than RNR, TrxR and
TS) two free ligands are biologically active while after coordination to
zinc they become inactive. A fitness value comparison between 4,4′-
bipyridine and DPPD could allow to conclude that the DPPD has better
binding ability toward proteins than the 4,4′-bipyridine.
Supplementary data associated with this article can be found, in the
online version, at https://doi.org/10.1016/j.ica.2018.07.014.
References
[1] H.-Y. Wang, L. Cui, J.-Z. Xie, C.F. Leong, D.M. D’Alessandro, J.-L. Zuo, Coord.
Chem. Rev. 345 (2017) 342–361.
[
2] H. Yao, F. Zhang, G. Zhang, H. Luo, L. Liu, M. Shen, Y. Yang, A novel two-di-
mensional coordination polymer-polypyrrole hybrid material as a high-perfor-
mance electrode for flexible supercapacitor, Chem. Eng. J. 334 (2018) 2547–2557.
3] S. Kitagawa, Angew. Chem. Int. Ed. 54 (2015) 10686–10687.
[
[
4] J. Goldsmith, A.G. Wong-Foy, M.J. Cafarella, D.J. Siegel, Chem. Mater. 25 (2013)
3
373–3382.
[5] D. Alezi, Y. Belmabkhout, M. Suyetin, P.M. Bhatt, Ł.J. Weseliński, V. Solovyeva,
K. Adil, I. Spanopoulos, P.N. Trikalitis, A.-H. Emwas, M. Eddaoudi, J. Am. Chem.
Soc. 137 (2015) 13308–13318.
[
6] C.V. McGuire, R.S. Forgan, Chem. Comm. 51 (2015) 5199–5217.
4
. Conclusion
[7] C.R. Pfeiffer, D.A. Fowler, J.L. Atwood, CrystEngComm 17 (2015) 4475–4485.
[
[
8] M. Fernandez, A.S. Barnard, A.C.S. Comb, Sci. 18 (2016) 243–252.
9] C. Pettinari, F. Marchetti, N. Mosca, G. Tosi, A. Drozdov, Polym. Int. 66 (2017)
Compounds of {(μ-OAc)(DPPD)Cd(μ-PYZ)Cd(DPPD)(μ-OAc)}
n
(1);
7
31–744.
HDPPD: 1,3-diphenylpropane-1,3-dione, {Cd(μ-4,4′-Bipy)(DPPD)
2
}
}
n
[10] R. Feng, Y.-Y. Jia, Z.-Y. Li, Z. Chang, X.-H. Bu, Chemical Science 9 (2018) 950–955.
[
[
[
11] Y. Cui, F. Zhu, B. Chen, G. Qian, Chem. Comm. 51 (2015) 7420–7431.
12] Z. Hu, B.J. Deibert, J. Li, Chem. Soc. Rev. 43 (2014) 5815–5840.
13] D. Zhao, Y. Cui, Y. Yang, G. Qian, CrystEngComm 18 (2016) 3746–3759.
(
(
2), [(DPPD)
2 2
Zn(μ-4,4′-Bipy)Zn(DPPD) ] (3), {Cd(μ-DPP)(DPPD)
2
n
4); DPP: 1,3-di(pyridin-4-yl)propane and (Z)-3-hydroxy-1,3-bis(4-
methoxyphenyl)prop-2-en-1-one (Z-HMPP) were prepared; their spec-
tral (IR, H NMR) and structural (single crystal X-ray diffraction)
[14] D. Ma, B. Li, X. Zhou, Q. Zhou, K. Liu, G. Zeng, G. Li, Z. Shi, S. Feng, Chem. Comm.
1
4
9 (2013) 8964–8966.
[
[
15] P. Kumar, A. Deep, K.-H. Kim, Trends Anal. Chem. 73 (2015) 39–53.
16] M.Y. Masoomi, A. Morsali, P.C. Junk, J. Wang, Ultrasonic assisted synthesis of two
new coordination polymers and their applications as precursors for preparation of
nano-materials, Ultrason. Sonochem. 34 (2017) 984–992.
properties were investigated. Among these structures, the cadmium
complexes 1, 2 and 4 have 1D polymeric structure with octahedral
geometry containing N-donor ligands as linkers (in 1, there are two
types of linker ligands, N-donor and O-donor). The complex 3 has bi-
nuclear structure and distorted square-pyramidal geometry at the zinc
atom. Among the different coordination modes of the acetate ligand
which is coordinated to the cadmium atom, the “(O,O)” mode is the
most observed ones (54%). In all complexes, the bond angle of the β-
diketone moiety and dihedral angles between phenyl groups with the
mean plan through the chelate ring of this moiety is increased with
respect to the free ligand. In addition to the hydrogen bonds in the
crystal network of the complexes, there are π–π stacking interactions
between aromatic rings, showing the high ability of these molecules to
interact with neighboring units and making them good choice to
docking studies. The docking studies on the 4,4'-bipyridine, DPPD and
complex 3 revealed that the these compounds might be biologically
active by interacting with the nine biomacromolecules (BRAF kinase,
CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II). The best
predicted targets for the 4,4'-bipyridine, DPPD and complex 3 is
HDAC7, TrxR and TS, respectively. Also 3 can interact selectively with
three biomacromolecules of RNR, TrxR and TS. Based on the calculated
[
[
[
17] M. Kurmoo, Chem. Soc. Rev. 38 (2009) 1353–1379.
18] J.S. Miller, Dalton Trans. (2006) 2742–2749.
19] D. Tiana, C.H. Hendon, A. Walsh, Chem. Comm. 50 (2014) 13990–13993.
[20] P. Kar, R. Haldar, C.J. Gómez-García, A. Ghosh, Inorg. Chem. 51 (2012) 4265–4273.
[
21] X.-Q. Wu, M.-L. Han, G.-W. Xu, B. Liu, D.-S. Li, J. Zhang, Inorg. Chem. Commun. 58
2015) 60–63.
22] Y. Cui, Y. Yue, G. Qian, B. Chen, Chem. Rev. 112 (2012) 1126–1162.
(
[
[23] D.F. Sava Gallis, L.E.S. Rohwer, M.A. Rodriguez, T.M. Nenoff, Chem. Mater. 26
2014) 2943–2951.
(
[
[
24] Z.-L. Fang, X.-Y. Wu, R.-M. Yu, C.-Z. Lu, CrystEngComm 16 (2014) 8769–8776.
25] C.A. Bauer, T.V. Timofeeva, T.B. Settersten, B.D. Patterson, V.H. Liu, B.A. Simmons,
M.D. Allendorf, J. Am. Chem. Soc. 129 (2007) 7136–7144.
[
26] J. Liu, L. Chen, H. Cui, J. Zhang, L. Zhang, C.-Y. Su, Chem. Soc. Rev. 43 (2014)
6
011–6061.
[
27] S. Kitagawa, R. Kitaura, S.-I. Noro, Angew. Chem. Int. Ed. 43 (2004) 2334–2375.
[28] J. Gascon, A. Corma, F. Kapteijn, F.X. Llabrés i Xamena, ACS Catal. 4 (2014)
61–378.
29] A.H. Chughtai, N. Ahmad, H.A. Younus, A. Laypkov, F. Verpoort, Chem. Soc. Rev.
4 (2015) 6804–6849.
3
[
4
[30] X. Zhang, M. Cui, R. Zhou, C. Chen, G. Zhang, Macromol. Rapid Commun. 35
(2014) 566–573.
[
31] S. Schwieger, R. Herzog, C. Wagner, D. Steinborn, J. Organomet. Chem. 694 (2009)
548–3558.
3
[
[
[
32] C.-J. Xu, B.-G. Li, J.-T. Wan, Z.-Y. Bu, J. Lumin. 131 (2011) 1566–1570.
33] K. Buczko, M. Karbowiak, J. Lumin. 136 (2013) 130–140.
34] Z. Ahmed, R.E. Aderne, J. Kai, J.A.L.C. Resende, H.I. Padilla-Chavarria,
M. Cremona, RSC Adv. 7 (2017) 18239–18251.
2
The compounds containing cadmium atom are not good choice for biolo-
[
35] Z. Ahmed, R.E. Aderne, J. Kai, H.I.P. Chavarria, M. Cremona, Thin Solid Films 620
gical active compounds.
724

F. Marandi et al.
Inorganica Chimica Acta 482 (2018) 717–725
(2016) 34–42.
G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato,
X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada,
M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda,
O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery Jr., J.E. Peralta, F. Ogliaro,
M.J. Bearpark, J. Heyd, E.N. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi,
J. Normand, K. Raghavachari, A.P. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi,
M. Cossi, N. Rega, N.J. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken,
C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin,
R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski,
G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas,
J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 09, in, Gaussian Inc,
Wallingford, CT, USA, 2009.
[
[
[
36] J.C.-H. Chan, W.H. Lam, H.-L. Wong, N. Zhu, W.-T. Wong, V.W.-W. Yam, J. Am.
Chem. Soc. 133 (2011) 12690–12705.
37] R. Yoshii, A. Hirose, K. Tanaka, Y. Chujo, J. Am. Chem. Soc. 136 (2014)
1
8131–18139.
38] T. Butler, W.A. Morris, J. Samonina-Kosicka, C.L. Fraser, ACS Appl. Mater.
Interfaces 8 (2016) 1242–1251.
[
[
39] G. Zhang, G.M. Palmer, M.W. Dewhirst, C.L. Fraser, Nat. Mater. 8 (2009) 747.
40] J. Samonina-Kosicka, C.A. DeRosa, W.A. Morris, Z. Fan, C.L. Fraser, Macromol. 47
(2014) 3736–3746.
[
[
41] S. Mukherjee, P. Thilagar, Chem. Comm. 51 (2015) 10988–11003.
42] M.N. Kopylovich, Y.Y. Karabach, K.T. Mahmudov, M. Haukka, A.M. Kirillov,
P.J. Figiel, A.J.L. Pombeiro, Crystal Growth & Design 11 (2011) 4247–4252.
43] K.T. Mahmudov, M.F.C. Guedes da Silva, A.M. Kirillov, M.N. Kopylovich, A. Mizar,
A.J.L. Pombeiro, Crystal Growth & Design 13 (2013) 5076–5084.
44] G.D. Diana, P.M. Carabateas, R.E. Johnson, G.L. Williams, F. Pancic, J.C. Collins, J.
Med. Chem. 21 (1978) 889–894.
45] R.K. Maheshwari, A.K. Singh, J. Gaddipati, R.C. Srimal, Life Sci. 78 (2006)
[62] J.P. Perdew, Phys. Rev. B 33 (1986) 8822–8824.
[63] G. Jones, P. Willett, R.C. Glen, A.R. Leach, R. Taylor, J. Mol. Biol. 267 (1997)
[
[
[
[
[
[
727–748.
[64] K. Nakamoto . in: 6 (Ed.), Infrared and raman spectra of inorganic and coordination
compounds 2009 John Wiley Hoboken 259 260.
[65] F. Marandi, J. Mol. Struct. 1059 (2014) 75–80.
2
081–2087.
[66] M. Hakimi, Z. Mardani, K. Moeini, E. Schuh, F. Mohr, Z. Naturforsch., 68b (2013)
46] H. Foks, D. Pancechowska-Ksepko, A. Kędzia, Z. Zwolska, M. Janowiec,
267.
E. Augustynowicz-Kopeć, Il Farmaco 60 (2005) 513–517.
[67] F. Marandi, K. Moeini, A. Rudbari Hadi, Z. Naturforsch., 71b (2016) 959.
[68] K. Nakamoto, in: 6 (Ed.) Infrared and raman spectra of inorganic and coordination
compounds, John Wiley, Hoboken, 2009, pp. 232.
[69] M. Hakimi, K. Moeini, Z. Mardani, F. Khorrami, J. Korean Chem. Soc. 57 (2013)
352–356.
47] M.M. Ghorab, A.Y. Hassan, Phosphorus Sulfur Silicon Relat. Elem. 141 (1998)
2
51–261.
48] R. Chen, C.-S. Liu, H. Zhang, Y. Guo, X.-H. Bu, M. Yang, J. Inorg. Biochem. 101
2007) 412–421.
(
[
[
49] H. Zhang, C.-S. Liu, X.-H. Bu, M. Yang, J. Inorg. Biochem. 99 (2005) 1119–1125.
50] M. Dardenne, J.M. Pléau, B. Nabarra, P. Lefrancier, M. Derrien, J. Choay, J.F. Bach,
Proc. Natl. Acad. Sci. 79 (1982) 5370–5373.
[70] Y. Akama, A. Tong, Microchem. J. 53 (1996) 34–41.
[71] M. Sánchez-Serratos, J. Raziel Álvarez, E. González-Zamora, I.A. Ibarra, J. Mex.
Chem. Soc. 60 (2017).
[
51] O. Bermingham-McDonogh, E.B. Gralla, J.S. Valentine, Proc. Natl. Acad. Sci. 85
[72] D. Williams, Acta Crystallogr., Sect. A: Found. Crystallogr. 21 (1966) 340–349.
[73] N.M. Boag, K.M. Coward, A.C. Jones, M.E. Pemble, J.R. Thompson, Acta
Crystallogr., Sect. A: Found. Crystallogr. C55 (1999) 672–674.
[74] A.W. Addison, T. Rao, J. Reedjik, J.V. Rijn, G. Verschoor, Dalton Trans. (1984)
1349.
(1988) 4789–4793.
[
[
[
52] A.H. Shankar, A.S. Prasad, Am. J. Clin. Nutr. 68 (1998) 447S–463S.
53] A.A. Adeniyi, P.A. Ajibade, Molecules 18 (2013) 3760–3778.
54] G. Mahmoudi, A. Morsali, A.D. Hunter, M. Zeller, CrystEngComm 9 (2007)
7
04–714.
55] F. Marandi, F. Amoopour, I. Pantenburg, G. Meyer, J. Mol. Struct. 973 (2010)
24–129.
[75] M. Hakimi, Z. Mardani, K. Moeini, F. Mohr, Polyhedron 102 (2015) 569.
[76] F. Marandi, K. Moeini, B. Mostafazadeh, H. Krautscheid, Polyhedron 133 (2017)
146–154.
[
[
[
1
56] APEX-II, Bruker Advanced X-ray Solutions (version 1-0), Bruker AXS Inc, Madison,
Wisconsin (USA), 2009.
57] G. Sheldrick, Acta crystallographica. Section A, Foundations of crystallography,
A64 (2008) 112–122.
[77] F. Marandi, K. Moeini, S. Ghasemzadeh, Z. Mardani, C.K. Quah, W.-S. Loh, J. Mol.
Struct. 1149 (2017) 92–98.
[78] C.F. Macrae, I.J. Bruno, J.A. Chisholm, P.R. Edgington, P. McCabe, E. Pidcock,
L. Rodriguez-Monge, R. Taylor, J. Van De Streek, P.A. Wood, J. Appl. Crystallogr.
41 (2008) 466–470.
[
58] L.J. Farrugia, J. Appl. Crystallogr. 30 (1997) 565.
[59] M.N. Burnett, C.K. Johnson, Ortep-III, Report ORNL-6895, Oak Ridge National
Laboratory, Oak Ridge, Tennessee, U.S., 1996.
[79] A. Gavezzotti, G. Filippini, J. Phys. Chem. 98 (1994) 4831–4837.
[80] A. Gavezzotti, Acc. Chem. Res. 27 (1994) 309–314.
[
60] G. Bergerhof, M. Berndt, K. Brandenburg, J. Res. Nat. Inst. Stand. Technol. 101
[81] Z. Mardani, V. Golsanamlou, S. Khodavandegar, K. Moeini, A.M.Z. Slawin,
J.D. Woollins, J. Coord. Chem. (2018) 1–15.
(1996) 221–225.
[61] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman,
725