Antimicrobial, computational, and molecular docking studies of Zn (II) and Pd (II) complexes derived from piperidine dithiocarbamate

Article abstract of DOI:10.1002/aoc.6108

Mixed ligand complexes of Zn (II) and Pd (II) have been prepared from piperidine dithiocarbamate (PipDT) and amine ligand {2,2′-bipyridine (Bipy), 1,10-phenanthroline (Phen), and 3-aminopyridine (3Apy)} to afford complexes of the type [M(κ¹-Pip

Full text of DOI:10.1002/aoc.6108

Received: 6 September 2020
DOI: 10.1002/aoc.6108
Revised: 27 October 2020
Accepted: 8 November 2020
F U L L P A P E R
Antimicrobial, computational, and molecular docking
studies of Zn (II) and Pd (II) complexes derived from
piperidine dithiocarbamate
Ahmed S.M. Al-Janabi1
Tarek A. Yousef 5,6
| Mustafa M. Kadhim2,3 | Amenah I.A. Al-Nassiry4
|
1Department of Biochemistry, College of
Veterinary Medicine, Tikrit University,
Tikrit, Iraq
2Department of Chemistry, College of
Science, Wasit University, Kut, Iraq
3Department of Chemistry, College of
Science, Baghdad University,
Baghdad, Iraq
4Department of Chemistry, College of
Education for Pure Science, Tikrit
University, Tikrit, Iraq
5Chemistry Department, Science College,
Imam Mohammad Ibn Saud Islamic
University, Riyadh, Saudi Arabia
6Toxic and Narcotic Drug, Forensic
Medicine Department, Mansoura
Laboratory, Medicolegal Organization,
Ministry of Justice, Egypt
Mixed ligand complexes of Zn (II) and Pd (II) have been prepared from piperi-
dine dithiocarbamate (PipDT) and amine ligand {2,20-bipyridine (Bipy),
1,10-phenanthroline (Phen), and 3-aminopyridine (3Apy)} to afford complexes
of the type [M(κ1-PipDT)(κ2-Bipy)] {MII Zn, Pd} (1,4), [M(κ1-PipDT)(κ2-Phen)]
(2,5), and [M(κ1-PipDT)(κ1-3Apy)2] (3,6). The reaction of equivalent molar of
sodium benzisothiazolinate (Nabit) or sodium saccharinate (Nasac) with cis-
[PdCl2(PPh3)2], followed by addition, sodium piperidine dithiocarbamate
(NaPipDT) afforded complexes of the type trans-[Pd(κ1-PipDT)(κ1-N-bit)
(PPh3)2] (7) and trans-[Pd(κ1-PipDT)(κ1-N-sac)(PPh3)2] (8). The obtained com-
plexes were characterized by elemental analysis and spectroscopic techniques.
The PipDT− was bonded as monodentate fashion via sulfur atom, whereas the
diamine ligands were coordinated as bidentate chelating, while the 3Apy
ligand bonded as monodentate mode through the nitrogen of heterocyclic ring.
In complexes (7) and (8), the bit− and sac− ligand coordinated as monodentate
through the nitrogen atom of heterocyclic ring. The antimicrobial activity of
the complexes was tested. All the complexes showed moderate to good activity
compared with standard antimicrobial. Moreover, the calculations of the den-
sity functional theory (DFT) were performed to estimate the thermal parame-
ters, dipole moment, polarizability, and molecular electrostatic potential of the
present complexes; in addition, Mulliken atomic charges of the complexes,
total electron density (TED), electrostatic surface potential (ESP), lethal con-
centration (LC50), and docking studies as well as the descriptors of chemical
reactivity were studied.
Correspondence
Ahmed S. M. Al-Janabi, Department of
Biochemistry, College of Veterinary
Medicine, Tikrit University, Tikrit, Iraq.
Email: dr.ahmed.chem@tu.edu.iq;
a_sh200683@yahoo.com
K E Y W O R D S
antimicrobial, dithiocarbamate, molecular docking, palladium, zinc
1 | INTRODUCTION
commonly utilized ligands such as xanthates, carba-
mates, dithiophosphates (Chart 1), and many others.[1–6]
Dithiocarbamate compounds (R2NCS2− or RNHCS2−) are
impartial one example of a general class of monoanionic
1,1-dithiolate ligands, which also contains other
The dithiocarbamate synthesis has a large variety,
depending on the final product. The traditional method
is based on the reaction of a primary or secondary amine
Appl Organomet Chem. 2020;e6108.
wileyonlinelibrary.com/journal/aoc
© 2020 John Wiley & Sons Ltd
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https://doi.org/10.1002/aoc.6108

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AL-JANABI ET AL.
CHART 1 Monoanionic 1,1-dithiolate
ligands
with carbon disulfide in the presence of metal or alkaline
salt, due to low stability of these acids.[6–22]
calculations, particularly Hartree–Fouck (HF) and
density functional theory (DFT), have been used to
predict the most stable conformation for different
compounds and isomers.[45–49]
Metal complexes of dithiocarbamate ligands have
been the subject of current and growing interest because
it possesses wide range of medical fields.[1–11] Dithiocar-
bamate can bond to metal ions in different coordination
modes (Chart 2) as (i) monodentate ligands through the
sulfur of the CSS− group (A);[10–15] (ii) bidentate chelat-
ing fashion through the sulfur atoms, through production
of two almost equal M–S bonds. In doing so, it forms a
small bite angle (S-M-S), ranging from 65ꢀ to 80ꢀ being
dependent upon the size of the ligand and metal ion
(B);[7,9,16–38] (iii) bidentate bridging mode through the
two sulfur atoms or through the one of the sulfur atom
only (C);[26,37,39–41] (iv) poly-dentate mode between three
center or more (D).[28,37,42–44] Metal complexes of dithio-
carbamate present a wide range of applications in agri-
cultural science, medicine as antibacterial, anti-fungal,
and anti-inflammatory, industry, analytical, and organic
chemistry.[1–11]
In the present work, we describe the synthesis, char-
acterization, and biological activity of Zn (II) and Pd
(II) mixed ligand complexes of piperidine dithiocarba-
mate (PipDT) and amine ligands {2,20-bipyridineine
(Bipy), 1,10-phenanthroline (Phen), and 3-aminopyridine
(3Apy)}, whereas the treatment of cis-[PdCl2(PPh3)2]
with sodium benzisothiazolinate (Nabit) or sodium
saccharinate (Nasac), followed by addition, sodium piper-
idine dithiocarbamate (NaPipDT) to give complexes of
the type trans-[Pd(κ1-PipDT)(κ1-N-bit)(PPh3)2] (7) and
trans-[Pd(κ1-PipDT)(κ1-N-sac)(PPh3)2] (8). Theoretical
2 | EXPERIMENTAL
2.1 | Materials and methods
All chemical materials and solvents required were pro-
vided from Sigma-Aldrich and used without additional
purification. Elemental analysis was determined on a
Vario El III elemental analyzer. Infrared spectra were
recorded
on
a
Shimadzu
Fourier
transform
infrared (FT-IR) 8400 spectrophotometer using KBr
discs in 400- to 4000-cm−1 range. 1H and 31P nuclear
magnetic resonance (NMR) spectra were recorded on
Bruker 400 apparatus in DMSO-d6. Molar conductivi-
ties were measured by using
conductivity meter (10−3 M—DMF). The melting point
was measured using SMP30 melting point
a digital CD-2005
apparatus. The sodium piperidine dithiocarbamate
(NaPipDT),[19] [Zn(κ2-PipDT)2],[19] [Pd(κ2-PipDT)2],[35]
and cis-[PdCl2(PPh3)2][50] were prepared by literature
methods. The antibacterial activities of the complexes
were tested by agar disc diffusion method originally
described by Bauer[51] against three bacteria types,
Staphylococcus aureus, Staphylococcus pyogenes, and
Escherichia coli in (10−3 μg/mL of freshly solution in
DMSO), also tested against two types of fungi,
Candida albicans and Aspergillus niger at same
concentration.
2.2 | Preparation of [Zn(κ1-
PipDT)2(Bipy)] (1)
A solution of 2,20-bipridyine (Bipy) (0.100 g, 0.64 mmol)
in chloroform (10 mL) was added to a suspension of [Zn
(κ2-PipDT)2] (0.247 g, 0.64 mmol) in chloroform (10 mL);
the mixture was stirred for 3 h at room temperature, then
refluxed for 4 h, and set aside for evaporate slowly. The
produced creamy solid was filtered off washed with
ethanol and dried under vacuum to afford a creamy
powder as [Zn(κ1-PipDT)2(Bipy)] (1).
The following complexes, [Zn(κ1-PipDT)2(Phen)] (2),
[Zn(κ1-PipDT)2(3Apy)2] (3), [Pd(κ1-PipDT)2(Bipy)] (4),
CHART 2 Coordination modes of dithiocarbamate ligands

AL-JANABI ET AL.
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[Pd(κ1-PipDT)2(Phen)] (5), and [Pd(κ1-PipDT)2(3Apy)2],
(6) were prepared in a similar method.
(Ω−1 cm−1 mol−1). IR (KBr) 3058w, 2973m, 2917w, 1598s,
1505s, 1438s, 1244s, 1163s, 988s, 891s, 672m, 417w, cm−1
.
1.69 (m, 4H, 2CH2-PipDT); 2.01 (m, 8H, 4CH2-PipDT);
4.08 (t, 8H, JHH = 7.8 Hz, 4CH2-PipDT); 7.46 (dd, 2H,
JHH = 7.8 Hz, H-Bipy); 7.69 (t, 2H, JHH = 7.6 Hz, H-Bipy);
8.40 (d, 2H, JHH = 7.6 Hz, H-Bipy); 8.69 (d, 2H,
JHH = 8.0 Hz, H-Bipy), ppm. Melting point: 260ꢀC
(decompose).
2.2.1 | [Zn(κ1-PipDT)2(Bipy)] (1)
Creamy solid. Yield: (0.282 g, 81%). Anal. calc. for
C22H28ZnN4S4: C, 48.74; H, 5.21; N, 10.34. Found: C,
48.96; H, 5.12; N, 10.56%. Molar conductivity in DMF: 8.5
(Ω−1 cm−1 mol−1). IR (KBr) 3058w, 2973m, 2917w, 1598s,
1505s, 1438s, 1244s, 1163s, 988s, 891s, 672m, 417w, cm−1
.
2.2.5 | [Pd(κ1-PipDT)2(Phen)] (5)
1H NMR (dmso-d6): δ 1.52(m, 4H, 2CH2-PipDT); 1.97 (m,
8H, 4CH2-PipDT); 4.06 (t, 8H, JHH = 7.8 Hz, 4CH2-
PipDT); 7.56 (dd, 2H, JHH = 7.8 Hz, H-Bipy); 7.85 (d, 2H,
JHH = 7.6 Hz, H-Bipy); 8.54 (dd, 2H, JHH = 7.6 Hz, H-
Bipy); 8.91 (d, 2H, JHH = 8.0 Hz, H-Bipy), ppm. Melting
point: 230–233ꢀC.
Off white solid. Yield: (0.289 g, 75%). Anal. calc. for
C24H28PdN4S4: C, 47.48; H, 4.65; N, 9.23. Found: C,
47.76; H, 4.81; N, 9.49%. Molar conductivity in DMF: 6.0
(Ω−1 cm−1 mol−1). IR (KBr) 3084w, 2966m, 2858w, 1573s,
1512s, 1434s, 1271s, 1152s, 993s, 908s, 662m, 423w, cm−1
.
1.58 (m, 4H, 2CH2-PipDT); 1.99 (m, 8H, 4CH2-PipDT);
4.05 (t, 8H, JHH = 8.00 Hz, 4CH2-PipDT); 7.49 (s, 2H, H-
Phen); 7.89 (d, 2H, JHH = 8.0 Hz, H-Phen); 8.56 (d, 2H,
JHH = 8.0 Hz, H-Phen); 8.98 (t, 2H, JHH = 8.0 Hz, H-
Phen), ppm. Melting point: 285ꢀC (decompose).
2.2.2 | [Zn(κ1-PipDT)2(Phen)] (2)
Off white solid. Yield: (0.319 g, 88%). Anal. calc. for
C24H28ZnN4S4: C, 50.92; H, 4.99; N, 9.90. Found: C,
50.89; H, 5.05; N, 10.13%. Molar conductivity in DMF: 6.0
(Ω−1 cm−1 mol−1). IR (KBr) 3082w, 2966 m, 2857w,
1573s, 1469s, 1434s, 1271s, 1152s, 995s, 941s, 827s, 664m,
2.2.6 | [Pd(κ1-PipDT)2(3Apy)2] (6)
1
447w, 423w, cm−1. H NMR (dmso-d6): δ 1.68(m, 4H,
Light brown powder. Yield: (0.329 g, 84%). Anal. Calc. for
C22H32PdN6S4: C, 42.95; H, 5.24; N, 13.66. Found: C,
42.75; H, 5.11; N, 13.72%. IR (KBr): 3295m, 3163m,
3058w, 2923m, 2871w, 1593s, 1504s, 1431s, 1266s, 1147s,
2CH2-PipDT); 2.08(m, 8H, 4CH2-PipDT); 4.12(t, 8H,
JHH = 8.00 Hz, 4CH2-PipDT); 7.49 (s, 2H, H-Phen); 7.89
(d, 2H, JHH = 8.0 Hz, H-Phen); 8.56 (d, 2H, JHH = 8.0 Hz,
H-Phen); 8.98 (t, 2H, JHH = 8.0 Hz, H-Phen), ppm. Melt-
ing point: 245ꢀC (decompose).
1
1063s, 956s, 657m, 443w cm−1. H NMR (DMSO-d6): δ
1.68 (m, 4H, 2CH2-PipDT); 2.09 (m, 8H, 4CH2-PipDT);
4.12 (t, 8H, JHH = 8.00 Hz, 4CH2-PipDT); 6.02 (bs, 4H,
NH2); 6.92 (s, 2H, H-3Apy); 7.39 (t, 2H, JHH = 7.8 Hz, H-
3Apy); 7.72 (d, 2H, JHH = 7.6 Hz, H-3Apy); 7.96 (d, 2H,
JHH = 7.8 Hz, H-3Apy). 240ꢀC (decompose).
2.2.3 | [Zn(κ1-PipDT)2(3Apy)2] (3)
Off white. Yield: (0.176 g, 85%). Anal. Calc. for
C22H32ZnN6S4: C, 46.02; H, 5.62; N, 14.64. Found: C,
45.94; H, 5.81; N, 14.72%. IR (KBr): 3345m, 3,159m,
3058w, 2923m, 2871w, 1587s, 1504s, 1431s, 1266s, 1147s,
2.3 | Preparation of trans-[Pd(κ1-PipDT)
(κ1-N-bit)(PPh3)2] (7)
1
1042s, 972s, 657m, 443w cm−1. H NMR (DMSO-d6): δ
1.73 (m, 4H, 2CH2-PipDT); 2.11 (m, 8H, 4CH2-PipDT);
4.08 (t, 8H, JHH = 8.00 Hz, 4CH2-PipDT); 5.56 (bs, 4H,
NH2); 6.78 (s, 2H, H-3Apy); 7.43 (dd, 2H, JHH = 7.6 Hz,
H-3Apy); 7.88 (d, 2H, JHH = 7.6 Hz, H-3Apy); 8.03(d, 2H,
JHH = 7.4 Hz, H-3Apy). Melting point: 159–162ꢀC.
A
hot solution of sodium benzisothiazolinate
(Nabit) (0.050 g, 0.289 mmol) in ethanol (10 mL) was
added to a yellow solution of trans-[PdCl2(PPh3)2]
(0.202 g,0.289 mmol) in dichloromethane (10 mL); the
mixture was stirred for 2 h then a solution of NaPipDT
(0.053 g, 0.289 mmol) in ethanol (5 mL) was added. The
mixture was refluxed for 4 h, to give light brown solution.
The produced brown solution was filtered off and set
aside to evaporate slowly. The brown solid formed was
filtered off washed with hot ethanol and dried under
vacuum. The trans-[Pd(κ1-PipDT)(κ1-N-sac)(PPh3)2] (8)
complex was prepared in a similar method.
2.2.4 | [Pd(κ1-PipDT)2(Bipy)] (4)
Creamy solid. Yield: (0.342 g, 92%). Anal. calc. for
C22H28PdN4S4: C, 45.31; H, 4.84; N, 9.61. Found: C,
45.20; H, 4.61; N, 9.88%. Molar conductivity in DMF: 8.5

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AL-JANABI ET AL.
2.3.1 | trans-[Pd(κ1-PipDT)(κ1-N-bit)
(PPh3)2] (7)
3 | RESULTS AND DISCUSSION
3.1 | Synthesis and characterization
[M(κ1-PipDT)2(κ2-Bipy)] {MII Zn, Pd} (1,4)
and [M(κ1-PipDT)2(κ2-Phen)] (2,5)
Yellowish brown powder. Yield: (0.239 g, 88%). Anal.
calc. for C49H44PdN2OP2S3: C, 62.51; H, 4.71; N, 2.98.
Found: C, 62.51; H, 4.71; N, 2.98%. Molar conductivity in
DMF: 4.30 (Ω−1 cm−1 mol−1). IR (KBr) 3072w, 2942w,
1618s, 1579s, 1520s, 1453s, 1436s, 1276s, 1123s, 1013m,
953m, 498s cm−1. 1H NMR (CDCl3): δ 1.56 (m, 4H, 2CH2-
PipDT); 1.98 (dd, 8H, JHH = 7.4 Hz, 4CH2-PipDT); 3.98 (t,
8H, JHH = 7.6 Hz, 4CH2-PipDT); 7.39–7.78 (m, 34H, H-
phenyl (bit + 2PPh3) ppm. Melting point: 231–233ꢀC.
The reactions of complexes (1) or (2) with equimolar
amounts of diamine ligands (Bipy or Phen) afforded com-
plexes of the type [M(κ1-PipDT)2(κ2-Bipy)] {MII = Zn, Pd}
(1,4) and [M(κ1-PipDT)2(κ2-Phen)] (2,5) (Scheme 1). The
dithiocarbamate ligand was coordinated through the sul-
fur atom as monodentate fashion, whereas the diamine
ligand was bonded as bidentate chelating ligand through
the nitrogen atoms. The prepared complexes are soluble
in DMSO and DMF and partially soluble in warm CHCl3
or CH2Cl2; the complexes were investigated by using ele-
mental analysis, molar conductivity, 1H-NMR, and IR
techniques, and data are given in Section 2. All attempts
to get crystals suitable for X-ray diffraction studies were
unsuccessful.
The IR spectra of the complexes (Figure S1) displayed
a strong bands within the 1602- to 1583-cm−1 range,
assigned to the υ(C N) of the diamine ligands. These
were shifted to lower frequencies of that in the free
ligands; this means that coordination of the amine took
place through the endocyclic nitrogen atoms.[20,25,32,33,57]
The PipDT ligand displayed two distinguishing bands
within 941–972 and 995–1063 cm−1 due to ν(C–S) and
ν(C S), respectively; the dithiocarbamate ligand dis-
played two characteristic bands compared with [M(κ2-
PipDT)2] {MII Zn, Pd} (showed one band) and indicated
that the PipDT¯ bonded as monodentate model to the M
(II) ion through the sulfur atom.[7,10,58] The spectra also
diplayed υ(M–N) within the 443- to 496-cm−1 range[50,59]
and υ(M–S) bond within the 418- to 455-cm−1 range.[50,59]
1H-NMR spectra of [M(κ1-PipDT)2(κ2-Bipy)] {MII Zn,
Pd} (1,4) and [M(κ1-PipDT)2(κ2-Phen)] (2,5) complexes
(Figure 1) clearly display the protons belong to the Bipy
or Phen and PipDT− ligands. The 1H NMR specrta
showed the protons of PipDT− ligand as three unglued
peaks within 1.47–1.69, 1.82–2.08, and 4.02–4.12 ppm,
due to the methylene groups. Whereas the protons of
phenyl rings in diamine ligands displayed as a resolved
peak in the aromatic region, and the integrations under
signals are in agreement with the number of protons. All
these peaks are listed in Section 2.
2.3.2 | trans-[Pd(κ1-PipDT)(κ1-N-sac)
(PPh3)2] (8)
Brown powder. Yield: (0.217 g, 77%). Anal. calc. for
C49H44PdN2O3P2S3: C, 60.46; H, 4.56; N, 2.88. Found: C,
60.71; H, 4.42; N, 3.14%. Molar conductivity in DMF: 4.30
(Ω−1 cm−1 mol−1). IR (KBr) 3035w, 2923w, 1648s, 1547s,
1512s, 1451s, 1434s, 1244s, 1153s, 997s, 936m,
1
487m cm−1. H NMR (DMSO-d6): δ 1.62 (m, 4H, 2CH2-
PipDT); 2.02 (dd, 8H, JHH = 7.4 Hz, 4CH2-PipDT); 4.10 (t,
8H, JHH = 7.6 Hz, 4CH2-PipDT); 7.23–7.86 (m, 34H, H-
phenyl (sac + 2PPh3)) ppm. Melting point: 231ꢀC
(decompose).
2.4 | Computational methods
Research Collaboratory for Structural Bioinformatics
(RCSB) used to download the protein structure
(3wze).[52] The protein and complexes structures were
processed to a format recognized by the AutoDock tools
(ADT) (*.pdbqt files) by adding all hydrogen atoms, Gas-
teiger charges, and merging the polar hydrogen atoms by
Molecular Graphic Laboratory (MGL) tools program.[53]
The root for the molecule identify by the Auto-dock auto-
matically. The atoms' specific affinity maps for all ligand
atom types, electrostatic, and desolation potentials were
computed with the help of Auto grid (version 4.2.6).[54]
The DFT calculations were performed with the hybrid
DFT functional B3LYP, as implemented by the Gaussian
09 program package. This function utilizes the Becke
three-parameter exchange functional (B3), combined
with the correlation functional of Lee, Yang, and Parr
(LYP). The Pd and Zn atoms were described by Stuttgart–
Dresden effective core potentials (ECP) and an SDD basis
set, while the 6-31G(d0) basis set was employed for the
remaining atoms.[55] Total electron density (TED) and
electrostatic surface potential (ESP) maps were calculated
by DFT/STO-3G method.[56]
3.2 | Synthesis and characterization
[M(κ1-PipDT)2(κ1-Apy)2] {MII Zn, Pd} (3,6)
Two moles of 3-aminopyridine ligand was reacted with
one mole of complex (1) or (2) to give complexes of the

AL-JANABI ET AL.
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SCHEME 1 Preparation of
complexes 1, 2, 4, and 5
FIGURE 1 1H nuclear magnetic
resonance (NMR) spectrum of complex
[Pd(κ1-PipDT)2(κ2-Bipy)2] (1)
type [M(κ1-PipDT)2(κ1-3Apy)2] {MII Zn, Pd} (3,6)
(Scheme 2). The 3Apy ligand was bonded as mono-
dentate model through the nitrogen of heterocyclic ring.
Also the PipDT− ligand was coordinated as mono-
dentate fashion through sulfur atom of CSS− group.
The complexes were investigated by using elemental
analysis, molar conductivity, 1H-NMR, and IR tech-
niques. Data are given in Section 2. All attempts to get
crystals suitable for X-ray diffraction studies were
unsuccessful.
Selected IR bands of the complexes (3) and (6) are
listed in Section 2. The IR spectra displayed the υ(C N)
at 1587 and 1593 cm−1 for the 3 and 6, respectively; this
band was shifted to lower frequency compared with the
free (3Apy) ligand, indicating that the coordination
occurred through the endocyclic nitrogen atom.[16,23,59]
SCHEME 2 Preparation of complexes
3 and 6

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AL-JANABI ET AL.
The asymmetric stretching of the NH2 group observed as
The 31P-{1H} NMR spectra of (7) and (8) showed a sin-
glet peak at δ P = 29.93 and 30.02 ppm, respectively
(Figure 2), indicating the presence of a single products
for each and the phosphorus atoms are equivalents.
The 1H-{31P} NMR spectra of (7) and (8) clearly
showed the protons of PipDT− ligand as three peaks
within δ 1.56–1.62, 1.98–2.02, and 3.98–4.10 ppm due to
methylene groups. Whereas, the protons of phenyl rings
in PPh3 and sac− ligands displayed as unresolved within
δ 7.39- to 7.78- and 7.23- to 7.86-ppm range for complexes
(7) and (8), respectively. Integration values under each
signal indicated that one of each of piperidine dithiocar-
bamate, saccharinate ligand, and two Ph3P is incorpo-
rated in each of the prepared complexes.
sharp to medium intensity bands at 3345 and 3295 cm−1
,
while the symmetric stretching appeared at 3159 and
3163 cm−1 for the complexes (3) and (6), respectively.
This band shifts slightly to higher wave number side rela-
tive to the free ligands indicating a noncoordination of
the NH2 group.[57,60] The PipDT ligand displayed two dis-
tinguishing bands within 956–972 and 1042–1063 cm−1
due to ν(C–S) and ν(C S), respectively; the appeared two
characteristic bands compared with [M(κ2-PipDT)2]
{MII Zn, Pd} (showed one band) indicated that the
PipDT¯ bonded as monodentate model to the M (II) ion
through the sulfur atom.[7,10,58]
1
In the H NMR spectra were particularly informative
for the protons of PipDT− and 3-aminpyridine ligands.
The protons of the heterocyclic ring of the 3Apy ligand
displayed as four separated peaks in the aromatic
range within δ (6.78–8.03 ppm for the complexes (3) and
(6). Whereas the protons of the NH2 group for
3-aminopyridine displayed a broad singlet at δ 5.56 and
6.02 ppm. The spectra also appeared the protons of the
dithiocarbamate ligand as three unglued peaks within
(1.68–1.73) ppm, (2.09–2.11) ppm and (4.08–4.12) ppm.
Integration values under each signal indicated
that two of each of piperidine dithiocarbamate and
3-aminopyrdine are incorporated in each of the prepared
complexes.
IR spectra of the complexes (7) and (8) showed the
ν(C O) of the sac− and bit− ligands at 1648 and
1618 cm−1, which slightly shifted compared with that of
the free saccharinate ligand, indicating that the carbonyl
group does not participate in the coordination to metal
ions.[61,62] The υ(C–N) band displayed at 1579 and
1547 cm−1; this band was shifted to low frequency region
compared with that of the free ligands; this is in agree-
ment with coordination of the sac− and bit− ligands with
the metal ions occurred through the nitrogen of heterocy-
clic ring.[62,63] The dithiocarbamate showed two diagnos-
tic bands in the IR spectra, at 936 and 959 and
997 and 1013 cm−1 corresponding to ν(C–S) and ν(C S),
respectively; the appeared two characteristic bands
compared with [M(κ2-PipDT)2] {MII Zn, Pd} (showed
one band) indicated that the dithiocarbamate coordinates
as monodentate fashion to the Pd (II) ion through the
sulfur atom.[7,10,58]
3.3 | Synthesis and characterization
trans-[Pd(κ1-PipDT)(κ1-N-bit)(PPh3)2] (7)
and trans-[Pd(κ1-PipDT)(κ1-N-sac)
(PPh3)2] (8)
Reaction of equimolar amount of cis-[PdCl2(PPh3)2] with
sodium benzisothiazolinate (Nabit) or sodium sac-
charinate (Nasac) followed by addition ethanolic solution
of sodium piperidine dithiocarbamate ligand led to for-
mation new products of (7) and (8) in good yield 88% and
77%, respectively (Scheme 3). The prepared complexes
were characterized by using spectroscopic and analytical
technical. All attempts to generate crystals suitable for
X-ray diffraction studies were unsuccessful. The molar
conductivity value referred the complexes (7) and (8) are
nonelectrolyte.
3.4 | Antimicrobial activity
Antimicrobial activity of the sodium piperidine dithio-
carbamate ligand and their complexes are listed in
Table 1 and summarized in Figure 3. The data were
obtained against three types of the pathogen bacteria
(E. coli, S. aureus, and S. pyogenes) and two fungi types
(C. albicans and A. niger) in 10−3 μg/mL. The standard
error for the experiment was 0.03%, and the experi-
ments were repeated three times at same conditions.
The diameter of the inhibitory zone (DIZ) was
SCHEME 3 Preparation of complexes (7)
and (8)

AL-JANABI ET AL.
7 of 15
FIGURE 2 The 31P-{1H}
nuclear magnetic resonance
(NMR) spectra of the
(a) complex (7) and
(b) complex (8)
TABLE 1 Results of antimicrobial activities of the compounds in (mm)
Dimeter inhibition zone (DIZ) in (mm)
Bacteria
Fungi
Escherichia
Coli
Staphylococcus
aureus
Pseudomonas
aeruginosa
Candida
albicans
Aspergillus
niger
Compounds
NaPipDT
8
12
19
12
17
20
24
23
NS
8
16
17
11
18
20
22
20
NS
11
14
18
12
16
14
20
25
NS
7
11
16
14
13
18
22
NS
21
9
10
12
10
16
15
19
NS
23
1
3
4
6
7
8
Streptomycin
Fluconazole
Note: Streptomycin: positive control for antibacterial screening; fluconazole: positive control for antifungal screening; NS denotes not screened.
compared with that of streptomycin (as control positive
of anti-bacteria) and fluconazole (as control positive
of anti-fungi), which is the positive control and
used DMSO as negative control. The complexes
displayed good activity against the pathogen bacteria.
1- The size of a complex could be considered a factor
that affects its permeability through the microbial cell
wall.[6,63] Arranging the complexes in order of increas-
ing molecular weight gives as follows:
Following
results
were
achieved
from
the
8 > 7 > 6 > 4 > 3 > 1 > NaPipDT.
obtained data:
2- Complexes 8 and 7 showed the highest anti-microbial
activity than the other complexes and free ligand.
These complexes have two phosphorus atoms with
one atom of nitrogen and sulfur around the palla-
dium; we assume that increased might be responsible
1- The complexes displayed high activity more than free
sodium piperidine dithiocarbamate ligand.
2- Biological activities of the compounds were in the
order of the following:
for
the
anti-microbial
activity,
and
the
8 > 7 > 3 > 6 > 4 > 1 > NaPipDT.
benzisothiazolinate (bit−) or saccharinate (sac−) has a

8 of 15
AL-JANABI ET AL.
FIGURE 3 A histogram representation of
the antimicrobial results of the complexes
heterocyclic ring with C O, CNS, and SO2 groups;
3.5 | Theoretical studies
these act to increase the activity.[64,65]
3- The complex 8 showed greater antibacterial activity
compared with streptomycin against E. coli and
S. aureus, also showed greater antifungal activity
compared with fluconazole against C. albicans.
3.5.1 | DFT calculations studies
In this part of this chapter, we propose to give the bases
for the understanding of the key concepts of DFT, which
provides access to a large number of properties. As it
cannot be exhaustive, the emphasis will be placed on the
theoretical foundations and the inevitable limits of this
theory.
Their activity of prepared complexes may be referring
to many factors:
1- Structure of starting materials such as saccharinate
and benzisothiazolinate are good examples of
hetero-aromatic organic compounds have biological
properties.
2- Chelating effect: The significant activity of metal
complexes in inhibiting ability due to incorporation
of metal ions increases the inhibition of cell
growth.[64–66]
We have analyzed, using DFT, with the aim of evalu-
ating the donor or electron acceptor capacities of these
ligands, as well as the analysis of its stability. Likewise,
the nature of the metal–ligand and metal–metal bonds of
the neutral species will be analyzed as a function of the
nature of the metal and of the donor or acceptor capaci-
ties of the auxiliary ligand linked to the metal atom.
The theoretical DFT calculations were performed in
gas phase by DFT method at B3LYP 6-311G (d,p) basis
set. The estimated DFT calculations for electronic energy,
heat capacity, entropy (S), thermal energy, polarizability,
and dipole moment for 1–8 are summarized in Table 2.
The DFT estimated data revealed that the dipole
moment of the complexes under investigation is in
the order: [Zn(κ2-PipDT)2] < 7 < 5 < 1 < [Pd(κ2-
PipDT)2] < 4 < 8 < 6 < 3 < 2. The high dipole moment 2,
3, 4, and 8 could illustrate their binding pose within a
specific target protein and their results of the predicted
binding affinity that will be discussed in the following
molecular docking part. The polarizability of the mate-
rials depends on how the susceptibility of molecular sys-
tem electron cloud be accepted by approaching of a
charge. Moreover, it depends on the complexity of the
compounds as well as the size of the molecular structure.
Molecules of the large size are more polarizable
compounds. It is worth noting that the [Pd(κ2-PipDT)2] is
the smallest in size and has the least polarizability
3- Effect of molecular weight: The molecular weight
plays a major role in interaction of materials with
biological system.
Although, the careful mechanism of biological
activity of our compounds is not fully understood
biochemically; style of action of biological agents may
include any of the following mechanism:
i. Interference with the cell membrane of bacteria or
fungi.
ii. Deactivate various cellular enzymes, which play a
vital role in different metabolic pathways of these
microorganisms.
iii. Formation of hydrogen bond between the function
groups with the active site of cell constituents,
producing in interference with the normal cell
action.[64–66]

AL-JANABI ET AL.
9 of 15
(218.93 a.u.); however, [Zn(κ2-PipDT)2] of the highest
complexity is predicted to have the highest polarizability
(617.48 a.u.).
In our study, the results show that the inhibition and
hindrance of protein activity of building complexes com-
plex 2, 4, [Zn(κ2-PipDT)2], 5, and 1 is higher compared
with other complexes with the highest occupied MO
(HOMO) and E energy indicating the capacity to donate
electrons and building complex stability, respectively,
inversely to other complexes.
3.5.2 | Mulliken atomic charges
Assessment of Mulliken atomic charges in the hypotheti-
cal estimation process of the molecular structure exhibits
considerable responsibility. The distribution of the all
complexes charge has been clarified (Table S1). The
positive charges of most C, Pd, and Zn atoms were due to
their ability to accept them, whereas the negative values
of most S, N, and O atoms were due to their ability
to give.
Recently, many reports showed that the Frontier
Orbital Theory in Organic Reactivity (FMOs) have to be
taken into consideration in investigation of the structure
activity relationships.[67–69] The FMOs theory showed
that the energy level of the HOMO and the LUMO is the
most significant aspects that impact the bioactivities of
small structural drugs. Mainly, HOMOs offer electrons;
however, the LUMOs accept electrons. Obviously, the
level of energy of HOMOs is different for all studied com-
pounds. [Zn(κ2-PipDT)2] showed the most lying HOMO
than the other compounds, and consequently, it could be
a better electron donor drug. Interestingly, [Zn(κ2-
PipDT)2] and 2 of the largest energy gap ΔE = 1.64 and
1.20 eV, respectively, there are several hydrophilic
interactions that could facilitate the binding with the
receptors. This suggests that such hydrophilic interac-
tions considerably impact the binding affinity of such
small drugs to the receptors. The HOMO of a certain drug
and the LUMO with the adjacent residues could share
the orbital interactions during the binding process.
3.5.3 | Chemical reactivity descriptors
The most essential orbitals to describe the compound's
optical properties and chemical and biological activity of
the chemical species are the highest occupied frontier
MO's and the lowest unoccupied MO's (highest occupied
molecular orbital [HOMO] and lowest unoccupied
molecular orbital [LUMO]). The higher value of a
molecule's HOMO implies that it acts as a “Lewis Base”
or may be oxidation and has the potential to donate
electrons to a convenient acceptor molecule with low
energy (or empty molecular orbitals), while the higher
value of a molecule's lowest unoccupied molecular
orbital LUMO implies that it acts as a “Lewis Acid” or is
capable of reducing and absorbing electrons from
convenient donor molecules.
Calculations, such as the energy of the highest occu-
pied molecular orbital (EHOMO) and energy of the low-
est unoccupied molecular orbital (ELUMO), obtain
quantium chemical parameters of organic compounds.
Additional parameters, such as separation energies (ΔE),
absolute electronegativities (v), chemical potentials (Pi),
TABLE 2 Electronic energy (Hartree/Particle), heat capacity (Cv), entropy (S) (cal/mol-Kelvin), thermal energy, polarizability α (a.u.),
and dipole moment (Debye) of [Zn(κ2-PipDT)2], [Pd(κ2-PipDT)2], and 1–8 complexes
Electronic
energy
Total dipole
moment
Polarizability
(α)
E
Heat
capacity (Cv)
Entropy
(S)
Compounds
(thermal)
[Zn(κ2-
−7846.63
3.31
617.48
439.06
122.88
196.05
PipDT)2]
[Pd(κ2-
−7069.78
8.76
218.93
228.98
60.84
126.83
PipDT)2]
1
2
3
4
5
6
7
8
−4412.43
−4487.56
−4523.25
−7558.09
−7633.05
−7668.55
−8981.71
−8832.96
8.36
14.82
12.99
10.05
7.62
298.76
313.09
304.11
377.16
380.36
267.63
566.39
565.61
329.99
339.47
371.41
329.42
330.18
362.29
574.29
569.22
81.57
88.17
90.49
80.27
82.18
86.04
135.50
132.34
142.69
153.76
157.78
144.52
143.29
150.16
188.91
190.92
12.02
6.54
10.49

10 of 15
AL-JANABI ET AL.
TABLE 3 Calculated EHOMO, ELUMO, energy band gap (EH–EL), chemical potential (μ), electronegativity (χ), global hardness (η),
global softness (S), global electrophilicity index (ω), and softness (σ) for [Zn(κ2-PipDT)2], [Pd(κ2-PipDT)2], and 1–8 complexes
Compounds
EH/eV
1.66
EL/eV
2.27
(EL–EH)/Ev
0.61
χ/eV
−1.96
−1.70
3.56
μ/eV
1.96
η/eV
0.31
0.74
0.75
0.42
0.82
0.56
0.57
0.55
0.71
0.72
S/eV−1
0.15
0.37
0.38
0.21
0.41
0.28
0.29
0.28
0.35
0.36
ω/eV
6.31
1.97
8.43
0.37
0.36
0.01
0.001
0.04
0.02
0.05
σ/eV−1
1.64
0.68
0.66
1.20
0.61
0.89
0.88
0.91
0.71
0.69
[Zn(κ2-PipDT)2]
[Pd(κ2-PipDT)2]
0.97
2.44
1.47
1.70
1
2
3
4
5
6
7
8
−4.32
−0.97
−0.05
−0.68
−0.62
−0.77
−0.55
−0.45
−2.81
−0.14
1.59
1.51
−3.56
−0.56
0.77
0.83
0.56
1.63
−0.77
0.12
0.44
1.11
−0.12
−0.05
−0.22
0.16
0.52
1.14
0.05
0.33
1.10
0.22
0.87
1.41
−0.16
−0.27
0.99
1.44
0.27
Abbreviations: EHOMO, energy of the highest occupied molecular orbital; ELUMO, energy of the lowest unoccupied molecular orbital.
absolute hardness (g), absolute softness (r), global
electrophilicity (x), and global and softness (S), were
calculated by Equations (1)–(5) (Table 3).[70–72]
parts so the TED and ESP are shown in Figure 4 (for
complexes 2, 4, 7, and 8). The palladium elements in all
complexes have a high electron density. Other than that,
the zinc complexes electron density focused on
oxygen atoms.
χ = −1=2 ðELUMO + EHOMOÞ,
μ = −χ = 1=2 ðELUMO + EHOMOÞ,
η = 1=2 ðELUMO −EHOMOÞ,
S = 1=2 η,
ð1Þ
ð2Þ
ð3Þ
ð4Þ
ð5Þ
3.5.5 | Lethal concentration
method (LC50)
LC50 is the maximum concentration anoxic of the com-
plexes studied that can be used in human body. HF/3–11
method is used to predict their values of LC50. Equation 7
is used to suggest the values.
ω = μ2=2 η:
HF−LogLC50 = 38:00 – 1:13Str + 1:38 × 10−3 ω H – 2:22 ð7Þ
× 10– 3 ω L – 0:36IA………,
The inverse value of the global hardness is designed
as the softness (σ) as follows:
σ = 1=η:
ð6Þ
where Str = translational entropy, ω = vibrational
wavenumber, and IA
=
principal moment of
inertia.[74] The heights value complex number
1 (84.8 × 10−10 mol/L) and the lowest value complex
6 (0.11 × 10−10 mol/L) Table 4. The results indicate to
the high concentrations could use in human body of
the complexes.
3.5.4 | Complexes interactions
ESP is the direct interactions of complexes onto the
protein functional groups. The present atoms and parts of
the complexes are not active in the linkage with protein
structure. There is high electron density (red color), low
electron density (blue color), and neutral by green color
according to TED[73] as shown in Figure S2. Complex 9 is
a good inhibition according to docking results in coming
3.6 | Docking results
The complexes mentioned were suggested as anticancer
by blocking vascular endothelial growth factor receptor

AL-JANABI ET AL.
11 of 15
FIGURE 4 Total electron density
(TED) and electrostatic surface potential
(ESP) of complexes 2, 4, 7, and 8
TABLE 4 LC50 suggested method
parameters
Complex
Str
IA
ωH
ωL
LC50 (mol/L)
[Zn(κ2-PipDT)2]
[Pd(κ2-PipDT)2]
45.802
44.052
44.745
44.875
44.917
44.968
45.089
45.128
46.398
46.497
0.99999
0.99999
0.99991
0.99981
0.9996
0.99943
0.99999
0.9954
0.99991
0.99983
2973.64
2977.53
3114.91
3098.55
3287.4
26.38
34.60
58.07
27.66
32.20
27.12
75.40
29.61
29.79
39.71
84.8 × 10−10
7.82 × 10−10
0.17 × 10−10
0.13 × 10−10
0.22 × 10−10
0.11 × 10−10
6.17 × 10−10
1.62 × 10−10
30.19 × 10−10
22.33 × 10−10
1
2
3
4
5
6
7
8
3118.35
3093.22
3354.03
3141.85
3143.91
Abbreviation: LC50, lethal concentration.

12 of 15
AL-JANABI ET AL.
FIGURE 4 Molecular interactions
between complexes 2, 7, and 8 with receptor
TABLE 5 Binding energy values
and ligand efficiency of the studied
complexes
Comp.
Eb (kcak/mol) LE
Eb (kcak/mol) range Best site number
[Zn(κ2-PipDT)2] −7.65
[Pd(κ2-PipDT)2] −5.47
−0.20 −6.05 to −7.65
3
3
4
7
5
5
6
4
9
4
−0.27 −5.11 to −5.47
−0.20 −4.10 to −6.3
−0.26 −3.35 to −8.68
−0.16 −1.91 to −5.36
−0.25 −4.54 to −7.83
−0.20 −3.98 to −6.54
−0.16 −2.26 to −5.13
−0.08 −1.98 to −4.74
−0.10 −1.69 to −6.25
1
2
3
4
5
6
7
8
−6.30
−8.68
−5.36
−7.83
−6.54
−5.13
−4.74
−6.25

AL-JANABI ET AL.
13 of 15
2 (VEGFRTK) (3wze).[75] The potency interaction of the
[Zn(κ2-PipDT)2], [Pd(κ2-PipDT)2], and (1–8) complexes
with receptor depending on binding energy and ligand
efficiency. The measure of the affinity of complexes and
the receptor is a binding energy (Eb) and ligand efficiency
(LE) is binding energy per atom of ligand to receptor
protein.[49] The best location in receptor in depending on
Eb for all complexes as and the range of Eb for the
complexes in different sites as present in Table 5.
The order of the ability to block the protein structure by
the Eb is
Formal analysis; investigation; methodology. Tarek
Yousef: Formal analysis; investigation; software.
ORCID
Ahmed S.M. Al-Janabi https://orcid.org/0000-0003-
2722-7419
Tarek A. Yousef https://orcid.org/0000-0003-3039-7646
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We synthesized eight mixed ligand complexes of Zn
(II) and Pd (II) complexes by the reaction of [M(κ2-
PipDT)2] {M Zn or Pd} complex with amine
ligands (2,2 bipyridyl, 1,10-phenanthroline, and
3-aminopyridine) or reaction of cis-[PdCl2(PPh3)2] with
sodium benzisothiazolinate (Nabit) or sodium sac-
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characterized by elemental analysis and spectroscopic
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was coordinated as monodentate fashion through the
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anticancer and the good, inhibitions are 2, 4, [Zn(κ2-
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