DFT investigations of linear Zn3-type complex with compartmental N/O-donor Schiff base: Synthesis, characterizations, crystal structure, fluorescence and molecular docking

Article abstract of DOI:10.1016/j.molstruc.2020.127936

A linear Zn(II) complex, [Zn₃(L^OMe-pn)₂(?¹-NCS)₂] (1) containing a N₂O₂O′₂ donor Schiff base, (H₂L^OMe-pn = N, N-bis(3-methoxysalicylidene)-2, 2-d

Full text of DOI:10.1016/j.molstruc.2020.127936

Journal Pre-proof
DFT investigations of linear Zn -type complex with compartmental N/O-donor Schiff
3
base: Synthesis, characterizations, crystal structure, fluorescence and molecular
docking
Dhrubajyoti Majumdar, Tapan kumar pal, Dheeraj Kumar Singh, Deepak K. Pandey,
Debaprasad Parai, Kalipada Bankura, Dipankar Mishra
PII:
S0022-2860(20)30260-X
DOI:
https://doi.org/10.1016/j.molstruc.2020.127936
MOLSTR 127936
Reference:
To appear in: Journal of Molecular Structure
Received Date: 17 January 2020
Revised Date: 18 February 2020
Accepted Date: 18 February 2020
Please cite this article as: D. Majumdar, T.k. pal, D.K. Singh, D.K. Pandey, D. Parai, K. Bankura, D.
Mishra, DFT investigations of linear Zn -type complex with compartmental N/O-donor Schiff base:
3
Synthesis, characterizations, crystal structure, fluorescence and molecular docking, Journal of Molecular
Structure (2020), doi: https://doi.org/10.1016/j.molstruc.2020.127936.
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DFT investigations of linear Zn3-type complex with compartmental N/O-donor Schiff
base: Synthesis, characterizations, crystal structure, fluorescence and molecular
docking
Credit Author Statements of Ms. Ref. No.: MOLSTRUC-D-20-00291:
1. Dhrubajyoti Majumdar—Main author, research concept, contributed synthesis, total
manuscript preparation and main research work carried out.
2. Tapan Pal contributed only X-ray crystallographic section
3. Dheeraj kumar Singh and Deepak K. Pandey contributed DFT section
4. Debaprasad Parai contributed only Molecular docking section
5. Dipankar Mishra Research guide and Supervisor
6.Kalipada Bankura contributed research proposal guide, fluorescence analysis, stokes shift
and preparation of different Molecular graphics.

GRAPHICAL ABSTRACT
Zn(OAc)2.2H2O
KSCN in MeOH
+ Few drops of
CH3CN + DMF
(1:1)
O
Me
OH
O
The perspective view of the
asymmetric unit
MeOH/Reflux
(2:1)M
N
N
[Zn3(LOMe-pn)2(η1-NCS)2] (1)
3h
OH
+
HO
Vaccum
Evaporation
MEP PLOT
SEM
O
O
Me
Me
NH2
H2N

1
DFT investigations of linear Zn3-type complex with compartmental N/O-donor Schiff
base: Synthesis, characterizations, crystal structure, fluorescence and molecular
docking
Dhrubajyoti Majumdar a, b, Tapan kumar pal c, Dheeraj Kumar Singh d, Deepak K. Pandey d,
Debaprasad Parai e, Kalipada Bankura a*, Dipankar Mishra a*
a Department of Chemistry, Tamralipta Mahavidyalaya, Tamluk-721636, West Bengal, India
b Department of Applied Chemistry, Indian Institute of Technology (Indian School of Mines),
Dhanbad, Jharkhand 826004, India
c
School of Liberal Studies, Pandit Deendayal Petroleum University, Gandhinagar-382421,
India
d Department of Physics; Institute of Infrastructure Technology Research and Management;
Near Khokhara Circle, Maninagar East, Ahmedabad-380026, Gujarat, India
e L V Prasad Eye Institute, Patia, Bhubaneswar, India-751024
AUTHOR EMAIL ADDRESS: dmishra.ic@gmail.com, kalipada2010@gmail.com

2
ABSTRACT
A linear Zn(II) complex, [Zn3(LOMe-pn)2(ƞ1-NCS)2] (1) containing a N2O2O'2 donor Schiff
base, (H2LOMe-pn =N, N-bis(3-methoxysalicylidene)-2, 2-dimethylpropane-1, 3 diamine) has
been synthesized and structurally well characterized. SCXRD study reveals that in 1, the
asymmetric section contains two identical discrete unit and each discrete unit contains three
zinc metal ions (Zn1, Zn2 and Zn3) which are crystallographic independent, two
deprotonated ligands [LOMe-pn]2- and [SCN-] ions which are linked with only terminal zinc ion
in a η1 mode where terminal zinc atoms (Zn1/Zn3) are distorted square pyramidal while Zn2
is square antiprismatic. All computational calculations were performed by the DFT/M06
functional and the 6-31G * basis set in the ground state. Complex optimized structure,
HOMO-LUMO energy gap, Hirshfeld surface, MEP and NLO property was nicely explained
with the help of DFT. Total dipole moment, average polarizability and first
hyperpolarizability were calculated where α and βhyp values are well demonstrate the NLO
property of complex (1). In addition, Bader’s “atoms-in-molecules” was analysed to delineate
complex non-covalent interactions using the same level of theory. Experimental electronic
spectra were explained using TD-DFT level of calculations with an IEFPCM solvent model.
DMF solvent explore complex (1) is a fluorescent material with maximum emission at 479
nm at an excitation wavelength of 300 nm. Finally, molecular docking was executed with
cytochrome P450 from B. megaterium and M. tuberculosis. Results of molecular docking and
HOMO-LUMO energy gap can provide new insights in the development of
antimycobacterial drugs and next-generation semiconductor devices.

3
Keywords: Schiff base, Zn(II), DFT, Molecular docking, Luminescence
1. Introduction
During (1834-1915) Prof. H. Schiff opened an unheard multidisciplinary research window
after his successful discovery of Schiff bases and other imines [1] and was responsible for
research into aldehydes. Now Schiff base ligands are ubiquitous in coordination chemistry of
transition metals due to its availability, easy synthetic approach, exhibit various denticities
and functional behaviours [2,3]. In recent decades, complexes derived from such privilege
ligands have become prime research area due to their attracting molecular structures and
interesting properties [4-6] which are utilized as fluorescent material, non-linear optics,
catalysis, magnetism, molecular recognition, biomedicine [7-12], optoelectronics [13-16],
involvement of many catalytic functions for biological and non-biological processes [17,18],
metallomesogens [19] and so forth. Spurred by the catalytic activity of various mono/di-
nuclear zinc complexes [20-24], usually heterometallic Zn2Cu calixarene complex have
greater catalytic efficiency than usual Zn3-type complexes [25-28]. In this juncture,
compartmental N2O2O'2 donor Schiff bases derived from salicylaldehyde derivatives (ortho
vanillin) and specific diamines, readily coordinate to d-block transition metal ions in a
tetradentate (N2O2) fashion to afford d-block mono/di-nuclear/homometallic/tri- and
tetranuclear complexes consisting of two molecules of parent salen ligands [29-31]. Herein
µ2-phenoxo bridging plays an important role in assembling metal ions and also two salen-
type ligands. The presence of alkoxy groups (-OR, R=Me, Et) at position 3 of salicylidene
moieties, an additional O4 coordination site and phenoxo oxygen is readily available in
conjunction with N2O2 site (Scheme 3). In fact, O4 site is particularly suitable for
heterometallic 3d-4f complex formation with interesting magnetic and photochemical

4
properties [32-34]. Similarly, introduction of hydroxyl groups at 3 position of salicylidene
moieties, reinforced the formations of mono/di/tri/heteronuclear complexes [35-38]. Such
common trimetallic structural motif has already portrayed by A. Mustapha et. al. (Scheme
S1B) [39]. Therefore, novel complex formations using hexadentate (N2O2O'2) Schiff base and
pseudo-halide [SCN-] ions are common synthetic strategy over many years where versatile
bridging mode of [SCN-] ions [40-42] were nicely explored (Scheme S2) without exception.
Herein the stereochemistry and coordination number attainment governed not only the
pseudo-halide spacers but also the steric requirements of the Schiff bases [43, 44]. The
unique selection of zinc metal ions is due to its zero-crystal field stabilization energy (CFSE)
and d10 configuration which permits favourable architecting with flexible coordination
environments [45].
Our motivated research group has already reported a number of pseudo-halide bridged
Zn(II)/Cd(II) discrete/polynuclear complexes with different compartmental N/O-donor Schiff
bases and explore their photoluminescence, DFT/TD-DFT, cytotoxic effect, apoptosis,
autophagy, necrosis type classical cell death, in vitro antibacterial and anti-biofilm properties
vividly [46-51]. Meanwhile, the outcome of previous works is the progressive response of
photoluminescence, cytotoxicity, antibacterial and anti-biofilm properties [52-54]. Although
till date various Zn3-salen type complexes [35-38] nicely explore their molecular architectures
but it is worth to mention here that always small amount of research efforts were devoted for
the synthesis of trinuclear zinc metal complex with current Schiff base ligand and [SCN-]
spacers followed by novel scientific analyses of DFT/TD-DFT, Hirshfeld surface (HS),
Bader’s “atoms-in-molecules” (AIM), Molecular electrostatic potential (MEP), Frontier
molecular orbital (FMO), Non-linear optics (NLO) and molecular docking with cytochrome
P450 from B. megaterium and M. tuberculosis as a representative model.

5
In this article, we report successfully synthesis, spectral characterizations including SEM-
EDAX analysis, single-crystal structure, DFT/TD-DFT, photophysical and molecular
docking with cytochrome P450 from B. megaterium and M. tuberculosis in favour of
complex [Zn3(LOMe-pn)2(ƞ1-NCS)2] (1).
2. Experimental section
2.1. Starting materials
All research chemicals were of analytical grade and used as received without any
purification. Zn(OAc)2.2H2O, KSCN, ortho vanillin, and 2, 2-dimethyl-1, 3-propanediamine
were directly purchased from Sigma Aldrich Company, USA. High grade solvents such as
CH3OH, CH3CN and DMF were purchased from Merck company.
2.2. Physical measurements
Elemental (CHN) analysis for ligand and the complex was carried out on a Perkin-Elmer
2400 elemental analyzer. FT-IR and Raman spectra were recorded as KBr pellets (4000–400
cm-1) using Perkin–Elmer spectrum RX 1 and BRUKER RFS 27 in the range 4000-50 cm-1.
1H NMR spectra was recorded on a Bruker 300MHz FT-NMR spectrometer using trimethyl
silane as internal standard in DMSO-d6 solvent. EDAX and SEM experiments was performed
on EDAX OXFORD XMX N (model) using Tungsten filament and JEOL Model JSM-
6390LV. UV-Visible spectra (200-1100 nm) were determined using Hitachi model U-3501
spectrophotometer. Fluorescence spectra in DMF solvent were measured at room temperature
using Perkin-Elmer LS50B Spectrofluorometer model. Phase purity of the trinuclear complex
(1) is carried out using Powder X-ray diffraction measurement by BRUKER AXS,
GERMANY X-ray diffractometer model using Cu Kα-1 radiation. Ligand and trinuclear

6
Zn(II) complex quantum yield (Φ) were determined using very popular equation (1) where
quinine sulphate used as secondary standard (Φ = 0.57 in water) [55].
ΦS AS (Abs)R nS2
=
×
×
------------------------------------------------------------------------------(1)
ΦR AR (Abs)S nR2
The meaning of each terms according to equation (1): A terms denote the fluorescence area
under the curve; Abs denotes absorbance; n is the refractive index of the medium; Φ is the
fluorescence quantum yield; and subscripts S and R denote parameters for the studied sample
and reference respectively.
2.3. X-ray crystallography
Crystals were grown by slow evaporation of CH3OH and few drops (1:1) mixture of
CH3CN+DMF at room temperature. Good quality crystals data was collected on a Bruker
SMART CCD [56] diffractometer using Mo Kα radiation at λ = 0.71073 Å. Judicious crystal
data collection purpose we have operated different popular programs such as SMART
program for collecting frames of data, indexing reflections and determining lattice
parameters, SAINT [57] for integration of the intensity of reflections and scaling, SADAB
[58] for absorption correction and SHELXTL for space group, structure determination and
least-squares refinements on F2. Crystal structure of complex (1) was fully solved after
refining by full-matrix least-squares methods against F2 using the program SHELXL-2014
[59] and Olex-2 software [60]. It is worth to mention here that the A-Level Alert in the
checkCIF (1) is related only to the ADP max/min Ratio ....7.1 oblate since examined single
crystal was a small-sized, brittle, weakly diffracting (despite using Mo Kα radiation) and
presence of atoms disorder. Herein data reported is the best one among the collected. Crystal
structure solving purpose all non-hydrogen atoms were refined with anisotropic displacement
parameters and all hydrogen positions were fixed at calculated positions which is refined iso-
tropically. Different crystallographic figures were designed using latest version of Diamond

7
software [61]. The crystallographic data and full structure refinement parameters for complex
(1) is submitted in Table 1. Crystallographic data (excluding structure factors) have been
deposited with the Cambridge Crystallographic Data Centre as supplementary publication
number CCDC 1904939.
Table 1 Crystal data and structure refinement parameters of complex (1)
Formula
M/g
C44H48N6O8S2Zn3
1049.11
Crystal system
Monoclinic
Space group
P21/c
a/Å
24.371(3)
b/Å
c/Å
19.435(2)
19.8118(19)
90
α (°)
β (°)
γ (°)
V/Å3
93.833(3)
90
9363.2(17)
Z
8
ρc/g cm-3
1.488
ꢀ/mm-1
1.671
F(000)
4320
Cryst size (mm3)
θ range (deg)
0.045× 0.031 × 0.022
0.997
Limiting indices
-26 ≤ h ≤ 29
-23 ≤ k ≤ 23
-23≤ l ≤ 24
Reflns collected
Ind reflns
84684
17391[Rint = 0.1790, Rsigma = 0.1789]
Completeness to θ (%)
Refinement method
Data/restraints/ parameters
Goodness-of-fit on F2
Final R indices
0.997
Full-matrix-block least-squares on F2
17391/0/1151
1.034
R1 = 0.0990

8
[I > 2θ(I)]
wR2 = 0.2050
R indices (all data)
R1 = 0.2076
wR2 = 0.2563
Largest diff. peak and hole (e ·Å-3)
0.964 and -2.486
2.4. Computational methodologies
Modelled complex (1) density functional theory (DFT) was implemented in GAUSSIAN 16
suite of programs [62]. Ground state energy of all the system is optimized in DMSO
(Dimethyl Sulfoxide) and the integral equation formalism Polarizable Continuum Model
(IEFPCM) was used to estimate the solvent effect [62]. The new highly parameterized
estimated exchange-correlation energy functional M06 (Meta-generalized gradient
approximation (GGA) functional exchange) chosen for the complete calculations within the
framework of the DFT method [62, 63] where over all the atoms, a valence double-zeta
polarized basis array 6-31 G* was applied. The vibrational analysis was performed based on
the second derivatives to confirm the existence of the minima of the potential surface which
confirms the absence of imaginary frequency. To obtain electronic absorption spectra,
vertical transition energies, oscillator strength, the time-dependent density functional theory
(TD-DFT) was employed at M06/6-31G* level of theory in DMSO by using same IEFPCM
model [62]. The GaussView 6 software was used to visualize optimized structures, molecular
electrostatic potential (MESP) map, frontier molecular orbital graphics and theoretically
calculated UV-Vis spectra [64]. Gauss sum [65] was utilized at the finale phase of
calculations to compute the fractional contribution of the various individual components in
the crystal to each molecular orbital. The first hyperpolarizability (βhyp) and its components

9
were theoretically calculated at M06/6-31G* level of theory by adopting the finite field (FF)
approach. The FF approach, which provides very constant results in accordance with the
experimental results, was used to calculate the first hyperpolarizability (βhyp) of a variety of
chemical systems. [66a] The total static dipole moment is determined by using equation (1)
as
μ = μꢁꢀ + μꢁꢂ + μꢁꢃ
(1)
The isotropic polarizability calculated by using equation (2) as:
ꢇꢅ ꢇꢅ
ꢉꢉ
ꢄ = ꢅ
ꢆꢆ
ꢈꢈ
ꢊ
(2)
The first-order hyperpolarizability (βhyp) is:
ꢒ
βꢋꢌꢍ = ꢎꢏβꢀꢋꢀꢌꢀꢍ + βꢋꢀꢂꢌꢍꢂ + βꢀꢋꢃꢌꢃꢍꢐꢁ + ꢏβꢋꢂꢌꢂꢍꢂ + βꢋꢌꢍ + βꢂꢋꢀꢌꢍꢀꢐꢁ + ꢏβꢋꢌꢍ + βꢋꢌꢍ + βꢃꢋꢂꢌꢂꢍꢐꢁꢑꢓ (3)
ꢂꢃꢃ
ꢃꢃꢃ
ꢃꢀꢀ
The Hirshfeld surfaces and the 2D fingerprint plots were calculated using the Crystal
Explorer [66b] software, which accepts a CIF-format structure input file obtained as a result
of single-crystal X-ray diffraction. HS is the external contour of the space consumed in a
crystalline environment by a molecule or an atom. The normalized contact distance dnorm is a
function of distances to the surface from nuclei (atoms) inside (di) and outside (de) the
Hirshfeld surface, compared with their respective van der Waals radii (ꢔꢖꢗꢘ and ꢔꢖꢗꢘ) and
ꢙ
ꢕ
expressed as:
ꢡꢢꢣ
ꢡꢢꢣ
ꢘ ꢠꢝ
ꢘ ꢠꢝ
ꢤ
ꢤ
ꢟ
ꢟ
ꢚꢛꢜꢝꢞ
=
+
ꢡꢢꢣ
ꢡꢢꢣ
ꢝ
ꢝ
ꢤ
ꢟ
(4)

10
The combination of ꢚꢙ and ꢚꢕ as a 2D fingerprint plot summarizes intermolecular contacts in
the crystal. The 2D fingerprint plots were displayed in the 0.5 – 3.0 Å range. The topological
analyses were performed by the Bader’s “atoms-in-molecules” theory by means of Multiwfn
software [66c].
2.5. Molecular docking
The bacterial cytochromes P450 are cytosolic heme-thiolate proteins from a superfamily of
heme-containing monooxygenases and analogous to eukaryotic mitochondrial P450 system.
These enzymes are involved in several important physiological processes like metabolism of
fatty acids and xenobiotics, catabolism of compounds used as carbon source and the
production of biologically active secondary metabolites such as antibiotics or antifungals
[67]. Bacillus and Mycobacteriam are two clinically significant bacterial genera due to their
deleterious roles in various human diseases [68-69]. Moreover, emergence of new drug
resistant strains from these genera has worsen the scenario nowadays and it needs new
alternatives of conventional treatment strategies. Bacterial cytochrome P450 can be a novel
therapeutic target as it coordinates many metabolically essential pathways [69-70]. In this
study, we selected cytochrome P450 from B. megaterium and M. tuberculosis as
representative model for docking analysis. Molecular docking was performed using
cytochrome P450 of B. megaterium (PDB ID: 1FAG; resolution=2.7 Å) and M. tuberculosis
(PDB ID: 3G5H; resolution=1.4 Å). The crystallographic structures of the protein with their
native ligands were downloaded from RCSB Protein Data Bank (PDB)
[https://www.rcsb.org/pdb]. The active site of the enzymes was defined using a radius of 5 Å
around natural ligand which was extracted from the PDB.
2.6. Synthesis of Schiff base

11
Schiff base (H2LOMe-pn) has been synthesized in our laboratory following the common
literature method (Scheme 1) [71]. Briefly, ligand was obtained by refluxing 2, 2-dimethyl-1,
3-propanediamine (0.0511 g, 0.5 mmol) with 3-methoxy-2-hydroxybenzaldehyde (0.152 g, 1
mmol) in (50 mL) in methanol at 70°C for 3 h. Vacuum evaporation of this yellow solution
gave the desired ligand in semisolid form. Ligand solution was evaporated to (15 mL) and the
concentrated solution used for complex preparation without further purification.
N, N-bis(3-methoxysalicylidene)-2, 2-dimethylpropane-1, 3diamine: Yield: (68%), elemental
analysis calcd (%) for C21H26N2O4: C 68.09, H 7.07, N 7.56; Found: C 68.07, H 7.03, N 7.52.
1
IR (KBr cm-1): ν=1652 (vs), 1252 (s), 3378 (s), H NMR (DMSO-d6, 300 MHz): δ (ppm):
3.3 (s, 3H1), 6.7-7.0 (m, 1H2, 1H3, 1H4), 8.5 (m, 1H5), 13.86 (1H6) (Scheme S3, Fig.
S2A),UV-Vis λmax (MeOH): 219 and 266 nm.

12
2.7. Synthesis of [Zn3(LOMe-pn)2(ƞ1-NCS)2] (1)
To the methanolic solution (15 mL) of zinc acetate dihydrate (0.2195 g, 1 mmol), (15 mL)
concentrated ligand (H2LOMe-pn) solution was added drop wise and the resulting solution was
stirred for 1 h. Then (10 mL) methanolic solution of KSCN (0.097 g, 1 mmol) was added to
it. The overall reaction mixture was refluxed for 25 min at 80 0C followed by addition of few
drops (1:1) mixture of (CH3CN+DMF). Further, stirring was continued for about 1 h. Finally,
colourless filtrate was kept for crystallization by slow evaporation at room temperature.
Single colourless crystals, suitable for X-ray diffraction were obtained after 7 days on slow
evaporation of the solution in open atmospheric condition. Crystals were isolated by filtration
and air dried. Yield: 0.290 g, Anal. Calc. for C44H48N6O8S2Zn3: C, 50.37; H, 4.61; N, 8.01.
Found: C, 50.40; H, 4.63; N, 8.04 %. IR (KBr cm-1) selected bands: ν(C꞊N), 1622 vs, ν(C-
OPhenolic) 1219 s, ν(SCN) 2086 vs, ν (Zn-N) 467 s, FT-Raman (cm-1) selected bands: ν(C꞊N),
1632 vs, ν(SCN) 2109 vs, UV-Vis λmax (DMF): 280 and 362 nm.
3. Results and discussion

13
3.1. Synthesis
The present study is based upon the employment of one N2O2O'2 donor compartmental Schiff
base which was synthesized by the condensation of 2, 2-dimethyl-1, 3-propanediamine with
ortho vanillin in MeOH at (1:2 M) ratio [71]. Complex (1) was derived from compartmental
ligand in moderate yield by taking the following procedure where (1:1:1 M) ratio of Zn(II)
acetate dihydrate, Schiff base and KSCN in minimum volume methanolic solution under
stirred and refluxing condition followed by few drops of (1:1) mixture (CH3CN+DMF)
(Scheme 1). Colourless block shaped crystals of complex (1) appeared at the junction of the
solutions after few days. Complex (1) possess trinuclear building blocks where two terminal
zinc metal centres (Zn1 & Zn2) presence in crystallographic asymmetric unit that are placed
at the inner N2O2 cavities. Further, [SCN-] ions function as η1 coordination mode (Scheme
S2, ESI) allowing distorted square pyramidal environment while terminal Zn(II) ion (Zn2) in
’
the outer O2O2 compartment fulfilled octa coordination with square antiprismatic geometry.
The above stereochemical occupancy of zinc metal ions are similar with other reported salen-
type compartmental Zn3-Schiff base complexes [72-76]. Structural skeleton of Schiff base
(Scheme S1, ESM) completely divulges its compartmental hexadentate nature since it
comprises two pockets (Scheme 2) and such pocketing nature is identical with other reported
salen-type compartmental ligands (Scheme S1A, ESM). Meanwhile, Table 2 further
highlighted few examples of Zn3-type Schiff base complexes basic structural motif where
most of the reported complexes are normal trinuclear Zn(II) without exception
{Zn(DMF)[Zn(L3)(H2O)(SCN)]}2 [73].Therefore, judicious literature survey received some
basic knowledge of current Schiff base compartment utilization (N2O2 vs O2O2) during
homo/heterometallic complex formations. Synthesized complex stoichiometry was confirmed
from different microanalytical results and characterized by FT-IR, Raman, UV-Vis, 1H NMR,
SEM-EDAX, PXRD, single X-ray crystal diffraction as well as fluorescence spectroscopy.

14
CH3
O
O
N
O
O
O2O2 Pocket 2
N
N2O2
Pocket 1
CH3
Scheme 3 Existing compartmental ligand showing N2O2 vs O2O2 pocket
Table 2 Structural motif of Zn3-type compartmental Schiff base complexes

15
Zn3-Schiff base complexes
[SCN-] ion bridging
Pockets (N2O2 vs Ref
O2O2) used
{Zn(DMF)[Zn(L3)(H2O)(SCN)]}2
ƞ1-NCS bonded only
yes
73
reported
Zn[Zn(L3)(µ2-HCOO)(DMF)]2.H2O
Zn[Zn(L3)( µ2-HCOO)]2
-
-
-
-
yes
73
Zn[Zn(L3)( µ2-OAC)]2
Zn[Zn(L3)( µ2-NO2)(EtOH)]2.2H2O
[Zn(Saldmen)3(OH)](ClO4)20.25H2O
-
-
yes
yes
75
74
[Zn3(H2L1)2(OAc)2]
[Zn3(H2L2)2(OAc)4]. EtOH. DMF
[Zn3(L)2(OAc)2]
-
yes
yes
76
[Zn3(LOMe-pn)2(ƞ1-NCS)2]
ƞ1-NCS coordinated
This
with terminal Zn
work
3.2. Spectral characterizations
Common spectroscopic tools (FT-IR, Raman, UV-Vis) have been used for Schiff base and
complex (1) characterizations purpose (Fig.S1, Fig.S2, Fig. S3, Fig. S4). The different FT-IR
stretching values are properly listed in Table 3. The characteristic imines (C=N) stretching
vibration of synthesized ligand was found nearly to be 1652 cm-1 [77]. The absence of the N-
H stretching band from trinuclear complex (at 3150 cm-1) conclusively confirmed the
condensation of all the primary amine groups [77]. FT-IR stretching value at 3378 cm-1 of
Schiff base is due to O-H stretching which is completely vanished from 1. In 1, FT-IR and
FT-Raman (C=N) stretching vibration bands are shifted to 1622 cm-1 (for IR) (Fig. S2) and
1632 cm-1 (for Raman) respectively (Fig.S3). These spectral data directly reflect the
coordination mode of the imine nitrogen atom to the zinc metal ion centre [78]. 1 displayed
strong bands at 2086 cm-1 (for FT-IR) and 2109 cm-1 (for FT-Raman) [79,80] which are

16
directly attributable to ν(SCN) binding mode (Fig.S2). Aliphatic C-H stretching resonance in
1 observed at 2932-2964 cm-1 (for FT-IR) and 2916 cm-1 (for FT-Raman) respectively. Also,
Ar-O stretching frequency observed at 1219 and 1221 cm-1 (for FT-IR and Raman) nearly
identical with previously reported salen-based ligands [81]. Herein the bridging fashion of
[SCN-] ions were compared thoroughly with previously reported pseudo-halide linked Zn(II)-
Schiff base complexes (Table S2 and Table S2A) to support the existence of [SCN-] spacers
in complex (1).
Table 3 FT-IR spectral data (cm-1) of Schiff base and complex (1)
Compounds ν(C=N) ν(C-OPhenolic
)
ν(O-H)/H2O
ν(N-H)
ν(Zn-N) ν(SCN-)
(H2LOMe-pn
)
1652
1622
1252
1219
3378
3150-3450
absence
-
-
467
2086 vs
1
-
-
3.3. UV-Vis spectra
The complexing behaviour of zinc metal ion on the absorption property of the compartmental
Schiff base ligand was explained using UV-Vis absorption spectra after measuring the same
experiment in DMF. Free Schiff base ligand in MeOH exhibit band near at 219 nm and 266
nm which can be attributed to π→π* and n→π* type of transitions within the Schiff base
ligand while for Zn3-nuclear metal complex in DMF exhibit ligand–based bathochromic
shifts UV-Vis spectra at 280 nm and 362 nm respectively (Fig. S4). This is mainly attributed
to L→M charge transfer π→π* or n→π* type transitions [78,82]. Fig.S4 confirmed the shape
and intensity of the absorption spectrum are typical of bis (iminophenolato) ligands [83].
Moreover, the UV-Vis absorption spectrum of Schiff base ligand and complex are almost
unchanged in presence of triethylamine base (TEA) but changes broadening peak by the
presence of HCl into the solution (Fig. S4A-S4B). This absorption behaviour is typically

17
observed for salen ligands when complexed with Zn [84,85]. Further, UV-Vis spectra divulge
the coordination mode of the ligand with zinc metal ions in 1 which are red shifted. Herein
the metal centric broad d-d absorption band was unexpected since d10 configuration zinc
metal ion is diamagnetic.
3.4. 1H NMR spectra
1H NMR spectroscopy is one of the essential tool to justify the Schiff base formation and its
effective binding ability with Zn(II) metal ion. At the same time, we have considered
1
standard ortho vanillin H NMR spectral data to explain the changes of reaction occur
between the aldehyde group (-CHO) in ortho vanillin and diamines during Schiff base
1
formation. The H NMR proton numbering scheme of synthesized Schiff base and Zn3-
1
nuclear metal complex are submitted in Scheme S3 and Fig. S2A-Fig.S2B. H NMR spectra
of ligand clarified that no broad peak was identified in the region δ 5.0-8.0 ppm that further
confirmed the absence of free -NH2 group function. Moreover, the formation of Schiff base
ligand was confirmed by the appearance of azomethine (-CH=N-) proton signal (5H) near δ
8.5 ppm [86]. Schiff base Ligand exhibit proton NMR signals specially for aromatic, OCH3
(1H) and phenolic OH (OH6) protons near at δ 6.7-7.0 ppm, δ 3.3-3.7 ppm and δ 13.86 ppm
respectively [87]. Now after comparison of the ligand chemical shift value with that of Zn3-
type metal complex, it confirms that phenolic proton (OH6) signals is totally vanished in the
synthesized Zn(II) complex suggesting coordination mode of the phenolic oxygen with Zn(II)
metal ion after deprotonating function of the Schiff base [88]. Apart from, the azomethine (-
CH=N-) proton (5H) undergoes a significant chemical shift further confirmed the
coordination motif of azomethine nitrogen to the zinc metal ion during formation of Zn3-
nuclear metal complex [86].

18
4. X-ray single crystal structure
4.1. Crystal structure of [Zn3(LOMe-pn)2(ƞ1-NCS)2] (1)
The single crystal of homo-trinuclear complex (1) has been grown in the mixture of solvent
CH3OH and few drops of (1:1) mixture of CH3CN+DMF in the ratio of metal ion (Zn2+):
ligand (H2LOMe-pn): co-ligand (KSCN) is 1:1:1. When the block shape colorless crystal was
subjected to the X-ray crystal diffraction, it reveals that the asymmetric unit contains two
identical discrete unit and each discrete unit contains three zinc metal ions which are
crystallographic independent, two deprotonated form of Schiff base [LOMe-pn]2- and two co-
ligands, [SCN-] ions. Thus, the formula of each discrete unit is [Zn3(LOMe-pn)2(ƞ1-NCS)2]. The
complex crystallizes in the monoclinic space group P121/c1 with Z=8 and further
crystallographic studies divulge that all the metal ions are full occupancy and the charge of
the complex is balanced by the co-ligand [SCN-] ions and the Schiff base [LOMe-pn]2-. The
ORTEP and the perspective view of asymmetric unit of complex (1) is shown in Fig.1 and
Fig.2. The selected some important bond lengths and bond angles are given in Table S1.
Fig.1. ORTEP diagram of complex (1) (30 % ellipsoid probability)

19
Fig.2. The perspective view of the asymmetric unit of 1 (Hydrogen atoms are omitted for
clarity)
From the design point of view, ligand (H2LOMe-pn) is having two tetradentate pockets and the
binding atoms of one pocket is O2N2 whereas in another pocket is 4O (Fig.3a). Additionally,
the ligand having two hydroxyl (-OH) groups which are deprotonated during complex
formation consequent to binding with the zinc metal ions. Further close inspection of the
crystal structure, it is found that each ligand (H2LOMe-pn) binds with the two zinc metal ions
and in each discrete unit the middle zinc metal ion having octa coordinated which is actually
the outer zinc metal ion (green circle in Fig. 3b), of each ligand (H2LOMe-pn) is symmetrically
shared by the these two ligands (H2LOMe-pn) leading to the linear homo-trinuclear zinc metal
cluster of formula [Zn3O8N4]2+.The octa coordinated stereochemical environment of zinc
metal ions (Zn2 & Zn5) is already identical with previously reported Zn(II)-Schiff base
complexes [72].To avoid steric interaction between –OMe groups at each end of (H2LOMe-pn
)
the position of the two ligands [LOMe-pn]2-in each discrete unit is almost perpendicular with
each other in order to attain maximum stability (Fig. 3b). Aside from, the coordination
activity afforded by the ligand [LOMe-pn]2-, two [SCN-] anions further attack on the linear
trimeric zinc metal cluster from at each end and offered a neutral linear trimeric zinc metal

20
cluster with the formula [Zn3O8N6] (Fig. 3c). The position of the each [SCN-] anion is
perpendicular with respect to the ligand [LOMe-pn]2- and looks like an insect trunk (Fig.3d).
Fig. 3. (a) The tetradentate pocket in the ligands (H2LOMe-pn), [Zn3O8N6] in complex (1), (b)
the position of the two ligands [LOMe-pn]2- unit (almost perpendicular to each other, green and
blue circle represent the presence of zinc metal ions.) (c) trimeric zinc metal cluster and (d)
the perpendicular position of the [SCN-] anion with respect to ligand (H2LOMe-pn
)
Moreover, further analysis of the crystal structure discloses the number of non-covalent
interaction (C-H····π, π ··π and hydrogen bonding interactions) (Fig. S7A) exist between the
two discrete part in the asymmetric unit (Fig. 4).

21
Fig.4. The non-covalent interaction in complex (1)
The binding fashion of each ligand [LOMe-pn]2- to the zinc metal ions in each discrete unit are
same and Fig.S6A represents the binding platform of the coordinating atoms and their
patterns are η1-oxygen, η2-oxygen and η1-nitrogen of the ligand [LOMe-pn]2-. The two [SCN-]
anions in each discrete unit acts as a monodentate fashion (η1-nitrogen) and binds to the at
each end on the metal center in the trimeric metal core. This bridging modes of [SCN-] ion as
well as bond lengths (Zn-NCS) (~1.981–2.091 Å) are similar to the previously reported
Zn(II)-Schiff base complexes (Table S3). Meanwhile using compartmental N/O-donor Schiff
base, we have successfully synthesized only homo trimetallic complex (1) while major
preferential encapsulation of metals by the reference ligand leads to heterometallic complex
formations (Table S6). To the best of our knowledge this is the first homo trimetallic system
where two compartments are solely occupied by zinc metal ions with η1-NCS coordination
mode of terminal zinc only.

22
The structural environment for five coordination number zinc metal centres (Zn1 and Zn3)
were calculated from Addison parameter Tau (ґ), (ґ =׀β-α׀/60° where β, α are the two largest
angles around zinc metal atom; ґ =0 for a perfect square pyramidal and 1 for a perfect
trigonal bipyramidal geometry [89]. Thus, coordination number of metals Zn1, Zn2 and Zn3
are five, eight and five respectively and these coordination numbers are fulfilled by 2O, 3N
for Zn1, 8O for Zn2 and 2O, 3N for Zn3, afforded distorted square pyramidal, square
antiprismatic and distorted square pyramidal respectively (Fig. S7C). The Addison tau (τ)
parameters are 0.611, 0.150 for Zn1 and Zn3 respectively (ideal value of tau for square
pyramidal geometry is 0). Similar geometry around the metal centers are shown by metals
(Zn4, Zn5 and Zn6) in the other discrete unit (Fig. S7B). As a result, it’s generated a homo
trimetallic system. The average distances between two Zn atoms is 3.531Å {Zn1-Zn2 =
3.525, Zn2-Zn3 = 3.530, Zn4-Zn5 = 3.552, Zn5-Zn6 = 3.520} and the average angle between
them is 106.33 ° {Zn1-O11-Zn21 = 105.4(3) °, Zn1-O10-Zn2 = 105.1(2)°, Zn3-O14-Zn2 =
106.7(3)°, Zn3-O15-Zn2 = 107.1(3)°, Zn6-O2-Zn = 106.1(3)°, Zn6-O3-Zn5 = 105.9(3)°,
Zn4-O6-Zn5 = 107(3)°, Zn4-O7-Zn5 = 107.5(3)°}. In fact, the Zn-Zn bond distances (Å) are
comparable to other trinuclear zinc metal complexes (Table S4).
4.2. SEM-EDAX
The chemical composition of the trinuclear complex (1) was analysed with the help of SEM-
EDAX profile analysis. Further, the chemical composition of the complex was confirmed
from EDAX profile. The weight percentage (%) contribution of the elements is shown in
Table S5 and their EDAX profile in Fig.S5A. The calculated and EDAX values of essential
elements in Zn3 complex are nearly good agreement. Preferably EDAX profile contained
only predictable elements and no impurity of other elements are present. Therefore, the
empirical formula of 1 is formulated as C44H48N6O8S2Zn3. Interestingly, the EDAX profile of
trinuclear complex reflects the highest peak of C followed by O, N, Zn which further agreed

23
the empirical formula. Besides, the important structural morphological features are supported
by SEM (scanning electron microscope) analysis. SEM images characterized the size and
morphological structure of the trinuclear zinc metal complex. Herein, micrograph of SEM
(Fig.S5B) clearly explores that the morphology of the complex (1) is plate shape up to 2 µm.
4.3. X-ray powder diffraction
Powder X-ray diffraction patterns for complex (1) were recorded at room temperature. The
PXRD patterns were recorded experimentally by scanning the compound in the range (2θ=40-
500). According to Fig.S6 the well-defined sharp PXRD peaks is due to crystalline nature of
the complex. The experimental PXRD patterns (Fig.S6) of the bulk materials of the complex
are similar with the patterns simulated from single X-ray crystal diffraction data (CIF for 1)
which is obtained from CCDC Mercury software consisting that single crystals and bulk
material are the same. The results of PXRD analysis can provide the additional confirmation
of the phase purity of each bulk samples of the complex.
5. DFT analyses
5.1. Hirshfeld Surface
The non-covalent supramolecular interactions in complex (1) were explained on the basis of
HS and 2D fingerprint analysis where Fig.5 provides the details of dnorm, shape index, curved
index, fragment patch and 2D finger print plots for complex (1). In 1, the total volume of the
surface was 2323.70 Å3, globularity is 0.635 and asphericity 0.285. 2D finger plots provide
information on various forms of interactions between these complexes and other atoms of the
surround molecules. The close inspection of Table 4 reveals that for complex (1), the major
contribution to the crystal packing is interactions H···H (56.8%) followed by 10% of
interaction is between the C-H and H-C (8.8%), 6.6% between the nearby hydrogen atom and
sulfur atoms, and 0.5% between oxygen and hydrogen atoms. Remaining contacts which are
less than 0.5% are negligible.

24
Table 4 Different type of interactions on HS in complex (1)
SL. No.
Type of interactions
C···C (i.e. π··· π)
C···H (i.e. C-H··· π)
S···H (i.e. C-S··· H)
N···H
Contribution (%)
1.
2.
3.
4.
5.
6.
7.
0.6
10
6.6
1.9
0.5
8.8
56.8
C-H··· O
H···C
H···H

25
Fig. 5. Hirshfeld surfaces analysis for complex (1): dnorm, Shape index, curvedness
and different 2D fingerprint plots
5.2. Energy and HOMO-LUMO analysis
Complex (1) was optimized in DMSO using a PCM model for including solvent effect at
M06/6-31G* level of theory. Fig. 6 portrays the ground state geometry of discrete unit of
complex (1). Theoretically calculated structure is in accordance with the crystal
structures where it depicts it is a trinuclear homometallic Zn(II) complex. In this structure
peripherals Zn atoms are pentacoordinate while central Zn-atoms is eight-
coordinated. Also, both the [SCN-] co-ligands and nitrogen atoms of [LOMe-pn]2- ligands are

26
attached with the peripheral Zn-atoms where central zinc atom is attached
with nearby oxygen atoms. The distance between two Zn-atoms are 3.23 Å which is
almost similar to crystal structure data (3.51 Å). Interesting outcome has been drawn on the
basis of mapping of the frontier molecular orbitals (FMOs) for complex (1). HOMO (highest
occupied molecular orbital) value dictates the electron donating ability of (1) and LUMO
(lowest unoccupied molecular orbital) indicates the electron accepting nature of the molecule.
It is also well known that information of the delocalization of the π electron cloud is
necessary to derive the non-linear optical properties of π conjugated complexes [90]. From
the close inspection of the HOMO-LUMO density plot, HOMO of 1 is largely contributed by
the Schiff base ligand (H2LOMe-pn) and its deprotonated hydroxyl group which coordinated
with the central Zn-atom of the one discrete unit of 1. Whereas in LUMO, the electron
density is mainly distributed over both the ligand (H2LOMe-pn) and on one co-ligand [SCN-].
Bridging is found to be strong and stable as it does not contribute much to HOMO or LUMO
in the bridging process and affects the stability of the complex.
Fig. 6. Ground state geometry of a discrete unit of 1 (black colour balls represent carbon
atoms)

27
Investigation of FMOs reveals that HOMO has energy of -5.63 eV and LUMO has -1.56 eV
and HOMO LUMO density plot (Fig.7) was used for the probing of FMOs of the complex
(1). HOMO-LUMO energy gap (∆ꢥ = ꢥꢦꢧꢨꢩ − ꢥꢪꢩꢨꢩ) is 4.07 eV which makes the
complex stable and can be associated with the band gap of the compound. Theoretical UV-
Vis spectra were also calculated to further confirm the semiconducting properties of 1 within
200-600 nm region of the wavelength (Fig.S9). The theoretical band gap here is within the
range of 3-6 ev described for the wide bandgap semiconductors [91, 92]. From this point of
view complex (1) possess the semiconducting property also since its bandgap is around ~4.07
eV (wide-bandgap semiconductor), its use in different devices will allow devices to work at
much higher voltages, frequencies and temperatures than traditional semiconductor-based
products. Recently Zn(II)-based 1-D CP observed similar theoretical bandgap so that CP can behave
as semiconducting property [92]. Complex (1) can be well used next-generation devices for
general semiconductor based on these wide-bandgap.