Spectral, structural, theoretical and docking studies of a Mn(II) complex with an n4-donor ligand

Article abstract of DOI:10.3184/174751918X15422215897056

The complex [Mn(EMMP)(OAc)₂]·3H₂O, [EMMP = N,N’-(ethane-1,2-diyl)bis(1-phenyl-1-{pyridin-2-yl}methanimine] has been prepared and has a distorted square-faced bicapped trigonal prismatic geometry. In the crystal network of the complex

Full text of DOI:10.3184/174751918X15422215897056

JOURNAL OF CHEMICAL RESEARCH 2018
VOL. 42 DECEMBER, 623–627
RESEARCH PAPER 623
Spectral, structural, theoretical and docking studies of a Mn(II) complex with
an N -donor ligand
4
a
a
b
a
Mohammad Hakimi *, Behjat Tarani , Zahra Mardani , Keyvan Moeini , Monika Kučeráková and
c
Michal Dušek
a
ChemistryDepartment, Payame Noor University, 19395-4697 Tehran, I.R. Iran
Inorganic Chemistry Department, Faculty of Chemistry, Urmia University, 57561-51818 Urmia, I.R. Iran
Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
b
c
The complex [Mn(EMMP)(OAc) ]·3H O, [EMMP = N,N’-(ethane-1,2-diyl)bis(1-phenyl-1-{pyridin-2-yl}methanimine] has been prepared and
2
2
has a distorted square-faced bicapped trigonal prismatic geometry. In the crystal network of the complex, the water molecules form
4
stronger hydrogen bonds than the complex molecules and participate in the formation of R (8) hydrogen bond motifs. The ability of the
4
complex and its ligand to interact with the biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II)
has been investigated by docking calculations and compared with that of doxorubicin.
Keywords: manganese complex, density functional theory studies, docking studies, crystal structure
Schiff bases and their complexes have played an important
role in the development of coordination chemistry, biological
and material science. They have a broad range of biological
DNA gyrase; histone deacetylase (HDAC7); recombinant
human albumin (rHA); ribonucleotide reductases (RNR);
thioredoxin reductase (TrxR), thymidylate synthase (TS); and
1–3
4
14,15
activities and have been used as metallo-biomolecules
topoisomerase II (Top II).
These proteins are used in this
5
–7
and catalysts. Similarly, pyridine base ligands have also
been used in many biochemical studies designed to develop
project either due to their reported roles in cancer growth or
as transport agents that affect drug pharmacokinetic properties
(e.g. rHA). In addition, DNA gyrase was included to study
the possibility of the compounds also acting as antimalarial
8
,9
molecular systems of biological and medicinal importance.
The coordination chemistry of manganese has long been a
10
16
subject of considerable interest in inorganic biochemistry
agents.
and the biological importance, diverse catalytic and magnetic
properties of manganese compounds have been broadly
Results and discussion
11
explored. Manganese(II) complexes are used successfully as
EMMP was prepared by the condensation of 1,2-diaminoethane
with 2-benzoyl pyridine. The reaction between manganese(II)
acetate with EMMP provided complex 1. This compound is air-
stable and soluble in DMSO.
12
catalysts of many oxidation reactions of organic compounds.
Manganese–salen complexes show considerable promise in
superoxide dismutase (SOD) and catalase-like activity which
could be a perspective for the creation of new medicines with
13
Spectral studies
wide applications. In order to extend the chemistry of this
class of compounds, in this work we present the preparation,
characterisation (elemental analysis and FTIR spectroscopy)
and crystal structure of a manganese(II) complex, [Mn(EMMP)
In the IR spectra of EMMP and 1, the relatively weak absorption
–1
bands at above and under 3000 cm are due to the C–H modes
of the aromatic rings (phenyl and benzene) and aliphatic
moieties (ethane moiety and acetate ligand of 1), respectively. In
the FTIR spectra of the imine and pyridine units of the ligand,
(
OAc) ]·3H O (1), [EMMP = N,N’-(ethane-1,2-diyl)bis(1-
2 2
phenyl-1-{pyridin-2-yl}methanimine] (Scheme 1).
−1 17
Binding of the manganese(II) ion to the EMMP ligand might
enhance its biological activity. For this reason, we performed
docking calculations to investigate interaction of 1 and its ligand
with nine protein targets: BRAF kinase; cathepsin B (CatB);
ν (C=N) values are in the region of 1550−1650 cm . These
−1
peaks are shifted by 29 and 42 cm to lower frequencies after
coordination to the manganese, confirming the N -donation of
the ligand.
4
1
0
11
9
12
1
3
8
4
7
6
N
N
4
3
5
3
N
1
2
N
2
1
Scheme 1 Structure of the EMMP ligand.
*
Correspondent. E-mail: mohakimi@yahoo.com

624 JOURNAL OF CHEMICAL RESEARCH 2018
The presence of the water molecules in 1 affects the IR
manganese atom is coordinated by four nitrogen atoms of one
EMMP and four oxygen atoms of two bidentate acetate-ligands
in the form of a distorted square-faced bicapped trigonal prism
–1
spectrum in three regions: 3300–3400 cm for asymmetric
–1
and symmetric OH stretches; 1640 cm for H O bending; and
2
–1
24
2
00–600 cm for ‘librational modes’. These modes are due
(MnN O ) (Fig. 2). Study of the CSD database revealed that
4
4
to rotational oscillations of the water molecules restricted by
interactions with neighbouring atoms and they are classified
25–31
this environment is rare and there are only eight examples
for such a geometry around the manganese in which all nitrogen
atoms belong to one tetradenate ligand. Among the four Mn–N
bonds, the bond lengths corresponding to the pyridine nitrogen
atoms are slightly (0.084 Å) longer than those of the imine. The
bond length average of all Mn–N (2.359 Å) is comparable with
the Mn–O (2.349 Å).
into three types (wagging [ρ ], twisting [ρ] and rocking [ρ ])
w
t
r
1
3,14
depending upon the direction of the principal axis of rotation.
In the FTIR spectrum of 1, three bands at 1560, 1436 and 667
–1
cm were assigned to the ν (COO), ν (COO) and δ (OCO)
as
s
18
respectively, confirming the presence of the acetate unit in
this complex. The differences between asymmetric (ν ) and
imine
py
as
The EMMP ligand acts as a tetradentate N2 N -donor,
2
symmetric (ν ) stretching of the acetate group (∆) can reveal its
s
forming three five-membered chelate rings. The central non-
coordination type. Compared with the Δ value for the acetate
3
planar chelate ring contains sp hybridised carbon atoms (root
salt, monodentate complexes exhibit much larger ∆ values (164
mean square deviation 0.255 Å for C16) while the two side
–1
cm ) while in bidentate complexes these values are significantly
2
rings with sp hybridised carbon atoms are almost planar (root
19,20
–1
lower.
The ∆ value for 1 is 124 cm which corresponds to
mean square deviations: 0.012 Å for C1; 0.063 Å for N4). The
two pyridine rings lie on a plane formed by four coordinated
nitrogen atoms of the EMMP while the benzene rings are
rotated by 72.71° (average angle).
the bidentate acetate ligand.
1
13
The H NMR and C NMR spectra of EMMP revealed
aromatic (7.5−9.0 ppm and 120−200 ppm, respectively) and
aliphatic (5.19 ppm and 85.6 ppm, respectively) moieties of
this structure. Among the aromatic protons, the nearest one to
the nitrogen atom of the pyridine ring is observed at the lowest
magnetic field.
In the crystal structure of 1, there are weak C–H···O and
strong O–H···O interactions, the latter existing between water
molecules as well as between water and the acetate ligand. In
addition to these hydrogen bonds, there are C–H···π interactions.
The O–H···O hydrogen bonds participate in the formation of
Structural studies
21, 22
23
4
Ortep
and Diamond plots of the investigated structures
one R (8) hydrogen bond motif (four acceptors and four donors
4
32,33
are shown in Figs 1–3. In the crystal structure of 1 (Fig. 1), the
with degree of 8)
between four water molecules (Fig. 3).
Fig. 1 The Ortep diagram of the crystal structure of complex 1. The
displacement ellipsoids are drawn at the 30% probability level.
Fig. 2 The distorted square-face bicapped trigonal prismatic geometry
around the manganese atom of 1.
4
Fig. 3 Packing of 1, showing the hydrogen bonds and R (8) hydrogen bond motifs. Only the hydrogen atoms involved in hydrogen bonding are shown.
4
Each MnN O is shown as a distorted square-face bicapped trigonal prism.
4
4

JOURNAL OF CHEMICAL RESEARCH 2018 625
Theoretical studies
interferes with the growth and spread of cancer cells in the
body ).
Analysis of Table 1 shows that all studied structures can be
3
8
For prediction of the molecular structure of the EMMP in the
gas phase a density functional theory calculation was performed.
In the optimised structure of the EMMP (Fig. 4), the nitrogen
atom N1 has a different position compared with its position in
considered as biologically active compounds (Figs 5 and 6). The
best predicted targets for 1 and EMMP is TrxR. Based on the
calculated fitness values, the ligand can interact with the CatB,
HDAC7, rHA and RNR proteins better than the complex; the
binding ability for other proteins are comparable. The data of
Table 1 revealed that the ligand and complex 1 both have higher
fitness values than doxorubicin, therefore we suggest that the
anticancer activities of these compounds should be studied.
1, because the (C H ) C–N moiety is rotated by ~ 180° around
6 5 2
the C–N bond. This illustrates the ability of this ligand to act as
helical ligand, which has been observed in reaction of EMMP
3
4
35
36
with copper nickel and mercury atoms.
Docking studies
For predicting and comparing the biological activity of complex
1
and its ligand, interactions of these compounds with nine
Conclusion
macromolecule receptors using the docking software, Genetic
In this work, a new complex [Mn(EMMP)(OAc) ]·3H O,
37
2
2
Optimisation for Ligand Docking (Gold), were studied. The
Gold docking results are reported in terms of the values of
fitness, where ‘fitness’ expresses the ability of the investigated
compound to take part in the docking interaction. Table 1
shows the best binding results out of the 10 favourable ones
predicted by Gold and compares the obtained scores with those
of the anticancer drug doxorubicin (a cancer medication that
[
EMMP = N,N’-(ethane-1,2-diyl)bis(1-phenyl-1-{pyridin-2-
yl}methanimine] (1) has been synthesised and spectral and
structural properties of both 1 and EMMP were investigated. In
the structure of 1, the manganese atom has an unusual distorted
square-faced bicapped trigonal prismatic coordination formed
by one N -donor EMMP ligand and two O -donor acetato-
16
4
2
ligands. In the crystal packing of 1, there are strong O–H···O,
weak C–H···O and C–H···π interactions; the O–H···O hydrogen
bonds participate in the formation of an R (8) hydrogen bond
4
4
motif. Docking studies on the complex and its ligand revealed
that these compounds might be biologically active by interacting
with nine biomacromolecules (BRAF kinase, CatB, DNA
gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II). The best
predicted targets for the ligand and complex is TrxR. Docking
calculations revealed that the fitness values of the ligand and
complex are higher than that of doxorubicin, thus we suggest
that studying anticancer activities of these compounds could
bring interesting results.
Experimental
All starting chemicals and solvents were reagent or analytical grade
and used as received. The infrared spectra of KBr pellets in the
–1
Fig. 4 Optimised structure of EMMP.
range of 400–4000 cm were recorded with a FTIR 8400-Shimadzu
Table 1 The calculated fitness values for the EPPM ligand and complex 1 along with doxorubicin
BRAF-kinase
CatB
DNA-gyrase
HDAC7
rHA
RNR
TrxR
TS
Top II
EMMP
60.95
61.67
54.21
47.29
34.74
25.95
66.70
68.04
52.97
66.75
62.65
50.73
54.98
51.95
50.10
58.90
45.04
49.18
72.51
70.56
66.70
58.24
57.92
53.34
64.52
67.06
59.05
Complex 1
Doxorubicin
Fig. 5 Docking study results, showing the interaction between the EMMP
ligand and BRAF kinase protein.
Fig. 6 Docking study results, showing the interaction between complex
1 and BRAF kinase protein.

626 JOURNAL OF CHEMICAL RESEARCH 2018
spectrometer. The carbon, hydrogen and nitrogen contents were
determined in a Thermo Finnigan Flash Elemental Analyzer 1112 EA.
The melting points were determined with a Barnsted Electrothermal
Table 2 Crystal data and structure refinement for complex 1
Empirical formula
C H MnN O
617.6
0.06 × 0.06 × 0.03
30 34 4 7
−1
Formula weight (g mol )
1
13
9
200 electrically heated apparatus. H and C NMR spectra were
3
Crystal size (mm )
recorded on a Inova 500 instrument operating at 250 and 63 MHz,
respectively; chemical shifts are given in ppm, with values in reference
to an internal standard of TMS.
Temperature (K)
Crystal system
Space group
Unit cell dimensions
A (Å)
95
Monoclinic
C2/c
Synthesis of N,N’-(ethane-1,2-diyl)bis(1-phenyl-1-{pyridin-2-yl}
methanimine, EMMP; general procedure
24.4771(6)
9
The EMMP ligand was prepared as described in the literature
B (Å)
8.0621(2)
with some modifications. The spectral data of this ligand were not
previously reported and are presented here. 1,2-Diaminoethane
C (Å)
30.5018(8)
Β (deg)
Volume (Å )
97.437(2)
5968.5(3)
(
1 mmol, 0.06 g) dissolved in methanol (5 mL), was added dropwise
with stirring to 0.37 g (2 mmol) of 2-benzoylpyridine in methanol
20 mL) and the resulting solution was stirred for 1 h at room
3
(
Z
8
−
3
temperature and then was refluxed for 6 h. The redundant precursors
and solvent were removed at the rotary evaporator to form the yellow
Calculated density (g cm )
Absorption coefficient (mm )
F(000), e
1.375
4.04
2584
−1
ar
hygroscopic ligand; yield 0.33 g (86%); IR (KBr disk): 3055 (ν CH) ,
py
2
960 (νas CH ), 2926 (ν CH ), 1665 (ν C=N), 1630 (ν C=N) , 1566
2
s
2
θ range for data collection (deg)
3.6–74.3
ar
and 1584 (ν C=C) , 1449 (δ CH ), 1395 (δ CH ), 1045 (ν CN), 750
as
2
s
2
–1
1
−30 ≤ h ≤ 17 −9 ≤ k ≤ 10,
and 698 (γ py) cm ; H NMR (250 MHz, DMSO-d ): 5.19 (s, 4H,
h, k, l ranges
6
−
36 ≤ l ≤ 37
13
9
11
2
3
C H ), 7.47 (t, 3H, C H−C H), 7.57 (t, 1H, C H), 7.87 (t, 1H, C H),
2
Reflections collected/independent/Rint
17030/5947/0.028
4
8
12
1
13
8
(
.01 (d, 1H, C H), 8.05 (d, 2H, C H, C H), 8.70 (d, 1H, C H); C NMR
63 MHz, DMSO-d ): 85.6 (C ), 124.6−193.8 (C −C ). Anal. calcd
13
1
12
Data/ref. parameters
Goodness-of-fit on F
5947/397
1.75
6
2
for C H N (390.49): C, 79.97; H, 5.68; N, 14.35; found: C, 79.89; H,
2
6
22
4
6
.02; N, 14.17%.
R1/wR2 (I ³ 2 σ(I))
R1/wR2 (all data)
Largest diff. peak/hole (e Å )
0.0336/0.0392
0.0423/0.0404
0.55/−0.27
Synthesis of N,N’-(ethane-1,2-diyl)bis(1-phenyl-1-{pyridin-2-yl}
methanimine]bisacetatomanganese(II) trihydrate, [Mn(EMMP)
–
3
(
OAc) ]·3H O; general procedure
2 2
Mn(OAc) ·H O (1) (1 mmol, 0.17 g) was dissolved in methanol (5 mL)
Table 3 Selected bond lengths and angles for complex 1 with estimated
2
2
standard deviations in parentheses
and added with stirring to a methanol solution (10 mL) of EMMP
1 mmol, 0.39 g). The reaction mixture was stirred at 60 °C for 4 h.
(
Bond length (Å)
Mn1–N1
Angle (deg)
N1−Mn1−N2
N1−Mn1−N3
N1−Mn1−N4
N1−Mn1−O1
N1−Mn1−O4
O1−Mn1−O3
O1−Mn1−O4
O2−Mn1−O4
The solution was left for slow evaporation at room temperature. The
resultant precipitate was filtered off, washed with methanol and
recrystallised from acetonitrile. After five days, yellow-brown crystals
of complex 1 were formed and collected by filtration. Yield 0.49 g
2.370(1)
2.390(1)
2.353(2)
2.323(2)
2.387(1)
2.425(2)
2.305(1)
2.278(1)
154.51(5)
138.10(5)
68.34(5)
94.72(5)
87.41(5)
Mn1–N2
Mn1–N3
Mn1–N4
(
3
1
79%); m.p. 145 °C; IR (KBr disk): 3393 (ν O−H), 3296 (ν O−H),
as
s
ar
Mn1–O1
059 (ν CH) , 2957 (ν CH and/or CH ), 2918 (ν CH and/or CH ),
as 2 3 s 2 3
py ar
640 (δ H O), 1636 (ν C=N), 1588 (ν C=N) , 1577 (νC=C) , 1560 (ν
Mn1–O2
Mn1–O3
Mn1–O4
55.81(5)
163.45(5)
55.58(5)
2
as
OAc
OAc
COO) , 1436 (ν COO ), 1420 (δ CH and/or CH ), 1356 (δ CH
s
as
2
3
s
2
Oac
and/or CH ), 1049 (ν CN), 750 and 708 (γ py), 667 (δ OCO) , ρ = 629
3
r
–1
(
H O), ρ = 548 (H O) cm . Anal. calcd for C H MnN O (617.56):
2 w 2 30 34 4 7
C, 58.35; H, 5.55; N, 9.07; found: C, 58.54; H, 5.42; N, 8.97%.
Computational details
39
tube, mirrors-collimated CuKα radiation (λ = 1.54184 Å), and
42
The structure of ligand was optimised with the Gaussian 09 software
CCD detector Atlas S2. The data was processed with CrysAlis.
The structure was solved with the charge flipping algorithm by
and calculated for an isolated molecule using density functional
4
0
theory at the B3LYP/6-31+G level of theory.
43
2
Superflip and refined by full-matrix least-squares on F using
Docking details
4
4
program Jana2006. Anisotropic displacement parameters were used
for all non-hydrogen atoms. Hydrogen atoms on carbon were kept at
geometrically expected positions and refined as riding atoms with
Uiso = 1.2 Ueq of the corresponding parent atom. Positions of hydrogen
atoms on water were refined using a restraint that all O–H bond lengths
as well as H–O–H angles are the same with s.u. of the constraint
The pdb files 4r5y, 3ai8, 5cdn, 3c0z, 2bx8, 1peo, 3qfa, 1njb and 4gfh
for the nine receptors, BRAF kinase, CatB, DNA gyrase, HDAC7,
rHA, RNR, TrxR, TS and Top II, respectively, used in this research
41
were obtained from the Protein Data Bank. The obtained full version
37
of GOLD 5.5 was used for the docking. The Hermes visualiser in
the GOLD Suite was used to further prepare the structures and the
receptors for docking. The optimised structure of EMMP and the cif
file of 1 were used for docking studies. The region of interest used for
Gold docking was defined as all the protein residues within the 6 Å
of the reference ligand ‘A’ that accompanied the downloaded protein.
All free water molecules in the structure of the proteins were deleted
before docking. Default values of all other parameters were used and
the complexes were submitted to 10 genetic algorithm runs using the
GOLDScore fitness function.
0.001 for bond lengths and 0.01 for bond angles. For hydrogen angles
of water, Uiso was kept as 1.2 Ueq of the corresponding parent oxygen.
Crystal data and details of the data collection and refinement are given
in Table 2. Selected bond lengths and angles of the compound are listed
in Table 3 and hydrogen bond geometries in Table 4.
Electronic Supplementary Information
CCDC 1857320 for complex 1 contains the supplementary
crystallographic data for this paper. These data can be obtained
free of charge from The Cambridge Crystallographic Data
Centre via www.ccdc.cam.ac.uk/data_request/cif.
X-Ray structure determination
A suitable crystal of 1 was chosen and its X-ray analysis was performed
at 95 K using a SuperNova diffractometer with a micro-focus sealed

JOURNAL OF CHEMICAL RESEARCH 2018 627
Table 4 Hydrogen bond dimensions (Å and deg) in complex 1
D–H···A
d(D–H)
0.960
0.960
0.960
0.960
0.960
0.98
0.98
0.98
0.97(2)
0.98(2)
0.98(2)
d(H···A)
2.558
2.534
2.682
2.524
2.600
1.83
1.87
1.76
1.84(2)
1.88(2)
1.94(2)
d(D···A)
3.339(2)
3.437(3)
3.539(2)
3.282(3)
3.480(2)
2.789(2)
2.796(2)
2.728(2)
2.807(2)
2.835(2)
2.910(2)
<(DHA)
138.6
156.7
148.9
135.9
152.6
169
158
168
170(2)
166(2)
176(2)
Symmetry code of A
0.5 − x, −0.5 + y, 0.5 − z
−x, −y, −z
C(14)–H(1c14)···O(1)
C(9)–H(1c9)···O(6)
C(11)–H(1c11)···O(6)
C(15)–H(1c15)···O(5)
C(13)–H(1c13)···O(7)
O(6)–H(2o6)···O(5)
O(6)–H(1o6)···O(2)
O(5)–H(2o5)···O(3)
O(5)–H(1o5)···O(6)
O(7)–H(1o7)···O(4)
O(7)–H(2o7)···O(1)
x, y, z
0.5 − x, 0.5 – y, −z
−0.5 + x, 0.5 + y, z
x, y, z
x, y, z
x, y, z
0.5 − x, 0.5 – y, −z
0.5 + x, 0.5 + y, z
0.5 + x, −0.5 + y, z
Acknowledgements
17 M. Hakimi, Z. Mardani, K. Moeini, E. Schuh and F. Mohr, Z. Naturforsch.,
013, 68b, 267.
F. Marandi, K. Moeini and A. Rudbari Hadi, Z. Naturforsch., 2016, 71b, 959.
19 K. Nakamoto (ed.), Infrared and raman spectra of inorganic and coordination
compounds, edn 6. John Wiley, Hoboken, 2009, p. 232.
2
We are grateful to Payame Noor University and Urmia
University of Iran for financial support. The crystallographic
part of this work was supported by the project 18-1054S of the
Czech Science Foundation using instruments of the ASTRA
Laboratory established within the operation programme Prague
Competitiveness (project CZ.2.16/3.1.00/24510).
18
20
M. Hakimi, K. Moeini, Z. Mardani and F. Khorrami, J. Korean Chem. Soc.,
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2
21
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G. Bergerhof, M. Berndt and K. Brandenburg, J. Res. Natl Stand. Technol.,
Received 11 August 2018; accepted 8 November 2018
Paper 1805578
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Published online: 28 November 2018
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