Cp and indenyl ruthenium complexes containing dithione derivatives: Synthesis, antibacterial and antifungal study

Article abstract of DOI:10.1016/j.jorganchem.2020.121418

A series of cationic complexes [(Cp/Ind)Ru(к²_(SS)-L)(PPh₃)]PF₆ (1–6) are obtained by the reaction of [CpRu(PPh₃)₂Cl] or [(Ind)Ru(PPh₃)₂Cl] (Cp = η⁵-C₅H₅, Ind = η⁵-C₉H₇) with respective dithione derivatives 1,2-di(piperidin-1-yl)ethane-1,2-dithione (L1), 1,2-dimorpholinoethane-1,2-dithione (L2) and 1,2-dithiomorpholinoethane-1,2-dithione (L3). All the compounds are characterized using spectroscopic techniques. The molecular structures of complexes 1, 2 and 4 are established by single-crystal X-ray diffraction studies. Antimicrobial studies were tested against three strains of bacterial microorganisms Staphylococcus aureus (gram + ve), Bacillus subtilis (gram + ve), Klebsiella pneumoniae (gram -ve) and one strain of fungal microorganism Candida albicans.

Full text of DOI:10.1016/j.jorganchem.2020.121418

Journal Pre-proof
Cp and indenyl ruthenium complexes containing dithione derivatives: Synthesis,
antibacterial and antifungal study
Lincoln Dkhar, Merrily Sawkmie, Agustine Lamin Ka-Ot, Santa Ram Joshi, Werner
Kaminsky, Mohan Rao Kollipara
PII:
S0022-328X(20)30320-X
DOI:
https://doi.org/10.1016/j.jorganchem.2020.121418
JOM 121418
Reference:
To appear in: Journal of Organometallic Chemistry
Received Date: 29 March 2020
Revised Date: 22 June 2020
Accepted Date: 24 June 2020
Please cite this article as: L. Dkhar, M. Sawkmie, A.L. Ka-Ot, S.R. Joshi, W. Kaminsky, M.R. Kollipara,
Cp and indenyl ruthenium complexes containing dithione derivatives: Synthesis, antibacterial
and antifungal study, Journal of Organometallic Chemistry (2020), doi: https://doi.org/10.1016/
j.jorganchem.2020.121418.
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Cp and indenyl ruthenium complexes containing dithione derivatives: Synthesis,
antibacterial and antifungal study
a
a
b
b
Lincoln Dkhar , Merrily Sawkmie , Agustine Lamin Ka-Ot , Santa Ram Joshi , Werner
c
a
Kaminsky , Mohan Rao Kollipara *
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a
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Centre for Advanced Studies in Chemistry, North-Eastern Hill University, Shillong 793 022,
India.
b
Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong 793
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1
022, India.
c
Department of Chemistry, University of Washington, Seattle, WA 98195, USA
Email: mohanrao59@gmail.com
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Graphical abstract
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Abstract
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A series of cationic complexes [(Cp/Ind)Ru(к
-L)(PPh )]PF (1-6) are obtained by the
3 6
(
SS)
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reaction of [CpRu(PPh ) Cl] or [(Ind)Ru(PPh ) Cl] (Cp= η -C H , Ind=η -C H ) with respective
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3 2
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dithione derivatives 1,2-di(piperidin-1-yl)ethane-1,2-dithione (L1), 1,2-dimorpholinoethane-1,2-
dithione (L2) and 1,2-dithiomorpholinoethane-1,2-dithione (L3). All the compounds are
characterized using spectroscopic techniques. The molecular structures of complexes 1, 2 and 4
are established by single-crystal X-ray diffraction studies. Antimicrobial studies were tested
against three strains of bacterial microorganisms Staphylococcus aureus (gram +ve), Bacillus
subtilis (gram +ve), Klebsiella pneumoniae (gram -ve) and one strain of fungal microorganism
Candida albicans.
______________________________________________________________________________
Keywords: indenyl, ruthenium, piperidine, morpholine, thiomorpholine, antifungal
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1. Introduction
Bacterial infections have remained the largest problem to humans due to their increasing
resistance towards multiple antibacterial drugs (multiple drug resistance) and even to new
antibacterial agents that the bacteria have never encountered before. Thus, the search for a new
and efficient antibacterial agent that can counteract this problem has become the emerging trend
in pharmaceutical and biological fields. This fact has driven us to synthesize and characterize
new complexes that have potential antimicrobial properties. We have zeroed-in/focussed our
attention to investigating new half-sandwich ruthenium complexes because of their ease to form
complexes with a variety of ligands [1, 2] and their vast applications in catalysis and biology.
Although transition metal complexes containing dithiolene ligands have been extensively
studied; those of half-sandwich ruthenium complexes have not been investigated yet. The study
of dithiolenes has long been associated with inorganic chemistry, only recently they have
become subject of interest to those scientists studying biological systems. Dithiolene ligands are
found in the biomolecule of organisms throughout the entire kingdom of life [3]. These
biomolecules are enzymes that help to catalyze chemical reactions crucial to the host organisms
[4, 5].
However, it is certainly the coordination of the metal and the dithiolene that is, along
with the protein, responsible for the biological function in these enzymes. Research on
dithiolenes was energized by the recognition that the majority of molybdenum and tungsten
enzymes contain dithiolene-like moiety in their active site [6, 7]. A metalladithiolene ring is a
five-membered ring consisting of one metal, two sulfur atoms and two unsaturated carbons.
Metalladithiolene complexes exhibit dual nature of both the aromatic and the unsaturated
characters [8]. The former property renders the metalladithiolene ring to carry out substitution
3
reactions [9], while the latter property allows addition reactions of Lewis bases (e.g., PR ) to the
unsaturated metal center [10]. It is worth mentioning that these ligands are also termed as ‘non-
innocent’ ligands as the manner in which they bond with the metal center is unclear. The
oxidation form (usually neutral or anionic) of the ‘non-innocent’ ligand present in the complex is
not certain. Consequently, the oxidation state of the central atom is not clear [11]. Dithiolene
bearing secondary amine substituents such as piperidine, morpholine and thiomorpholine are
chosen for this work. These secondary amines were chosen because of their good antibacterial
property in the biological system. Several researchers have reported compounds containing
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piperidine or morpholine or thiomorpholine showed better antimicrobial and anticancer activity
(Chart 1) [12].
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3
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Chart 1: Ligands used in this study
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2. Experimental Section
2.1
Physical methods and materials
All the reagents were purchased from commercial sources and used as received. Glyoxal
and elemental sulfur were obtained from Sigma Aldrich. Piperidine, morpholine and
thiomorpholine were obtained from Alfa Aesar. The solvents were purified and dried according
to standard procedures. The starting metal precursor [CpRu(PPh ) Cl] [13] and
3
2
[(Ind)Ru(PPh ) Cl] [14] were prepared following the reported procedure. Infrared spectra were
3
2
recorded on a Perkin-Elmer 983 spectrophotometer by using KBr pellets in the range of 400-
-1 1
4000 cm . H NMR spectra were recorded on a Bruker Avance II 400 MHz spectrometer using
DMSO-d and CDCl as solvents. Absorption spectra were recorded on a Perkin-Elmer Lambda
6
3
25 UV/Visible spectrophotometer in the range of 200-800 nm at room temperature in
acetonitrile. Perkin-Elmer 2400 CHN/S analyzer was used for elemental analyses of the ligands
and complexes.
2.2
Single-crystal X-ray structures analyses
Single crystal X-ray diffraction data for complexes 1 and 2 were collected on an Oxford
Diffraction Xcalibur Eos Gemini diffractometer at 293 K using graphite monochromated Mo-Kα
radiation (λ = 0.71073 Å). Single crystal X-ray diffraction data of complex 4 was collected on a
Nonius Kappa CCD FR590 single-crystal X-ray diffractometer at 100 K using graphite
monochromated Mo-Kα radiation (λ = 0.71073 Å). Suitable crystals were selected and each
mounted on a glass fiber. The strategy for the data collection on an Oxford Diffraction Xcalibur
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Eos Gemini diffractometer was evaluated using the CrysAlisPro CCD software [15]. Crystal data
were collected by standard ‘‘phi–omega scan’’ techniques and were scaled and reduced using
CrysAlisPro RED software. Using Olex2 [16] the structures of complex 2 was solved with
SHELXT [17] solution program using the direct method and refined with olex2.refine [18]
refinement package using Gauss-Newton minimization. The strategy for the data collection on a
Nonius Kappa CCD FR590 single-crystal X-ray diffractometer was integrated and scaled using
hkl-SCALEPACK [19]. This program applies a multiplicative correction factor (S) to the
observed intensities (I) and has the following form:
−
2B(sin2 )/λ2
θ
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S = (e
)/scale
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S is calculated from the scale and the B factor determined for each frame and is then applied to I
to give the corrected intensity (Icorr).
Complexes 1 and 4 were solved by direct methods (SHELXT [17] or SIR97 [20])
produced a complete heavy atom phasing model consistent with the proposed structure. The
structure was completed by difference Fourier synthesis with SHELXL [21, 22]. Scattering
factors are from Waasmair and Kirfel [23]. Hydrogen atoms were placed in geometrically
idealized positions and constrained to ride on their parent atoms with C---H distances in the
range 0.95-1.00 Angstrom. Isotropic thermal parameters U were fixed such that they are 1.2U
1
1
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1
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1
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1
1
1
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1
1
1
00
01
02
03
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09
10
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12
13
14
eq
eq
of their parent atom U for CH's and 1.5U of their parent atom U in case of methyl groups.
eq
eq
eq
All non-hydrogen atoms were refined anisotropically by full-matrix least-squares. The
contribution of a disordered anion to the diffraction pattern was removed with SQUEEZE [24].
Crystallographic and structure refinement details for the complexes are summarized in Table 1
and selected bond lengths and bond angles are presented in Table 2. Figure 1 was drawn with
ORTEP3 program [25]. Figures S12-S14 were drawn with MERCURY3.6 program.
2.3
In vitro antimicrobial evaluation
Antimicrobial activity of ligands and complexes were tested against the three bacterial
strains, i.e., Staphylococcus aureus MTCC 96, Bacillus subtilis MTTC 441, Klebsiella
pneumoniae MTCC 109 and one fungal strain, Candida albicans MTCC 183. All strains were
tested for purity by standard microbiological methods. The bacterial stock cultures were
maintained on Mueller-Hinton agar slants and stored at 4˚C. An agar-well diffusion method [26]
was employed for the evaluation of the antimicrobial activity of test compounds. DMSO was
used as a negative control. The stock solutions for ligands (L1-L3) and complexes 1–6 were
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prepared freshly in DMSO before use. The stock concentrations of the tested samples were
~10,000 μg/mL. Mueller Hilton agar plates were swabbed with bacterial cell suspensions of the
8
indicator of bacterial strains adjusted to 1.5 x 10 colony forming units (CFU)/mL. Then, the
agar surface was bored by using a sterilized cork borer to generate wells of 5 mm diameter,
which were filled with a 100 μl aliquot of the corresponding test compound solution. A disc with
the broad-spectrum antibiotic chloramphenicol (30 mcg) was used as a positive control and a
DMSO solution as a negative control. Plates were incubated at 37 °C for 24 hours and the
inhibition zones (mm) formed around the wells were measured using a Vernier caliper. For each
organism, the experiments were conducted in triplicate and the result thus obtained is taken as
the mean of the three reading (Table 3). The antibacterial activity was evaluated by measuring
the growth inhibition zone diameter (IZD, in mm). The activity was classified as high sensitivity
for IZD ≥ 20 mm, medium sensitivity for IZD = 14–20 mm, low sensitivity for IZD = 7–13 mm,
and insignificant for IZD < 7 mm.
2.4 General preparation of ligands (L1, L2 and L3)
Dithiolene derivatives (Scheme 1) were obtained following the procedure reported in the
literature with slight modification [27]. A mixture of glyoxal (10 mmol), secondary amines such
as piperidine for L1, morpholine for L2, thiomorpholine for L3 (25 mmol) and elemental sulfur
(25 mmol) was refluxed for 4 hours (Scheme 1). The dark brown oil formed was allowed to cool
and then transfer slowly into a beaker containing cold water with vigorous stirring. The solid
precipitate was then filtered and washed thoroughly with water. The crude product obtained was
then purified by passing through column chromatography on silica gel (60-120 mesh) using ethyl
acetate and hexane as eluent.
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Scheme 1: Schematic representation for the synthesis of ligands L1-L3
2.4.1 1,2-di(piperidin-1-yl)ethane-1,2-dithione (L1)
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
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-
1
3
Color: Orange; Yield: 55%; FT-IR (KBr, cm ): 2992 (sp ʋC-H), 1504, 1482 and 999 (ʋC=S), 1444
1
and 1348 (ʋCH2); H NMR (400 MHz, CDCl ): δ 4.36-4.30 (m, 2H), 4.06-4.00 (m, 2H), 3.79-3.73
3
(m, 2H), 3.55-3.49 (m, 2H), 1.97-1.88 (m, 2H), 1.85-1.66 (m, 8H), 1.58-1.50 (m, 2H); UV-Vis
-4
-1
-1
{Acetonitrile, λmax nm (ε/10 M cm )}: 276 (7.030). Anal. Calc. for C H N S (256.53): (%)
12
20
2 2
C, 56.21; H, 7.86; N, 10.92. Found: C, 53.41; H, 4.96; N, 3.32.
2.4.2 1,2-dimorpholinoethane-1,2-dithione (L2)
-1
3
Color: Light yellow; Yield: 61%; FT-IR (KBr, cm ): 2957 (sp ʋC-H), 1511, 1489 and 1005
1
(ʋC=S), 1429 and 1361 (ʋCH2), 1104 (ʋC-O); H NMR (400 MHz, CDCl
3
): δ 4.52-4.46 (m, 2H),
4.06-4.00 (m, 2H), 3.93-3.79 (m, 8H), 3.70-3.64 (m, 2H), 3.58-3.52 (m, 2H); UV-Vis
-4
-1
-1
{Acetonitrile, λmax nm (ε/10 M cm )}: 276 (5.896). Anal. Calc. for C H O N S (260.38):
10
16
2
2 2
(%) C, 46.13; H, 6.19; N, 10.76. Found: C, 53.41; H, 4.96; N, 3.32.
2.4.3 1,2-dithiomorpholinoethane-1,2-dithione (L3)
-1
3
Color: Yellow; Yield: 65%; FT-IR (KBr, cm ): 2984 (sp ʋC-H), 1513, 1497 and 1006 (ʋC=S),
1
1422 and 1359 (ʋCH2), 662 (ʋC-S); H NMR (400 MHz, CDCl ): δ 5.13-5.08 (m, 2H), 4.16-4.11
3
(m, 2H), 3.97-3.90 (m, 2H), 3.78-3.71 (m, 2H), 3.23-3.17 (m, 2H), 3.03-2.96 (m, 2H), 2.69-2.63
-4
-1
-1
(m, 2H), 2.50-2.44 (m, 2H); UV-Vis {Acetonitrile, λmax nm (ε/10 M cm )}: 278 (5.630).
Anal. Calc. for C H N S (292.51): (%) C, 41.06; H, 5.51; N, 9.58. Found: C, 53.41; H, 4.96;
1
0
16
2 4
N, 3.32.
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2.5
General procedure for the synthesis of metal complexes (1-6)
To a solution of metal precursor [(arene)Ru(PPh ) Cl] (arene = cyclopentadienyl /
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2
indenyl) complexes (0.1 mmol), dithione derivatives (L1, L2 and L3) (0.1 mmol) and excess of
NH PF were added and reflux in dry methanol (10 mL) for 6 hours (Scheme 2). The mixture
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was allowed to cool and evaporated to dryness. DCM was added to dissolve the compound and
filter through celite. This mixture was then concentrated to about 1 mL and excess hexane was
added to precipitate the compound. The solid precipitate was washed thoroughly with diethyl
ether and dried.
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Scheme 2: Schematic representation for the synthesis of complexes 1-6.
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2.5.1 [CpRu(к
-L1)(PPh )]PF (1)
SS) 3 6
(
-1
3
Color: dark brown; Yield: 87%; FT-IR (KBr, cm ): 2932 (sp ʋC-H), 1527, 1483 and 1006 (ʋC=S),
1
1439 and 1361 (ʋCH2), 840 (ʋ ); H NMR (400 MHz, CDCl ): δ 7.43-7.36 (m, 15H, CH(PPh3)),
P-F
3
4.49 (s, 5H, CH(Cp)), 3.73 (t, J = 8 Hz, 9H), 1.74 (d, J = 8 Hz, 3H), 1.26 (s, 2H), 0.90-0.83 (m,
9

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3H); UV-Vis {Acetonitrile, λmax nm (ε/10 M cm )}: 273 (2.786), 561 (0.319). Anal. Calc. for
C H N RuS P F (829.84): (%) C, 50.66; H, 4.86; N, 3.38. Found: C, 50.84; H, 5.03; N, 3.54.
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2
2 2 6
2
2.5.2 [(Ind)Ru(к
-L1)(PPh )]PF (2)
3 6
(
SS)
-1
3
Color: dark brown; Yield: 86%; FT-IR (KBr, cm ): 2929 (sp ʋC-H), 1523, 1482 and 1004 (ʋC=S),
1
1438 and 1326 (ʋCH2), 841 (ʋ ); H NMR (400 MHz, CDCl ): δ 7.43-7.35 (m, 16H, CH(PPh3)),
P-F
3
7.22-7.20 (m, 3H), 4.94 (d, J = 4 Hz, 2H, CH(Ind)), 4.33 (quint, J = 4 Hz, 1H, CH(Ind)), 3.63-3.47
-4
-1
-1
(m, 8H), 1.65 (s, 6H), 1.51 (s, 6H); UV-Vis {Acetonitrile, λmax nm (ε/10 M cm )}: 256
(4.190), 587 (0.535). Anal. Calc. for C H N RuS P F (879.90): (%) C, 53.24; H, 4.81; N, 3.18.
3
9
42
2
2 2 6
Found: C, 53.41; H, 4.96; N, 3.32.
2
2.5.3 [CpRu(к
-L2)(PPh )]PF (3)
3 6
(
SS)
-1
3
Color: dark blue; Yield: 89%; FT-IR (KBr, cm ): 2970 (sp ʋC-H), 1517, 1482 and 1030 (ʋC=S),
1
1435 and 1360 (ʋCH2), 1114 (ʋC-O), 841 (ʋ ); H NMR (400 MHz, CDCl ): δ 7.46-7.26 (m, 15H,
P-F
3
CH(PPh3)), 4.86 (s, 5H, CH(Cp)), 3.77 (t, J = 4 Hz, 8H), 3.62 (q, J = 4 Hz, 8H); UV-Vis
-4
{Acetonitrile, λmax nm (ε/10 M-1 cm-1)}: 273 (2.356), 583 (0.710). Anal. Calc. for
C H N O RuS P F (833.78): (%) C, 47.54; H, 4.35; N, 3.36. Found: C, 47.73; H, 4.51; N,
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2
2
2 2 6
3.50.
2.5.4 [(Ind)Ru(к
2
-L2)(PPh )]PF (4)
(
SS)
3
6
-1
3
Color: dark green; Yield: 87%; FT-IR (KBr, cm ): 2938 (sp ʋC-H), 1521, 1481 and 1034 (ʋC=S),
1
1436 and 1385 (ʋCH2), 1115 (ʋC-O), 842 (ʋP-F); H NMR (400 MHz, CDCl
3
): δ 7.48-7.39 (m,
10H), 7.35-7.30 (m, 8H), 7.24-7.22 (m, 2H), 5.18 (d, J = 4 Hz, 2H, CH(Ind)), 4.60 (quint, J = 4
Hz, 1H, CH(Ind)), 3.76-3.70 (m, 4H), 3.67-3.65 (m, 3H), 3.62 (s, 2H), 3.59-3.57 (m, 3H), 3.54-
-4
-1
-1
3.47 (m, 4H); UV-Vis {Acetonitrile, λmax nm (ε/10 M cm )}: 259 (4.110), 602 (0.764). Anal.
Calc. for C H N O RuS P F (883.84): (%) C, 50.28; H, 4.33; N, 3.17. Found: C, 50.46; H,
3
7
38
2
2
2 2 6
4.49; N, 3.32.
2.5.5 [CpRu(к
2
-L3)(PPh )]PF (5)
(
SS)
3
6
-1
3
Color: dark blue; Yield: 88%; FT-IR (KBr, cm ): 2920 (sp ʋC-H), 1515, 1481 and 1030 (ʋC=S),
1
1434 and 1365 (ʋCH2), 841 (ʋ ), 698 (ʋ ); H NMR (400 MHz, CDCl ): δ 7.47-7.30 (m, 15H,
P-F
C-S
3
CH(PPh3)), 4.80 (s, 5H, CH(Cp)), 4.00-3.94 (m, 4H), 3.86-3.80 (m, 4H), 2.69-2.66 (m, 8H); UV-Vis
-4
-1
-1
{Acetonitrile, λmax nm (ε/10
M
cm )}: 273 (2.475), 583 (0.344). Anal. Calc. for
C H N RuS P F (865.92): (%) C, 45.77; H, 4.19; N, 3.24. Found: C, 45.77; H, 4.35; N, 3.38.
33
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2
4 2 6
2
3 6
2.5.6 [(Ind)Ru(к (SS)-L3)(PPh )]PF (6)
1
0

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Color: dark green; Yield: 84%; FT-IR (KBr, cm ): 2951 (sp ʋC-H), 1523, 1483 and 1007 (ʋC=S),
1
1435 and 1385 (ʋCH2), 842 (ʋ ), 697 (ʋ ); H NMR (400 MHz, CDCl ): δ 7.90-7.34 (m, 19H),
P-F
C-S
3
5.14 (d, J = 4 Hz, 2H), 4.55 (quint, J = 4 Hz, 1H), 3.90 (t, J = 8 Hz, 8H), 2.69-2.63 (m, 4H),
-4
-1
-1
2.54-2.48 (m, 4H); UV-Vis {Acetonitrile, λmax nm (ε/10 M cm )}: 256 (4.243), 586 (0.665).
Anal. Calc. for C H N RuS P F (915.97): (%) C, 48.52; H, 4.18; N, 3.06. Found: C, 48.71; H,
3
7
38
2
4 2 6
4.35; N, 3.21.
3. Result and Discussion
3.1 Synthesis of ligands and complexes
In this work, we have carried out the synthesis, characterization and antimicrobial activity
evaluation of dithiolene ligands and complexes of ruthenium (Cp/Ind) containing dithiolene
derivatives. On reacting [(arene)Ru(PPh
3 2
) Cl] (arene = cyclopentadienyl, indenyl) with ligand
(L1/L2/L3) in 1:1 (M:L) ratio, a series of cationic bidentate sulfur-sulfur bonded five-membered
2
+
chelating ruthenium complexes 1-6 with the chemical formula [(arene)Ru{κ ( L}(PPh )] , L =
S∩S)
3
L1/L2/L3 were obtained. The ligands are light orange to yellow in color whereas the complexes
are dark brown to dark green in color. The ligands and complexes are highly soluble in an
organic solvent such as chloroform, dichloromethane, acetone, acetonitrile, etc., and insoluble in
solvents like hexane, diethyl ether and petroleum ether. They are also highly stable in air as well
1
as in a solution. All ligands and complexes were characterized by IR, H-NMR, CHN analysis,
UV spectroscopic technique and the analytical data of all the compounds are consistent with the
formulations. Further characterization of the complexes was done by single-crystal X-ray
diffraction technique. The molecular structure obtained for some complexes further confirm the
formation of desired compounds. The molecular structure of complexes also revealed the
bonding of the respective ruthenium complex towards the dithiolene derivatives which take place
6
through the two sulfur atoms. The presence of a PF counter ion in all the complexes shows that
the two sulfur atoms of the dithiolene derivatives bonded as C=S towards the metal center. This
observation was also confirmed from the bond distance of the carbon-sulfur double bond which
agrees well with the reported data [28]. Antimicrobial activity of ligands tested against three
strains of bacterial microorganisms Staphylococcus aureus (gram +ve), Bacillus subtilis (gram
+ve), Klebsiella pneumoniae (gram -ve) and one fungal strain Candida albicans shows that
ligands lacked antimicrobial activity. The antimicrobial activity of all complexes displays good
activity against both gram-positive and gram-negative bacteria and also against fungal strain.
1
1

2
2
2
2
2
2
2
2
2
2
2
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3.2
Spectral Studies of ligands (L1, L2 and L3) and complexes (1-6)
3.2.1 Infrared Spectra (IR) of ligands and complexes
The IR spectra of ligands and complexes provide information on the nature of the
substituents and functional group attached to the compounds. The free ligands IR spectrum
3
displayed bands corresponding to sp C-H, C=S, CH , C-O and C-S stretching frequencies only.
2
3
The complexes, on the other hand, displayed bands corresponding to sp C-H, C=C, C=S, CH
2
,
-
1
C-O, C-S and P-F stretching frequencies. The band at 2920-2970 cm corresponds to the
3
stretching frequencies of sp C-H of secondary amine derivatives of dithiolene. The band at
-1
-1
-1
1515-1527 cm , 1481-1483 cm and 1004-1034 cm corresponds to the stretching frequencies
-1
-1
of C=S of dithiolene ligands. The band at 1439-1434 cm and 1365-1326 cm corresponds to
the stretching frequencies of the CH group of secondary amine derivatives of dithiolene.
2
-1
-1
Complexes 3 and 4 display the extra band at 1114 cm and 1115 cm respectively which
corresponds to the C-O stretching frequencies of morpholine derivatives. Also, complexes 5 and
-1
-1
6 display extra band at 698 cm and 697 cm respectively which corresponds to the C-S
-1
stretching frequencies of thiomorpholine derivatives. A very sharp band at 840-842 cm which
corresponds to the P-F stretching frequencies of PF
6
counter ion suggests the formation of the
desired complexes.
1
3.2.2
H-NMR spectra of ligands and complexes
1
The bulk purity of ligands and complexes were obtained from their H-NMR spectra. The
1
1
H NMR spectra of all the compounds were recorded in CDCl . H-NMR spectrum of ligand L1
3
displayed six multiplets in the range of 4.36-1.88 ppm and 1.58-1.50 ppm which corresponds to
the chemical shift of two protons each of the piperidine derivatives. Multiplet at 1.85-1.66 ppm
1
which corresponds to the chemical shift of eight protons was also observed. The H-NMR
spectrum of ligand L2 displayed four multiplets in the range of 4.52-4.00 ppm and 3.70-3.52
ppm which corresponds to the chemical shift of two protons each of the morpholine derivatives.
Multiplet at 3.93-3.79 ppm which corresponds to the chemical shift of eight protons was also
1
observed. The H-NMR spectrum of ligand L3 displayed eight multiplets in the range of 5.13-
2.44 ppm which corresponds to the chemical shift of two protons each of the thiomorpholine
derivatives.
1
The H-NMR of complexes displayed signals associated with the ligand protons, signals
due to cyclopentadienyl (Cp) for 1, 3 and 5 or indenyl (ind.) ring protons for 2, 4 and 6 and also
1
2

2
2
2
2
2
2
2
2
2
2
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2
2
2
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2
2
2
2
2
2
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93
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95
96
3
signal corresponding to the PPh group. Complexes 1, 3 and 5 displayed signals at 7.47-7.26
ppm which corresponds to the multiplets of 15 protons of the PPh group. The five protons
3
singlet signal of Cp group were observed in the range of 4.86-4.49 ppm and the chemical shift of
ligands proton were observed in the range of 4.00-0.83 ppm. Complexes 2, 4 and 6 displayed a
set of multiplets in the range of 7.90-7.20 ppm which corresponds to the protons of PPh and the
3
four protons of aromatic indenyl group. The other three protons of the indenyl group split into a
doublet at 5.18-4.94 ppm for two protons and a quintet at 4.61-4.32 ppm for one proton. The
1
ligand protons signal of indenyl complexes were observed in the range of 3.90-1.51 ppm. The H
NMR of all the ligands and complexes were given in supplementary data (Figures S1 to S9).
3.2.3 UV-visible spectra of ligands and complexes
-4
The electronic spectra of ligands and complexes were recorded in acetonitrile at 10 M
concentration at room temperature and the respective plots are shown in (Figures S10 and S11).
The electronic spectra of ligands display one absorption band in the higher energy region around
276-278 nm which can be assigned as ligand centered or intra ligand π-π* [29, 30]. Complexes,
on the other hand, displayed two bands, one in the higher energy region of 273-256 nm and one
in the low energy region at 561-602 nm corresponding to the metal to ligand charge transfer from
Ru (4d) orbitals to the low-lying empty orbitals π* orbitals of the ligand [31].
3.3
Description of the molecular structures of complexes
The solid-state structures of some of the complexes were established by single-crystal X-
ray crystallography. The ORTEP view of complexes along with the atom numbering scheme are
shown in Figure 1. The summary of the crystal data, data collection and structure refinement
parameters are summarized in Table 1. Selected bond lengths, bond angles and metal atom
involving ring centroid values are listed in Table 2.
Single crystal X-ray study helps us to understand the type of bonding, the distance
between the bonded atoms and the angle which they made while bonding. The black crystal of
complex 1 was obtained by slow diffusion of hexane into a concentrated solution of the
compound dissolved in DCM. The crystal data of 1 shows that the complex crystallized in the
triclinic system with Pī space group. From the molecular structure of 1 depicted in Figure 1,
3
ruthenium metal Ru(1) is coordinated to one Cp ring, one PPh group and the two sulfur atoms of
the dithiolene derivatives. The distance between the centroid of the Cp ring and the ruthenium
metal is 1.826 Å. The bond distances between Ru(1) and P(1) is 2.2982(19) Å which fall under
1
3

2
2
2
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
97
98
99
00
01
02
03
04
05
06
07
08
09
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
the usual range of Ru-P bond distances (2.20-2.43 Å) [32]. The bond distances between Ru(1)
and S(1) and also between Ru(1) and S(2) are 2.361(2) Å and 2.425(2) Å respectively which is
close to the previously reported data [33]. The carbon-sulfur double bond distances changes
slightly on coordination to the metal, in which the C(6) and S(1) bond length is slightly longer at
1.696(9) Å and the C(7) and S(2) bond length is almost the same as in free ligand at 1.673(9) Å.
The bond angle between S(1)-Ru(1)-S(2), P(1)-Ru(1)-S(1) and P(1)-Ru(1)-S(2) are 88.59(8)º,
89.72(7)º and 91.07(7)º respectively are close to that of a perfect octahedral geometry with a
bond angle equal to 90º. Assuming that the Cp ring occupies the three coordinate sites while the
ligand (S∩S) and PPh
group occupy the other three coordinating sites and also the evidence
3
from its bond angle (close to 90º) confirms that the geometry of complex 1 is pseudo-octahedral.
The crystal of both complexes 2 and 4 are black in color obtained by slow diffusion of
hexane into the concentrated solution of compound dissolved in DCM. Both the complexes
contain an indenyl ring and a PPh group in their structure. The dithiolene with piperidine
3
substituent is present in complex 2 while complex 4 contain dithiolene with morpholine
substituent. Complex 2 crystallized in the monoclinic system with P2 /n space group whereas
1
complex 4 crystallized in the orthorhombic system with Pbca space group. From the molecular
structure of 2 and 4 shown in Figure 1, both the complexes coordinate to the metal center
through the two sulfur atoms forming five-membered cationic complexes with PF counter ion.
6
5
The distance between the centroid of the η -indenyl ring and the ruthenium metal Ru(1) in 2 and
4 are 1.891 Å and 1.883 Å respectively. The Ru(1)-P(1) bond distances in both complexes are
2.2687(11) Å and 2.2748(10) Å respectively which is in agreement with similar reported
complexes [32]. The Ru(1)-S(1) and Ru(1)-S(2) bond distances are in the range of 2.2991 Å -
2.4223 Å which also falls under the reported range [33]. The S(1)-Ru(1)-S(2), P(1)-Ru(1)-S(1)
and P(1)-Ru(1)-S(2) bond angle in both the complexes are in the range of 85.35º-94.45º which is
close to that of an octahedral geometry bond angle (90º) thus attaining a pseudo-octahedral
geometry. The coordination of the indenyl ring to the ruthenium metal is in a pentahapto fashion
and also display asymmetric coordination between the metal center and the carbon atoms of the
five-membered ring. In both the indenyl complexes, three of the Ru-C bond distances are
significantly shorter than the two Ru-C bond distances (Table 2). This observation is due to the
5
3
ring slippage from a η -coordination to a η -coordination [34].
3.4 Non-covalent interaction
1
4

3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
28
29
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31
32
33
34
35
36
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38
39
40
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42
43
44
45
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47
48
49
50
51
52
53
54
55
56
57
58
The stability of the complexes can be governed from their non-covalent interaction
obtained from the crystal packing diagram of the complexes (Figures S12-S14). Complex 1
possessed intermolecular hydrogen-hydrogen interaction N-CH∙∙∙∙∙H-C between the hydrogen of
two different piperidine ring (H43A and H10A) with 2.189 Å bond distance. The complex is
further stabilized by two types of intermolecular CH-π interaction, one between the centroid of
3 3
the phenyl ring of PPh group and the hydrogen atom (H19) of the phenyl ring of PPh group
with 3.464 Å bond distance. Another CH-π interaction was observed between the centroid of the
phenyl ring of PPh group and the hydrogen atom (H52A) of the piperidine derivatives with
3
3.107 Å bond distance. Complex 2 is stabilized by only one type of intermolecular CH-π
interaction between the centroid of the phenyl ring of PPh group and the hydrogen atom (H3A)
3
of the piperidine derivatives with 3.464 Å bond distance forming a supramolecular unit.
Complex 4, on the other hand, possessed one intermolecular hydrogen-hydrogen interaction N-
CH∙∙∙∙∙H-C between one of the hydrogen atom of morpholine ring (H14A) and the hydrogen
3
atom of one of the phenyl ring (H35) of PPh group derivatives with 2.205 Å bond distance. An
intermolecular hydrogen bonding between the morpholine derivatives O2∙∙∙∙∙H18B was also
observed with 2.474 Å bond distance. Intermolecular CH-π interaction between the centroid of
the phenyl ring of PPh group and the hydrogen atom (H28) of the phenyl ring of another PPh
3
3
group with 3.792 Å bond distance further stabilizes the complex.
3.5
In vitro antimicrobial activity of complexes and ligands
The synthesized ligands and complexes were evaluated for their in-vitro antimicrobial
activity against two gram-positive bacteria; Staphylococcus aureus MTCC 96, Bacillus subtilis
MTCC 441 strains; one gram-negative; Klebsiella pneumoniae MTCC 109 strain and one fungal
strain Candida albicans MTCC 183 by using standard techniques. The inhibition zone diameter
(IZD, in mm) in comparison with chloramphenicol and fluconazole as reported in the previous
paper [35] was given in Table (3) and the chart representation was given in Figures 2 and 3. Petri
dishes showing the antibacterial and antifungal activity of the ligands and complexes against the
representative strains were given in Figures S15 and S16. DMSO solvent was used as a negative
control. In the previous article, we have reported the antimicrobial activity of metal precursors
[36] and the result shows that these metal precursors lacked activity. The antimicrobial activity
of the ligands has also been evaluated and the result shows that they lacked activity towards the
tested strains. Thus the activity of the complexes is purely attributed to the combination of these
1
5

3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
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3
3
3
3
3
3
3
3
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3
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85
86
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88
89
metal precursors and ligands. All the complexes exhibited potent antibacterial activity against the
tested organism. The antibacterial activity of all complexes displays better activity against both
gram-positive and gram-negative bacteria. Amongst all the complexes, complexes 3 and 4 with
IZD ≥ 20 mm are considered to be highly sensitive for the tested strains. Both these complexes
contain dithiolene with morpholine substituent. Also, complexes 5 and 6 containing dithiolene
with thiomorpholine derivatives display good antimicrobial activity with IZD = 14-20 mm. It is
important to note that antibacterial activity of complexes 1 and 2 with dithiolene containing
piperidine derivatives were active only towards S. aureus (gram +ve) and K. pneumoniae (gram -
ve) whereas complexes 3-6 were active towards S. aureus (gram +ve) and B. subtilis (gram +ve).
Perhaps the structural similarity between morpholine and thiomorpholine in complexes 3-6 is
responsible for the result in their antimicrobial activity. On the other hand, antifungal activity of
all complexes except complex 1 were active towards the tested fungal strain. Complexes 2-4
with IZD ≥ 20 mm are considered to be a better antifungal activity with high sensitivity towards
the tested strain whereas complexes 5 and 6 with IZD = 15 mm are considered to be a good
antifungal activity with medium sensitivity towards the tested strain. It is important to note that
the biological application such as the antimicrobial study has not been explored with these
dithiolene ruthenium complexes. Thus, it is difficult to predict exactly why certain complexes are
more active than others with the studied bacterial and fungi strains. However, results obtained
from their inhibition study show that complexes containing morpholine substituent are very
active whereas the same ligand is inactive towards the studied bacterial and fungi strains. This
shows that for the studied compound to be active it has to contain a specific metal such as the
ruthenium center, a specific hydrocarbons group with either a cyclopentadienyl or an indenyl
group and specific dithiolene derivatives.
4. Conclusion:
All the complexes were isolated as cationic species with PF counter ion. The ligands and
6
complexes were obtained in good yields and were characterized by analytical and spectral
methods. Single crystal X-ray diffraction study reveals that the dithiolene derivatives ligands
coordinated to the metal center through the two sulfur atoms forming cationic five-membered
chelate complexes. Antimicrobial activity against Staphylococcus aureus MTCC 96, Bacillus
subtilis MTCC 441 strains, Klebsiella pneumoniae MTCC 109 and one fungal strain Candida
albicans MTCC 183 have been carried out. The result shows that ligands lacked activity whereas
1
6

3
3
3
90
91
92
complexes display potent activity towards the tested bacterial and fungal strains. In particular
complexes, 3 and 4 are highly active towards gram-positive bacteria as well as against fungal
strain but inactive towards gram-negative bacteria.
3
93
5. Acknowledgment
3
3
3
3
94
95
96
97
Lincoln Dkhar thanks the Department of Science and Technology (DST), India for providing
financial assistance under the Innovation in Science Pursuit for Inspired Research (INSPIRE)
fellowship. Lincoln Dkhar also thanks SAIF-NEHU for spectral analyses and DST-PURSE
SCXRD, India for providing Single Crystal X-ray analysis.
3
98
6. Supplementary Material
3
4
4
4
4
99
00
01
02
03
CCDC 1993141 (1), 1993142 (2) and 1993143 (4) contains the supplementary crystallographic
data for this paper. These data can be obtained free of charge via
www.ccdc.cam.ac.uk/data_request/cif, by e-mailing data_request@ccdc.cam.ac.uk, or by
contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ,
UK; Fax: +44 1223 336033.
4
4
04
05
7. References
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16
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1
9

Figure 1: Therminal ellipsoid plots of complexes 1, 2 with 50% thermal ellipsoid probability collected at a temperature of 293 K each and
complex 4 with 80% thermal ellipsoid probability collected at a temperature of 100 K generated using ORTEP program. Hydrogen atoms and
PF counter ions have been omitted for clarity.
6
2
0

Figure 2: Histogram showing the zone of inhibition of the tested compounds against the
bacterial strains (Staphylococcus aureus MTCC-96, Bacillus subtilis MTCC-441 and Klebsiella
pneumoneae MTCC-109).
2
1

Figure 3: Histogram showing the zone of inhibition of the tested compounds against the fungal
strain (Candida albicans MTCC-183).
2
2

1
Table 1: Crystal structure data and refinement of complexes 1, 2 and 4
Complexes
[1]
[2]
[4]
Empirical formula
Formula weight
Temperature (K)
Wavelength (Å)
Crystal system
Space group
C H N RuS P F
C H N RuS P F
879.87
293(2)
0.71073
monoclinic
P2 /n
1
C H O N RuS P F
2 2 6
883.82
100(2)
0.71073
Orthorhombic
Pbca
35
40
2
2
2
6
39 42
2
2
2
6
37 38
2
2
829.82
293(2)
0.71073
triclinic
Pī
a (Å)/α (°)
b (Å)/β (°)
c (Å)/γ (°)
Volume (Å )
13.2445(8)/91.172(4)
14.4121(7)/105.628(5)
21.7873(13)/102.494(4)
3896.5(4)
15.7980(5)/90
8.57970(10)/90
25.1844(4)/90
34.2594(9)/90
7402.6(2)
8
1.586
0.690
3600
0.23 x 0.20 x0.17
10.8457(5)/99.415(3)
23.0318(8)/90
3893.1(3)
3
Z
4
4
-3
Density (calc) (Mg/m )
Absorption coefficient
F(000)
1.415
0.647
1696
0.25 x 0.21 x 0.19
1.501
0.652
1800.0
0.23 x 0.12 x 0.09
3
Crystal size (mm )
Theta range for data collection
3.077 to 25.350°
6.354 to 52.746°.
2.655 to 28.287°
Index ranges
-14<=h<=15, -13<=k<=17, -
-19<=h<=13, -13<=k<=8, -
23<=l<=28
-11<=h<=11, -33<=k<=33, -
44<=l<45
2
6<=l<=24
Reflections collected
23004
14286
15860
Independent reflections
Completeness to theta = 25.00°
Absorption correction
Refinement method
14134 [Rint = 0.0501]
99.3 %
7901 [Rint = 0.0256]
99.04 %
8898 [Rint = 0.0681]
96.6 %
Semi-empirical from equivalents Semi-empirical from equivalents Semi-empirical from equivalents
2
2
2
Full-matrix least-squares on F
14134/965/1032
1.025
Full-matrix least-squares on F
7901/0/469
1.024
Full-matrix least-squares on F
8898/21/491
0.976
Data/restraints/parameters
2
Goodness-of-fit on F
Final R indices [I>2sigma(I)]
R1 = 0.0792, wR2 = 0.1975
R1 = 0.0509, wR2 = 0.1223
R1 = 0.0494, wR2 = 0.0925
R indices (all data)
Absolute structure parameter
Largest diff. peak and hole (e.Å ) 1.141 and -0.752
R1 = 0.1333, wR2 = 0.2410
n/a
R1 = 0.0737, wR2 = 0.1374
n/a
R1 = 0.1200, wR2 = 0.1072
n/a
-
3
0.87 and -0.84
1993142
1.944 and -0.918
1993143
CCDC No.
Structures were refined on F
1993141
2
2
2 2
2 2 1/2
-1
2
2
2
2
2
3
0
: wR
2
0 c 0 0 0 c
= [Σ[w(F - F ) ]/Σw(F ) ] , where w = [Σ(F )+(aP) +bP] and P = [max(F ,0)+2F ]/3
2
3

4
Table 2: Selected bond lengths (Å) and bond angles (°) of complexes 1, 2 and 4.
Ligand/Complexes
Ru(1)-CNT
1
2
4
1.826
1.891
1.883
Ru(1)-P(1)
2.2982(19) 2.2687(11) 2.2748(10)
Ru(1)-S(1)
2.361(2)
2.425(2)
2.4223(11) 2.2991(10)
2.3616(12) 2.3320(10)
Ru(1)-S(2)
Ru(1)-C(4)/C(20)
Ru(1)-C(5)/C(21)
Ru(1)-C(6)/C(13)
Ru(1)-C(7)/C(14)
Ru(1)-C(8)/C(15)
C(6)/C(10)=S(1)
C(7)/C(15)=S(2)
P(1)-Ru(1)-S(1)
P(1)-Ru(1)-S(2)
S(1)-Ru(1)-S(2)
2.347(4)
2.191(5)
2.153(5)
2.178(5)
2.338(4)
1.713(4)
1.680(4)
90.34(4)
92.54(4)
85.89(4)
2.300(4)
2.194(3)
2.175(4)
2.216(4)
2.321(4)
1.680(4)
1.702(4)
89.69(4)
94.45(4)
85.35(3)
1.696(9)
1.673(9)
89.72(7)
91.07(7)
88.59(8)
5
6
CNT represents the centroid of the Cp/Ind ring to the Ruthenium metal.
2
4

7
8
Table 3: Antimicrobial activity (Agar well) of tested compounds against representative bacterial
and fungal strains.
Zone of inhibition (Diameter in mm)
S.
No.
Compound
Names
MTCC-96 MTCC-441
MTCC-109
K. pneumoniae
0
MTCC-183
C. albicans
0
S. aureus
B. subtilis
1
2
3
4
5
6
7
8
9
Ligand L1
Ligand L2
Ligand L3
Complex 1
Complex 2
Complex 3
Complex 4
Complex 5
Complex 6
0
0
0
0
0
0
0
0
0
0
15
19
30
20
18
18
0
11
10
0
0
0
22
29
25
15
15
35
27
20
20
0
0
0
DMSO (negative
control)
Chloramphenicol
C30
1
0
1
0
0
29
0
0
22
0
0
0
1
26
1
2
Fluconazole
0
18
(
FLC 25)
9
0
1
2
S. aureus
=
Staphylococcus aureus
;
B. subtilis
=
Bacillus subtilis
;
K. pneumoniae
=
Klebsiella
1
1
1
pneumoniae
,
C. albicans Candida albicans.
=
N.B.: For each organism, the experiments were conducted in triplicate and the result thus
obtained was taken as the mean of the three reading.
2
5

HIGHLIGHTS
∑
∑
∑
Ruthenium binds preferentially through the sulfur atoms of dithione derivatives
The dithione ligands (L1, L2 & L3) lacked antibacterial and antifungal activity
Complexes 3 and 4 shows exceptional antibacterial and antifungal activity

Professor K. Mohan Rao
Department of Chemistry
North Eastern Hill University
Shillong 793022
e mail: mohanrao59@gmail.com
mobile: 9436166937 (M)
tel. no. 0364 272 2620
th
The Editor
29 March 2020
Journal of Organometallic Chemistry
Declaration of interest statement
'Declarations of interest: none'
Yours truly,
Mohan Rao Kollipara