Palladium(II) Complexes Based on N,S-Donor Ligands: Synthesis and Molecular Structures

Article abstract of DOI:10.1134/S0022476619010220

Phenyl(chloro)dithioformate is treated with pyrazole derivatives and phenyl(Pz-1-carbodithioate) ligands (Pz = pyrazole (1), 3-methylpyrazole (2), and 3,5-dimethylpyrazole (3)) are obtained. These ligands are treated with PdCl₂ in acetonitrile and complexes of the general formula Pd(L)Cl₂ form in an essentially quantitative yield. The ligands are found to be N,S-bidentate linkers, and 5-membered palladacycles are obtained. Precursors 1–3 are oily materials and characterized by ¹H and ¹³C NMR spectroscopy. Due to a partial solubility of Pd complexes, the complete set of NMR data cannot be collected. The structural elucidation is also accompanied by elemental and mass spectrometric analyses. Solid-state structures of complexes 5 and 6 are determined by X-ray diffraction. The data obtained for complexes 5 and 6 are also calculated by DFT using the TURBOMOLE program package. Experimental and calculated data sets are found to be in close agreement with each other.

Full text of DOI:10.1134/S0022476619010220

Journal of Structural Chemistry. Vol. 60, No. 1, pp. 159-167, 2019.
Text © 2019 S. A. Khan, E. Khan, A. Noor, S. Schwarz.
PALLADIUM(II) COMPLEXES BASED ON N,S-DONOR
LIGANDS: SYNTHESIS AND MOLECULAR STRUCTURES
1,2
S. A. Khan , E. Khan *, A. Noor ,
1
3
3
and S. Schwarz
Phenyl(chloro)dithioformate is treated with pyrazole derivatives and phenyl(Pz-1-carbodithioate) ligands
(Pz = pyrazole (1), 3-methylpyrazole (2), and 3,5-dimethylpyrazole (3)) are obtained. These ligands are
treated with PdCl in acetonitrile and complexes of the general formula Pd(L)Cl form in an essentially
2
2
quantitative yield. The ligands are found to be N,S-bidentate linkers, and 5-membered palladacycles are
1
13
obtained. Precursors 1-3 are oily materials and characterized by H and C NMR spectroscopy. Due to
a partial solubility of Pd complexes, the complete set of NMR data cannot be collected. The structural
elucidation is also accompanied by elemental and mass spectrometric analyses. Solid-state structures of
complexes 5 and 6 are determined by X-ray diffraction. The data obtained for complexes 5 and 6 are also
calculated by DFT using the TURBOMOLE program package. Experimental and calculated data sets are
found to be in close agreement with each other.
DOI: 10.1134/S0022476619010220
Keywords: phenyl(chloro)dithioformate, phenyl(pyrazol-1-carbodithioate) derivatives, N,S ligands,
palladacycles, DFT calculations.
INTRODUCTION
The synthesis of dithocarbamic acid, its salts and esters is of great interest due to their wide potential as radicals,
starting materials, and intermediates in the synthesis of many compounds [1-3]. They are used in Diels-Alder reactions [4]
and have wide applications in the field of agriculture as pesticides [5] and polymerization reactions at the industrial scale [6].
Moreover, they are potent antioxidant, antifungal, antimicrobial, anticancer agents and possess the cytostatic activity [7-11].
The esters of dithiocarbamates are synthesized via different methods, i.e. treatment of dithiocarbamic acid salt with
teraflouroborate salts [12], reactions of alkyl halide derivatives with dithiocarbamic acid salts [13], the Markovnikov addition
reaction in the aqueous medium [14], regioselective thiolation [15], the reaction of alkyl halides with thiocarbamic salts [16],
the Ullman reaction from phenyl diazonium tetrafluoroborate, carbon disulphide, and amines in water, and CuI-catalyzed
coupling reactions [17].
The S and N donor ligands such as thioureas [18], thiocarbamates [19], and alkyl or aryl esters of thiocarbamates [9]
are useful precursors in chemistry. Bidentate ligands are widely used in coordination chemistry with various metal centers to
1
Department of Chemistry, University of Malakand, Khyber Pakhtunkhwa, Pakistan; *ekhan@uom.edu.pk.
3
2
Department of Chemistry, University of Education, D. G. Khan. Anorganische Chemie II, Universität Bayreuth, Bayreuth,
Germany. Zhurnal Strukturnoi Khimii, Vol. 60, No. 1, pp. 166-173, January, 2019. Original article submitted September 06,
2017; revised October 03, 2017; accepted October 09, 2017.
0022-4766/19/6001-0159 © 2019 by Pleiades Publishing, Ltd.
159

fix terminal ligands (halogens or organic groups) in the cis position for the specific reactivity, such as biological and catalytic
8
applications. Better reactivity has been shown by d metal centers (Ni(II), Pd(II), Pt(II)) with bidentate ligands. Considerable
literature is available on Pd(II) complexes with bidentate neutral ligands with a residual MX moiety (where X can be halogen
or an organic group coming from starting salt). The geometry around the metal center in normal cases is distorted square
planar [20], a distortion being caused by bidentate chelating ligands.
In continuation of our previous work [21] here we report the synthesis of N,S ligands and their Pd(II) complexes.
1 13
The final complexes contain the MCl moiety, which can be used for secondary reactions. The NMR ( H and C)
2
characterization and the X-ray structure of complexes 5 and 6 are discussed. The experimental data have also been
reproduced theoretically by DFT.
EXPERIMENTAL
General considerations. Pyrazole, 3-methylpyrazole, 3,5-dimethylpyrazole, phenyldithioformate are commercial
products (Sigma Aldrich) and were used without further purification. Triethylamine was distilled (bp 89.5 °C) prior to the use
and dry toluene (sodium metal and benzophenone) was used throughout. Elemental analyses (CHN) were performed on
1 13
a Vario EL III instrument. NMR spectra were recorded on Varian INOVA 300 ( H 300 MHz; C 75 MHz) at 23 1 °C.
Chemical shifts are reported in ppm, proton NMR spectra were referenced to the chemical shifts of residual proton signals
13
(CHCl δ 7.27 and DMSO δ 2.50). The spectra of carbon were referenced to the C resonance of the respective solvent
3
(CDCl δ 77.00 and DMSO δ 39.51). Mass spectra (EI, 70 eV) were measured using Finnigan MAT 8500 with a direct inlet
3
system.
Synthesis of carbodithioate derivatives 1-3. To a solution of phenylchlorodithioformate (1.5 ml, 10 mmol) in
toluene (30 ml) pyrazol was added (0.96 g, 10 mmol) followed by an equimolar amount of Et N (1.5 ml, 10 mmol). The
3
mixture was left stirred for few hours, and after some time the Et N⋅HCl precipitate appeared, indicating the progress in the
3
chemical reaction [22]. The reaction mixture was further stirred for 48 h. After the reaction was completed, the reaction
mixture was filtered and the filtrate was washed with water and dried over Na SO . After the evaporation of the solvent and
2
4
other volatiles, deep orange-red oil was collected and analyzed by NMR and elemental analyses. Compounds 2 and 3 were
prepared in the same way.
1
1. Yield: 76%, C H N S . Elemental, found (Cal): C 55.16 (54.52); H 3.47 (3.66); N 11.53 (12.72). H NMR
10
8
2 2
13
(CDCl ) δ (ppm) = 8.62 (br, 2H, pz), 7.55-7.83 (m, aromatic protons, Ph/Pz), 6.51 (br, 1H, pz). C NMR (CDCl )
3
3
δ (ppm) = 201.2, 145.0, 136.5, 130.9, 130.8, 130.5, 129.9, 111.0.
1
2. Yield: 77%, C H N S . Elemental, found (Cal): C 57.50 (56.38); H 4.71(4.30), N 11.20 (11.95). H NMR
11 10
2 2
1
(CDCl ) δ (ppm) = 8.52 (d, 1H, pz, J( H, H) = 2.9 Hz), 7.53-7.73 (m, 5H, Ph), 6.31 (d, 1H, 4-pz, J( H, H) = 2.9 Hz), 2.46
1
1
1
3
13
(s, 3H, 3-Me). C NMR (CDCl ) δ (ppm) = 200.2, 141.6, 136.4, 136.3, 131.2, 130.4, 129.4, 111.8, 14.1.
3
1
3. Yield: 89%, C H N S . Elemental, found (Cal): C 57.50 (58.03); H 4.49 (4.87), N 11.20 (11.28). H NMR
12 12
2 2
13
(CDCl ) δ (ppm) = 7.21-7.51 (m, 5H, Ph), 6.13 (s, 1H, pz), 2.64 (s, 3H, Me), 2.35 (s, 3H, Me). C NMR (CDCl )
3
3
δ (ppm) = 201.3, 152.6, 146.2, 136.9, 131.7, 130.6, 129.7, 113.8, 17.7, 14.0.
Synthesis of complexes 4-6. Palladium(II) chloride (0.177 g, 1 mmol) was dissolved in acetonitrile (20 ml). The
solution was stirred overnight to afford the [Pd(CH CN) Cl ] adduct. The desired adduct was obtained as a yellow solution.
3 2 2
A solution of compound 1 (0.2 g, 1 mmol) in acetonitrile (5 ml) was prepared in a separate flask and added to the Pd(II)
solution. Immediately after the addition orange precipitates formed. The reaction was allowed to continue overnight. The
precipitate was separated by filtration and washed with an excess amount of acetonitrile. Desired complex 4 was obtained in
1
13
an essentially quantitative yield. The complex thus obtained was characterized by NMR ( H and C) spectroscopy, mass
spectrometry, and elemental analysis. The same procedure was followed for the synthesis of complexes 5 and 6. All
complexes were obtained as yellow precipitates from their respective reaction mixtures.
160

4. Yield: 78%, C H Cl N PdS . Elemental analysis found (Cal.): C 30.42 (30.20), H 2.02 (2.03), N 7.22 (7.04). MS
10 8 2 2 2
1
(EI-MS), m/z (%): 220(18), 111(80), 144(100). H NMR (DMSO-d ), ppm: 9.65 (br, 1H, Pz), 8.69, 8.23, 8.09 (m, m, m, 5H,
6
13
Ph), 6.75 (m, 1H, Pz), 6.67 (d, 1H, Pz). C NMR (DMSO-d ), ppm: 173.5, 142.9, 129.8, 129.5, 129.5, 127.6, 127.2, 108.3.
6
5. Yield: 76%, C H C N PdS . Elemental analysis found (Cal.): C 32.55 (32.09), H 2.45 (2.45), N 6.99 (6.80). MS
11 10 l2 2 2
(EI-MS), m/z (%): 234 (19), 125 (78), 158 (100).
6. Yield: 70%, C H Cl N PdS . Elemental analysis found (Cal.): C 33.77 (33.86), H 3.79 (2.84), N 6.60 (6.58). MS
12 12 2 2 2
(EI-MS), m/z (%): 248 (20), 139 (70), 172 (100).
X-ray crystallography. Details pertinent to the crystal structure determination of Pd(II) complexes 5 and 6 are
listed in Table 1. Crystals of the appropriate size were selected (in perfluorinated oil [23] at room temperature) and the data
were collected at 133 2 K using a STOE IPDS II diffractometer with graphite-monochromated MoK radiation
α
2
(λ = 0.71069 Å). The system was equipped with an Oxford Cryostream low-temperature unit. Final refinement on F was
carried out by the full-matrix least-squares technique. Structure solutions and refinements were accomplished using SIR97
[24], SHELXL-97 [25], and WinGX [26].
Computational methods. Density functional theory (DFT) calculations were performed with the TURBOMOLE
3
program package [27]. The RI-DFT method [28] applying the B–P86 functional [29] with the default grid size m was used
for all calculations. The starting structure was obtained from the X-ray crystal structure of the corresponding molecule. The
initial geometry optimization was performed with the split-valence basis set def2-SV(P) [30] for all atoms. The obtained
geometry was optimized for the second time applying the triple zeta basis set def2-TZVP [30] for all atoms.
TABLE 1. Crystal Data and Structure Refinement Parameters for Complexes 5 and 6
Empirical formula
Formula weight
Temperature
C H Cl N PdS (6)
12 12 2 2 2
C H Cl N PdS ⋅CH Cl (5)
11 10 2 2 2 2
2
496.56
133(2)
425.66
133(2)
Wavelength, Å
0.71069 (MoK )
α
Crystal system
Triclinic
Monoclinic
C(2)/c
Space group
P-1
Unit cell dimensions a, b, c, Å
α, β, γ, deg.
7.02(12), 9.08(13), 14.14(2)
25.70(14), 8.68(7), 16.10(12)
71.62(12), 85.38(13), 88.32(13)
–, 111.29(7), –
3349.2(4)
8
3
Volume, Å
851.9 (2)
2
Z
3
Density, mg/m
1.936
1.688
–1
Absorption coefficient, mm
1.953
1.664
F(000)
488
1680
Crystal size, mm
0.11×0.07×0.06
1.52 to 27.32
0.17×0.15×0.09
1.70 to 27.38
θ range, deg.
Index ranges
h 9; k 11; l 18
13418 / 3823
27.32, 99.8
3823 / 0 / 191
0.839
h 33; k 11; l 20
25126 /3776
27.38, 98.9
3776 / 0 / 174
1.059
Collected / independent reflections
Completeness to θ
Data / restraints / parameters
2
Goodness-of-fit on F
2 2
Final R indices [F > 2σ(F )]
0.0864
0.0470
R indices (all data)
0.1903
0.0588
3
Largest diff. peak and hole, e/Å
1.696 and –0.964
0.953 and –1.733
161

RESULTS AND DISCUSSION
Scheme 1 shows an overview of the synthetic route for compounds 1-3. The reactions are straightforward, efficient
and performed at ambient temperature adopting the literature procedure [22]. The coupling reactions between pyrazole
derivatives and phenyl(chloro)dithioformate were carried out in the presence of an equimolar amount of trimethylamine. The
Et N⋅HCl adduct can easily be removed by filtration from the solution, leaving behind the desired compounds. The reactions
3
afforded the desired products in a reasonably pure form and an excellent quantity of the required compounds (yield 76-89%)
was obtained. No side reactions/products were observed during the synthesis of compounds 1-3 (NMR analysis). All
compounds of this series are air and moisture stable, viscous oil and can be stored under aerobic conditions for a reasonably
1
13
long period of time. These compounds were characterized by H and C NMR spectroscopy in the solution state (see
EXPERIMENTAL). The structure of the compounds could easily be deduced from the consistent set of NMR parameters.
13 13
Carbon CSS in C NMR spectra in the range 200-201 ppm supports the formation of the products (1-3). All other C signals
corresponding to pyrazole and phenyl groups appear in their characteristic region of 111-155 ppm.
Scheme 1.
Synthesis
of
N,S
ligands
derived
from
phenylchlorodithioformate and pyrazole derivatives 1-3.
Ligands 1-3 show very good solubility in common organic solvents. They were dissolved in acetonitrile and treated
with an equimolar amount of the [PdCl (CH CN) ] adduct (based on PdCl contents) at room temperature (Scheme 2). The
2 3 2 2
progress in the chemical reaction can easily be monitored by the physical appearance of orange-colored precipitates within
few minutes (<5 min). The desired compound can easily be separated from the mother liquor by filtration. Palladium
complexes 5 and 6 were insoluble in polar organic solvents such as DMSO, CH Cl , and CH Cl at room temperature,
2
2
3
however, the solubility of complex 4 could be improved at high temperatures (30-40 °C) in DMSO. The structural elucidation
of the complexes was carried out by the elemental analysis and mass spectrometry. The fragmentation pattern deduced from
the MS data was quite supportive towards the expected structures. For complexes 4-6 molecular ion peaks were not observed
and the peak with the highest m/z value corresponds to the respective free ligand. It indicates that ligands are loosely bound to
metal and detached in the presence of 70 eV energy. After the dissociation of the complex the further fragmentation of
ligands takes place (see EXPERIMENTAL).
Scheme 2. Five-membered palladacycles 4-6 derived from pyrazole-1-carbodithioate
derivatives.
162

The extremely limited solubility of the synthesized complexes excludes the solution-state NMR characterization;
only complex 4 is sparingly soluble in DMSO, which allowed for the required NMR data [31]. The data obtained for complex
4 shows a characteristic carbon signal at 173.47 ppm which could be assigned unambiguously to the C=S carbon atom. The
C=S chemical shift is a good indication of the ligand coordination to metal through the S atom. Other carbon atoms and all
protons appear in the expected region with slight changes in their chemical shifts.
The orange-colored powder material obtained for all three complexes containing Pd(II) as a central metal ion was
dissolved in hot dichloromethane. Orange needle-like crystals were obtained for complexes 5 and 6 in 5 and 7 days,
respectively. Such attempts were unsuccessful to get crystals of compound 4.
Structural description of compound 5. The X-ray diffraction analysis of compound 5 (Fig. 1) reveals that it
crystallizes in the triclinic crystal system with the space group P-1. The palladium metal ion is four-coordinated (S,N sites of
ligand 2 and two chloro functions) and adopts a distorted square planar geometry with the sum of all bond angles around the
metal ion being 360°. The distortion is obvious because of the ligand, making a five-membered metallacycle. The five-
membered metallacycle contains an acute angle ∠N8–Pd1–S1 of 84.61°, as expected. Other angles around the Pd(II) ion
were in the expected range, i.e. ∠Cl1–Pd1–Cl2 90.85°, ∠Cl2–Pd1–S1 85.05, except ∠N8–Pd1–Cl1 99.53° [32]. The methyl
group attached to the ligand pyrazolyl moiety is predominantly involved to cause the change. Bond lengths around the metal
center are within the expected limits: Pd–Cl1 233.4 pm, Pd1–Cl2 228.1 pm, and Pd1–N8 201.1 pm while the Pd1–S1 bond is
shorter (223.4 pm) than the Pd–S (DTC) bond (227.9 pm, 229.7 pm) [33]. The elongation of the Pd1–Cl1 bond in the
2
complex clearly reflects the greater trans effect of S compared with that of N. The C17 atom being sp -hybridized bears
a trigonal planar geometry with bond lengths C17–S1 166.1, C17–S5 171.3, and C17–N9 134.7. The data show that the π
electron pair is localized on S1 which causes an elongation in the CS bond (Table 2).
The Pd(Ph(3-Me–Pz)CS )Cl building units of complex 5 are associated with each other via Cl2---S5 and Cl1---H22
2 2
interactions (316.3 pm and 261.6 pm), respectively, making a 1D supramolecular chain. The two adjacent chains are held
together via CH Cl molecules, as shown in Fig. 2.
2 2
Description of compound 6. The molecular structure of palladium complex 6 is shown in Fig. 3 and the data
pertinent to the structure solution and refinements are summarized in Table 1. It crystallizes in the monoclinic crystal system
with the space group C2/c. The coordination number of the palladium ion is four (S,N sites of ligand 3 and two chloro ions).
Fig. 1. Molecular structure of
compound 5 with partial numbering
scheme, thermal ellipsoids drawn at
a 50% probability level, a CH Cl
2
2
solvent molecule and hydrogen
atoms are omitted for clarity.
163

TABLE 2. Comparison of Selected Bond Lengths (Å) and Bond Angles (deg.), Experimental and Calculated for Complexes
5 and 6
Complex 5
Experimental
Calculated
Complex 6
Experimental
Calculated
Pd1–N8
Pd1–S1
2.011(13)
2.234(4)
2.281(4)
2.335(3)
1.662(12)
1.713(12)
1.346(17)
99.5(3)
2.069
2.251
2.281
2.303
1.668
1.758
1.385
97.8
Pd1–N1
Pd1–S1
2.034(4)
2.223(11)
2.278(11)
2.323(11)
1.738(4)
1.668(4)
1.358(5)
84.33(10)
85.91(4)
99.72(10)
90.19(4)
120.2(3)
119.0(3)
120.8(2)
2.071
2.233
2.285
2.311
1.763
1.672
1.389
84.2
Pd1–Cl2
Pd1–Cl1
Pd1–Cl1
Pd1–Cl2
S1–C17
S2–C1
S5–C17
S1–C1
N9–C17
C1–N2
N8–Pd1–Cl1
Cl2–Pd1–Cl1
S1–Pd1–Cl2
N9–C17–S1
N9–C17–S5
S1–C17–S5
N1–Pd1–S1
S1–Pd1–Cl1
N1–Pd1–Cl2
Cl1–Pd1–Cl2
N2–C1–S1
N2–C1–S2
S1–C1–S2
90.9(12)
85.1(13)
119.3(9)
114.8(9)
125.9(8)
90.6
86.3
86.6
99.3
119.8
114.2
126.0
90.2
120.0
117.6
122.4
Fig. 2. 2D supramolecular network of compound 5 stabilized by Cl⋯S and Cl⋯H
interactions. The adjacent chains are linked through solvent molecules; hanging
contacts are omitted for clarity.
Palladium adopts a distorted square planar surrounding similar to that in complex 5, with the sum of all bond angles of 360°
(around the metal ion). The complex bears an endocyclic acute angle ∠N1–Pd1–S1 of 84.33°, as expected. Other angles
around the Pd ion are within the permissible range ∠Cl1–Pd1–Cl2 90.19°, ∠Cl1–Pd1–S1 85.91°, and ∠N1–Pd1–Cl2 99.72°
as observed for the complex discussed above. The Pd–Cl/S/N bond lengths are within the expected limits: Pd–Cl1 227.8 pm,
Pd1–Cl2 232.3 pm, Pd1–N1 203.4 pm, and Pd1–S1 222.3 pm. The difference in Pd1–Cl1 and Pd1–Cl2 bonds is due to the
presence of different donor atoms, i.e., N and S of the ligand in the trans position. Other structural features are very close to
molecule 5.
The solid-state structure of compound 6 shows that the molecules assemble into a layer structure through Cl---H(pz)
non-bonding intermolecular interactions: Cl1–H5B 293.8 pm, Cl1–H12A 288.0 pm, Cl2–H3 272.2 pm, and Cl2–H7
280.6 pm (Fig. 4).
The secondary interactions in the molecules, as discussed above, are very useful to make the parent compound
biologically active. These interactions make the molecule efficient to bind with polar biological macromolecules such as
DNA and can be used for treatment of diseases such as cancer [34-36].
164

Fig. 3. Molecular structure of
compound with partial
6
a
numbering scheme, ellipsoids are
drawn at a 50% probability level,
all hydrogen atoms are omitted
for clarity.
Fig. 4. 2D supramolecular layered network of compound 6 stabilized by Cl⋯H interactions. The
five-membered ring containing Pd is shown shaded and hanging contacts are omitted for clarity.
The solid-state data for bond lengths and angles of complexes 5 and 6 were reproduced by DFT calculations using
the TURBOMOLE program package. The data obtained were compared with the experiment and found to be in close
agreement (Table 2).
CONCLUSIONS
Three ligands, namely phenyl-1H-pyrazole-1-carbodithioate, phenyl-3-methyl-1H-carbodithioate, and phenyl-3,5-
dimethyl-1H-carbodithioate were prepared and treated with PdCl . All reactions were carried out at ambient temperature. The
2
ligand derivatives showed the excellent reactivity towards Pd(II) metal. Three complexes containing the Pd(II) ion were
isolated in a reasonably pure form. All complexes bear the PdCl function, which can be used for secondary reactions.
2
Complexes are mononuclear and exhibit poor solubility in CH Cl, CH Cl , and C H , which did not allow the full NMR
3 2 2 6 6
165

characterization, except complex 4. To study the secondary reactivity and applications in the field of bio-inorganic chemistry
these complexes are under investigation.
S. A. Khan is grateful to Higher Education Commission (HEC) Pakistan for SRGP No. 21-
1217/SRGP//R&D/HEC/2016 University of Education Lahore. E. Khan thanks the Higher Education Commission (HEC),
Pakistan under National Research Funds for Universities (NRPU) No. 20-1488.
The crystallographic data corresponding to compounds 5 and 6, have been deposited with the Cambridge
Crystallographic Data Centre (CCDC) as supplementary publications Nos. CCDC 1014352 and 1014353. These data can be
obtained free of charge at www.ccdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystallographic Data Centre,
12 Union Road, Cambridge CB2 1EZ, UK; Fax: + 44-1223-336-033; e-mail: deposit@ccdc.cam.ac.uk).
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