X-ray Diffraction Study of Fluorine-Functionalized Thiosemicarbazones and Cyclometallated Compounds †
Department of Inorganic Chemistry, Faculty of Chemistry, University of Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
*
Author to whom correspondence should be addressed.
†
Presented at the 3rd International Online Conference on Crystals, 15–30 January 2022; Available online: https://iocc_2022.sciforum.net/ .
Chem. Proc. 2022, 9(1), 3; https://doi.org/10.3390/IOCC_2022-12140
Published: 12 January 2022
(This article belongs to the Proceedings of The 3rd International Online Conference on Crystals)
Abstract
:In this work, an X-ray diffraction study of fluorine-functionalized thiosemicarbazone ligands and their corresponding cyclometallated compounds is discussed. The results are in agreement with previous characterization by IR spectroscopy, 1H and 19F NMR spectroscopy. Suitable crystals were obtained for a thiosemicarbazone ligand and a cyclometallated compound. The crystal structure analyses are in accordance with the proposed structures: a fluorine-functionalized thiosemicarbazone ligand and a cyclometallated compound in which the thiosemicarbazone is a tridentate [C, N, S] ligand. A comparative study of bond distances and angles is shown, providing information about the coordination of the ligand to the metal center.
1. Introduction
In this work, fluorine-thiosemicarbazone ligands were used to synthesize cyclometallated palladium compounds. The fluorine functionality increases their solubility, which is one of the main issues when dealing with this type of species [1,2].
The ligands are widely used in coordination and organometallic chemistry due to the number of different heteroatoms and their versatile coordination to metal centers [3], generating a wide range of compounds. In addition, these ligands are relevant in the biological field; the free ligands themselves possess a certain degree of biological activity [4,5], usually enhanced by coordination to one or more metal atoms [6,7].
Furthermore, cyclometallated compounds are a large family of complexes that contain a chelate ring comprising a coordinated heteroatom–metal bond or a σ carbon–metal bond [8,9]. The metalated atom may be an aromatic [10,11] or alkenyl [12] sp2 carbon or an sp3 carbon [13]. Many of these compounds are used in catalysis, and they produce very good results in cross-coupling reactions with carbon–carbon bond formation (Suzuki–Miyaura [14,15] and Mizoroki–Heck [16,17]) and carbon–nitrogen bond formation (Buchwald–Hartwig [18,19]). Likewise, their biological activity has been shown to be quite high, and it has been tested for a huge variety of metals and ligands [20,21,22,23].
2. Results and Discussion
An X-ray diffraction study of a thiosemicarbazone ligand and the ensuing palladium cyclometallated product is discussed (see Scheme 1). The results agree with a previous characterization by IR, 1H NMR and 19F NMR spectroscopies [24]. In addition, a structural study and comparison between the two structures were carried out.
2.1. X-ray Diffraction Study
Suitable crystals for compounds were obtained by slow evaporation of a DMSO−acetone (3a) or chloroform (4b) solution, shown in Scheme 2. The X-ray diffraction study showed the proposed structures. The structures were solved by direct methods and refined by full-matrix least-squares on F2. Hydrogen atoms were included in calculated positions. Refinement converged at a final R1 = 0.0302 and wR2 = 0.0712 (compound 3a) and R1 = 0.0299 and wR2 = 0.0625 (compound 4b) with allowance for thermal anisotropy of all non-hydrogen atoms. The structure solution and refinement were carried out using the program OLEX2 [25].
2.1.1. Compound 3a
Compound 3a crystallizes in a monoclinic system, P21/n space group. The unit cell contains four molecules of thiosemicarbazone (see Figure 1). Crystal data is shown in Appendix A (Table A1).
The structure shows thiosemicarbazone in the thionic form, with E conformation [26], probably due to the intramolecular interaction (2.179 Å) between the imine nitrogen and the thioamide proton, shown in Figure 2a.
In addition, intramolecular interaction (2.378 Å) between the fluorine atom and the imine methyl group is observed. Consequently, in Figure 2b, the aromatic ring is turned away from the thiosemicarbazone plane, with a 34.34° deviation.
2.1.2. Compound 4b
Compound 4b crystallizes in a triclinic system, P-1 space group. The unit cell contains two cyclometallated molecules and eight chloroform molecules. Crystal data is shown in Appendix A (Table A2).
The thiosemicarbazone acts as a tridentate ligand (see Figure 3a), generating two five-membered chelate rings, and the compound shows a tetranuclear structure in Figure 3b, with the ligands assuming an antiparallel arrangement and being perpendicular to each other.
In one of the monomers, the palladium center (Pd1) is surrounded by the ortho aromatic carbon of the phenyl ring (C5), the imine nitrogen (N1) and two sulfur atoms (S1 and S2) exhibiting two different bonds with palladium: Pd−Schelate (S1) and Pd−Sbridging (S2).
As in the thiosemicarbazone ligand, an intramolecular interaction of ca. 2.5 Å (Figure 4) is observed between the fluorine atom and the imine methyl group. In this case, the aromatic ring is unable to rotate due to metallation, so the methyl group displays an eclipsed conformation.
2.1.3. Comparison between Bond Distances (Å) and Angles (°)
A comparative study of bond distances (Table 1) and angles (Table 2) between the thiosemicarbazone ligand 3a and the cyclometallated compound 4b was carried out.
The N(1)-C(7) and C(5)-C(6) bonds are somewhat longer in the cyclometallated compound due to the back-bonding of the palladium metal to the N(1) and the C(5) atoms, respectively.
The C(9)-N(2) and C(9)-S(1) bond differences are because of metallation; since it occurs in the thiolic form of the thiosemicarbazone, tautomerization of the C(9)=S(1) double bond is thus needed.
The C(9)-N(3) bond is slightly longer, probably due to the tautomerization of the thionic bond and the coordination of the sulfur atom.
The N(2)-C(9)-S(1), N(2)-C(9)-N(3) and N(3)-C(9)-S(1) angles change upon going to the cyclometallated compound due to the tautomerization and the coordination of the sulfur atom to palladium.
The C(5)-C(6)-C(7) and N(1)-N(2)-C(9) are smaller due to the formation of the five-membered chelate ring upon cyclometallation.
2.1.4. Palladium Bonds and Angles in Compound 4b
3. Conclusions
- X-ray structural analysis was carried out for a thiosemicarbazone ligand and its cyclometallated palladium derivative.
- A comparative study allowed the determination of variations in bond distances and angles in the structure of the ligand after the cyclometallation process.
- The metal atom displays the typical square-planar geometry for palladium.
Author Contributions
Conceptualization, M.R.-S. and P.M.-C.; methodology, M.R.-S.; software, M.R.-S.; validation, M.R.-S. and P.M.-C.; formal analysis, M.R.-S.; investigation, M.R.-S. and P.M.-C.; resources, J.M.O. and J.M.V.; data curation, M.R.-S. and P.M.-C.; writing—original draft preparation, M.R.-S.; writing—review and editing, M.R.-S.; visualization, M.R.-S. and P.M.-C.; supervision, J.M.O. and J.M.V.; project administration, M.R.-S. and J.M.V.; funding acquisition, J.M.O. and J.M.V. All authors have read and agreed to the published version of the manuscript.
Funding
This research was funded by Xunta de Galicia (Galicia, Spain) under the Grupos de Referencia program (GRC 2019/014).
Conflicts of Interest
The authors declare no conflict of interest.
Appendix A
Table A1.
Crystal data and structure refinement for 3a.
| Identification code | 3a |
| Empirical formula | C11H14FN3S |
| Formula weight | 239.31 |
| Temperature | 100(2) K |
| Wavelength | 0.71073 Å |
| Crystal system | Monoclinic |
| Space group | P21/n |
| Unit cell dimensions | a = 5.8663(2) Å, α = 90° |
| b = 19.5573(6) Å, β = 105.0047(10)°. | |
| c = 10.5485(3) Å, γ = 90°. | |
| Volume | 1168.96(6) Å3 |
| Z | 4 |
| Density (calculated) | 1.360 Mg/m3 |
| Absorption coefficient | 0.266 mm−1 |
| F(000) | 504 |
| Crystal size | 0.240 × 0.127 × 0.119 mm3 |
| Theta range for data collection | 2.083 to 26.366°. |
| Index ranges | −6 ≤ h ≤ 7, −24 ≤ k ≤ 24, −13 ≤ l ≤ 13 |
| Reflections collected | 32894 |
| Independent reflections | 2399 [R(int) = 0.0527] |
| Completeness to theta = 25.242° | 100.0% |
| Refinement method | Full-matrix least-squares on F2 |
| Data/restraints/parameters | 2399/0/147 |
| Goodness-of-fit on F2 | 1.050 |
| Final R indices [I > 2sigma(I)] | R1 = 0.0302, wR2 = 0.0712 |
| R indices (all data) | R1 = 0.0372, wR2 = 0.0751 |
| Largest diff. peak and hole | 0.246 and −0.266 e·Å−3 |
Table A2.
Crystal data and structure refinement for 4b.
| Identification code | 4b |
| Empirical formula | C64H52Cl12F4N12Pd4S4 |
| Formula weight | 2044.41 |
| Temperature | 100(2) K |
| Wavelength | 0.71073 Å |
| Crystal system | Triclinic |
| Space group | P-1 |
| Unit cell dimensions | a = 13.6814(4) Å, α = 87.1620(10)° |
| b = 15.1512(4) Å, β = 79.4790(10)° | |
| c = 19.9092(5) Å, γ = 64.1110(10)° | |
| Volume | 3648.25(17) Å3 |
| Z | 2 |
| Density (calculated) | 1.861 Mg/m3 |
| Absorption coefficient | 1.585 mm−1 |
| F(000) | 2016 |
| Crystal size | 0.180 × 0.160 × 0.070 mm3 |
| Theta range for data collection | 2.082 to 28.342°. |
| Index ranges | −18 ≤ h ≤ 18, −20 ≤ k ≤ 20, −26 ≤ l ≤ 26 |
| Reflections collected | 112138 |
| Independent reflections | 18195 [R(int) = 0.0390] |
| Completeness to theta = 25.242° | 99.9% |
| Refinement method | Full-matrix least-squares on F2 |
| Data/restraints/parameters | 18195/0/1020 |
| Goodness-of-fit on F2 | 1.049 |
| Final R indices [I>2sigma(I)] | R1 = 0.0299, wR2 = 0.0625 |
| R indices (all data) | R1 = 0.0390, wR2 = 0.0666 |
| Largest diff. peak and hole | 2.352 and −1.613 e·Å−3 |
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Scheme 1.
Reaction sequence leading to the synthesis of cyclometallated complexes containing fluor atoms.
Scheme 1.
Reaction sequence leading to the synthesis of cyclometallated complexes containing fluor atoms.
Scheme 2.
Compounds 3a and 4b were studied by X-ray diffraction study.
Figure 1.
Molecular structure of ligand 3a. Thermal ellipsoids are shown at 50% probability level.
Figure 2.
(a) Intramolecular interactions between F(1)-H and N(1)-H. (b) Deviation of the phenyl ring from the thiosemicarbazone plane.
Figure 2.
(a) Intramolecular interactions between F(1)-H and N(1)-H. (b) Deviation of the phenyl ring from the thiosemicarbazone plane.
Figure 3.
(a) Molecular structure of a monomer of 4b. Thermal ellipsoids are shown at 50% probability level. (b) Molecular structure of 4b, with antiparallel and perpendicular arrangement of each thiosemicarbazone.
Figure 3.
(a) Molecular structure of a monomer of 4b. Thermal ellipsoids are shown at 50% probability level. (b) Molecular structure of 4b, with antiparallel and perpendicular arrangement of each thiosemicarbazone.
Figure 4.
Intramolecular interaction of F(1)-H in compound 4b.
Table 1.
Comparison between bonds in compounds 3a and 4b.
| Bond | 3a/Å | 4b/Å |
|---|---|---|
| N(1)-C(7) | 1.2870(18) | 1.304(3) |
| C(9)-N(2) | 1.3677(18) | 1.297(3) |
| C(9)-S(1) | 1.6816(14) | 1.807(3) |
| C(9)-N(3) | 1.3297(18) | 1.361(3) |
| C(5)-C(6) | 1.399(2) | 1.424(4) |
Table 2.
Comparison between angles in compounds 3a and 4b.
| Angle | 3a/° | 4b/° |
|---|---|---|
| C(5)-C(6)-C(7) | 121.14(12) | 116.3(2) |
| N(1)-N(2)-C(9) | 117.90(11) | 114.1(2) |
| N(2)-C(9)-S(1) | 119.57(11) | 125.16(19) |
| N(2)-C(9)-N(3) | 115.62(12) | 120.6(2) |
| N(3)-C(9)-S(1) | 124.81(11) | 114.08(18) |
Table 3.
Distance bonds (Å) and angles (°) around palladium metal center.
| Bond | /Å | Angle | /° |
|---|---|---|---|
| Pd(1)-N(1) | 1.996(2) | N(1)-Pd(1)-C(5) | 81.24(9) |
| Pd(1)-C(5) | 2.003(2) | N(1)-Pd(1)-S(1) | 83.31(6) |
| Pd(1)-S(2) | 2.3060(6) | C(5)-Pd(1)-S(2) | 94.39(8) |
| Pd(1)-S(1) | 2.3729(6) | S(2)-Pd(1)-S(1) | 100.81(2) |
| N(1)-Pd(1)-S(2) | 174.68(6) | ||
| C(5)-Pd(1)-S(1) | 164.07(8) |
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Rúa-Sueiro, M.; Munín-Cruz, P.; Ortigueira, J.M.; Vila, J.M. X-ray Diffraction Study of Fluorine-Functionalized Thiosemicarbazones and Cyclometallated Compounds. Chem. Proc. 2022, 9, 3. https://doi.org/10.3390/IOCC_2022-12140
AMA Style
Rúa-Sueiro M, Munín-Cruz P, Ortigueira JM, Vila JM. X-ray Diffraction Study of Fluorine-Functionalized Thiosemicarbazones and Cyclometallated Compounds. Chemistry Proceedings. 2022; 9(1):3. https://doi.org/10.3390/IOCC_2022-12140
Chicago/Turabian StyleRúa-Sueiro, Marcos, Paula Munín-Cruz, Juan M. Ortigueira, and José M. Vila. 2022. "X-ray Diffraction Study of Fluorine-Functionalized Thiosemicarbazones and Cyclometallated Compounds" Chemistry Proceedings 9, no. 1: 3. https://doi.org/10.3390/IOCC_2022-12140
