Theoretical and Comparative Study of the Complex [RuCl₃(H₂O)₂(Gly)] by Density Functional Theory

Kátia Meirelles D. de Sousa^1*, Marcio Adriano S. Chagas², Jesyca Mayra F. D. dos Santos¹, Anderson D. Galvão¹, Fabrício Tarso de Moraes¹, Andressa Teixeira Barros Nunes Ribeiro¹, Dário Batista Fortaleza¹, Kelly Aparecida da Encarnação Amorim¹, Wagner B. dos Santos¹

¹Materials Research Lab, Federal University of Mato Grosso—Campus II, Barra do Garças, Brazil.
²Institute of Chemistry, Brasília University, UNB, Brasília, Brazil.

DOI: 10.4236/ojic.2018.81004                

Abstract

In this work, the use of computational methods was essential to distinguish the three possible isomeric structures of the [RuCl₃(H₂O)₂(Gly)] molecule. The characterization of these molecules was performed using IR, NMR and UV-VIS simulations. Some calculations related to the optimization of structures and properties such as chemical hardness and dipole moment were also conducted. The fac-cis isomer presented promising data when compared to the experimental data, indicating that this is the likely experimentally synthesized isomer. This study demonstrates the technical utility of the computational calculations by virtue of situations that prevent the realization of X-ray diffraction.

Keywords

Computational Methods, Isomeric Structures, Simulations

1. Introduction

Computational calculations are widely used in research to confirm geometric structures and to determine the properties of coordination compounds [1] [2] [3] [4] , especially in cases where obtaining a single crystal for X-ray diffraction is not possible [5] [6] or inconclusive [3] [7] .

Chagas [8] began to develop the study of the complex [RuCl₃(H₂O)₂(Gly)] in 2012. In biological tests performed by Salama [9] , Chagas [8] observed the potential Leishmanicidal activity of its complex. Martínez et al. [10] , Iniguez et al. [11] and Barbosa et al. [12] demonstrated that some of their ruthenium compounds exhibited improved antileishmanial activity compared with the reference compound and their free ligand.

Structural variations depending on the size of the molecule, the position of the ligands and their spatial characteristics such as flatness and three-dimensionality help to understand the action of these molecules in the biological environment, as the interaction of a molecule with a biological receptor depends on this type of structural information [13] [14] . Previous research has shown the utility and exploitation of structural knowledge in areas such as catalytic activity and the use of computational calculations in these studies [15] [16] . Gianferrara, Bratsos and Alessio [17] give a good account of the conditions mentioned in the paragraph beginning, based on some examples such as cisplatin and ruthenium compounds (NAMI-A and KP1019), which are anticancer drugs currently in use and under development, respectively.

This study used computational methods to determine the possible geometric isomers of the compound [RuCl₃(H₂O)₂(Gly)], in comparison with experimental data, illustrating the usefulness of computational methods to elucidate the possible geometrical structures of a compound in situations in which a single crystal for X-ray diffraction cannot be obtained.

2. Methodology

All calculations were performed using the Gaussian program package 09 [18] . The geometries were optimized by the DFT method (Density Functional Theory) and the functional hybrid meta-GGA M06-2x [19] , and confirmed by vibrational analysis. The basis set used was 6-311++G(d,p) [20] for all atoms except for Ruthenium, which was treated with the basis sets SDD (Stuttgart/double-ζ Dresden) and ECP (effective core potential) for the innermost electrons of the ruthenium atom [21] . The harmonic vibrational frequencies were calculated with the analytical second derivative, without the presence of imaginary frequencies. For the calculations of 35 excited states, the time dependent method (TDDFT) with an open layer was used with a polarized solid model to determine the effect of the solvent water molecule through IEF (integral equation formalism). For the comparison of nuclear magnetic resonance, the calculation was performed by the GIAO method (Atomic Orbital Measure Independent) [22] for ¹³C and ¹H in the presence of the solvent water. All DFT calculations employed the keyword int (grid = ultrafine). All calculations were performed at the Federal University of Mato Grosso, Laboratório de Estudos de Materiais. All experimental data were obtained for comparison of the findings [8] .

3. Results and Discussion

The [RuCl₃(H₂O)₂(Gly)] molecule described by Chagas [8] , can generate three possible geometric isomers: fac-cis-diaquotrischloroglycinatoruthenium III, mer-cis-diaquotrischloroglycinatoruthenium III and mer-trans-diaquotrischloroglycinatoruthenium III. As shown in Figure 1.

To determine which isomer was synthesized by Chagas [8] , computational methods were used to investigate the characteristics of each isomer compared to the experimental data.

3.1. Energy of the Geometrical Isomers

Table 1 shows the data obtained from the energy optimization of each isomer. The data show that the mer-trans isomer showed the largest relative difference when compared to the fac-cis molecule with the lowest energy. The fac-cis molecule, with lower energy compared to the other two isomers, had greater stability. However, the energies of the three structures were very close and the lowest energy does not guarantee formation of the compound experimentally. Thus, IR, UV-vis and NMR simulations were performed to elucidate the structure [5] [6] [23] .

3.2. Infrared Simulation

The infrared frequencies of the three isomers showed similar values to each other. It was also observed that, when compared to the experimental data, the fac-cis and mer-trans isomers demonstrated a closer approximation as show in Table 2.

The fac isomer showed lower frequencies than the mer isomers for the same bandwidth allocations in regions below 1000 cm⁻¹. However, a difference was

Figure 1. Structure of the molecule isomers [RuCl₃(H₂O)₂gly].

Table 1. Relative energies of isomers of the molecule [RuCl₃(H₂O)₂gly].

Table 2. Calculated frequency by DFT of isomers [RuCl₃(H₂O)₂(Gly)], and FTIR_med (4000 - 600 cm⁻¹) with approximate assignment bands.

Not observed. νa: Asymmetrical stretch; νs: Symmetrical stretch; δa: Asymmetrical bending; δs: symmetrical bending; ρw: Wagging deformation; ρr: Rocking deformation.

not observed between mer-trans and mer-cis, which did not conform to any general pattern.

$RMS=\sqrt{\frac{1}{n-1}\underset{i}{\overset{n}{{\displaystyle \sum }}}{\left(v_i^{cal}-v_i^{\exp }\right)}^2}$

The root mean square error (RMSE) between the experimental and the calculated frequency of the molecules were 42.44 cm⁻¹ (fac-cis), 75.67 cm⁻¹ (mer-cis) and 37.36 cm⁻¹ (mer-trans), with the lowest RMSE found for the mer-trans molecule, according to the above equation [24] . The overestimated values of the calculated frequency were due to neglecting anharmonicity. The calculation was performed on a single molecule, disregarding intermolecular interactions [25] .

The theoretical and experimental spectra in Figure 2 and Figure 3 showed characteristic peaks related to the glycine molecule and the compound. The carboxylate group showed variations between asymmetric and symmetric peaks, which assisted in the distinction of the three isomeric structures of the theoretical spectra as fac-cis (396 cm⁻¹), mer-cis (558 cm⁻¹) and mer-trans (276 cm⁻¹). This distinction was observed in a previous work was well Alam et al. [26] . The

Figure 2. Theoretical spectrum.

Figure 3. Experimental spectrum.

experimental spectrum showed a variation between asymmetric and symmetric peaks of 276 cm⁻¹. The peak at 676 cm⁻¹ was assigned to a “wagging” group (COO⁻) in the fac-cis isomer and was not observed in the mer isomers.

3.3. Ultraviolet-Visible Simulation

Table 3 shows the data on electron density-related oscillator strength. Ligand charge transfer to the metal (LMCT) can be evidenced by the HOMO and

Table 3. Electronic density of the molecular frontier orbitals.

LUMO, referring to the excited states shown in Table 4. The excited state closest to the experimental value was presented by the fac-cis molecule.

The values related to states 19 and 26 (fac-cis), 19 and 22 (mer-cis) and 22 and 27 (mer-trans) show π-π* type transitions relating to the glycine binder. The greatest contribution of the chlorides to the metal center occurred in states 19, 16 and 19 of the fac-cis structures, mer-cis and mer-trans, respectively.

3.4. Molecular Properties

The HOMO is the occupied orbital with the highest energy that has the ability to donate electrons, while the LUMO is the unoccupied orbital with the least energy that has the ability to accept electrons; the difference between them can explain charge transfer within a molecule [27] [28] . The HOMO and LUMO data energies as well as their differences are shown in Table 5.

The range of energy between HOMO and LUMO as well as the hardness and chemical dipole moment may provide additional information. The fac-cis molecule had the largest energy difference and greater chemical hardness, making it more stable kinetically and less favorable to adding electrons to LUMO or extracting electrons from HOMO, i.e. this molecule had low chemical reactivity [29] [30] .

The dipole moment implies that the higher the stronger value is an intermolecular interaction [30] , The mer-trans molecule should form stronger intermolecular bonds than the other two isomers, for example with other molecules or DNA bases, as shown previously Pramanik et al. [30] and Das et al. [31] .

Table 4. Excitation energies (eV), Oscillator strength (f) and wave length (nm) calculated and experimental.

Table 5. Calculated data of some molecular properties.

According to the Koopman theorem, the chemical hardness η can be described by the following equation, $\eta =\frac{E_{Lumo}-E_{Homo}}{2}$ [32] .

3.5. Nuclear Magnetic Resonance Simulation (nmr)

Table 6 is presented the magnetic resonance of ¹³C and ¹H in comparison with experimental data.

The NMR theoretical data indicate overestimated values. These overestimated values can be explained by the method and the basis set, resulting in poor results [33] . Another explanation for such high values is that the simulation was performed on a single molecule, meaning that various types of chemical interactions were not considered theoretically [25] .

The NMR data for the mer-cis isomer provided a close approximation to the experimental data of the group (COO⁻), but the other NMR results were poorly related to the other two structures. Therefore, a correction of the basis sets and/or the method may provide better results in general.

4. Conclusions

Although some experimental data showed overestimated values, the spectral characteristics were maintained according to the experimental data.

Table 6. Magnetic resonance ¹³C and ¹H.

The fac-cis-diaquotrischloroglycinatoruthenium III and mer-trans-diaquo- trischloroglycinatoruthenium III isomer presented data indicating greater stability compared to the other two isomers and was confirmed by optimizing data from the UV-vis simulation, the energy of the frontier orbitals and the chemical hardness, which supported its greater stability.

The fac-cis-diaquotrischloroglycinatoruthenium III and mer-trans-diaquo- trischloroglycinatoruthenium III isomer presented the lowest RMSE in comparison with the other structures. The difference between the RMSE of the mer-trans and fac-cis isomers was relatively small compared to the mer-cis isomer, which had the highest value. Thus, observing only the frequency values cannot differentiate between two isomers, but allowed us to discard the mer-cis isomer, which showed the worst results.

The observation of the theoretical spectrum suggests the mer-trans structure. The mer-trans structure showed higher reactivity compared to the other structures, which implies that this molecule can be modified easily as a function of applied energy compared to the other two structures.

Analyzing the results in general, the fac-cis-diaquotrischloroglycinatoruthe- nium III isomer presented results suggesting that this was the molecule synthesized by Chagas [8] .

The data relating to the properties of these three molecules may assist in future studies addressing structural modifications and interactions with the biological environment, since the molecule [RuCl₃(H₂O)₂(Gly)] has been shown to possess antileishmanial activity.

Acknowledgements

This work was supported by CAPES.

Supporting Information

The orientation of the three structures is presented.

Conflicts of Interest

The authors declare no conflicts of interest.

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