Abstract
In this data article, density functional theory (DFT) calculated data for the optimized geometries and electronic structure data of the neutral, oxidized and reduced forms of the fac and mer isomers of tris(amino-pent-3-en-2-onato-N,O)ruthenium(III) as representative example of tris(β-ketoiminato)ruthenium(III) complexes is provided. Energy-level diagrams of the neutral, oxidized and reduced molecules, show the effect on the molecular energy levels and the electron occupation of the frontier orbitals, when the neutral complex is oxidized or reduced. The DFT calculated data also confirms the spin state of the molecules and show that the fac and mer isomers of tris(amino-pent-3-en-2-onato-N,O)ruthenium(III) are equi-energetic.
Keywords: Bidentate N,O ligands; (Z)-4-Aminopent-3-en-2-one; Ruthenium(III); DFT; Low-spin
Specifications Table
| Subject | Chemistry |
| Specific subject area | Computational chemistry. |
| Type of data | Table Image Figure |
| How data were acquired | Electronic structure calculations, using the Gaussian 2016 programme. |
| Data format | Raw Analyzed |
| Parameters for data collection | Suitable xyz coordinates for the input geometries were constructed using CHEMCRAFT. The input coordinates were used in the input file of the DFT program, example input files are provided in the supplementary information. |
| Description of data collection | Data were collected from DFT output files |
| Data source location | Department of Chemistry, University of the Free State, Nelson Mandela Street, Bloemfontein, South Africa |
| Data accessibility | With the article |
| Related research article | Tankiso Lawrence Ngake, Johannes. H. Potgieter and Jeanet Conradie, Tris(β-ketoiminato)ruthenium(III) complexes: Electrochemical and computational chemistry study. Electrochimica Acta 320 (2019) 134635 DOI 10.1016/j.electacta.2019.134635. |
Value of the Data
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1. Data
This data article provides the density functional theory (DFT) calculated geometrical and electronic structure data of the neutral, oxidized and reduced forms of the fac and mer isomers of tris(amino-pent-3-en-2-onato-N,O)ruthenium(III), 1 (Fig. 1), as representative example of tris(β-ketoiminato)ruthenium(III) complexes, that can electrochemically be oxidized and reduced [1]. Table 1 provides the DFT calculated energies for the different spin states possible for 1, namely ½, 3/2 or 5/2, obtained by different DFT methods. The data shows that the neutral d5 molecule has a low spin state of ½, therefore contains one unpaired electron, as is experimentally observed for Ru(III) complexes [2,3]. The data in Table 1 further shows that the fac and mer isomers of 1 are near equi-energetic, thus both isomers are energetically possible. The data in Table 2 shows that the oxidized tris(β-ketoiminato)ruthenium(III) complexes are doublets (S = 1, two unpaired electrons), while the reduced complexes are singlets (S = 0, no unpaired electrons). The data in Table 3 provides the density functional theory calculated ionization potential and electron affinity for fac and mer isomers of tris(amino-pent-3-en-2-onato-N,O)ruthenium(III). Fig. 2 illustrates the effect on the energy of the molecular energy levels and the electron occupation of the frontier orbitals, when the neutral complex is oxidized or reduced for the fac and mer isomers of 1 respectively. The mainly d-based anti-bonding molecular orbitals of the fac and mer isomers of 1 are shown in Fig. 3 and Fig. 4 respectively.
Fig. 1.
Structure of fac and mer tris(amino-pent-3-en-2-onato-N,O)ruthenium(III).
Table 1.
Relative energies (ΔE) for different spin states (S) of fac and mer tris(amino-pent-3-en-2-onato-N,O)ruthenium(III), as calculated with the indicated functional.
| Isomer | S | B3LYPa | B3LYP-D3a | PBE-D2 | OLYP-D3 | BP86-D3 | PW91-D3 |
|---|---|---|---|---|---|---|---|
| fac | ½ | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| 3/2 | 1.93 | 2.38 | 1.97 | 1.90 | 1.94 | 1.97 | |
| 5/2 | 3.27 | 3.80 | 3.58 | 3.09 | 3.41 | 3.52 | |
| mer | ½ | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.01 |
| 3/2 | 1.59 | 2.07 | 1.68 | 1.41 | 1.67 | 1.71 | |
| 5/2 | 3.09 | 3.65 | 3.45 | 2.94 | 3.33 | 3.39 |
From Ref. [1].
Table 2.
Relative energies (ΔE) for different spin states (S), of reduced and oxidized fac and mer tris(amino-pent-3-en-2-onato-N,O)ruthenium(III), calculated with the indicated functional.
| S | B3LYP | B3LYP-D3 | PBE-D2 | BP86-D3 | OLYP-D3 | PW91-D3 | |
|---|---|---|---|---|---|---|---|
| Fac anion | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| 1 | 1.56 | 1.57 | 1.55 | 1.53 | 1.57 | 1.54 | |
| Mer anion | 0 | 0.02 | 0.07 | 0.07 | 0.05 | 0.08 | 0.05 |
| 1 | 1.51 | 1.53 | 1.53 | 1.51 | 1.54 | 1.53 | |
| Fac cation | 0 | 0.20 | 0.15 | 0.00 | 0.01 | 0.03 | 0.03 |
| 1 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | |
| Mer cation | 0 | 0.26 | 0.22 | 0.10 | 0.07 | 0.12 | 0.05 |
| 1 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 |
Table 3.
Ionization potential (IP) and electron affinity (EA) of fac and mer tris(amino-pent-3-en-2-onato-N,O)ruthenium(III), calculated with the indicated functional.
| B3LYP | B3LYP-D3 | PBE-D2 | BP86-D3 | OLYP-D3 | PW91 | |
|---|---|---|---|---|---|---|
| IP fac | 5.80 | 5.83 | 5.68 | 5.86 | 5.59 | 5.83 |
| IP mer | 5.82 | 5.82 | 5.66 | 5.86 | 5.60 | 5.83 |
| EA fac | 1.21 | 1.18 | 1.36 | 1.62 | 1.36 | 1.60 |
| EA mer | 1.17 | 1.15 | 1.33 | 1.57 | 1.32 | 1.55 |
Fig. 2.
The OLYP/TZP Kohn-Sham MO energy level (in eV, on the y-axis) diagrams of the frontier MOs, for all three forms of fac (left) and mer (right) of tris(amino-pent-3-en-2-onato-N,O)ruthenium(III), namely the reduced (anion, left), neutral (middle) and oxidized (cation, right) forms. The energy levels of filled MOs are shown in solid blue (for Ru-d based MOs) or dotted blue (for ligand based MOs), and the energy levels of empty MOs in red (solid red Ru-d-based, dotted red ligand based). The arrows indicate the α-electrons (up spin) and β electrons (down spin), solid arrows indicate mainly Ru-d based MOs and the dotted arrow a mainly ligand based MO.
Fig. 3.
The BP86-D3/TZ2P(C,H,O,N)/ZORA/TZ2P(Ru) metal d-based anti-bonding MOs fac tris(amino-pent-3-en-2-onato-N,O)ruthenium(III. Contour = 0.06 e/Å3.
Fig. 4.
The BP86-D3/TZ2P(C,H,O,N)/ZORA/TZ2P(Ru) metal d-based anti-bonding MOs mer tris(amino-pent-3-en-2-onato-N,O)ruthenium(III. Contour = 0.06 e/Å3.
2. Experimental design, materials, and methods
Density functional theory (DFT) calculations were performed in the gas phase on the neutral, oxidized and reduced compounds using the Gaussian 16 package [4] and the Amsterdam Density Functional (ADF) 2018 programme [5]. The data presented is obtained by different DFT methods (functional and basis set combination): (i) B3LYP functional [6,7] and the triple-ζ basis set 6-311G(d,p) on all atoms except for Ru where the Stuttgart/Dresden (SDD) pseudopotential was used to describe the metal electronic core, while the metal valence electrons were described using the def2-TZVPP basis set [8], (ii) B3LYP-D3/6-311G(d,p)/def2-TZVPP/SDD (B3LYP with the Grimme empirical dispersion correction D3) [9]), (iii) PBE-D2 (PBE with the Grimme empirical dispersion correction D3) with 6-311G(d,p) on all nonmetallic atoms and LANL2DZ with included ECP [(c), (d), [10], (a), (b)] augmented with one f-polarization function (1.235) [11] on Ru, (iv) OLYP (Handy-Cohen and Lee-Yang-Parr) [6,[12], [13], [14]] with the TZ2P (Triple ζ double polarized) basis set on all atoms (C,H,O,N) except for Ru where the ZORA/TZ2P was used, (v) BP86/TZ2P(C,H,O,N)/ZORA/TZ2P(Ru) [15,16], (vi) PW91/TZ2P(C,H,O,N)/ZORA/TZ2P(Ru) (Perdew-Wang 1991 [[b], [17], [a]]. Input coordinates were constructed using ChemCraft [18]. ADF Graphical User Interface (GUI) and Chemcraft were used to visualize the output files. The optimized coordinates, as well as example input files, are provided in the supplementary information.
Acknowledgments
This work has received support from the South African National Research Foundation (Grant numbers 113327 and 96111) and the Central Research Fund of the University of the Free State, Bloemfontein, South Africa. The High Performance Computing facility of the UFS, the CHPC of South Africa and the Norwegian Supercomputing Program (UNINETT Sigma2, Grant No. NN9684K) are acknowledged for computer time.
Footnotes
Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2019.104833.
Conflict of Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Appendix A. Supplementary data
The following is the Supplementary data to this article:
Input and output files and optimized coordinates of DFT calculations.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Input and output files and optimized coordinates of DFT calculations.