Journal of Chemistry

Journal of Chemistry / 2016 / Article

Research Article | Open Access

Volume 2016 |Article ID 3672062 | https://doi.org/10.1155/2016/3672062

Adebayo A. Adeniyi, Peter A. Ajibade, "Exploring the Ruthenium-Ligands Bond and Their Relative Properties at Different Computational Methods", Journal of Chemistry, vol. 2016, Article ID 3672062, 15 pages, 2016. https://doi.org/10.1155/2016/3672062

Exploring the Ruthenium-Ligands Bond and Their Relative Properties at Different Computational Methods

Academic Editor: Maria F. Carvalho
Received21 Sep 2015
Revised17 Nov 2015
Accepted25 Nov 2015
Published05 Jan 2016

Abstract

We report some experimental bond distances and computational models of six ruthenium bonds obtained from DFT to higher computational methods like MP2 and CCSD. The bonds distances, geometrical RMSD, and the thermodynamic properties of the models from different computational methods are similar. It is observed that optimization of molecules of many light atoms with different functional methods results in significant geometrical variation in the values and order of the computed properties. The values of the hyperpolarizabilities, HOMO, LUMO, and isotropic and anisotropic shielding are found to depend greatly on the type of the functional used and the geometrical variation rather than on the nature of basis set used. However, all the methods rated modelled Ru-S, Ru-Cl, and Ru-O bonds as having the highest hyperpolarizabilities values. The infrared spectra data obtained from the different computational methods are significantly different from each other except for MP2 and CCSD which are found to be very similar.

1. Introduction

Ruthenium complexes have received significant consideration as conductive, optical, anticancer, and antibiotic applications [116]. Besides great number of ruthenium complexes, there are many of the ruthenium-ligand bonds which are found relevant to their biological activities. The covalent bonding between Ru and N7 (guanine) is considered the predominant mode of action with DNA for Ru antitumor compounds [1719]. It was also assumed that metals can form chelates with N7 and O6 atoms of guanine [20]. The formation of a hydrolyzed Ru-O bond is very significant for the activation of ruthenium complexes for biological activities [19, 21]. The rate of hydrolysis has significant effect on the anticancer activities [2224]. Ruthenium has also been reported to bind to S of Cys. residue of Cathepsin B [2527]. Mostly for Ru anticancer activities, bonding between Ru and N7 (guanine) is considered to be the predominant mode of action with DNA [17]. However, it is also possible that binding to guanine N7 atoms is less important than other types of interaction like interaction with phosphate groups, hydrogen bonds, and so forth [28].

The computational approach is very significant for the optimization of the complexes and design of novel complexes for various applications, studying their electronic, conductive, and spectroscopic properties in relation to their stability. However, it is computationally expensive to compute the properties of ruthenium complexes using higher basis set like aug-cc-pVTZ and high perturbation method like MP2. It is therefore highly important to optimize the computational methods which are affordable for the ruthenium complexes. In this paper, we have presented different models of ruthenium complexes which are different by the type of the ruthenium-ligand (Ru-L) bonds. The types of the Ru-L bond of interest to us are Ru-C, Ru-N, Ru-O, Ru-P, Ru-S, Ru-Cl, and Ru-H which are common to many of the synthesised ruthenium complexes for various applications as shown in Table 1. The effects of the functional methods and the level of basis sets on the Ru-L bond length and their relative properties are presented with the intention to find cheaper and approachable computational methods for ruthenium complexes.


Ru-CRu-NRu-ORu-PRu-SRu-ClRu-H

1.827 [44]1.940 to 2.137 [45]2.00 to 2.01 [46]2.2587 to 2.3141 [47]2.246 to 2.266 [48]2.2971 to 2.3680 [49]1.494 [44]
1.845 to 2.220 [50]2.00 to 2.053 [46]2.0514 to 2.091 [47]2.277 [50]2.2777 to 2.3050 [51]2.327 to 3.366 [51]1.57 to 1.59 [52]
1.865 to 2.035 [53]2.0190 to 2.0914 [49]2.058 to 2.074 [54]2.279 to 2.298 [54]2.3436 to 2.3737 [55]2.359 to 2.388 [45]
2.083 [1]2.024 to 2.114 [51]2.0656 [51]2.2812 to 2.4188 [52]2.3726 to 2.3885 [53]
2.109 to 2.287 [55]2.025 to 2.047 [46]2.066 to 2.092 [44]2.31 to 2.389 [47]2.407 to 2.418 [37]
2.116 to 2.1777 [43]2.066 to 2.196 [56]2.076 to 2.109 [49]2.3165 to 2.3679 [57]2.407 to 2.4511 [46]
2.199 to 2.281 [58]2.0703 to 2.183 [53]2.0783 to 2.118 [53]2.336 [46]2.411 to 2.434 [54]
2.0792 [58]2.18 to 2.23 [59]2.363 to 2.378 [44]2.431 to 2.4823 [47]
2.107 to 2.122 [60]2.412 [56]2.434 to 2.4567 [51]
2.141 to 2.196 [44]2.4357 [1]

2. Computational Method

Six models of common ruthenium-ligand bonds which are H5Ru-CH3, H5Ru-NH2, H5Ru-OH, H5Ru-Cl, H5Ru-PH3, and H5Ru-SH3 were built to represent common types of bonds in ruthenium-ligand complexes and in ruthenium-receptor interactions. The models were optimized with DFT hybrid functional like PBE [29] and B3LYP [30] and other higher computational methods like MP2 and CCSD using mixed basis sets of SBKJC VDZ [31] for Ru atom and 6-31+G(d,p) for other atoms. Many of the properties are computed using DGDZVP for Ru, while others were treated with 6-31+G(d,p). Also, for better simulation results, the models were treated with higher perturbation method, MP2, and at higher basis set, aug-cc-pVTZ, for all the atoms including ruthenium. In all the methods, all atoms besides the Ru atom are treated with 6-31+G(d,p) basis set except when basis sets aug-cc-pVTZ was applied on all atoms. Therefore, in the methods where different basis set is applied on Ru atom, the method will be reference based on the type of basis set applied on the Ru atom. All the computational methods, B3LYP/SBKJC-VDZ, PBE/SBKJC-VDZ, MP2/SBKJC-VDZ, CCSD/SBKJC-VDZ, B3LYP/DGDZVP, PBE/DGDZVP, MP2/DGDZVP, and CCSD/DGDZVP, and all other atoms beside Ru atom were treated with 6-31+G(d,p) while in the MP2/aug-cc-pVTZ method, all the atoms were treated with the same basis set. All the computation was done using Gaussian 09 [32] and external basis set aug-cc-pVTZ for Ru atom EMSL Basis Set Library [33, 34] and incorporated into the input file in a format that Gaussian 09 programs can read. The first hyperpolarizability tensors were calculated from the Gaussian output using , where , , and [35, 36]. The atomic units (a.u.) of ß in G09 were converted into electrostatic units (esu) (1 a.u. = 8.6393 × 10−33 esu). The IR spectra of the molecules were assigned through the method of potential energy distribution (PED) contributions as implemented in VEDA package [37] and explained in the literatures [38, 39].

3. Results and Discussion

Six models of ruthenium-ligand bonds (Ru-C, Ru-N, Ru-O, Ru-Cl, Ru-P, and Ru-S) are modelled and were optimized using the functionals MP2, CCSD, PBE, and B3LYP. Many of their properties like their hyperpolarizabilities and isotropic and anisotropic shielding tensors are computed using the functionals with different basis sets like SBKJC-VDZ6-31+G(d,p), DGDZVP6-31+G(d,p), and aug-cc-pVTZ.

3.1. Bonds and the Thermodynamic Properties Dependent on Functional Methods

Different bond distances of ruthenium-ligands (Ru-L) which are reported in the literatures from their crystal structures are shown in Table 1. From the crystal structures of ruthenium complexes, the range of the experimental bond length for Ru-C is 1.827 to 2.281, that of Ru-N is 1.940 to 2.196, that of Ru-O is 2.00 to 2.23, that of Ru-Cl is 2.2971 to 2.4357, that of Ru-P is 2.2587 to 2.412, that of Ru-S is 2.246 to 2.3737, and that of Ru-H is 1.494 to 1.59 (Table 1). The general features of the experimental Ru-L bond lengths are in the order of Ru-Cl > Ru-P > Ru-S > Ru-O > Ru-N > Ru-C > Ru-H. The Ru-L bond distances of the six models which are obtained from the optimized geometries at MP2, CCSD, PBE, and B3LYP level of theories are shown in Figure 1. The general features of the Ru-L bond lengths of the six models using different computational methods show a common order of Ru-P > Ru-S > Ru-Cl > Ru-C > Ru-O > Ru-N. The observed similarity in the bond orders between the experimental and theoretical is that they both rated Ru-Cl, Ru-P, and Ru-S higher than Ru-O, Ru-N, and Ru-C. The computed range of bond values for Ru-C is 1.94 to 1.98 in the order of MP2 < PBE < B3LYP < CCSD, that of Ru-N is 1.83 to 1.87 in the order of MP2 < B3LYP < CCSD < PBE, that of Ru-O is 1.85 to 1.87 in the order of MP2 < CCSD < B3LYP < PBE, that of Ru-Cl is 2.17 to 2.21 in the order of MP2 < CCSD < B3LYP < PBE, that of Ru-P is 2.39 to 2.45 in the order of MP2 < PBE < B3LYP < CCSD, and that of Ru-S is 2.21 to 2.24 in the order of MP2 < PBE < B3LYP < CCSD. In both Ru-N and Ru-Cl, the functional PBE overestimates the bonds above other functional methods. Ru-C bond values of our model are within the common experimental bond values for Ru-C, while the values obtained for other modelled bonds are little below the common experimental values. If the bond values obtained using the MP2 are compared to the analytical values, the differences in the values of other computational methods from MP2 are calculated using simple expression and are presented in Table 2. The differences in bond values obtained using PBE compared to the analytical values from MP2 are smaller in magnitude compared to other methods (Table 2) but the order of the bond distances in the model was not perfectly reproduced as in B3LYP and CCSD (Table 3). All the thermodynamic properties were computed at 298.150 Kelvin and pressure 1 Atm. The magnitude of the differences in thermodynamic properties (Table 2) shows that CCSD and PBE give closer values to MP2 than B3LYP. Also, considering the reproducibility of the order of bond distances obtained from MP2 in the other methods, all the computational methods produced a perfect order for the thermodynamic energies except PBE which gave a relatively better order for the CV and the entropy (Table 3). This is an indication that PBE performs better for geometrical optimization and computation of thermodynamic properties which agree well with the literatures that reported PBE correlation in combination with SBKJC VDZ ECP basis set as a good method for the optimization of metal complexes [40, 41]. The computed types of energies using other methods of computation are higher in negative values than MP2, while their bond distance, CV, and S are higher in positive values. Considering the RMSD of all the atoms in each of the models as shown in Table 4 and Figure 2, the optimized geometries obtained for the models Ru-C, Ru-O, and Ru-S at various computational methods are very similar to lower RMSD compared to what was obtained for the models Ru-N, Ru-Cl, and Ru-P. Also, the RMSD of the optimized geometries obtained from the functional PBE are lower than those obtained from B3LYP and CCSD which further supports PBE as a good method for the optimization of ruthenium complexes.


Method/bondsDistanceEnergyZero energyThermal energyEnthalpyGibbs-free CV KJ/Mol-K KJ/Mol-K

Ru-C-MP2-ECP1.9485
Ru-N-MP2-ECP1.8342
Ru-O-MP2-ECP1.8501
Ru-Cl-MP2-ECP2.1711
Ru-P-MP2-ECP2.3969
Ru-S-MP2-ECP2.2157

Difference of the other methods from MP2/SBKJC VDZ
Ru-C-PBE-ECP0.0024
Ru-N-PBE-ECP0.0120
Ru-O-PBE-ECP0.0243
Ru-Cl-PBE-ECP0.3088
Ru-P-PBE-ECP0.0219
Ru-S-PBE-ECP0.0074
Ru-C-B3LYP-ECP0.0159
Ru-N-B3LYP-ECP0.0047
Ru-O-B3LYP-ECP0.0144
Ru-Cl-B3LYP-ECP0.0392
Ru-P-B3LYP-ECP0.0398
Ru-S-B3LYP-ECP0.0125
Ru-C-CCSD-ECP0.0316
Ru-N-CCSD-ECP0.0436
Ru-O-CCSD-ECP0.0109
Ru-Cl-CCSD-ECP0.0368
Ru-P-CCSD-ECP0.0512
Ru-S-CCSD-ECP0.0211


MP2-ECPPBEB3LYPCCSD

Ru-L-dist1.001.001.00
Energy1.001.001.00
Zero energy1.001.001.00
Thermal energy1.001.001.00
Enthalpy1.001.001.00
Gibbs-free1.001.001.00
CV0.990.970.95
Entropy0.980.950.92


B3LYPCCSDPBE

Ru-C0.9631.3470.637
Ru-N1.0301.0321.035
Ru-O0.0560.0720.065
Ru-Cl1.3021.0301.268
Ru-P1.2031.2211.190
Ru-S0.2650.2660.252

3.2. Energy, HOMO, LUMO, Shielding Tensors, and J-Coupling

The values of the energy, HOMO, LUMO, and isotropic and anisotropic shielding computed at MP2/aug-cc-pVTZ and the variations obtained when computed with other methods are presented in Table 5. The shielding tensors were computed using Gauge-Independent Atomic Orbital (GIAO) method. The values of the energy and the variation obtained at different functional and basis sets show that variation in the energy values using different functional is lower compared to variation in the energy values using different basis sets. This is an indication that the energy values depend more on the type of basis sets rather than on the type of the functional. However, the variation in the values of HOMO, LUMO, and isotropic and anisotropic shielding at different functional methods shows that they depend more on the type of the functional and the geometrical change rather than on the type of the basis sets. The difference in the values of HOMO, LUMO, and isotropic and anisotropic shielding within MP2 methods at different basis set is lower compared to changing the functional to PBE and B3LYP. Also, B3LYP seems to perform better than PBE as the differences obtained at B3LYP are far lower compared to PBE. Also, considering the reproducibility of the order of these properties at different computational methods (Table 6), only the energy order is perfectly reproduced by all the methods. There is a very high similarity in the order of HOMO and LUMO, especially LUMO computed using B3LYP. In addition, B3LYP is found to also perform better in reproducing the shielding tensors of Ru and other atoms compared to PBE except for the order of the isotropic shielding of other atoms besides Ru atom. The correlation obtained from B3LYP in computing shielding tensors further supports its reported better performance for these properties [42].


EnergyHOMOLUMORu-IsoRu-AnisoX-IsoX-Aniso

Ru-C-MP2-acc
Ru-N-MP2-acc
Ru-O-MP2-acc
Ru-Cl-MP2-acc
Ru-P-MP2-acc
Ru-S-MP2-acc

0.00
Ru-C-MP2-dv
Ru-N-MP2-dv
Ru-O-MP2-dv
Ru-Cl-MP2-dv
Ru-P-MP2-dv
Ru-S-MP2-dv