Preface
Chapter 3: Method for calculating steric strain 3.1 Introduction
3.4 Evaluation and application of SterixLB
3.4.2 Application
The size of the dissociating ligand was calculated for the G (Figure 3.4), B (Figure 3.5) and A (Figure 3.6) complexes with the use of the outer pocket and the inner pocket techniques within SterixLB.
Thereafter, the size of the vacant space was calculated for the G (Figure 3.4), B (Figure 3.5) and A (Figure 3.6) complexes with the use of modified Tolman, outer pocket, inner pocket and the inner-inner pocket techniques within SterixLB.
The computer programs solid-G[7] (which incorporates solid angle calculations) and sambVca[8](which uses percentage buried volume calculations) were used to calculate the steric strain in the G, B and A complexes. The trends obtained from solid-G[7] and sambVca[8]were then compared to the trends obtained from SterixLB.
Moreover, the close contact distance between non-bonded atoms was calculated with the use of SterixLB.
3.4.2.1 Calculations with SterixLB
SterixLB is divided into three sections, i.e. input data, close contacts and results, as shown in Figure 3.24. Results are divided into two sections, namely graph plots and tabled data for each technique.
Figure 3.24: Screenshot of SterixLB 3.4.2.1.1 Input data
In this section of SterixLB, the parameters were selected and the input file was loaded. The first parameter was the number of atoms in the complex. For example, the number of atoms in the A complexes (Figure 3.6) is 14, while there are 24 atoms in the B complexes (Figure 3.5) and 120 in the well-known Grubbs 1 catalyst (Figure 3.2). The next parameter was to select the substituents on the dissociating ligand and adding the atom numbers (as given in PES output file) of said substituents. The last parameter was the selection of the radii of the substituents, the chlorine and the carbon atoms. This parameter was added so that the user can select his/her own radii (depending on the source used[9]). Thereafter, run was selected and the user was prompted to select his/her input file. After the input file is selected, the calculations are performed. The bond lengths needed for all the techniques are calculated, while the potential energy is imported from Materials Studio output file.
3.4.2.1.2 Close contacts
In the close contact section, a table of the distances between non-bonded atoms in the dissociating ligand and the vacant space is shown. The minimum allowed distance between non-bonded atoms is also shown. The differences between the distances and minimum allowed distances of non-bonded atoms are determined. These values of the differences are listed in the violation column. The violation is calculated by subtracting the sum of the radii of two non-bonded atoms from the distance between these atoms. Therefore, if a negative
number was obtained, the sum of the radii of the non-bonded atoms is greater than the distance between them, resulting in close contacts.
3.4.2.1.3 Results
The results section was divided into graphs and tables. The user is able to select his/her prefered x-axis and y-axis for the graph. In addition, it is possible for the user to zoom in and out of the graph and also move the graph around while zoomed in. Furthermore, the user is allowed to select the technique for the data he/she requires. This data are provided in table format. In addition, the user can export the tabled data to an Excel spreadsheet; however, the graph cannot be exported.
3.4.2.2 Calculations with solid-G
In order to use solid-G, the input file must be in a .xyz format. In Materials Studio[3] the arc files .xtd of the PES scan are sets of files containing the coordinate data of the complex under investigation for each step of the scan. The separate coordinate data were exported as .car files. Thereafter, the program Open Babel[10] was used to convert the .car files to .xyz files. Finally, the .xyz files were edited with Notepad before solid-G could be used. The editing of the .xyz files consisted of uniquely numbering each atom in the file and removing all other data except the Cartesian coordinates of the atoms. The input file for the A1 complex is shown in Appendix D.1. As mentioned earlier, solid-G is not a dynamic technique, but a static (complex at a stationary point) technique. Therefore, each step of the PES scan data had to be converted to .xyz files, edited and run separately.
After opening solid-G, the user is asked to select the input file .xyz. After the input file has been selected, the user must select the Ru3 metal. Thereafter, the user selects the Select Atom button (1), the identify ligands button (2) then the calculate angles button (3), as shown in Figure 3.25.
Figure 3.25: Screenshot of Solid-G
Solid-G outputs the data as shown in Figure 3.26 and also saves the data as a text file in the solid-G directory. Solid-G calculates the ligand composition and coordination, the coordinated atom data, ligand angles and unfavourable contacts between atoms. The normalisation to M-L (metal to ligand distance) is 2.28 Å. The complete result output file for complex A1 can be seen in Appendix D.2 (for step 1) and in Appendix D.3 (for step 17), respectively.
Figure 3.26: Screenshot of solid-G output
1 2 3
The output file for complex A1, step 17, has non-ligands, which is the ligand after it has dissociated. Therefore, solid-G does not calculate data for a ligand that has dissociated or is no longer bonded to the ruthenium. However, if the input file is edited in such a way that the complex is removed, and only the Cartesian coordinates of the dissociated ligand are in the input file, then it is possible to obtain steric data for the dissociating ligand.
3.4.2.3 Calculations with percentage buried volume (sambVca)
Before sambVca can be used, the input file must be edited. The correct editing method is shown in Appendix D.5. The main screen of sambVca is shown in Figure 3.27. In Figure 3.27, the file type used in this study was the XYZ coordinate files. Furthermore, in the edited file, the P atoms were numbered 1 and the PX3 ligand is 3, since there are three substituents, where these substituent numbers were 2, 3 and 4, as shown in the purple square. According to Cavallo[8], the recommended values for the sphere radius is 3.5 Å, the distance from the centre of the sphere is 2.10 Å and the mesh spacing is 0.05 Å, so it was left as is for the calculations in this study. Lastly, the radii used in the percentage buried volume calculations were the Bondi radii.
Figure 3.27: Screenshot of sambVca
Notably, sambVca[8] was recently updated to sambVca2. However, the original sambVca was used in this study and not the latest version.