Preface
Chapter 4: Results and discussions 4.1 Introduction
4.4 Calculation of the vacant space size
4.4.1 Calculation of the vacant space size with the new defined techniques
4.4.1.1 Vacant space size calculations performed with the modified Tolman technique
structure, because the change is very small. According to the change in the angles, the vacant space size increased from 139.40° to 140.56°. Therefore, the increase in size was 1.16°, which is too small to be shown in the visual comparison of the molecular structure. On the other hand, the Ph ring (2) shifted towards the ligand that was busy dissociating from the ruthenium metal. This shift was a large enough to be observed in the visual comparison of the molecular structure. After the dissociation, the dissociating ligand will leave an unoccupied space that the Ph ring will move into. Furthermore, the PCy3 groups (3) shifted in various directions, since the Ph ring has shifted away from the PCy3 groups.
Figure 4.22: Overlay of step 4-5 of the molecular structures for the G1 complex, where step 4 is red and step 5 is blue
The molecular structures for the change in the angle that occurs in the G1 complex at steps 11-12 in Figure 4.21 (b) are shown in Figure 4.23. However, due to the small change of 1.20°
in size of the vacant space (1) between steps 11-12, the change could not be observed in Figure 4.23. However, the change in the angles calculated for the vacant space size is more descriptive than the molecular structures for small changes whereas larger shifts is shown in the molecular structures. In addition, the Ph ring (2) has rotated slightly and shifted towards the unoccupied space left by the dissociating ligand. Furthermore, the PCy3 groups (3) changed their positions slightly, since the Ph ring has shifted away from the PCy3 groups.
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Figure 4.23: Overlay of steps 11-12 of the molecular structures for the G1 complex, where step 11 is red and step 12 is blue
The molecular structure at steps 3-4 in the G5 complex (c) is shown in Figure 4.24. In this figure the vacant space size (1) is inconclusive. It looks like the vacant space decreased.
However, according to the change in the vacant space size, it increased from 137.98° to 139.20°. Consequently, the vacant space size increased by 1.22°, which is too small to be detected with the molecular structures. Therefore, it is more conclusive to use the calculated vacant space sizes than the molecular structure. In addition, the position and orientation of the Ph ring (2) shifted slightly towards the dissociating ligand that is moving away from the ruthenium. Furthermore, the PCy3 groups (3) changed position during steps 3-4.
Figure 4.24: Overlay of steps 3-4 of the molecular structures for the G5 complex, where step 3 is red and step 4 is purple
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The molecular structures of steps 14-15 in the G5 complex (d) are shown in Figure 4.25. The change in the vacant space (1) is unclear in the molecular structures. According to the calculated size, the vacant space decreased from 138.39° to 137.32°. Therefore, the vacant space size decreased by 1.05°. This decrease in size is small enough not to be shown in the molecular structure. In addition, the Ph ring (2) shifted towards the unoccupied space left behind by the dissociating ligand. The Ph ring rotated around the C-C bond when comparing Figure 4.24 and Figure 4.25. Furthermore, the PCy3 groups (3) changed their orientation/position during steps 14-15.
Figure 4.25: Overlay of step 14-15 of the molecular structures for the G5 complex, where step 14 is red and step 15 is blue
The vacant space size was calculated with the modified Tolman technique for the B complexes and plotted against the increasing P(4)-Ru bond length as shown in Figure 4.26.
This figure shows that the change in the vacant space size increased before dissociation and decreased thereafter. However, the rate at which the change in the vacant space size increased for the small B1 and B5 complexes was less than the rate observed for the larger B2, B3 and B4 complexes. Furthermore, the change in the vacant space size was small for the large chlorine, bromine and iodine containing complexes.
In Figure 4.26, four changes in the angles were observed. These changes were in the B2 complex at steps 13-14 (a), in the B3 complex at steps 8-9 (b) and the B5 complex at steps 11-12 and 21-22 (c, d). In addition, the molecular structures are shown in Figure 4.27 for the B2 complex (a), Figure 4.28 for the B3 complex (b), Figure 4.29 for the B3 complex (c) and
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Figure 4.26: Change in the modified Tolman size of the vacant space for the B complexes The molecular structures of steps 13-14 in the B2 complex (a) are shown in Figure 4.27. In Figure 4.27, the size of the vacant space (1) is inconclusive, since the decrease is only 0.08°.
The vacant space size decreased from 147.75° to 147.67°. The Ph ring (2) shifted towards the dissociating ligand that consequently resulted in the observed change in angles in Figure 4.26.
Figure 4.27: Overlay of steps 11-12 of the molecular structures for the B2 complex, where step 11 is red and step 12 is blue
The molecular structures of steps 8-9 in the B3 complex (b) are shown in Figure 4.28. The change in the vacant space (1) is unclear, because the decrease in the vacant space size is 1.04°. This is small enough to be undetectable in the molecular structure. The calculated
-10 -8 -6 -4 -2 0 2 4 6
2 2.5 3 3.5 4 4.5 5
Change in the modified Tolman (ᵒ)
P(4)-Ru (Ǻ)
B1 B2 B3 B4 B5
b a
c
d
1 2
vacant space sizes decreased from 148.02° to 146.98°. The Ph ring (2) shifted towards the unoccupied space left by the dissociating ligand. The change in the vacant space size observed in Figure 4.26 is a consequence of the shifting Ph ring.
Figure 4.28: Overlay of steps 8-9 of the molecular structures for the B3 complex, where step 8 is red and step 9 is blue
The molecular structures of the B3 complex between steps 11-12 (c) are shown in Figure 4.29. In Figure 4.29, the vacant space size (1) looks like it increased in size. According to the calculated vacant space size, the vacant space decreased in size from 146.26° to 145.67°. The decrease in the vacant space size is 0.57 °, which is too small to be detected in the molecular structure. When comparing Figure 4.28 with Figure 4.29, it can be seen that the Ph ring (2) shifted largely towards the unoccupied space. Furthermore, the orientation of the Ph ring changes as the Ph ring rotated around the C-C axis.
Figure 4.29: Overlay of steps11-12 of the molecular structures for the B3 complex, where step 11 is red and step 12 is blue
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The molecular structure of the B5 complex between steps 21-22 (d) is shown in Figure 4.30.
In Figure 4.30, the size of the vacant space (1) increased when comparing the red molecule to the blue molecule. According to the calculated vacant space sizes, the vacant space size decreased from 147.45° to 146.07°. The change in the vacant space size that occurred between steps 21-22 was 1.38°, which is small enough to not show in the molecular structure.
Therefore, it is inconclusive to base the size of the vacant space from pictures of the molecular structure that cannot show small amounts of changes in the size of the vacant space. The Ph ring (2) shifted towards the unoccupied space that was left by the dissociating ligand. Consequently, the Ph ligands shifted towards the unoccupied space to lessen the steric strain in the B5 complex.
Figure 4.30: Overlay of steps 21-22 of the molecular structures for the B5 complex, where step 21 is red and step 22 is blue
The change in the modified Tolman for the vacant space for the A complexes was plotted against the increasing P(4)-Ru bond length as shown in Figure 4.31. In Figure 4.31, a change in the vacant space size was observed in the A1 and A5 complexes as the vacant space size increased before decreasing. On the other hand, the larger A3 and A5 complexes decreased immediately. The A2 complex increased slightly during steps 3-4 before decreasing. There is a minimum change in the vacant space observed for the larger A2, A3 and A4 complexes.
The change in the vacant space for the A1 and A5 complexes is shown in the molecular structures in Figures 4.32 and 4.33.
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Figure 4.31: Change in the modified Tolman size of the vacant space for the A complexes
In Figure 4.32, the size of the vacant space (1) increased. The increase in the vacant space is clearer than the previous molecular structures since this is between steps 1-5 of the dissociation. According to the calculated vacant space sizes, the vacant space increased in size from 145.90° to 150.32°. This increase in the vacant space size is 4.42°, which is large enough for it to be observed in the molecular structure. Therefore, the molecular structures can be used to determine whether the vacant space size increased or decreased with large changes in the vacant space size. However, smaller changes in the vacant space size cannot be observed with the molecular structure.
Figure 4.32: Overlay of steps 1 and 5 of the molecular structures for the A1 complex, where step 1 is red and step 5 is green
The molecular structures of steps 1-5 for the A5 complex (b) are shown in Figure 4.33. In
-6 -4 -2 0 2 4 6
2 2.5 3 3.5 4 4.5 5
Change in the modified Tolman (ᵒ)
P(4)-Ru (Ǻ)
A1 A2 A3 A4 A5
a b
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space sizes, the vacant space increased in size from 144.72° to 147.87°. The increase in the vacant space between the first and fifth step of the dissociation is clearer since the increase is 3.15°.
Figure 4.33: Overlay of steps 1 and 5 of the molecular structures for the A5 complex, where step 1 is red and step 5 is green
To summarise, the smaller van der Waals radii according to Bondi[3]lead to larger absolute vacant space size. Complexes with substituents having smaller radii showed less change in vacant space than those with larger radii.
4.4.1.2 Vacant space size calculations performed with the outer pocket technique