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
4.4.1.2 Vacant space size calculations performed with the outer pocket technique The change in the outer pocket size of the vacant space for the G complexes was plotted
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
dissociation, as shown in Figure 4.34. This trend with the outer pocket technique was also observed in the modified Tolman technique.
Figure 4.34: Change in the outer pocket size of the vacant space for the G complexes The molecular structures for steps 8-9 in the G1 complex (b) are shown in Figure 4.35. In Figure 4.35, the size of the vacant space increased when comparing the red molecule to the blue molecule. According to the calculated vacant space size, the vacant space size decreased from 142.70° to 141.16°. The change in the vacant space size was 1.54°, which is too small to be observed in the molecular structure. Therefore, the change in size of the vacant space is inconclusive from viewing the molecular structures alone. In addition, the Ph group (2) shifted towards the unoccupied space left by the dissociating ligand. Therefore, the change in the angles is a consequence of the Ph ring shifting towards the space previously occupied by the dissociating ligand. Furthermore, the PCy3 ligands (3) changed their positioning in the G1 complex. However, the change in the PCy3 groups is small.
-10 -8 -6 -4 -2 0 2 4 6
2 2.5 3 3.5 4 4.5 5
Change in the outer pocket (ᵒ)
P(4)-Ru (Ǻ)
G1 G2 G3 G4 G5
a b
c d
e
Figure 4.35: Overlay of steps 8-9 of the molecular structures for the G1 complex, where step 8 is red and step 9 is blue.
The change in the vacant space sizes of the B complexes was calculated with the outer pocket technique and plotted against the increasing P(4)-Ru bond length, as shown in Figure 4.36.
The size of the vacant space increased initially (only for the first points, thereafter it decreased) for the B1 and B5 complexes, while the vacant space decreased with the B2, B3 and B4 complexes as also seen in the modified Tolman technique.
The pair of structures are shown in Figure 4.37 for the B1 complex at steps 15-16 (a), Figure 4.38 for the B2 complex at steps 13-14 (b), Figure 4.39 for the B3 complex at steps 13-14 (c), Figure 4.40 for the B3 complex at steps 23-24 (d), Figure 4.41 for the B4 complex at steps 9- 10 (e), Figure 4.42 for the B5 complex at steps 13-14 (f) and Figure 4.43 for the B5 complex at steps 21-22 (g).
Figure 4.36: Change in the outer pocket size of the vacant space for the B complexes
-14 -12 -10 -8 -6 -4 -2 0 2 4 6 8
2 2.5 3 3.5 4 4.5 5
Change in the outer pocket (ᵒ)
P(4)-Ru (Ǻ)
B1 B2 B3 B4 B5
a
b
c g
e
d f
1
2
3
The molecular structures for the B1 complex at step 15-16 (a) are shown in Figure 4.37. The vacant space (1) size decreased from 152.21° to 151.62°. Consequently, the vacant space size deceased a mere 0.59°, which would not necessarily be observed in the molecular structure, since the change in the vacant space is small. Therefore, the determination of the vacant space from the molecular structure is inconclusive. Moreover, the Ph ring (2) shifted towards the unoccupied space left by the dissociating ligand, which will indirectly influence the size of the dissociating ligand. Overall, the shift in the position and orientation of the Ph ring is what caused the change in the vacant space size observed in Figure 4.36.
Figure 4.37: Overlay of step 15-16 of the molecular structures for the B1 complex.
The molecular structures for the B2 complex at steps 13-14(b) are shown in Figure 4.38. The change in vacant space (1) size is inconclusive, since determining whether the vacant space increased or decreased is not possible from the molecular structure. According to the calculated vacant space sizes, the vacant space decreased from 150.01° to 146.04°.
Consequently, the vacant space size deceased by 3.97°. This decrease is larger than that observed in the B1 complex. Moreover, the Ph ring (2) shifted in position and orientation towards the unoccupied space left by the dissociating ligand. Therefore, the shift in the position and orientation of the Ph ring is what caused the change in the vacant space size, observed in Figure 4.36.
1
2
Figure 4.38: Overlay of steps 13-14 of the molecular structures for the B2 complex The molecular structures of the B3 complex at steps 13-14 (c) are shown in Figure 4.39. The calculated vacant space size (1) increased from 145.39° to 145.40°. However, this small increase in the vacant space size cannot be observed in the picture of the molecular structure shown in Figure 4.39. Furthermore, the change in the vacant space size observed in Figure 4.36 is a consequence of the Ph ring (2) shifting position and orientation around the axis.
Figure 4.39: Overlay of steps 13-14 of the molecular structures for the B3 complex The molecular structures at steps 23-24 in the B3 complex (d) are shown in Figure 4.40.
According to the calculated vacant space sizes, the vacant space decreased from 142.70° to 140.70°. Consequently, the change in the vacant space is 2.00°. The change in the vacant space size is small enough that it would not appear in the molecular structure and overlapping of the molecular structure (3) occurs that makes the determination unclear. Furthermore, the Ph ring (2) shifted largely towards the unoccupied space and the orientation changed. This shift in orientation and position of the Ph ring is what caused the change in the angles calculated with this technique.
1
2
1
2
Figure 4.40: Overlay of steps 23-24 of the molecular structures for the B3 complex The molecular structures for the B4 complex at steps 9-10 (e) are shown in Figure 4.41.
According to the calculated data, the change in the vacant space size was 2.94°, which decreased from 148.49° to 145.55°. Therefore, it is no surprise that the small change in the vacant space (1) size is not observed in the molecular structure. The Ph ring (2) started to shift towards the unoccupied space left by the dissociating ligand. This unoccupied site will allow the complex to lessen steric strain by moving the large Ph ring in a position where it will cause less steric strain in the complex. Consequently, the vacant space size decreased with the lessened steric strain.
Figure 4.41: Overlay of steps 9-10 of the molecular structures for the B4 complex The molecular structures of the B5 complex at steps13-14 (f) are shown in Figure 4.42. In Figure 4.42, the size of the vacant space (1) is unclear in the molecular structure since it is difficult to determine how the size of the vacant space changed. According to the calculated data, the vacant space size decreased from 155.04° to 150.99°. Furthermore, the Ph ring (2) shifted slightly towards the unoccupied space. This shift in the Ph ring caused the vacant
1
2
1
2 3
space to decrease in size. The shift of the Ph ring is less than what was observed in the other complexes since the hydrogen containing B5 complex is smaller in comparison to the other complexes.
Figure 4.42: Overlay of steps13-14 of the molecular structures for the B5 complex The molecular structures for steps 13-14 in the B5 complex (g) are shown in Figure 4.43. In Figure 4.43, the determination of the vacant space (1) is unclear from the molecular structure, since the change in the vacant space is small enough to not be noticeable. The calculated vacant space size data shows that the vacant space size decreased from 148.62° to 144.52°.
The change in the vacant space size was 4.10°, which is a small change. On the other hand, the Ph ring (2) can shift into the unoccupied space and change its orientation to find a less steric strained conformer.
Figure 4.43: Overlay of step 21-22 of the molecular structures for the B5 complex The change in the vacant space sizes calculated with the outer pocket technique for the A complexes is plotted against the increasing P(4)-Ru bond length, as shown in Figure 4.44. The
1
2
1
2
changes in vacant space that were observed in the G and B complexes are not observed in the smaller A complexes that do not have the large Ph groups.
The trend observed in the change in the vacant space is similar to that of the modified Tolman technique for the A complexes. Furthermore, the same five changes in the vacant space size in steps 1-5 of the A1 complex (a) and steps 1-5 of the A5 complex (b) were observed in both the modified Tolman and the outer pocket technique for the A complexes.
The molecular structures for the A1 (a) and A5 (b) complexes were shown in the modified Tolman section at Figures 4.32 and Figure 4.33. In both the modified Tolman and the outer pocket techniques, the fluorine containing complexes had the largest vacant space sizes, while hydrogen was the second largest for the A complexes.
Figure 4.44: Change in the outer pocket size of the vacant space for the A complexes Overall, the trend observed in the outer pocket technique is comparable to the trend observed in the modified Tolman technique except for a few changes in the vacant space sizes that were not observed in the modified Tolman technique. The smaller van der Waals radii resulted in larger vacant space sizes, while the largest van der Waals radii resulted in the smallest vacant space size for the G complexes. In contrast, the highly electronegative (second smallest van der Waals radius according to Bondi[3]) fluorine containing complex had the largest vacant space over the smaller (least electronegative) hydrogen containing complex observed in the B and A complexes. Free movement in the B and A complexes is more likely than in the sterically strained G complexes.
-6 -4 -2 0 2 4 6
2 2.5 3 3.5 4 4.5 5
Change in the outer pocket (ᵒ)
P(4)-Ru (Ǻ)
A1 A2 A3 A4 A5
a
b
4.4.1.3 Vacant space size calculations performed with the inner pocket technique