Preface
Chapter 4: Results and discussions 4.1 Introduction
4.3 Calculation of dissociating ligand size
4.3.2 Calculation of the dissociating ligand size using the percentage buried volume technique
The percentage buried volume technique is different from the outer and inner pocket techniques within SterixLB, since it calculates how much of the ligand is buried in the metal sphere. Therefore, to obtain a deeper understanding of the dissociating mechanism, the G, B and A complexes were calculated with sambVca.[6] The detailed results are shown in Appendix H. Only the coordinates of the dissociating ligand were used in the percentage buried volume technique.
-5 -4 -3 -2 -1 0 1 2 3 4
2 2.5 3 3.5 4 4.5 5
Change in the inner pocket (ᵒ)
P(4)-Ru (Ǻ)
A1 A2 A3 A4 A5
The dissociating ligand calculations performed with the percentage buried volume technique use the coordinates of the phosphorous atom and the substituents bonded to it. All the coordinates are uniformly translated so that the metal is at (0.0.0). The percentage buried volume then calculates how much of the phosphine ligand is buried in the metal sphere. The change in the percentage buried volume is plotted against the increasing P(4)-Ru bond length for the G, B and A complexes.
The change in the percentage buried volume (%VBur) for the G1, B1 and A1 complexes was plotted against the increasing P(4)-Ru bond length as shown in Figure 4.16. In Figure 4.16, the change in the percentage buried volume of the G1, B1 and A1 complexes decreases as the dissociating ligand dissociates.
The changes in the B1 and A1 complexes are identical and the curves lie on top of each other in Figure 4.16. On the other hand, the changes in the G1 complex is different from the B1 and A1 complexes, since it has the large PCy3 ligand that increases the volume of the sphere while decreasing the percentage buried volume of the ligand. However, the change in the percentage buried volume for the G1 complex increased (a) momentarily before decreasing as the phosphine ligand dissociated. The increase in the change in the percentage buried volume can be a consequence of the large G1 complex shifting positions and orientations. In addition, an increase at (d) was observed at a P(4)-Ru bond length of 3.41 Å. This 0.1%
increase in the change of the %VBur was not observed with the modified techniques at this bond length. At this bond length the Ph ring rotated, while one of the PCy3 rings also rotated around the P(5)-C axis, which lead to the change in %VBur. This rotation of the PCy3 ring can be observed in the molecular structures (a-d), the decrease in the distance between the iodine and one of the hydrogens of the ring is what causes the point observed at (d).
Overall, the square (e) indicates that the G1, B1 and A1 complexes have reached equilibrium and that the change in the percentage buried volume is constant. The change in percentage buried volume for the G1 complex is 0.1%, the percentage buried volume for the B1 complex is 16.7%, while for the A1 complex it is 16.8%. The detailed percentage buried volume information for the complexes can be found in Appendix H.
(a) (b )
(c) (d )
aa
Figure 4.16: Change in the %VBur of G1, B1 and A1 complexes, plotted against the P(4)-Ru bond length
0.05 0.1 0.15 0.2 0.25 0.3 0.35
2 2.5 3 3.5 4
Change in the %VBur (%)
P(4)-Ru (Å)
G1 B1 A1
a
d
e b
c
There is no outlier observed in Figure 4.17 for the G2, B2 and A2 complexes. The (a) G2 and (b) B2 complexes increased in percentage buried volume (0.1 %), while the A2 complex stays constant before decreasing. The G2 and B2 complexes are larger in size than the A2 complex and the small increase in the change in percentage buried volume can be a consequence of the shifting of the large Ph ring in the large complexes. However, in the percentage buried volume technique, only the Cartesian coordinates of the phosphine ligand is used. Consequently, the Ph ring (or the PCy3 ligands) will still interfere in the dissociating ligand size.
The change in the percentage buried volume for the B2 (19.6%) and A2 (19.9%) complexes decreased until the dissociating ligand was (c) no longer part of the Grubbs 1-type complex.
The dissociating ligand size calculated with the outer pocket technique was 245.0° for B2 and 248.3° for A2. Therefore, the larger dissociating ligand of the A2 complex resulted in a larger percentage buried volume value. On the other hand, the dissociating ligand size for the G2 complex was 241.7° that resulted in a (d) percentage buried volume for G2 of 19.3%.
Therefore, the smallest dissociating ligand size resulted in the smallest percentage buried volume.
Figure 4.17: Change in the %VBur of G2, B2 and A2 complexes against the P(4)-Ru bond length
The change in the percentage buried volume for the bromine containing complexes was plotted against the increasing P(4)-Ru bond length, as shown in Figure 4.18. The change in the
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
2 2.5 3 3.5 4 4.5 5
Change in the %VBur (%)
P(4)-Ru (Å)
G2 B2 A2
c a
b
d
percentage buried volume increased (a) initially for the bulky G3 and B3 complexes with the large bromine substituents. The calculated dissociating ligand sizes with the outer pocket technique was 238.4°, 241.2 - 241.1° and 243.3° for G3, B3 and A3, respectively. The G3 (20.1%) and A3 (19.9%) complexes decreased until they reached (b) the point where the dissociating ligand has moved far away from the metal centre. Furthermore, for the B3 (20.3 - 20.4%) complex this occurred at (c). The dissociating ligand size for the B3 complex decreased at the last step, which resulted in an increase in the percentage buried volume.
The largest dissociating ligand size of the A3 complex resulted in the smallest percentage buried volume for the bromine containing complexes. Furthermore, the smallest dissociating ligand size of the B3 complex resulted in the largest percentage buried volume.
Figure 4.18: Change in the %VBur of G3, B3 and A3 complexes against the P(4)-Ru bond length
The change in the percentage buried volume for the large iodine containing complexes was plotted against the increasing P(4)-Ru bond length as shown in Figure 4.19. The change in the percentage buried volume increased (a) initially for all three the complexes. The molecular structure for the G4 (1) and B4 (2) complexes shows that during step 1 (red) to step 2 (green) , the Ph ring rotates around the C=C bond. On the other hand, in the A4 (3) complex, only the chlorine atoms rearranged their position between steps 1-2. Therefore, this initial increase in the percentage buried volume is due to the increase in the dissociating ligand size as the ligand prepared for dissociation. The calculated dissociating ligand size with the outer pocket
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
2 2.5 3 3.5 4 4.5 5
Change in the %VBur (%)
P(4)-Ru (Å)
G3 B3 A3
a
b
c
technique was 235.1°, 236.03-236.00° and 236.93-236.95°for the G4, B4 and A4 complexes, respectively.
The G4 (20.8%) and A4 (21.1-21.2%) complexes decreased until they reached the point (b) where the P(4)-Ru distance was long enough that the dissociating ligand was no longer buried in the metal sphere. This point was at (c) for the B3 (20.3-20.4%) complex. Therefore, the largest dissociating ligand resulted in the smallest percentage buried volume for the iodine containing complex. The small change in the percentage buried volume at the second last step is because the size of the dissociating ligand increased, resulting in a decreased percentage buried volume.
(1) (2) (3)
Figure 4.19: Change in the %VBur of G4, B4 and A4 complexes against the P(4)-Ru bond length
The change in the percentage buried volume for the hydrogen containing complexes was plotted against the increasing P(4)-Ru bond length as shown in Figure 4.20. In Figure 4.20, the
-0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
2 2.5 3 3.5 4 4.5 5
Change in the %VBur (%)
P(4)-Ru (Å)
G4 B4 A4
c b a
1 2
3
change in the percentage buried volume increased (a) initially for only the G5 complex, while the smaller B5 and A5 complexes did not increase. The complexes with H as the substituent in the dissociating ligand are smaller than where the substituents in the phosphine ligand are halogens, so the percentage buried volume size does not change in large quantities.
The calculated dissociating ligand sizes with the outer pocket technique for complexes G5, B5 and A5 are 230.8°, 234.5° and 237.9°, respectively. The largest dissociating ligand size resulted in the largest percentage buried volume size for the A5 complex (14.2%) at (b) while the second largest was B5 (14.1%) at point (c). The smaller dissociating ligand sized G5 (14%) complex has the smallest percentage buried volume. This is the opposite trend as was found for the complexes with halogen substituents. However, the hydrogen atom is small in comparison to the halogens and the size of the hydrogen does not influence the size of the dissociating ligand much.
In conclusion, the size of the dissociating ligand influences the percentage buried volume value. The decrease in the percentage buried volume is a consequence of the dissociating ligand moving away from the metal centre of the sphere. Therefore, the percentage buried volume correlates with the dissociating ligand size calculated with the outer pocket technique. The dissociating ligand size is influenced by the type of substituent on the phosphine ligand and the size of the Grubbs 1-type complex.
Figure 4.20: Change in the %VBur of G5, B5 and A5 complexes against the P(4)-Ru bond length
-0.35 -0.3 -0.25 -0.2 -0.15 -0.1 -0.05 0 0.05 0.1 0.15
2 2.5 3 3.5 4 4.5 5
Change in the %VBur (%)
P(4)-Ru (Å)
G5 B5 A5
a
b
c
d