Chapter 6 Computational Chemistry
6.2 Results and Discussion
6.2.2 Geometry Optimisation of the Heteroleptic Copper(II) Chelates
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Page | 111 The RMSDs for the heteroleptic complexes are in most cases smaller than those of the single- ligand complexes. The bidentate ligands have fewer degrees of freedom and allow for fewer conformational distortions. Hence there is greater similarity between the experimental and calculated structures.
The RMSD for [Cu(L1)(Bpy)](Cl) measures 0.372 Γ with the gas-phase structure being 42.9 kJ mol-1 lower in energy than the solid-state structure. The similarity of the calculated and experimental structures suggests the level of theory used for the calculations was appropriate and the simulations are likely to be reliable. The structural overlay for [Cu(L1)(Bpy)](Cl) (an overlay of the quinoline and salicylideneimine moiety only) shows an RMSD of 0.133 Γ and is depicted in Figure 6.2.5. This shows a similar trend to that observed previously: the most significant difference between the structures lies in the angle between the tridentate ligand and the co-ligands.
Figure 6.2.5: Structural overlay of the experimental (green) and DFT-simulated (purple) for the quinoline and salicylideneimine moiety only of [Cu(L1)(Bpy)](Cl).
A summary of key calculated and experimental bond lengths and bond angles is given in Table 6.2.5 along with the percentage difference between these data.
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Table 6.2.4: Comparison of experimental and DFT-calculated bond lengths (Γ ) and bond angles (Β°) for [Cu(L1)(Bpy)](Cl).
Percentage Difference = (πΆπππβπΈπ₯π)πΆπππ π₯ 100
From Table 6.2.4 it can be concluded that all bond lengths are in good agreement as indicated by the small percentage differences. From the structural overlay in Figure 6.2.5 it is evident that the quinoline and salicylideneimine region of the calculated structure has been accurately simulated when compared to the experimental structure. The key difference lies in the angle N1-Cu1-N4 which shows a very large deviation between the gas-phase and solid state structures. The angle is larger for the gas-phase structure by 13.39Β°; this significantly changes the overall geometry of the chelate. In the gas phase, the copper(II) chelate is not restricted by lattice packing and so the geometry optimisation yields a chelate structure with the lowest steric strain and correspondingly the lowest energy.
Bond lengths (Γ )
Experimental Calculated Difference (%)
Cu1-N1 2.214(4) 2.295 3.53
Cu1-N2 2.017(3) 2.076 2.84
Cu1-N3 2.022(3) 2.030 0.39
Cu1-N4 1.954(3) 1.973 0.96
Cu1-O1 1.931(2) 1.911 -1.05
C=Nimine 1.311(5) 1.314 0.23
Bond angles (o)
Experimental Calculated Difference (%)
N1-Cu1-N2 78.1(1) 75.64 -3.25
N4-Cu1-O1 93.3(1) 93.12 -0.19
N3-Cu1-N4 82.6(1) 82.57 -0.04
N1-Cu1-N4 97.80(1) 111.49 12.28
Page | 113 The RMSD for [Cu(L1)(Phen)](Cl) measures 0.307 Γ with the gas-phase structure being 35.4 kJ mol-1 lower in energy than the solid-state structure (Figure 6.2.4). The structural overlay for [Cu(L1)(Phen)](Cl) (an overlay of the quinoline and salicylideneimine moiety only) shows a RMSD of 0.174 Γ and is illustrated in Figure 6.2.6.
Figure 6.2.6: Structural overlay of the experimental (green) and DFT-simulated (purple) of the quinoline and salicylideneimine moiety only for [Cu(L1)(Phen)](Cl).
Figure 6.2.6 shows a similar result to that previously discussed where the quinoline and salicylideneimine regions are in good agreement with each other in the gas phase and the solid state structures. The most significant deviations are observed in the angle between the co-ligand and primary ligand. The relevant bond lengths and bond angles for [Cu(L1)(Phen)](Cl) are summarised in Table 6.2.5 and Table 6.2.6. The consequence of this small deviation, however, is a significantly different molecular geometry.
Table 6.2.5: Comparison of experimental and DFT-calculated bond lengths (Γ ) for [Cu(L1)(Phen)](Cl).
Bond lengths (Γ )
Experimental Calculated Difference (%)
Cu1-N1 1.962(3) 1.972 0.51
Cu1-N2 2.014(3) 2.031 0.84
Cu1-N3 2.293(3) 2.331 1.63
Cu1-N4 2.034(3) 2.071 1.79
Cu1-O1 1.911(3) 1.909 -0.10
C=Nimine 1.287(4) 1.313 1.98
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Table 6.2.6: Comparison of experimental and DFT-calculated bond angles (Β°) for [Cu(L1)(Phen)](Cl).
Percentage Difference = (πΆπππβπΈπ₯π)πΆπππ π₯ 100
All bond angles and bond lengths around the coordination sphere lie within good agreement of each other in the gas-phase and solid state structures. This is confirmed by the small percentage differences which range from 0.10 β 1.98 %. The exception is the N1-Cu1-N3 bond angle which measures 96.74(1)Β° in the solid state while the in vacuo structure shows a corresponding angle of 109.49Β°. The reason for the deviation in the bond angle is likely that the solid state structure has to deviate from the lowest energy structure to allow for optimal packing in the lattice.
The most interesting of the three structures is [Cu(L1)(Phen-NH2)](Cl) since this is the only heteroleptic compound with the potential to hydrogen bond. This is significant as hydrogen bonding has been previously shown to lead to marked deviations between the lowest energy structures and those observed experimentally.51 The RMSD for [Cu(L1)(Phen-NH2)](Cl) measures 0.365 Γ with the gas-phase structure being 30.0 kJ mol-1 lower in energy than the solid-state structure. The structural overlay for [Cu(L1)(Phen-NH2)](Cl) (an overlay of the quinoline and salicylideneimine moiety only) shows a RMSD of 0.0896 Γ and is illustrated in Figure 6.2.7.
Bond angles (o)
Experimental Calculated Difference (%)
N1-Cu1-N2 83.05(1) 82.57 -0.58
N1-Cu1-O1 93.42(1) 93.15 -0.29
N3-Cu1-N4 77.52(1) 76.62 -1.17
N1-Cu1-N3 96.74(1) 109.49 11.64
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Figure 6.2.7: Structural overlay of the experimental (green) and DFT-simulated (purple) of the quinoline and salicylideneimine moiety only for [Cu(L1)(Phen-NH2)](Cl).
As was observed with the previous two heteroleptic chelates, the quinoline and salicylideneimine moieties have a low RMSD value indicating that the geometry optimisation results are reliable. From the crystallographic studies, it was observed that the NH2 group was involved in hydrogen bonding with the chloride counter ion as well as the oxygen atom of the Schiff base ligand. The molecule has seemingly had to undergo minimal deviation from the lowest energy conformation to allow for optimum hydrogen bonding. This is an unusual result and suggests that the hydrogen bonding groups are coincidentally pre-organised for optimum hydrogen bonding. This is an encouraging result as it shows that the complex will likely be able to hydrogen bond with the DNA helix with minimal distortion, stabilising the DNA/drug conjugate. Key bond lengths and bond angles are summarised in Table 6.2.7.
Table 6.2.7: Comparison of experimental and DFT-calculated bond lengths (Γ ) and angles (Β°) for [Cu(L1) )(Phen-NH2)](Cl).
Bond lengths (Γ )
Experimental Calculated Difference (%)
Cu1-N1 1.957(2) 1.974 0.86
Cu1-N2 2.010(1) 2.032 1.08
Cu1-N3 2.013(2) 2.061 2.33
Cu1-N4 2.241(2) 2.333 3.94
Cu1-O1 1.940 (9) 1.912 -1.46
C=Nimine 1.305(2) 1.314 0.68
Page | 116 Table 6.2.7 continuedβ¦
Percentage Difference = (πΆπππβπΈπ₯π)πΆπππ π₯ 100
Table 6.2.7 shows a summary of the bond angles and lengths defining the coordination sphere of the copper(II) ion. The calculated bond lengths are all similar, as expected, with Cu1-N4 being slightly longer in the gas phase. Once again, the bond angle of interest, N1-Cu1-N4, is larger in the gas phase than in the solid state structure. This angle deviation is ubiquitous in all six structures studied. This is an interesting result as it shows that the simulated structures are tending towards a trigonal bipyramidal structure as opposed to the square pyramidal structure observed in the solid state. These geometries are both well known for copper(II) chelates, however, trigonal bipyramidal structures tend to be lower in energy as there is reduced steric strain in the complexes. It therefore stands to reason that in the gas phase, in the absence of packing constraints, the molecules are tending as far as possible towards a trigonal bipyramidal geometry.