3.4 X-ray crystallographic characterisation of nickel complexes
3.4.2 Solid-state structures of alkylated nickel complexes
Four alkylated nickel Schiff base complexes were crystallised by slow evaporation of solvent from saturated solutions. The latter were prepared by initially suspending a small amount of complex in a solvent in which it had limited solubility, such as acetone, methanol or hexane. A second solvent that the complexes were very soluble in, such as DCM, was then slowly added until the complex just dissolved. In contrast to the above procedure, crystals of (81) suitable for crystallographic examination were collected from a solution of the complex in DMSO- d6 in an NMR tube. Table 3.7 summarises the solvents used to obtain crystals of complexes for determining their solid-state structures.
Table 3.7 Conditions used to obtains crystals of alkylated nickel Schiff base complexes suitable for X-ray crystallography.
Complexes Mass (mg) Solvents Time (days)
(71) 19.6 Acetone/DCM 13
(75) 20.1 Acetone/DCM 15
(81) 11.3 DMSO-d6 21
(89) 12.5 MeOH/DCM 4
Most of the unit cells of the complexes contained only the alkylated molecules.
The one exception to this was (75), which also had one molecule of DCM in the unit cell. Information obtained during crystallographic data acquisition and refinement is shown in Table 3.8, while ORTEPs for the complexes are shown in Figure 3.25, and selected bond lengths, bond angles and coplanar ring angles in Table 3.9.
Complexes (71) and (75) crystallised in the monoclinic space group P21/c, and each had an asymmetric unit cell that contained four nickel molecules. The unit cells of (89) and (81) were also asymmetric, but belonged to the triclinic system. These complexes were found to have the space group P1, and their unit cells contained two and eight molecules of complex, respectively.
141 Table 3.8 Crystallographic data for alkylated nickel Schiff base complexes.
(71) (75) (81) (89)
Formula C42H48N4NiO4 C43H50N4NiO4.(CH2Cl2) C42H48N4NiO4 C56H74N6NiO6
Mr 731.56 830.54 731.56 985.94
Crystal system Monoclinic Monoclinic Triclinic Triclinic
Crystal colour Orange Green yellow Orange Orange
Space group P21/c P21/c P1 P1
a (Å) 15.6742 (16) 14.6486 (1) 10.6471 (4) 10.5477 (5)
b (Å) 9.0717 (8) 8.8879 (1) 26.9276 (13) 15.4745 (6)
c (Å) 26.436 (3) 31.2974 (3) 28.5309 (16) 16.5986 (8)
(o) ---- ---- 65.563 (5) 88.093 (3)
(o) 94.398 (9) 91.8126 (8) 84.047 (4) 83.802 (4)
(o) ---- ---- 83.883 (3) 70.576 (4)
V (Å3) 3747.9 (7) 4072.74 (7) 7388.6 (7) 2540.1 (2)
Dx (Mg m-3) 1.296 1.354 1.315 1.289
Z 4 4 8 2
(h,k,l)
-19<h<18 -7<k<11 -32<l<29
-18<h<18 -11<k<8 -38<l<38
-12<h<9 -32<k<33
-35<l<33
-12<h<11 -19<k<18 -20<l<20 Number of unique
reflections 7203 8211 27960 9968
Refinement Rint = 0.074 R[F2 > 2σ(F2)] = 0.081
Rint = 0.032 R[F2 > 2σ(F2)] = 0.052
Rint= 0.056 R[F2 > 2σ(F2)] = 0.097
Rint= 0.054, wR(F2) = 0.177,
R[F2 > 2σ(F2)] = 0.064
142 Figure 3.25 Molecular structures for (71), (75), (81) and (89), with ellipsoids drawn at the 30% probability level.
(71) (75)
(81)
(89)
143 The nickel atoms in all four alkylated complexes also possessed the square planar coordination geometry exhibited by their non-alkylated analogues, and showed similar Ni–O and Ni–N bond distances and bond angles to other nickel Schiff base complexes previously reported.[126, 127, 130] The largest deviations were observed for complex (75) which exhibited an atypical green colour, and features a diamine moiety that forms a six-membered chelate ring with the nickel ion.
Table 3.9 Selected bond length (Å), angles (°) and separation (Å) for alkylated benzophenone derivatives complexes.
Geometric parameters
Nickel complexes
(71) (75) (81) (89)
Ni1–O1 (Å) 1.834 (3) 1.8372 (15) 1.833 (5) 1.822 (2) Ni1–O2 (Å) 1.818 (4) 1.8625 (14) 1.827 (5) 1.829 (2) Ni1–N1 (Å) 1.846 (4) 1.8909 (17) 1.860 (5) 1.854 (3) Ni1–N2 (Å) 1.851 (4) 1.8716 (17) 1.853 (5) 1.850 (3) O1–Ni1–O2 (°) 84.03 (15) 85.87 (6) 84.3 (2) 84.18 (9) O2–Ni1–N2 (°) 94.10 (17) 91.54 (7) 93.9 (2) 93.49 (10) O1–Ni1–N2 (°) 176.16 (18) 166.18 (7) 176.4 (2) 177.67 (10) O2–Ni1–N1 (°) 176.26 (18) 167.03 (7) 175.1 (2) 178.39 (12) O1–Ni1–N1 (°) 94.42 (16) 94.23 (7) 93.3 (2) 94.40 (10) N1–Ni1–N2 (°) 87.64 (18) 91.31 (7) 88.7 (2) 87.92 (11)
N1—C8—C9—N2 (°) 35.9 (5) ---- 39.7 (7) 40.1 (3)
Ring A/Ring B (°) 15.90 24.90 5.62 11.28
Ring A/Ring C (°) 4.23 15.84 4.50 1.59
Ring B/Ring D (°) 4.27 5.51 1.92 8.32
Ring C/Ring E (°) 82.91 83.20 79.37 79.85
Ring D/Ring F (°) 89.54 87.01 75.22 61.48
The solid-state structures shown in Figure 3.25 confirm that the alkylation reactions were successful, including for (89), which features four pendant groups. In the case of (81), one pendant group is orientated above the coordination sphere of the metal ion, while the second is located beneath (Figure 3.26 (b)). This configuration appears to have had the effect of inducing a greater degree of coplanarity between the two bottom aromatic rings in (81) (coplanar angle for rings A and B = 5.62°) compared to its non-alkylated analogue (80), for which the corresponding angle was 21.30°, (Table 3.6 and Figure 3.26 (a)). In contrast, the corresponding coplanar angle for rings A and B in the alkylated complex (75), which
144 features two pendant groups located below the metal ion’s coordination sphere, was 24.90°, which was larger than what was found for its non-alkylated analogue (74) (coplanar angle for rings A and B = 13.27°).
(a) (b)
Figure 3.26 Molecular structures of nickel Schiff base complexes viewed parallel to the coordination sphere of the metal ion: (a) (80) and (b) (81).
Similar to what was observed with the non-alkylated complexes, there was typically a much higher degree of coplanarity between ring systems located solely in the bottom half of the molecules, than between those located in the top and bottom halves. This is exemplified by the coplanar ring angles for rings C and E, and between rings D and F, varying from 61.48° to 89.54°, (Table 3.9). In contrast, all other coplanar ring angles were < 25°. The lack of coplanarity between ring systems in the top and bottom halves of the molecule could inhibit -stacking interactions with G-tetrads, which is usually the most important binding mode for this class of complexes with G-quadruplexes. It must be noted, however, that there is free rotation around the C-C bonds connecting the upper aromatic rings to those in the bottom halves of the complexes, which may mean that alternative conformations to those observed in the solid state may occur in solution, and which are more suitable for binding to G-quadruplexes.
145 The crystal lattices of (71), (89) and (75) consisted of molecules arranged in pairs around crystallographic inversion centres. In the case of (71) and (89) the molecules were packed in a slipped co-facial arrangement, with separations of 4.647 Å and 4.254 Å, respectively between the mean molecular planes calculated excluding the pendant groups. This packing arrangement is illustrated for (89) in Figure 3.27. In contrast to the solid-state structures of the non-alkylated complexes, there were no hydrogen bonds between the metal complexes and solvent molecules, as the former lack free hydroxyl groups and the latter were generally absent from the structures.
(a)
(b)
Figure 3.27 Different views of the packing of molecules of (89) in the crystal lattice: (a) two molecules of (89) in the unit cell; and (b) the view parallel to the molecular planes, showing the separation between the molecules (side arms omitted for clarity).
4.254 Å
146