CHAPTER 3 X-ray Crystallography
N, N'-bis[(pyridin-2-yl)methylene]cyclohexane-1,2-diamine (L5)
3.4.3 X-ray structures of the Schiff base ligands
All the above ligands gave white or colourless crystals suitable for X-ray diffraction studies. Some of the single crystals were grown by allowing slow evaporation, undisturbed for a few days, from diethyl ether (L1, L4 and L5). Others were formed from the reaction mixture on standing (L2h, L6h and L4bh) or were a minor product which
precipitated out in a crystalline form along with the powder of the major product (L1bh and L2bh). All of the ligands that crystallised were found to be of either the monoclinic or orthorhombic systems, with the exception of L4 and L2bh, which crystallised in the triclinic crystal system (P1). All nonhydrogen atoms were refined anisotropically.
Hydrogen atoms were inserted with standard SHELXL291 idealisation parameters in their geometrically idealised positions for L4b and constrained to ride on their parent atoms, with distances in the range 0.95–1.00 Å. Hydrogen atoms for L1, L5 and L4 were located by difference Fourier synthesis and refined isotropically.
Figure 3.14: Thermal ellipsoid views (with the nitrogen atoms labelled) of the X-ray structures of L1, L4 and L5 (50% probability displacement ellipsoids), showing the overall molecular conformations. (Hydrogen atoms have been calculated for L1 and L5 and located for L4.)
L1, L4 and L5 are novel examples of structurally characterised N4-donor Schiff base ligands; their molecular structures are shown in the thermal ellipsoid plots in Figure 3.14.
Due to the cis-configuration of the cyclohexane bridge there is no centre of inversion for L5 and all the nitrogen atoms are unique. However, L1 has inversion symmetry due to its symmetrical ethyl bridge and hence the ligand contains two identical halves. Although
L5 L1
L4
that the bridging group has been distorted. Selected bond lengths and angles are shown in Table 3.2. The standard uncertainty (estimated standard deviation) is given in parenthesis. Note that for bonds to differ by a statistically significant amount, the difference must be > 4 x the esd (estimated standard deviation). The lengths of the C=N bonds are experimentally equivalent: 1.267(2) (L1), 1.267(2) (L4) and 1.268(2) (L5) Å.
These lengths fall within the expected range for imine bonds: 1.250 to 1.270 Å.158,302 Table 3.2: Selected average bond lengths (Å) and angles (°) of the free Schiff base ligands.
L1 L4 L5
Ni=Ci 1.267(2) 1.267(2) 1.268(2) Np-Cp 1.342(2) 1.347(2) 1.348(2) Cf-Cg 1.519(3) 1.539(2) 1.533(2) Ci-He 0.981(1) 0.989(2) 0.994(2) Ci=Ni-Cf 117.0(1) 116.9(1) 116.5(1) Ni-Cf-Cg 111.5(1) 112.2(1) 110.7(1) Np-Cp-Ci 115.3(1) 114.9(1) 115.0(1) Cp-Ci-Ni 121.9(1) 121.8(1) 122.6(1)
There is no indication of π–π stacking for the pyridine rings in these ligand structures, even though such interactions might be expected to occur due to their abundance in heteroaromatic systems.303 Complementary short contacts are seen for all three of these ligands (as shown in Figure 3.15). Short intermolecular contacts have been observed between two neighbouring Schiff base units for the ligand L5 (Ca-Ha···Np and Np···Ha-Ca).
A similar contact involving the pyridine-nitrogen takes place in L1 between Ci-He···Np and Np···He-Ci for adjacent molecules. Because the imine C-H group functions similarly to an aromatic C-H group as a known unconventional H-bond donor304, the pair of C-H···N interactions between neighbouring molecules is consistent with complemenary H- bonding. Meanwhile, L4 has a complementary relationship between the bridging hydrogens of one molecule with the pyridyl carbon atoms from another molecule. There is also a second set of complementary short contacts observed for L5 invloving the imine-nitrogen, Cc-Hc···Ni.
Figure 3.15: Complimentary short intermolecular contacts of L5 (2.621(10) and 2.745(10) Å), L1 (2.656(10) Å) and L4 (2.857(10) Å and 2.814(10) Å).
Figure 3.16: Crystal packing diagrams of the unit-cell for L1 (Z = 4), L4 (Z = 2) and L5 (Z = 4),
Np
He
He
Np
2.656(10)Å
Hf
Hf Cc
Cc Cd
Cd
2.814(10)Å 2.857(10)Å
Ha
Ha
Np
2.621(10)Å
Np
Hc
Hc
Ni
Ni
2.745(10)Å
L5
L5
L1
L4
L5 L1
L4
Thus, L1 and L5 represent systems with unconventional complementary (sp2) C-H···N hydrogen bonding, while L4 simply has a pair of molecules related by inversion with some short non-bonded contacts. The latter are not in any way stabilising, in contrast to the former H-bonded dimers. The unit-cell packing diagrams for each of the ligands are depicted in Figures 3.16 and display the patterns in which the molecules are located in the solid state. They reveal the infinite two-dimensional network structure for each of the compounds.
The ligands with the larger steric bulk on the imine carbon have more difficulty in crystallising. None of the methyl-substituted ligands have thus far produced X-ray quality crystals and only one structure has been obtained for the phenyl-substituted ligands;
L4b. The structure of this ligand is shown in Figure 3.17 along with its complementary short contacts between Ch-Hh···Ce2 and Ce2···Hh-Ch. This space-filling model clearly shows the extra bulk on this ligand.
The other ligands that have formed X-ray quality crystals are mono(imine) ligands (1:1 ratio of aldehyde to diamine) resulting in an N3 Schiff base ligand. This structure then cyclises intramolecularly at the imine carbon atom to produce an imidazole-containing or hexahydropyrimidine-containing bidentate ligand. X-ray quality crystals have been obtained for: L2h, L6h, L1bh, L2bh and L4bh. Not much success has thus far been had in obtaining crystals from their fully reacted ligands (2:1 ratio of aldehyde to diamine).
Most of these ligands are viscous oils, except for L4b, for which the data has been presented here. These bidentate imidazole- or hexahydropyrimidine-containing ligands present the possibility of metallation in a 2:1 ligand to metal ratio. This has been attempted for L6h with Pt(II) and Pd(II), where metallated adducts in powder form have been obtained (see Chapter 2 – Experimental).
The imidazoline derivative, L1bh305, has been reported in the literature with the same space group as in this work. L1bh crystallises in the monoclinic space group C2/c and displays an interesting supramolecular structure – a “zip” – that involves corresponding hydrogen bonding between neighbouring molecules (Figure 3.18). A similar interlocking hydrogen-bonded polymer has been seen by Munro and co-workers for a novel crystalline steroidal sapogenin306 and Barboiu et al. have reported metallosupramolecular zippers stabilised by strong π–π stacking interactions.307
Figure 3.17: Left: The complementary short contacts of 2.842 Å for L4b. Right: The space filling model of L4b (top) and a thermal ellipsoid view of the X-ray structure of L4b (50% probability displacement ellipsoids), showing the overall molecular conformation where hydrogen atoms are rendered with arbitrary radii (bottom).
Figure 3.18: The packing “zip” of the imidazoline derivative, L1bh, showing short contacts C2
C2
H
h
H
h
N1 N2
N3
N4
Although L6h has also been synthesised before, it has been reported with space groups of Pbca308 and P2/c309. Here our space group setting for L6h is Pbna albeit with a slightly higher R-factor (Rint = 0.0972) than those reported for the Pbca and P2/c polymorphs.
L2h and L2bh are both novel structures, with the only difference between them being either a hydrogen atom or a phenyl ring. These structures were synthesised when the aldehyde and diamine starting materials reacted in a 1:1 ratio (see page 41). The bulk of this group clearly has an effect on the structure as the two molecules show very different crystallographic arrangements. L2h has interesting hydrogen bonding which involves the water and chloride counter ions. The π–π stacking seen for this molecule is at a distance of 3.355 Å which presumably stabilises the crystal structure (Figure 3.19). L2bh does not possess this π–π stacking and the molecules pack in an alternating pattern (zig-zag strucrure) using hydrogen bonding to stabilise them (Figure 3.20). Cd-Hd···Np
complementary hydrogen bonding favours the formation of one-dimensional chains; this repeated packing chain of these molecules can be seen in Figure 3.21.
Figure 3.19: Ball and stick model to show the π–π stacking interactions (left) and a thermal ellipsoid view (at 50% probability) of the hydrogen bonding (right) for L2h.
3.355(2) Å 3.355(2) Å
3.355(2) Å
Cp
Ca
Cp
Ca
Cp
Ca
2.568 Å 3.339 Å
Figure 3.20: The complimentary short contacts of 2.722 Å between neighbouring molecules (left) and the packing diagram for the unit cell of L2bh, hydrogen atoms have been omitted for clarity (right).
Figure 3.21: The hydrogen-bonded chain of L2bh with two alternating intermolecular separations: 2.742 and 2.722 Å.
Hd
N2 Hd
N2
2.722 Å
2.742 Å 2.742 Å
2.722 Å
The structure of L4bh is rather similar to that of L2bh, differing only by the dimethyl substitution of the central carbon of the propyl bridge of the diamine starting material.
This results in greater bulk on the cyclised hexahydropyrimidine ring and subsequently very different packing to that of the triclinic L2bh. There are no complimentary short contacts for L4bh; but rather a “circular” arrangement of four molecules (Figure 3.22).
These four molecules are connected to each other to form a symmetrical pattern, with Hf···H3 and C3/C4···Hb short contacts on either side. Chains of these circular four molecules are then linked to other chains through Hh···Hh (2.2563 Å) short contacts.
There is no π–π stacking observed for L4bh, as in L2bh.
Figure 3.22: Top: The intermolecular short contacts between neighbouring molecules of L4bh.
Bottom left: a thermal ellipsoid view (at 50% probability). Bottom right: the packing diagram for the monoclinic unit cell of L4bh.
Hf
Hb
H3
2.364 Å Hf
Hb
C4 C3
H3
C4
C3
2.845 Å 2.840 Å 2.364 Å
2.845 Å 2.840 Å