Materials and methods

5.1.1 Reagents.

All chemicals and solvents were of reagent grade (unless otherwise stated) and purchased from Aldrich Chem. Co. Ltd., Fluka Chemika-Biochemica (U.K.), Lancaster Synthesis Ltd. or local solvent suppliers, and were used as received, unless otherwise stated. Water was deionised in house before use.

5.1.2 Elemental analysis.

Elemental Analysis was carried out at University College Dublin by Ms. Ann Connelly using a Carlo Erba 1006 automatic analyser. Expected range C, N ± 0.3 %, H ± 0.5 %.

5.1.3 Nuclear magnetic resonance spectroscopy.

NMR spectra were carried out by Dr. John O’Brien and recorded on a Bruker DPX 400 machine operating at 400.14 MHz for 1H, 100.63 MHz for 13C. Samples were run in deuterated solvents as listed for each spectrum. Standard abbreviations for spectra: s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet; br, broad.

5.1.4 Infrared spectroscopy.

Infrared spectra were recorded in the range 4000 – 400 cm-1 on a Mattson Genesis II FTIR. Samples were run as 8 mm diameter potassium bromide pellets prepared under vacuum. The following abbreviations were used to describe the intensities: vs, very strong; s, strong; m, medium; w, weak; vw, very weak; sh, shoulder; br, broad; vbr, very broad.

5.1.5 Single crystal X-ray diffraction.

X-Ray analyses for all the crystals were performed by Dr. Paul Jensen and Dr. Sandrine Goetz within the Kruger group at Trinity College, Dublin, with a Bruker SMART APEX CCD diffractometer. The candidate was involved in all aspects of structure determination. The final refinements were performed by the candidate, with assistance provided by Dr. Sandrine Goetz where necessary.

The diffractometer utilised graphite-monochromated Mo-Kα radiation (λ = 0.71073 Å). The omega scan method was used to collect either a full sphere or hemisphere of data for each crystal with detector-to-crystal distance of either 5 or 6 cm at temperatures of 153 or 293 K. Data were collected, processed, and corrected for Lorentz and polarisation effects using SMART and SAINT-NT software.276, 217 Absorption corrections for single crystals were applied using SADABS.277 The

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structures were solved using either Patterson or direct methods and refined on HKLF4 data with the SHELXTL program package.278 Data for the non-merohedral twinned crystal of 12 were indexed using the GEMINI program213 rather than the usual SMART routine. The twinned data were processed using the twin output option of SAINT217 and corrected for absorption using TWINABS.216 The twinned structure 12 was solved as for the single crystals using HKLF4 data for the main domain, however attempts to refine this structure using HKLF5 data were not successful.

All non-hydrogen atoms were refined anisotropically except for some atoms which were ”non-positive definite” and thus refined isotropically or their isotropic thermal parameters were fixed to 0.08 when too high. Hydrogen atoms for CH, CH2 and CH3 were assigned to calculated positions using a riding model with appropriately fixed isotropic thermal parameters. Hydrogen atoms of alcohol or ammonium functions, however, were located from difference maps and their positions refined with O-H or N-H distance restraints (DFIX 0.84 Å, SAME, SADI)278 and isotropic thermal parameters either fixed at 1.5 or 1.2 times that of the adjoining oxygen or nitrogen atom or refined isotropically. The hydrogen atom of the phenolic function in 8 was assigned to a calculated position using a riding model with appropriately fixed isotropic thermal parameter. Hydrogen atoms of some disordered water or methanol molecules were not added.

The CrystalMaker software282 was used to generate all the pictures of crystal structures included in this thesis, by reading the ‘cif’ files of either previously reported structures, whose reference was listed for each picture, or crystal structures resulting from the research carried out by the candidate and presented within this thesis. The colour code used is that from IUPAC: black represents carbon atoms; blue, nitrogen atoms; red, oxygen atoms; cream, hydrogen atoms; green, Ni(II) or Cu(II); pink, Mn(II); orange, Mn(III); purple, Mn(IV). Where specifically needed the colour codes were listed for each picture.

5.1.6 Magnetic susceptibility measurements.

Variable temperature magnetic measurements for crystalline samples of complex 2, the mixture of complexes 3 and 4, complexes 15 and 17 were performed by Dr. Boujemaa Moubaraki (School of Chemistry, Monash University, Clayton, Victoria, Australia) using a Quantum Design MPMS 5 SQUID (Superconducting Quantum Interference Device) magnetometer in the range 4-300 K with an applied magnetic field of 1 Tesla. The machine was calibrated by use of a standard palladium sample (Quantum Design) of accurately known magnetisation or by use of magnetochemical calibrants such as CuSO4·5H2O and [Ni(en)3]S2O3. Crystalline samples of the complexes (typically 40 mg) were air-dried, powdered in a mortar and used for the

H₃N H₃N NH₃ H₃N H₃N NH₃ + + + + + + .3Cl .3Cl - - L1a.3HCl a c a a c c b b b a' a' a' b' b' b' c' c' c' L1b.3HCl bbbb

measurements. Samples were contained in gelatine capsules held at the end of a plastic straw, which was fixed to the end of the sample rod. Prof. Keith Murray is thanked for his assistance with the interpretation of the magnetic data.

5.1.7 Electrospray mass spectrometry.

Electrospray mass spectrometry was carried out by Dr. Martin Feeney on a Micromass LCT Electrospray mass spectrometer. Samples were dissolved in HPLC grade solvent which are listed for each spectrum at a concentration of ~2 ng/L. Spectra are reported in the following manner: m/z and assignment.