Chemistry and biology are full of examples of aggregation phenomena; from the useful applications in drug molecule stabilisation and tissue engineering, to the negative effects of causing diseases such as Alzheimer's and Parkinson's. NMR is a useful tool for probing aggregation as it can provide detail at the atomic scale; however, the molecular size of the aggregates can lead to poor resolution and spectral broadening, issues which require some development to solve. The research detailed in this thesis aims to develop NMR tools to investigate aggregation phenomena from two angles; firstly, to directly monitor aggregation using diffusion-ordered NMR spectroscopy and secondly to probe the effects of aggregates on biomimetic constructs using NMR techniques. To achieve the first aim, diffusion-ordered NMR Spectroscopy in conjunction with a size-exclusion chromatography stationary phase was developed for the purpose of monitoring aggregation in a time-resolved manner. The size-exclusion stationary phases, commonly used to separate molecules of different sizes, such as proteins from salts, in liquid chromatography methods, provide an additional perturbation of the diffusion profile of molecules of different sizes when added to NMR samples for diffusion-ordered spectroscopy analysis. The development of this method and a selection of applications are detailed within two chapters of the thesis. These studies have been published in Journal of Magnetic Resonancei and Journal of Physical Chemistry Cii. A complementary study of the interactions between aggregates and biological structures such as biomimetic cell membranes using NMR methods such as time-resolved 31P NMR and the implementation of paramagnetic shift reagents is discussed in the final two chapters. Changes in chemical shift caused by additional interactions between the shift reagent and the solvent are fully investigated and the method is applied to the study of membrane permeation by amyloid-β oligomers.

A range of fluorescence fluctuation analysis methods were developed and applied to labels commonly used in biological samples. Various super-resolution techniques were demonstrated in vitro and in vivo using objective-type Total Internal Reflection Fluorescence Microscopy (TIRFM). An experimental Fluorescence Correlation Spectroscopy (FCS) setup was developed along with associated post-acquisition data algorithms. The technique was applied to investigate the stoichiometry of a protein subunit of ribonucleotide reductase (RNR). FCS method was adapted with an Electron Multiplying Charge Coupled Device (EMMCD) detection scheme and applied to inorganic Quantum Dots (QDs) diffusing in solutions of different viscosities. Super-resolution Optical Fluctuation Imaging (SOFI) algorithm was implemented in ImageJ software and conclusive results obtained on reference samples of QDs and combed DNA. Potential applications of temporal correlation analysis to the study of diffusive processes and single particle tracking were also discussed. A new super-resolution technique applicable to multiple adjacent fluorescent molecules called Direct Object Resolution by Image Subtraction (DORIS) was developed and tested with QD complexes. The method enables one to accurately map the position of two emitters displaying intermittency in their fluorescence emission and separated by a distance below the diffraction limit, without the need of complex instrumentation or analysis. The technique relies on the subtraction of the Point Spread Function (PSF) of each single fluorescent probe, and is in theory applicable to any blinking or flickering dye. The principle was first demonstrated on simulated data and experimentally on QDs coupled by 100-basepair double-stranded DNA constructs. Super-resolution by image subtraction was further applied in vivo in S. pombe cells, where distances between clustered fluorescent fusion proteins were accurately determined. The selective activation of photoswitchable probes mEos3 was exploited to optimise the DORIS subtraction process and provided a simple method to determine the relative positions of closely spaced emitters within an aggregate, as encountered in association sites or multimeric complexes.

For genome integrity, adequate levels of deoxyribonucleotide (dNTPs) are essential to maintain faithful DNA replication and repair via the regulation of ribonucleotide reductase (RNR). In the fission yeast, RNR is composed of two subunits: Cdc22 and Suc22. The importance of Spd1 (RNR inhibitor) in Cdc22-Suc22 complex formation has been demonstrated by imaging of S. pombe containing fluorescent protein (FP) modified RNR subunit proteins in the presence of Spd1 and absence of Spd1 cells using confocal laser scanning microscopy. To investigate further the significant role of Spd1 in the regulation of RNR, 41 mutants created by Nestoras group. We used fluorescence resonance energy transfer (FRET) by acceptor photobleaching to investigate the RNR subunit interaction and provide evidence for a new model for the role of Spd1 in RNR regulation. Different treatments such as HU, 4NQO and heat shock have been used to investigate the effect of radical scavenging on the inhibition of RNR activity and induced DNA damage on S. pombe cell viability to elucidate further the role of Spd1 in the regulation of RNR. Finally a novel imaging technique, near-total internal reflection microscopy has been developed and applied with dual-view detection. The technique has been applied to image, simultaneously, the donor CFP and acceptor YFP channels of the FP-tagged RNR complex in the wild-type S. pombe cells and perform FRET measurements that are consistent with the confocal fluorescence results. In conclusion, a new hypothesis for the role of Spd1 has been drawn from the results, which is that the inhibitory role of Spd1 mediates the Suc22-Cdc22 (R1-R2) interaction to form a FRET competent but immature and inactive RNR complex, while with Spd1 deleted RNR is clearly active in a conformation that lacks FRET.

The work in this thesis deals with computational studies of manganese ions and atoms in the gas-phase and in the solid phase. The results are divided into three chapters, and the theory and methods used are explained and discussed in a separate theory chapter. The first results on manganese and its coordination to water and methanol molecules in the gas-phase are discussed in the light of physical properties for different ligands including water and methanol. Preferred coordination of a specific ligand type, preferred complex or cluster size as well as coordination modes are thoroughly investigated. Also discussed is stability against proton-transfer reactions for a few manganese-water and manganese-methanol clusters. The work is carried out at the HF/6- 31G(d), MP2/6-311G(d,p) and B3LYP/6-311(3df,3pd)-level of theory using the computer code Gaussian. The results presented here are in good agreement with experimental results and findings. It is concluded that mixing between 4s and 3d orbitals on the manganese atom is responsible for preference for a specific cluster size and that occupation of anti-bonding orbitals destabilizes the cluster, for a specific coordination mode. The next results are for manganese atoms in a double layer of graphite, using the computer code Aimpro. Different coordination modes are investigated as are magnetic properties upon adsorption and modification of the band structure compared to a pristine double layer of graphene. Only one case of a significantly high spin polarization is encountered, and the spin polarization on the manganese atom and the surrounding carbon atoms is investigated with Mulliken analysis. This study is in agreement with previous work in the same field, but provides a more realistic picture since a larger system is considered here. The final chapter deals with manganese atoms in metal-organic frameworks, MOFs, using the Aimpro code. Magnetic properties and binding energies for adsorption of selected molecules are discussed in this chapter. Magnetic properties are discussed using Mulliken analysis. Modification of the band structure upon coordination of these gas molecules is shown and investigated. Very few experimental results exist in this field for this structure, but its role as a potential candidate for hydrogen storage will specifically be discussed.

A range of experimental techniques for application in reaction studies between ionic and neutral atoms/molecules and high resolution spectroscopy experiments with sympathetically cooled molecular ions are presented. A novel ion trap loading scheme using the photo-ionisation of atoms generated by the pulsed laser ablation of a solid calcium target has been characterised. We have identified the range of ablation laser fluences that must be used in order to produce a flux of neutral calcium atoms, which is a prerequisite for isotope selective ion trap loading. Calcium ions are trapped and laser cooled in a linear radio-frequency ion trap. We have developed a spectroscopy scheme that allows the entire fluorescence spectrum of trapped ions to be rapidly collected with high precision while maintaining a low ion temperature and good ion localisation throughout interrogation. The scheme has been demonstrated by measuring the saturation intensity of the calcium ion 4S1/2→4P1/2 transition. We have developed a novel scheme to measure the secular motion of trapped ions and demonstrated the application of the technique to ion-neutral collision reaction experiments. Employing pulsed excitation and Doppler velocimetry, we have measured the centre-of-mass mode frequency of single ions as well as large ion crystals with a frequency precision better than 2x10-3 within an interrogation time on the order of seconds. This method has been used to measure the mass of ions and observe charge exchange collisions between trapped calcium isotopes. In particular, we have measured the 44Ca++40Ca!40Ca++44Ca reaction cross section and demonstrated the single-event resolution of the technique. Finally, we have developed a novel all-optical broadband scheme for exciting, amplifying and measuring the secular motion of ions in the trap. Oscillation induced by optical excitation has been coherently amplified to control and measure the ion's secular motion. Requiring only a single interrogation laser, the ion's oscillation amplitude can be precisely controlled. The application of this technique to non-destructive spectroscopy of trapped molecular ions is discussed.