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Radiation chemistry is concerned with understanding the chemical kinetics following the application of ionising radiation. There are two main methods for modelling recom- bination and spin dynamics in radiation chemical systems: The Monte Carlo random flights algorithm, in which the trajectories of the diffusing species are followed ex- plicitly and the Independent Reaction Times (IRT) algorithm, where reaction times are sampled from appropriate marginal distribution functions. This thesis reports develop- ments to both methods, and applies them to better understand experimental findings, particularly spin relaxation effects. Chapter 4 introduces current simulation techniques and presents newly developed algorithms and simulation programs (namely Hybrid and Slice) for modelling spatially dependent spin effects. A new analytical approximation for accurately treating ion-pair recombination in low-permittivity solvents in also presented in this chapter. Chapter 5 explores the photodissociation of H₂O₂, where there is some controversy in the literature on the spin state of the precursor. This chapter explores the possibility of reproducing the observed spin polarisation phase using the Radical Pair Mechanism. Chapter 6 presents two new algorithms for treating reactive products in the IRT framework. These have been tested for two chemical systems: (i) photodissociation of H₂O₂ where the ·OH are scavengeable; (ii) water photolysis which produces H⁺, ·OH and e⁻__aq. In the latter case a careful handling of three body correlations is required. Chapter 7 presents simulation results which suggest a strong correlation between scavenging and ion recombination in low permittivity solvents. A path decomposition method has been devised that allows IRT simulations to be corrected for this effect. Chapter 8 presents evidence for spin-entanglement and cross-recombination to act as an extra source of relaxation for ion-recombination in low permittivity solvents. It is hypothesised this effect contributes to the anomalous relaxation times observed for certain cyclic hydrocarbons. Chapter 9 presents an extension of the IRT simulation method to micelles. The kinetics are shown to be accurately described using the mean reaction time and the exponential approximation.

Pulsed ultraviolet lasers can be used to induce clean etching in organic and some inorganic materials. This effect is called photoablation or ablative photodecomposition. Although the precise cause remains unknown, this phenomenon is becoming of vital importance in micromachining, materials processing, and medicine. To better understand the photoablation process, a theoretical description of the process has been developed. This description is based on a treatment of the radiation transport of intense ultraviolet light pulses through absorbing organic material. The theory predicts deviations from Beer's Absorption Law at high intensities which are in fact observed. These discrepancies are due to three main effects: saturation of the finite number of chromophores in the material, multiphoton absorption, and attenuation of laser light by ablation products. Using the analysis to model the ablation process it is possible to describe observed ablation behaviors for a variety of synthetic and biological substrates. Excimer laser photoablation has also been studied experimentally as a means of removing occlusive arterial thrombi. Thrombi induced in canine coronary arteries were removed with XeF excimer laser light (351 nm) delivered via flexible optical fiber. The results of this study indicated that it was possible to remove significant thrombi (27 mg mass) within 3 minutes, without causing injury to the adjacent arterial wall. In addition, the ablation products consisted of a minute volume of gas and small particulate debris ($>$100 $\mu$m), which would not be a cause of concern in a clinical procedure. Excimer laser induced autofluorescence signatures have been analyzed as possible diagnostic aids in laser angioplasty procedures. Spectra acquired from cadaver artery samples using low intensity laser light revealed distinct differences in fluorescence response between healthy and atherosclerotic arterial wall. Fluorescence spectra acquired during tissue ablation with intense laser pulses also exhibited variation between healthy and diseased sites. Spectral examination of tissue sites after ablative tissue removal showed changes in fluorescence response which coincided with penetration of diseased lesions. These findings indicated that it should be possible to use UV laser fluorescence spectroscopy to target atherosclerotic lesions and to monitor in real time the ablative removal of these vessel obstructions.

Doctor of Philosophy / Department of Biochemistry and Molecular Biophysics / John M. Tomich / Branched Amphiphilic Peptide Capsules (BAPCs) are peptide nano-spheres comprised of equimolar proportions of two branched peptide sequences bis(FLIVI)-K-KKKK and bis(FLIVIGSII)-K-KKKK that self-assemble in water to form bilayer delimited poly-cationic capsules capable of trapping solutes. We examined the lipid-like properties of this system including assembly, fusion, solute encapsulation, and resizing by membrane extrusion as well as their capability to be maintained at a specific size by storage at 4˚C. These studies along with earlier work from the lab (Gudlur et al. (2012) PLOS ONE 7(9): e45374) demonstrated that the capsules, while sharing many properties with lipid vesicles, were much more robust. We next investigated the stability, size limitations of encapsulation, cellular localization, retention and, bio-distribution of the BAPCs. We demonstrated that the BAPCs are readily taken up by epithelial cells in culture, escape or evade the endocytotic pathway, and accumulate in the peri-nuclear region where they persist without any apparent degradation. The stability and persistence of the capsules suggested they might be useful in delivering radionuclides. The BAPCs encapsulated alpha particle emitting radionuclides without any apparent leakage, were taken up by cells and were retained for extended periods of time. Their potential in this clinical application is being currently pursued. Lastly we studied the temperature dependence of capsule formation by examining the biophysical characteristics of temperature induced conformational changes in BAPCs and examined the structural parameters within the sequences that contribute to their remarkable stability. A region in the nine-residue sequence was identified as the critical element in this process. The ability to prepare stable uniform nano-scale capsules of desired sizes makes BAPCs potentially attractive as delivery vehicles for various solutes/drugs.

This Thesis aims to examine the effects of substituents on the adjacent proton accepting phenyl ring with respect to a new type of excited state intramolecular proton transfer (ESIPT) process discovered by Wan and co-workers. Therefore, a number of 2-phenylphenols 23-28 were synthesized with electron-donor and electron-acceptor substituents such as methyl, methoxy, and ketone moieties on the adjacent proton accepting phenyl ring. The results obtained from examination of photochemical deuterium exchange showed that all derivatives except for ketone 27 underwent deuterium exchange (Фex = 0.019 - 0.079), primarily at the 2’-position on photolysis in D2O-CH3CN. In general, compounds with methoxy moiety (ies) on the adjacent proton accepting ring showed higher deuterium exchange yields. Diol 28 has the potential to undergo photosolvolysis as well as ESIPT process since it has both a benzyl alcohol and a phenol chromophore on the same molecule. Irradiation of 28 in 1:1 H2O-CH3OH gave the corresponding methyl ether product in high yield. Photolysis of 28 in 1:1 D2O-CH3OH also showed that ESIPT competes very well with photosolvolysis. Thus, this work has established that ESIPT can compete efficiently with photosolvolysis. Semi-empirical AM1 (examination of HOMOs and LUMOs) calculations show a large degree of charge transfer in the electronic excited state (except 27), from the phenol ring to the attached phenyl ring of the studied compounds. The AM1 calculation for ketone 27 showed that the carbonyl oxygen is more basic than the carbon atoms of the benzene ring, which explains the lack of deuterium exchange observed for 27.

Protein structure models obtained from X-ray crystallography are subject to radiation damage. The resulting specific alterations to protein structures can be mistaken for biological features, or may obscure actual protein mechanisms, leading to misidentification or obscuration of biological insight. The radiation chemistry behind this site-specific damage is not well understood. Radiation damage processes progress in proportion to the dose absorbed by the crystal in the diffraction experiment. Doses can be estimated using existing software, but these assume idealised experimental conditions. To simulate complex diffraction experiments, including treatment of imperfect X-ray beam profiles and inhomogeneous dose distributions, a new program, RADDOSE-3D, was developed. RADDOSE-3D can be integrated into beamline software to provide convenient, more accurate, comparative, and publishable dose figures, also facilitating informed data collection decisions. There is currently no method to automatically detect specific radiation damage in protein structure models in the absence of an 'undamaged' reference model. Radiation damage research therefore generally relies on detailed observation of a few model proteins. A new metric, B_Damage, is designed and used to identify and quantify specific radiation damage in the first large-scale statistical survey of 2,704 published protein models, which are examined for the effects of local environments on site-specific radiation damage susceptibility. A significant positive correlation between susceptibility and solvent accessibility is identified. Current understanding of radiation damage progression is mostly based on a few consecutive structure model 'snapshots' at coarse dose intervals. The low sampling rate considerably limits the ability to identify varying site susceptibility and its causes. Real space electron density data are obtained for crystals of different mutants of a RhoGDI protein with very high sequence identity, to determine sensitising and stabilising factors for radiation induced structural changes. Utilising a newly developed data collection and analysis protocol, these changes could be tracked with unprecedented time resolution.

La tomographie par émission de positons (TEP) est une modalité d’imagerie nucléaire puissante, permettant des mesures fonctionnelles non-invasive dans les cellules, les animaux et les humains avec une haute sensibilité et résolution. Les exosomes sont des vésicules extracellulaires de 30 à 120 nm qui peuvent transférer leur contenu cytoplasmique entre cellules, mais comprendre leurs cheminements in vivo reste un défi. Les hydrogels thermosensibles à base de chitosane ont été développés et sont sous optimisation pour diverses applications telles que l'embolisation des vaisseaux sanguins, l'administration de médicaments, l’'administration de lymphocytes et la réparation du cartilage et des disques intervertébraux. Il y a un besoin urgent de suivi in vivo à court terme pour évaluer la rétention des hydrogels et des exosomes. Le Hexadécyl-4- [18F]-fluorobenzoate ([18F]HFB) est un radiotraceur lipophile à longue chaîne qui est retenu dans les membranes cellulaires et les biomatériaux. Le but de ce travail était d'automatiser la radiosynthèse de [18F]HFB pour marquer des exosomes et des hydrogels. La radiosynthèse et la purification de [18F]HFB ont été réalisées en utilisant le synthétiseur de chimie commercial IBA Synthera®. [18F]HFB a été préparé via substitution du précurseur d’ammonium quaternaire par [18F]F-. Après une première purification via une cartouche C18, [18F]HFB a été élué avec de l'acétonitrile et purifié par HPLC. [18F]HFB a ensuite été reformulé dans une solution de DMSO (10%) après élimination du solvant HPLC sous azote, filtré et dilué dans une solution saline stérile. [18F]HFB a été obtenu en rendement radiochimique allant de 15 à 45% (corrigé pour désintégration), en haute pureté radiochimique et chimique, et dans un temps de synthèse total de 60 minutes. Les exosomes n'ont pas été marqués avec succès. Cependant, les hydrogels de chitosane ont démontré un marquage élevé, avec une stabilité du complexe >90%, même après 8 heures d’incubation en solution saline. La TEP avec [18F]HFB d'exosomes et de biomatériaux présente une approche novatrice pour déterminer leur distribution in vivo. / Positron emission tomography (PET) is a powerful nuclear imaging modality allowing for non-invasive functional measures in cells, animals and humans with high sensitivity. Exosomes are 30-120 nm extracellular vesicles that can transfer their cytoplasmic contents between cells, however, understanding where exosomes traffic in the body remains a challenge. Chitosan-based thermosensitive hydrogels have been developed and are currently under optimization for various applications such as blood vessel embolization, drug delivery, lymphocyte delivery systems, and cartilage and intervertebral disc repair. There is an urgent need for in vivo, short term follow-up of such procedures to assess the retention of hydrogels and exosomes at the site of injection. Hexadecyl-4-[18F]fluorobenzoate ([18F]HFB) is a long chain lipophilic radiotracer that has been reported to be retained within cell membranes or biomaterials. The aim of this work was to automate the radiosynthesis of [18F]HFB for labeling exosomes and chitosan-based hydrogels. The radiosynthesis and purification of [18F]HFB was done using the commercial IBA Synthera® chemistry synthesiser with the R&D IFP-cassette and HPLC module. As previously reported, [18F]HFB was prepared by [18F]F- substitution of the trimethyl ammonium triflate precursor in DMSO. After removal of unreacted [18F]F- and DMSO via a C18 light cartridge, [18F]HFB was eluted with acetonitrile and purified by semi-prep C18 HPLC. [18F]HFB was then reformulated in DMSO (10%) solution after removal of the HPLC solvent from the radioactive product peak under nitrogen, filtered, and diluted in sterile saline. [18F]HFB was obtained in radiochemical yield (isolated after HPLC and evaporation) ranging from 15 – 45% (decay-corrected), high radiochemical and chemical purities, and within a total synthesis time of 60 mins. Exosomes were not successfully labeled. However, high labeling efficiency was observed with the chitosan hydrogels displaying a stability >90%, even after 8 hours incubation in saline. PET imaging with [18F]HFB of exosomes and biomaterials presents a novel approach to determining their in vivo distribution.