Chemistry - Masters by Research Theses

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https://hdl.handle.net/10468/10433

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Synthesis and reactivity of α-diazosulfoxides and α-diazosulfones
(University College Cork, 2024) Ní Thuama, Eilís; Maguire, Anita; Collins, Stuart
The focus of this body of work has been the synthesis of stable mono and bicyclic α-diazosulfoxides and their subsequent reactivity. A range of α-diazosulfoxides have been synthesised by the Maguire-Collins research group since the mid-1990s using a Regitz diazo transfer method. In this work in situ NMR monitoring has been used to gain a deeper understanding of the relative reactivity of diastereomeric sulfoxides in this reaction. α-Diazosulfoxides were synthesised using flow and batch reaction conditions. Continuous flow processing enabled the α-diazosulfoxide synthesis using an in situ generated sulfonyl azide for the first time, resulting in a greater safety profile for the process. Investigations into the synthesis of related mono and bicyclic α-diazosulfones were also undertaken, in both batch and flow. The α-diazosulfoxides are known to react via a hetero-Wolff rearrangement to form α-oxo sulfines. The 1,3-dipolar cycloadditions of these α-oxo sulfines were investigated further under Rh catalysis and a study into the photoreactivity of the α-diazosulfoxides on flow was also performed.
Atomic layer deposition and electrochemical characterization of TiO2 as a potential candidate for a photoanode protective layer
(University College Cork, 2024) Shine, Micheál; Povey, Ian; SFI Manufacturing
The search for alternative fuel sources has become more prevalent in recent years due to increasing energy demands as well as the detrimental effects fossil fuels have on the environment. Solar water splitting using semiconductor photoelectrochemical cells has long been viewed as a potential means of large-scale H2 production from renewable resources. A study was carried out to test the corrosion resistance performance of thin TiO2 layers deposited by means of atomic layer deposition under oxidative conditions. Despite Silicon being considered one of the most promising semiconductors for use in photoelectrodes, its instability in aqueous solutions is one of its main limiting factors. TiO2 film (~6 nm) were deposited on the anode surface, using atomic layer deposition and plasma enhanced atomic layer deposition (ALD), to act as corrosion protection and to passivate the electrode surface along with a 5 nm Nickel over layer to act as an oxygen evolution catalyst. The longevity of these photoanodes was the main focus of this work employing the techniques of cyclic voltammetry and chronoamperometry to evaluate electrochemical performance. Electron microscopy SEM was carried out, before and after the anodes underwent electrochemical testing, to gain insight into any surface degradation and morphological changes of the TiO2 and Ni layers that may influence charge transfer and performance. Comparisons were drawn between photoanodes prepared by ALD and plasma enhanced atomic layer deposition (PE-ALD) to give a clearer picture of the limiting factors of charge carrier mobility and photoactivity. The estimated ratio of Ti3+ to Ti4+ and hence the oxygen vacancies, played an important role in the overall conduction of the device along with the % composition of impurities present due to incomplete reactions in the deposition process. This was tested by producing films with different oxygen doses during the deposition stage.
Differential regulation of the phosphorylated and dephosphorylated forms of the ubiquitin-conjugating enzyme Ubc6e
(University College Cork, 2024) Burns, Stephanie; Fleming, John V (Eoin)
The ubiquitin proteasome system (UPS) is a key stress response employed by cells to remove damaged and misfolded proteins that accumulate in the endoplasmic reticulum (ER) during energy deprivation, hypoxia, or viral infection. Ubc6e is an ER-localised ubiquitin-conjugating enzyme that plays an important role in the proteasomal degradation of misfolded proteins and can be phosphorylated at serine residue 184. Recent studies have demonstrated that Ubc6e is co-localised with p62/sequestrosome, which is a cargo receptor that delivers ubiquitinated cargo to autophagosomes for degradation. To further investigate the possible role that Ubc6e may play in autophagy, we aimed to investigate any protein-protein interactions between p62 and Ubc6e and we also aimed to investigate the effect of autophagic-related proteins, p62 and ULK1 on Ubc6e. From our research, we saw that Ubc6e levels are reduced when co-expressed with proteins that promote autophagy. Specifically for the autophagy inducer ULK1, we saw differential regulation between the phosphorylated and dephosphorylated forms of Ubc6e, suggesting that the S184 phosphorylation may protect the protein from autophagic degradation. Degradation of the dephosphorylated form, on the other hand, did not depend on S184 phosphorylation, or the catalytic activity of Ubc6e. Neither was it dependent absolutely on ER localisation. Finally, although ULK1 co-expression did not appear to specifically alter the ER/ perinuclear localisation of Ubc6e, it was noted that amino-terminal tagging with GFP led to a ULK1-related localisation of Ubc6e to intracellular vesicles. Together our results suggest that Ubc6e does play a role in autophagy however it is not mediated by the direct interaction with p62.
Enhancing the potential of hydrolases in enantioselective synthesis
(University College Cork, 2024) Torley, Rachel; Maguire, Anita; Collins, Stuart; Synthesis and Solid State Pharmaceutical Centre; Thermo Fisher Scientific
This interdisciplinary research project focuses on the utilisation of a novel hydrolase of marine origin as a biocatalyst in asymmetric synthesis, bringing together synthetic organic chemistry and molecular biology. The primary objective of this research was to investigate the effect of histidine tags on the activity and selectivity of this biocatalyst. Chapter 1 summarises literature reports of the applications of biocatalysts in asymmetric processes and, specifically, the reported effects of histidine tags on enzyme activity. Chapter 2 describes the synthesis and use of ester substrates for biocatalysis screening against three variants of the novel marine esterase, esterase 26D. The enzyme variants included the wild-type, non-histidine tagged strain, and two histidine tagged enzymes (C-terminal and N-terminal tagged). Overall, the investigation showed that the histidine tag had no detectable effect on the selectivity or activity of the esterase 26D. An important outcome of the work was development of a standard procedure to be undertaken at the outset of future investigations of novel biocatalysts to definitively establish whether the histidine tag impacts on the enzyme activity. Chapter 3 details the expression of the novel esterase, esterase 26D, variants. The non-histidine tag variant was cloned into E. coli where it was subsequently expressed alongside the readily available histidine tagged counterparts. Additionally, variants of other enzymes, esterase 32C and 51C, were cloned and expressed to provide another set of enzymes that could be screened for activity in the future. Lastly, Chapter 4 contains the full experimental details and spectroscopic characterisation of the compounds synthesised in the work, the biocatalysis studies, along with the general methods employed for generating the desired enzymes.
Rhodium catalysed 1,4-addition of N-Boc-indol-3-ylboronic acid to α,β-unsaturated carbonyls
(University College Cork, 2024) O'Driscoll, Conor C.; McGlacken, Gerard; Irish Research Council for Science, Engineering and Technology
In recent years, work within the McGlacken group has focused on the asymmetric conjugate additions of indole boronic acids. The work presented in this thesis is concerned with the exploration of the asymmetric rhodium-catalysed conjugate addition of indol-3-ylboronic acids to α,β-unsaturated carbonyl compounds. Optimisation studies towards the asymmetric addition of N-Boc-indol-3-ylboronic acid to 2-cyclohexen-1-one are described herein. With the optimised reaction conditions, a variety of substrates was explored and the synthesis of a number of novel compounds is described. Modest yields of up to 39% were achieved, with excellent enantioselectivities of up to 96%.

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