# School of Chemistry - Theses

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Investigating Photo-luminescent Materials with Advanced Micro-spectroscopic Methods
Xu, Yang ( 2022)
Microscopic and spectroscopic techniques are very practical tools for investigating details of energy relocation processes in solar cell materials. However, this is always challenging as energy migration processes occur on ultrafast timescales and are usually very complex as several processes could take place either simultaneously or sequentially. On the other hand, morphological variations in thin films lead to different charge separation behavior. This usually needs to be distinguished spatially at the nanoscale, which is beyond the resolution limit of conventional optical microscopy methods. To address the challenges mentioned above, this thesis focuses on the development of advanced microscopic and spectroscopic techniques, and exploring their applications in studying the morphology of thin-film materials of opto-electronic applications, including solar cells and organic light-emitting diodes (OLEDs). Novel and versatile approaches with high spatial and temporal resolutions, as well as polarisation sensitivity, have been explored to reveal the relationship between morphology and photo-physical properties of thin-film excitonic materials. First of all, the design and construction of two advanced techniques, a time-resolved fluorescence anisotropy imaging microscope (TR-FAI) and a super-resolution structured illumination microscope (SR-SIM), have been elucidated in detail. The TR-FAI system provides the ability to collect a time-resolved fluorescence image, a fluorescence anisotropy image and a polarised transmission image simultaneously over the same area. The home-built SR-SIM system has been applied to various samples, including standard fluorophores and excitonic materials, providing obviously enhanced spatial resolution compared to wide-field imaging. Moreover, the possibility of using evanescent wave (EW) excitation to probe interfacial dynamics of thin-film excitonic materials has been explored. Time-resolved fluorescence anisotropy measurements (TR-FAM) of Acridine-doped PAA thin films of various concentrations reveal complex time-dependent dynamics inside these films. Numerical simulations have been conducted using the COMSOL Multiphysics platform, suggesting that a proposed multi-layer approach for EW generation in materials of high refractive indices is not reliable. Finally, the molecular conformation and alignment of a polyfluorene-based polymer, PODPF, has been successfully altered by thermal annealing and physical stretching. The developed TR-FAI, together with multi-dimensional microspectroscopic techniques, have been applied to thin-films of PODPF and its derivatives, to monitor the morphological variations and the related photo-physical properties. These techniques have been shown to be very powerful for characterising the morphological variations and excitonic processes in thin films. In summary, this thesis demonstrates that SIM, EW, and TR-FAI are practical and powerful tools to investigate morphological variations and photo-induced processes in thin-film excitonic materials.
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Extrusion-Insertion Reactions for Organic Synthesis: a Mechanism-Based Approach to Transition-Metal Assisted Synthesis of Amides and Alkenes
Yang, Yang ( 2022)
The imperative to achieve highly efficient and environmentally benign chemical synthesis stimulates the endless exploration of new reactions. The isoelectronic nature of heterocumulene species has been known for a long time. Extrusion and insertion reactions are well-known elementary reactions in organometallic chemistry. However, few cases have combined these concepts to invent new procedures for use in organic synthesis. This thesis describes a mechanism-based approach to establish a series of new classes of extrusion-insertion (ExIn) reactions for use in organic synthesis. Multistage mass spectrometry (MSn) experiments, solution-phase experiments in which either NMR or GC-MS are deployed to monitor formation of products, and density functional theory (DFT) are used to underpin the subsequent synthetic method development. In Chapters 3 and 4, the role of organometallic intermediates in the palladium mediated extrusion of carbon dioxide from carboxylic acids followed by insertion of isocyanates or allenes was investigated in the gas phase via mass spectrometry experiments and DFT calculations. Subsequent condensed phase studies led to the development of one pot methods for the synthesis of amides or alkenes with moderate to good yield under mild conditions. In the case of allene insertion, a crystalline sample of the organopalladium intermediate was isolated and its structure was determined via X-ray crystallography, thereby confirming the regioselectivity of the inserted product. To extend the scope of ExIn reactions, in Chapters 5 and 6, copper(I) and silver(I) salts were used in amide synthesis via CO2 extrusion from carboxylic acids and isocyanate insertion. The initial gas-phase experiments showed the formation of an organometallic species via decarboxylation of copper or silver carboxylate ions. Only the organoargentate ion reacted with phenyl isocyanate. The silver mediated reaction between carboxylic acids and isocyanates successfully yielded amides in the condensed phase. However, mechanistic studies based on 13C labelled experiments, gas-phase studies and DFT calculations uncovered a new base-catalysed condensation mechanism as an alternative pathway, whereby the acyl group is transferred from the carboxylate to the N atom of an isocyanate molecule. In Chapter 7, desulfination was explored as an alternative to decarboxylation for the formation of the crucial organometallic intermediate. Thus, a new type of ExIn reaction using sulfinate salts and phenyl isocyanate in the presence of palladium(II) salts was explored. The initial gas phase experiments and DFT calculations were carried out on phenanthroline ligated palladium cations and revealed that the sulfinate more readily undergoes extrusion due to its flexible coordination mode. The translation of this desulfination ExIn variant from the gas phase reactions into condensed phase was not successful. This is due to the fact that a biaryl homocoupling side reaction is preferred, as supported by DFT calculations, which revealed that the barriers for this side reaction are below that of the insertion reaction.
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Sono-Assembled Peptide Biofunctional Nanoparticles and Ultrasound-driven Metal Nanostructures
BARAL, ANSHUL ( 2022)
Amino acids and peptides are biological molecules that can self-assemble to construct several multifunctional nanostructures with potential applications as biomedical devices. Despite the advantages of self-assembling biomolecules, precise control over the morphology and size of the obtained nanostructures is vital to control their functionality in a biological milieu. Although several techniques have been explored and applied to control the self-assembly phenomenon, they often require salts, metal ions, and organic solvents. Therefore, the development of facile, one-pot, and efficient green synthesis techniques to construct biofunctional nanomaterials is always in high demand. In the current PhD work, we have investigated the application of high-frequency ultrasound to generate multifunctional nanostructures from biomolecules, metals, and oxides. Ultrasound-assisted biofunctional nanoparticles were fabricated from self-assembling oligopeptides with potential bioimaging and drug delivery applications. High-frequency ultrasound also triggered the formation of magnetic tryptophan nanoparticles with interesting optical properties which can be utilized in biosensing applications and as a contrast agent in magnetic resonance imaging. A sonochemical technique was invented to construct 2D gold nanostructures with controlled morphology and excellent catalytic properties.
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Neutron Spectroscopy and Magnetic Properties of Lanthanoid(III)-dioxolene Compounds
Dunstan, Maja Anna ( 2022)
This thesis presents a series of studies on the electronic structure and magnetic properties of several families of lanthanoid(III)-dioxolene compounds. Compounds of the trivalent lanthanoid (Ln) ions are the current best performing single-molecule magnets (SMMs), and efforts to improve their properties include design of the coordination geometry, as well as control of spin-phonon, magnetic exchange, and intermolecular dipolar interactions. This thesis presents an exploration of the effect of Ln(III)-radical magnetic exchange coupling, as well as other solid-state effects, on the SMM behaviour of Ln(III) dioxolene compounds. Slow magnetic relaxation in Ln-SMMs can be modulated by the introduction of magnetic exchange coupling, however, quantifying the magnitude of magnetic exchange coupling in many Ln(III) systems is difficult using conventional magnetometric techniques, due to the often large orbital angular momentum contribution to the magnetic moment of Ln(III) ions. Spectroscopic techniques are therefore required to determine the magnetic exchange coupling for non Gd(III) systems. Inelastic neutron scattering (INS) is used in this work, alongside magnetometry, EPR spectroscopy, and luminescence measurements, to experimentally determine both the crystal field (CF) splitting and magnetic exchange coupling in several families of Ln(III)-dioxolene compounds. The two families of compounds [LnTp2trop] (Tp– = tris-pyrazolylborate; tropH = tropolone) and [LnTp2dbsq] (dbsqH = 3,5-di-tert-butylsemiquinone) are investigated, and a trend in the magnitude of the antiferromagnetic magnetic exchange coupling |JLn-SQ| is found, increasing from Tb to Yb in the isostructural series of compounds. For the compound [Tb(18-c-6) Br4CatNO3] (18-c-6 = 18-crown-6; Br4CatH2 = tetrabromocatecholate), INS is used to measure the magnitude of the CF splitting of the Tb(III) in a highly axial coordination environment. The one electron oxidised compounds [Ln(18-c-6)X4SQNO3] . I3 (X4SQH = tetrahalosemiquinone; X = Cl, Br) were then synthesised, and the magnetic exchange coupling was determined for the Gd(III) analogues by magnetometry, and the Nd(III) and Tb(III) congeners by INS. The implications of the magnetic exchange coupling on the slow magnetic relaxation of both the [LnTp2dbsq] and [Ln(18-c-6)X4SQNO3] . I3 families of compounds is investigated. Slow magnetic relaxation in zero-field is engendered for the Tb(III) congeners by the magnetic exchange bias. For the case of stronger magnetic exchange coupling in the Kramers systems, the Ln(III) radical exchange coupling leads to the loss of a doubly degenerate ground state and the magnetic bistability. For the [Ln(18-c-6)X4SQNO3] . I3 compounds, the axial ligand environment and magnetic exchange coupling leads to unusual slow magnetic relaxation for the Gd(III) and Eu(III) congeners. Modulation of the slow magnetic relaxation in these systems by effects other than Ln(III)- radical exchange is also observed for several of the compounds. The effect of intermolecular dipolar interactions and crystal packing on the magnetic relaxation of the SMM analogues adds to the understanding of the contributing factors on the observed relaxation of Ln(III)-SMMs.
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Photochemistry and Electronic Spectroscopy of Gas-Phase Ions
Buntine, Jack Thomas ( 2022)
This dissertation focuses on investigations of gas-phase molecular and cluster ions -- deprotonated dithienylethene molecular photoswitches and positively charged carbon clusters -- using electronic action spectroscopy. Dithienylethene (DTE) photoswitches are members of the diarylethene (DAE) class of molecules that undergo rapid, reversible photoisomerisation between two isomeric forms in response to light, and have been incorporated into functionalised materials as light-triggered switches. Carbon clusters are structurally diverse molecules that exist as several different conformational isomers and allotropes, and are astrophysically important species. By measuring gas-phase electronic spectra for these species, information concerning their electronic and molecular structures can be obtained in an environment where potential sources of complications are absent. The experiments described in this thesis utilise ion mobility spectrometry (IMS) to separate isomeric forms of gas-phase ions prior to spectroscopic interrogation. DTE photoswitches undergo 6$\pi$-electrocyclisation (ring closing) and cycloreversion (ring opening) reactions upon exposure to light in the ultraviolet (UV) and visible spectral regions, respectively, making them ideal photoswitches for a range of applications. The experiments described in this thesis are concerned with the photoisomerisation of \textit{meta}- (\textit{m}) and \textit{para}- (\textit{p}) substituted DTE carboxylate anions using a tandem ion mobility mass spectrometer coupled with laser excitation. Density functional theory calculations were used to aid in the interpretation of the gas-phase photoisomerisation action (PISA) spectra. Gas-phase PISA spectra for \textit{p}-DTE$^-$ and \textit{m}-DTE$^-$ were obtained by measuring the wavelength-dependent photoisomerisation yields over the 300--700\,nm range. For \textit{p}-DTE$^-$, the PISA spectrum for 6$\pi$-electrocyclisation has an onset at $\approx$360\,nm and likely reaches a maximum at a wavelength just shorter than 300\,nm. For the ring-closed isomer, the cycloreversion PISA spectrum exhibits a band in the 450-700\,nm range with a maximum response at $\approx$615\,nm and a smaller band in the 320-415\,nm range peaking at $\approx$365\,nm. For \textit{m}-DTE$^-$, 6$\pi$-electrocyclisation of the ring-open isomer was not observed, presumably due to this isomer adopting a structure in the gas phase that is not suitable for cyclisation. This emphasises the importance of the carboxylate substitution position on the gas-phase photochemistry of DTE photoswitches. For the ring-closed isomer, the cycloreversion PISA spectrum shows an intense band spanning the 430-680\,nm range peaking at $\approx$590\,nm and a second band of comparable intensity in the 330-420\,nm range with a maximum at 355\,nm. Furthermore, the gas-phase investigations show no evidence for the formation of the cyclic byproduct, the main cause of fatigue for DAE-based photoswitches in solution, when either \textit{p}-DTE$^-$ or \textit{m}-DTE$^-$ were exposed to UV light. The PISA spectra for the DTE anions should help to develop more robust and efficient DTE-based photoswitches for use in a wide variety of functional materials. The work reported in the rest of this thesis involves the spectroscopic characterisation of isomer- and mass-selected cluster ions produced by laser ablation. This thesis describes an instrument that has been designed and built for obtaining electronic spectra of positively charged carbon clusters produced by laser ablation of graphite that have been selected according to both their isomeric form and their mass-to-charge ratio. Prior to the work presented here, there have been no previous isomer-specific spectroscopic investigations of carbon clusters. Gas-phase electronic spectra were measured for monocyclic C$_{2n}^+$ (\textit{n}=6--18) clusters over the 400--2000\,nm range by photodissociating C$_n^+$-(N$_2$)$_m$ complexes in a cryogenically cooled, three-dimensional quadrupole ion trap (QIT). The most striking feature of the spectral series is the linear shift of the wavelength for the origin band transitions to longer wavelength with the number of carbon atoms, indicating a common structural motif supporting the assignment of the electronic spectra to monocyclic structures. The spectra also exhibit a series of weaker transitions that lie to higher energy from the origin bands that are probably vibronic progressions in the ring deformation vibrational modes. The bands for the C$_{4k}^+$ cluster series (C$_{12}^+$, C$_{16}^+$, C$_{20}^+$, C$_{24}^+$, C$_{28}^+$, C$_{32}^+$ and C$_{36}^+$) are relatively broad (FWHM$>$100\,cm$^{-1}$), presumably due to rapid non-radiative deactivation from the excited state, whereas those for the C$_{4k+2}^+$ clusters (C$_{14}^+$, C$_{18}^+$, C$_{22}^+$, C$_{26}^+$ and C$_{30}^+$) are much narrower (FWHM$\approx$10--20\,cm$^{-1}$), consistent with slower non-radiative deactivation. The C$_{2n}^+$ ($n$=6--14) clusters are possibly connected to the diffuse interstellar bands (DIBs) as their electronic absorptions lie in the visible wavelength region where most DIBs are found. The electronic spectra of C$_{n}^+$ clusters should provide benchmark data for the development of quantum chemical methods for modelling the electronic structure of these clusters.
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Towards Total Synthesis of Icumazole A
Salimimarand, Mina ( 2022)
Detailed is work towards the enantioselective synthesis of the NADH oxidase inhibitor icumazole A. Key reactions include an organocatalysed asymmetric self-aldol reaction of propionaldehyde towards the synthesis of the oxazole containing fragment. An enantioselective synthesis of the Diels-Alder precursor of the isochromanone fragment has been performed. Key steps included an enzyme catalysed enantioselective desymmetrisation which was then substituted with epoxide formation and ozonolysis. Further work towards the intramolecular [4+2] cycloaddition/aromatisation sequence to give aryl bromide followed by elaboration of product to the desired isochromanone fragment through borylation and obtaining the aldehyde constituted a formal total synthesis of noricumazole B.
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Experimental and Numerical Investigations of Chemical and Physical Effects by Oscillating Bubbles
MONDAL, JOYDIP ( 2022)
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Structural and functional characterisation of bacterial proteins that act in the utilisation of arsenic oxyanions for respiration
Poddar, Nilakhi ( 2022)
Arsenic is a toxic metalloid present as a contaminant in drinking water, affecting more than 140 million people worldwide. Ingestion of arsenic as the soluble oxyanions arsenite and arsenate, is linked to neurological, reproductive and respiratory disorders, cancer and diabetes mellitus. Although toxic to human health, arsenite and arsenate can be utilised by some prokaryotes as sources of energy from the environment. Such prokaryotes are Pseudorhizobium banfieldiae sp. str. NT-26 (NT-26) and Chrysiogenes arsenatis (C.arenatis) respire using these oxyanions by the actions of arsenite oxidase (AioAB) and arsenate reductase enzymes (ArrAB), respectively. The focus of the present work details structural and functional characterisation of proteins that allow these bacteria to use arsenic oxyanions for respiration. This includes characterisation of periplasmic binding proteins, ArrX and AioX that bind to arsenic oxyanions, the interaction of these proteins with the sensor histidine kinase, AioS and the respiratory arsenite oxidase enzyme, AioAB, and its interaction with its electron acceptor, cytochrome c552. The substrate specificity of periplasmic binding proteins, AioX and ArrX to arsenite and arsenate, from NT-26 and C.arsenatis, respectively were investigated. The aims of this study were to establish how both these proteins distinguish between arsenite and arsenate, and to determine the structure of ArrX protein in an apo- and arsenate-bound state. The X-ray crystal structure of ArrX with arsenate was determined to 1.74 Angstrom resolution. Structural comparison of the AioX and the ArrX proteins and isothermal titration calorimetry (ITC) analyses of mutant proteins identified a conserved Cys residue in their substrate binding sites that play a key role in the discrimination between arsenite and arsenate for both proteins. Structural analyses also revealed that the nature of neighbouring residues (Gly in AioX and Thr in ArrX) may provide varied structural flexibilities that contribute to the differential interaction of the conserved Cys residue to arsenic oxyanions. The biophysical characterisation of the interaction between the AioX protein and its sensor histidine kinase AioS was performed to investigate the processes that control the expression of the AioAB enzyme in NT-26. Size exclusion chromatography (SEC) and analytical ultracentrifugation (AUC) experiments revealed that AioX and AioS proteins can form a stable heterodimer complex in the absence of arsenite. These findings also revealed that the oligomeric state of the complex does not change in the presence of arsenite. A loop in the AioX protein, which was proposed to be involved in the interaction with AioS was shown experimentally not to directly participate in the interface between the two proteins. Structural and functional characterisation of the interaction between the AioAB enzyme with its electron acceptor cytochrome c552 was carried out to investigate the structural basis of the electron transfer process that underpins the respiration of Pseudorhizobium banfieldiae sp. str. NT-26. The crystal structure of the AioAB/cytc552 was determined to 2.25 Angstrom resolution. The structure showed two AioA2B2/(cytc552)2 complexes per asymmetric unit. Three of the four AioAB/cytc552 complexes revealed that the cytc552 molecule docks in a cleft at the interface of between the AioA and AioB subunits. The positioning of the cytc552 proteins in these complexes revealed an edge-edge distance of 7.5 Angstrom between the heme of cytc552 and the Rieske 2Fe-2S cluster in the AioB subunit, which is considered an ideal distance for fast electron transfer between proteins. The interface of the AioAB and the cytc552 protein also shows electrostatic interactions and is stabilised by two salt bridges, a classic example of transient complex formation for fast electron transfer. Additionally, the structure also highlights the unique positioning of one of the four cytc552 proteins that sit at a long distance from the redox cofactors of AioAB subunits and presumably aid in crystallisation. Enzyme kinetics analysis also revealed the AioAB/cytc552 system to be catalytically very efficient.
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Development and characterisation of micro polymer inclusion beads (µPIBs) for the separation of rare earth elements
Croft, Charles Frederick ( 2022)
The global demand for rare earth elements (REEs) is predicted to significantly increase in the near future. This is due to expanding production of green technologies heavily dependent on the incorporation of REEs, such as electric vehicles (EVs) and wind turbines. However, REEs are currently supplied by mining REE minerals, which require high intensity industrial processing and releases REEs into the environment. As a result, our demand for REEs is causing a significant environmental impact. Therefore, there is a considerable interest in the development of more sustainable extraction technologies and their application to alternative sources of REEs, namely recycling from end-of-life (EOL) electronics. This thesis details the development of a new polymer-based extraction material, denominated as micro polymer inclusion beads (uPIBs), and its application to the separation of REEs. The thesis covers the development and optimisation of uPIBs composed of the base polymers poly(vinyl chloride) (PVC) or poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) which immobilise between their entangled chains the extractant di-(2-ethyl hexyl)phosphoric acid (D2EHPA). The uPIBs were fabricated via a recently developed phase inversion microfluidic method, which was modified to allow effective fabrication of the PVC and PVDF-HFP-based uPIBs containing up to 60 wt% D2EHPA. These modifications included acidification of the fabrication solutions to 0.1 M sulfuric acid, and increasing desolvation solution salinity from 5 to 15 wt% NaCl. The uPIBs demonstrated superior extraction performance over their polymer inclusion membrane (PIM) counterparts, attributed to the higher surface area exposed to the feed and receiving solutions. This thesis also covers the uPIBs characterisation via thermogravimetric analysis (TGA), which was used to confirm the uPIB’s D2EHPA content, using PIMs with equivalent composition as reference standards. Negligible D2EHPA leaching occurred from both the PVC and PVDF-HFP-based uPIBs under the fabrication conditions applied here. Characterisation of PVC-based uPIBs using an isothermal step highlighted the presence of Na+, extracted during the fabrication process, which was successfully removed through a 1 M sulfuric acid washing step. The removal of Na+ was found to significantly improve the extraction performance of the uPIBs and would not have been identified if not for the application of the isothermal TGA method developed here. The performance of the newly developed uPIBs (60 wt% D2EHPA, 40 wt% PVC) was characterised for the on-line separation of REEs by packing a column with uPIBs. La3+ and Gd3+ were initially used as model REE ions and could be separated by selective extraction or back-extraction. The column separation method was then applied successfully to the recovery of the REE ions Nd3+ and Dy3+ from EOL rare earth permanent magnet (REPM), which was digested in 2 M sulfuric acid. Upon decreasing the acidity of the digest to 0.03 M sulfuric acid, Nd3+ and Dy3+ were selectively extracted after the introduction of ascorbic acid at a 3:1 ratio with Fe to reduce Fe3+ to Fe2+. Nd3+ and Dy3+ could then be selectively back-extracted from the uPIB-column using 0.3 and 2.0 M sulfuric acid solutions, respectively. On the basis of the results presented in this thesis it can be concluded that the column separation method based on the newly developed uPIBs has shown promising potential as a future sustainable method for recycling REEs from digested EOL electronics.
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Sonosynthesis of Functional Micro/Nano-structures using Biomolecules
Zhu, Haiyan ( 2022)