School of Chemistry - Theses

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Self Assembly Nano Particle Simulation and Modelling of Organic Photovoltaic Materials

Bhasin, Mayank ( 2022-05)

This work contributes in predicting effects of OPV materials in solar cell active layers through MD simulations. Through general coarse grained simulations, the rate of change of component solubility, demixing tendency, and the difference in interaction energies, were studied for nano-composite self-assemblies. Routes to form uni- form, core-shell, Janus, and eccentric morphologies were established. Using atom- istic simulations it was established that increasing P3HT chain length the stability of the nanocomposite (P3HT:PCBM/ICBA) decreases, whereas increasing PDI stability increases. Also addressed is why two specific members of the entire BXR series (benzodithiophene- X-thiophene-rhodamine) exhibit liquid-crystalline phase and highest PCE in solar cell usage, compared to the other members. These members exhibit optimum aggregation which is necessary for liquid crystalline phase formation.
Synthesis of tyrosine-derived diketopiperazines and investigation of their inhibition of CYP121, an essential enzyme of Mycobacterium tuberculosis.

Kurosz, Luke Sebastian ( 2022-12)

The growing incidence and degree of resistance exhibited by Mycobacterium tuberculosis (Mtb), the major causative agent of tuberculosis (TB), to currently available treatments is of great concern. With multi-drug resistant (MDR-TB) and extensively-drug resistant (XDR-TB) strains being reported, alternative chemotherapies are required to maintain viable approaches to treat TB. Treatments exploiting new therapeutic targets are a key avenue of exploration. In the pursuit of drug discovery, analysis of an organism’s genome is imperative to determine essential gene products. Genomic analysis has revealed the presence of 20 cytochrome P450 encoding genes, with subsequent knockout studies uncovering CYP121 and CYP128 as proteins essential to bacterial survival and growth in vitro. The only unique and essential Mtb CYP that has been functionally characterized is CYP121, known to catalyze the production of the secondary metabolite, mycocyclosin, from the cyclic dipeptide cyclo(L-tyrosinyl-L-tyrosine) (cYY). With a known substrate and product, the generation of substrate-like mimics and pursuit of transition state analogues are two possible avenues of inhibitor development. A series of cYY analogues were synthesized to investigate the effect of incorporating various P450 inhibitory functionalities, in the hope to develop selective Mtb inhibitors. Biochemical analysis shows that the incorporation of nitrogen containing heterocycles is tolerated by the enzyme. Numerous substrate analogues display potent binding to CYP121. Additionally, analogues of postulated transition states on the enzymatic reaction pathway to mycocyclosin were designed. The biaryl distance of these macrocycles was calculated to identify the most appropriate linker that closely mimics the calculated transition state distance.
Synthesis of Myxobacteria Metabolites and Analogues and Development of Metal Complexes for the Mukaiyama Hydrogen Atom Transfer Reaction

Ricca, Michael ( 2022)

The spirangiens are a series of spiroketal containing polyketide natural products which are potently active against human and mouse cancer cell lines, and interleukin 8 expression. Oxidation at the C20 position occurs after polyketide synthesis is complete. Acyclic compounds lacking oxidation at the C20 position have been isolated, but never cyclic species; as such C20 deshydroxy spirangiens could be undiscovered natural products. This work saw the completion of the synthesis of a C20 deshydroxy derivative of spirangien M522, utilising a series of asymmetric aldol reactions to construct the polyketide backbone. A cross metathesis reaction followed by spirocyclisation forged the core, which was elaborated to by a Roush crotylation/Weix coupling sequence. Cell death, and cell growth inhibition assays in immortalised bone marrow derived macrophages (murine) and colon adenocarcinoma cells (murine), indicated that derivative retained its activity, and that C20 oxidation was not crucial for bioactivity. The Mukaiyama-Isayama hydration reaction hydrates a polar or non polar alkene to an alcohol via a C centred radical. Under Mn, Co or Fe catalysis, with phenylsilane in an alcoholic solvent, a metal hydride species forms which is able to facilitate hydrogen atom transfer (HAT) and generate the requisite radical. In the absence of oxygen alkene reduction occurs, and this also represents a major side product in the Mukaiyama hydration. In the presence of a Michael acceptor, the radical can undergo coupling, forging a new C-C bond. Three cis-beta octahedral complexes with a SALPN type ligand; Mn(SALPN)acac and Co(SALPN)acac were synthesised. These complexes were active in the Mukaiyama hydration of esters and ketones, and Fe(SALPN)acac successfully catalysed olefin coupling reactions. Compared to the control catalysts, the new complexes, showed superior reactivity (reduced side product formation, lower catalyst loading) or unusual reactivity (promotion of an acyloin rearrangement). Furthermore, the cobalt complex facilitated the synthesis of 7 acyloin natural products.
Biochemical Characterisation of C. elegans Ferritins

Mohamed Mubarak, Samsun Sanjeedha ( 2022)

Ferritin plays an important role in maintaining optimum cellular iron concentrations. Consisting of 24 protein subunits in a spherical architecture, it creates an interior cavity that stores iron atoms in the form of a ferric oxy-hydroxide. Extensive in-vitro enzymological studies have greatly assisted our understanding but it is not yet fully understood how iron is released from ferritin in-vivo. A clearer understanding could aid iron related disorders, including iron overload or deficiency. The use of the model organism Caenorhabditis elegans will allow genetic manipulation to further understand the mechanisms involved in iron metabolism within a whole organism. C. elegans expresses two types of ferritin, FTN-1 and FTN-2 which have not been biochemically characterised. The aim of this thesis is to establish the mechanism of iron storage for these proteins to develop strategies to control and manipulate the protein for in vivo and ex vivo studies. C. elegans ferritins have been expressed, purified, and characterised through a range of techniques. Both ferritins show ferroxidase activity but with L-type ferritin nucleation properties. Even with identical ferroxidase active sites, FTN-2 is shown to react ~10 times faster than FTN-1. Combined structural and stopped-flow spectroscopy studies revealed the source of the difference in rates to be iron transport to the ferroxidase site. Both FTN-1 and FTN-2 react initially to form a mu-1,2-peroxo diferric intermediate that absorbs at 595 nm. Structural comparison showed an asparagine residue (Asn106) near the ferroxidase active site, which is a valine in most other ferritins including human H ferritin. The mu-1,2-peroxo diferric intermediate of human H ferritin absorbs at 665 nm and replacement of Asn106 to valine in FTN-2 shows a similar absorption. This may explain the variation in wavelength of the peroxide-to-iron(III) charge transfer band observed for ferritin across taxa.
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.
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.
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.
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.
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.
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.

School of Chemistry - Theses

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