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    Asymmetric catalysis via spatially separated chiral and catalytic motifs in multicomponent metal-organic frameworks : a thesis presented in partial fulfilment of the requirements of the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2025-11-18) Petters, Ludwig
    Modern life without catalysis is inconceivable. Asymmetric catalysts are a special type of catalyst that preferentially produce one of two possible enantiomers over the other. The ability to selectively obtain exclusively one of the possible enantiomers is of highest importance for modern synthetic chemistry. To enable the transfer of chiral information from the catalyst to the reaction substrates, asymmetric catalysts must be chiral. In conventional asymmetric catalysts, the catalytic and chiral motifs are held close together within one single molecule. In this work, we break the design limitation of conventional asymmetric catalysts with a strategy we call ‘remote asymmetric induction’ (RAI). In RAI catalysts, the catalytic and chiral motifs are independent of each other in their design and synthesis. To achieve this, we use the multicomponent metal-organic framework MUF-77 (MUF = Massey University Framework). MUF-77 consists of three chemically distinct linkers that each occupy a specific position in the framework without disorder or randomness. To create RAI catalysts, the catalytic and chiral motifs are individually anchored to the different building blocks of MUF-77. By virtue of the MUF-77 structure, the catalytic and chiral motifs are in close proximity to one another in a catalytic pore, which creates an active site. This enables the transfer of chiral information to the reaction participants. Initially the reaction scope of the RAI catalyst was expanded by screening a variety of RAI-MOFs incorporating different catalytic and chiral functionalities across a range of model reactions. A promising catalyst for one model reaction was identified and investigated in depth. Through systematic modification of important reaction variables, the variation in enantioselectivity of this system was explored. After parameter optimisation, very good to excellent enantioselectivity was achieved. Control experiments confirmed that the origin of enantioselectivity arises from remote cooperative interactions between the functionalities in the active site. The catalysts were then tested for classical performance metrics and a hypothetical transition state within the MOF pore was proposed. This work establishes RAI as an alternative platform to develop high-performing asymmetric catalysts.
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    Biofilm formation of Vibrio parahaemolyticus : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Food Microbiology at Massey University, Campus Manawatū, New Zealand
    (Massey University, 2024-05-20) Wang, Dan
    Vibrio parahaemolyticus in seafood can cause food poisoning. There is increasing concern with the increase in reports of illness globally believed to be due to climate change affecting sea temperatures. Biofilm formation of V. parahaemolyticus is an additional concern as biofilms are more resistant to cleaning and sanitation than planktonic cells. However, little is known about the biofilm formation of V. parahaemolyticus. Strain variation and the factors determining biofilm formation were investigated in this study with the aim to provide information that can be used to design more effective control strategies. This study identified two robust biofilm forming strains (PFR30J09 and PFR34B02) from nine V. parahaemolyticus seafood isolates. Comparative genome analysis unveiled 136 unique accessory genes in robust biofilm formers. Protein-protein-interaction analysis showed interactions between UDP-glucose metabolism (Gene ontology (GO): 0006011), cellulose biosynthesis (GO: 0030244), rhamnose metabolism (GO: 0019299) and O antigen biosynthesis (GO: 0009243). Cellulose contributed to robust biofilm formation. Cellulose biosynthesis was identified as being acquired from within the order Vibrionales. The cellulose synthase operons consisting of genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC were present in 15.94% (22/138) of V. parahaemolyticus. Strong biofilm-forming V. parahaemolyticus showed greater resistance to sanitizers of biofilm cells than the weaker biofilm forming cells. The effective concentrations of sodium hypochlorite for inactivating most V. parahaemolyticus biofilm cells were higher than the recommended concentration. Available chlorine of 1176 mg/L inactivated 1.74-2.28 log10 CFU/cm2 of biofilm on stainless steel surfaces and 4704 mg/L inactivated > 7.00 log10 CFU/cm2 of biofilm (to undetectable levels, < 10 CFU/cm2), except for biofilms formed by the strong biofilm formers. Peracetic acid (PAA) at 200 ppm (89.56 mg/L PAA, 471.64 mg/L hydrogen peroxide) inactivated > 5.00 log10 CFU/cm2 of biofilm from stainless steel surfaces (except for those the strong biofilm formers, see Figure 4.4). RNA sequencing (RNA-seq) identified 74 differentially expressed genes when comparing planktonic and biofilm cells of V. parahaemolyticus. These represented the rearrangement of nucleotide and energy metabolism in biofilm cells. Biosynthesis of secondary metabolites, purine and pyrimidine metabolism, propanoate metabolism, and valine, leucine and isoleucine degradation were deemed essential in the young V. parahaemolyticus biofilms. Genes of purH, purF, pdhA are potential genetic targets for biofilm prevention and control of V. parahaemolyticus. Understanding V. parahaemolyticus biofilm formation will help to design strategies to overcome the limitations of chemical sanitizers, improving product safety and quality in the seafood industry.
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    Synthetic studies towards dictyoxetane and the dolabellanes : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Chemistry, Massey University, New Zealand
    (Massey University, 1997) MacKenzie, Karla Ruth
    Dictyoxetane (1) has been isolated from Dictyota dichotoma, a brown alga found in the Indian Ocean. It has an unusual pentacyclic structure which has not yet been synthesised. It is a diterpene which is closely related to the dolabellanes, an important class of bioactive compounds. A stereoselective synthesis of the linearly fused cyclohept[f]indene system is described. Selective epoxidation of cycle-octadiene (142), followed by hydrolysis to the diol (143) and oxidative cleavage allowed preparation of the dialdehyde (141) on large scale. Treatment of this with potassium carbonate causes an intramolecular aldol reaction to form cycloheptadiene- carboxaldehyde (140). An E- selective Wittig reaction is performed with 4- carboxybutyl-triphenylphosphium bromide, to produce the acid (139). This is subsequently converted to the vinyl ketone (138) followed by an intramolecular Diels Alder reaction to produce the desired cyclohept[f]indene (137a). Utilisation of a Z- selective Wittig reaction produced methyl ester (145z). Conversion to cyclohept[f]indene occurred via an intramolecular Diels-Alder of the subsequent vinyl ketone (138z). Conversion of acid (139) to the methyl ester (145) followed by an intermolecular Diels Alder gave the endo- product. Subsequent attempts to cyclise this to the cyclohept[f]indene via an intramolecular Claisen reaction to give the third isomer were unsuccessful. Cyclohept[f]indene is the backbone for dictyoxetane and can be efficiently synthesised in eight steps from 1,5-cyclo-octadiene (142) in a diastereoselective synthesis. This route allows for further modification of functionality to the linearly fused ring system and paves the way for further synthetic studies towards the dolabellanes.
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    Studies towards thermodynamically stable G-quadruplexes embedded in canonical DNA duplexes : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2023) Chilton, Bruce
    DNA is the polymer responsible for the storage of genetic information and, ultimately, all processes that occur within the cell. Our understanding of DNA structure and function has developed considerably, but some areas are still unclear. In particular, a range of non-canonical DNA secondary structures such as G-quadruplexes (G4s), i-motifs and triplexes, have also been shown to form in genomic DNA sequences and these structures also appear to have a role in genome function. Better understanding of the interactions of non-canonical secondary structures is hindered by their transient nature in the context of larger DNA structures, making it difficult to accurately study them using in vitro analytical techniques (e.g., NMR spectroscopy, X-ray crystallography, etc.). They are typically less thermodynamically stable than canonical DNA duplexes and are formed within the genome only in equilibrium with many secondary structures, typically favouring the canonical duplex. They can often only be formed reliably under specific conditions in vitro (e.g., single-stranded, low pH etc.). This thesis presents several strategies designed to stabilise non-canonical G4 secondary structures, which are of interest because they are often found in the promoter regions of oncogenes. The most commonly used existing G4 stabilisation technique utilises small-molecule ligands which specifically bind to and stabilise G4 structures. This thesis includes an investigation into both a widely used G4-binding ligand and several newly developed ligands, but their potential to block binding sites and disrupt G4 topology makes them less suitable for our intended applications. Hydrophobic modifications can encourage aggregation of DNA strands and therefore increase stability of secondary structures. Hydrophobic phosphate modifications in G4s proved effective at disrupting duplexes and stabilising G4s but was limited by coupling efficiency of the modification and resulting difficulties with purification. Intentional mismatches in the G4-forming sequence were introduced by inverting sequence direction or incorporating α-anomers of nucleotides. This strategy was able to completely disrupt duplex formation while preserving G4 structures, but modification sites have to be carefully considered to avoid significant changes in G4 topology. Internal cross-links were incorporated into DNA using modified nucleotides designed for copper(I)-catalysed azide-alkyne cycloaddition. These cross-links prevent G4 structures from unfolding, but the location of these cross-links must also be carefully considered to prevent disruption of the native G4 topology and blocking protein binding sites. All three of these methods present potential routes for stabilising G4s within larger DNA structures. Furthermore, all three modifications could potentially be expanded to stabilise other non-canonical structures, such as imotifs or triplexes.
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    Catalysts derived from metal-organic frameworks : a thesis presented in partial fulfilment of the requirements of the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatu, New Zealand
    (Massey University, 2021) Bandara, W. R. L. Nisansala
    The synthesis of atomic-scale catalysts is a blooming field, and these replace the conventional nanocatalysts due to their high atom utilization, selectivity, and unique catalytic activity. Metal-organic frameworks (MOFs) serve as promising precursors for the synthesis of single-atom catalysts (SACs). This study focused on the synthesis of SACs on nitrogen-doped hollow carbon by using MOFs and MOF composites followed by pyrolysis. The synthesis of two SACs namely rhodium SACs (Rh SACs) and cobalt SACs (Co SACs) by different methods, their characterization, and catalysis was explored. Rh SAC synthesized in this work hydrogenates nitroarenes with high consumption and high selectivity. Moreover, Co SAC did little or no hydrogenation of the nitroarenes. Further applications of these SACs were explored by employing them in oxygen reduction reaction (ORR), NO abatement, and Fenton-like catalysis. Moreover, the synthesis of two types of hollow nanoboxes (HNB) namely HNB-1 and HNB-2; using MOFs and MOF composites, their characterization and applications were also investigated. HNB-1 was used to make electrode supercapacitors and it showed comparable activity to activated carbon. Further attempts were made to use HNB-2 as a fluorescence sensor. Finally, several ideas on synthesising SACs and HNBs were proposed as a part of future work.
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    The synthesis and chemistry of Quinolino(7,8-h)quinoline derivatives : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatu, New Zealand
    (Massey University, 2021) Severinsen, Rebecca
    Proton sponges are a class of neutral organic superbases. Quinolino[7,8-h]quinoline (QQ) is one such molecule. Structurally it has two closely positioned nitrogen atoms which cause a destabilising lone electron overlap which manifests as a helical torsional twist that can be relieved by monoprotonation or complexation. These compounds are highly basic and are chelators that can accommodate a variety of ion sizes. Exploration of the structural properties of QQ provides an avenue for non-symmetric compound synthesis. Research interest arose in developing original synthetic pathways and exploring the chemistry of this QQ moiety, and its potential uses. This work primarily focussed on the development of methods towards new derivatives containing the QQ core structure, of which several were developed. Exploration of their properties as bases was begun in the context of both experimental measurements and theoretical calculations, allowing some to be classified as superbases. Computational analysis also gave insight into structural changes taking place during the protonation process. Potential uses of QQ derivatives as chelators for metals were examined. An X-ray crystal structure of a beryllium containing 4,9-dihydroxyquinolino[7,8-h]quinoline was achieved, the 7th reported ion to be chelated by a QQ compound.
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    Hydrothermal synthesis of inorganic nanoparticles for potential technological applications : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2021) Etemadi, Hossein
    Iron oxide nanoparticles (IONPs) are of interest in a diverse range of environmental and biomedical applications due to their intrinsic chemical, physical and thermal features such as superparamagnetism, high surface-to-volume ratios, high biocompatibility, low toxicity and easy magnetic separation. Many technological applications necessitate small (diameter < 20 nm) nanoparticles with narrow size distributions (< 5 %) and pronounced saturation magnetisation (Ms) for uniform physical and chemical effects. Historically, the synthesis of IONPs with controlled size and size distribution without particle agglomeration has proved challenging. In this thesis, we utilised an easy hydrothermal route and successfully synthesized two common phases of IONPs, namely Fe₃O₄ (magnetite) and α-Fe₂O₃ (hematite), using Fe(acac)₃ as iron source. By controlling the reaction conditions such as time, temperature, and the concentration of surfactants such as PVP and oleic acid, the different phases were selectively synthesized. The prepared nanoparticles were fully characterized with X-ray diffraction (XRD), transmission electron microscopy (TEM), dynamic light scattering (DLS), energy dispersive X-Ray spectroscopy (EDS), atomic absorption spectroscopy (AAS), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), vibrating-sample magnetometry (VSM), Brunauer-Emmett-Teller (BET) surface area measurements, photoluminescence (PL) and UV–Vis diffuse reflectance spectroscopy (UV–Vis/DRS). In Part I of this thesis, Fe₃O₄ and metal-doped spinel MxFe₃−xO₄ (M = Fe, Mg, Mn, Zn) nanoferrites were synthesised as agents for cancer treatment via a method called magnetic fluid hyperthermia (MFH). In Part II, α-Fe₂O₃ nanoparticles were hybridized with tin (II) sulfide (SnS) to create p-n heterojunction photocatalysts for efficient H2 production via ethanol photoreforming.
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    The synthesis and chemistry of [2.2]paracyclophane amino acid derivatives : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry at Massey University, Manawatū, New Zealand
    (Massey University, 2020) Etheridge, Leonie
    Due to the ever-growing requirement for chiral compounds, new conditions for stereoselective synthesis are in constant development. Asymmetric organocatalysis is well-studied, with peptide catalysts popular due to their modular and highlyfunctionalisable nature. One such example of their utility is in the Michael reaction, a well-studied carbon-carbon bond forming reaction. [2.2]Paracyclophane is an aromatic industrial precursor compound with remarkable structural and electronic properties. Its conformational bulk and rigidity make it an attractive target for integration into sterically-hindered unnatural amino acids for incorporation into peptides that may be effective organocatalysts. An updated route to 4-amino-13-[2.2]paracyclophane-carboxylic acid (Pca) was developed and optimised. The synthetic route comprises four steps with an overall yield of 50%. This compares with previous routes which had yields between 7 and 48% for 6 - 7 steps. Peptide coupling conditions for the poorly-reactive Pca were developed with some success; including devising a route for direct synthesis of a glycine residue on Pca’s aniline. Four new Pca-containing peptides were described. The above work sets the stage for development of interesting new planar chiral peptide compounds with diverse chemistry. Three Pca-containing peptides were studied as asymmetric organocatalysts in Michael addition between trans-β-nitrostyrene and hexanal and were compared to proline, a known catalyst for this reaction. These tests were performed to probe the relationship between relative conformation between the carboxylic acid and amine moieties of the catalyst, and the catalyst’s stereoselectivity. The Pca-containing catalysts showed an interesting trend to reversal of the prevailing syn product configuration.
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    Modular functionalization of engineered polyhydroxyalkanoate scaffolds : a thesis presented in partial fulfilment of the requirements for degree Doctor of Philosophy in Microbiology at Massey University, New Zealand
    (Massey University, 2019) Wong, Jin Xiang
    Microbial polyhydroxyalkanoates (PHAs) are spherical polyesters that are naturally synthesized in vivo by a variety of microorganisms as carbon and energy reserves under imbalanced nutrition environments. Notably, PHA particles can be functionalized by the genetic modification of surface-exposed PHA-associated proteins, e.g. PHA synthase (PhaC), and this approach has led to multiple successful proof-of-concept demonstrations for bio-technology applications. However, current recombinant methods to functionalize PHAs require a certain biological complexity, such as simultaneous polyester and protein synthesis within a single cell. The less defined nature of this technology means limited control over particle morphology and surface functionalization. Seeking to overcome these limitations, the work presented in this thesis is to introduce the concept of modularity to the PHA particle technology, by merging the PHA particle technology with Tag/Catcher protein ligation systems. The Catcher domain can rapidly form a covalent bond with its pairing short peptide tag in a site-specific manner, without the need of additional reagents nor enzymes at broad ligation conditions. The SpyTag/SpyCatcher pair was merged recombinantly with PHA particle technology, where the resulting SpyCatcher-coated PHA particles were able to immobilize various SpyTagged proteins in vitro in a tunable manner and remained functional. This thesis further demonstrates several functionalization processes to streamline this modular strategy by assessing the possibility of whether non-purified SpyTagged proteins could ligate with the PHA particles in complex environments. The results demonstrated that SpyCatcher-coated PHA particles could be functionalized adequately using two of the proposed methods. To further expand the design space of this generic modular platform towards programmable multi-functionalization, various bimodular PHA particles utilizing alternative Tag/Catcher pairs (e.g. SdyTag/SdyCatcher and SnoopTag/Snoop-Catcher pairs) were designed and studied. One of the constructs resulted in the simultaneous multi-functionalization of plain PHA particles in one-step with two differently tagged proteins in in vivo and ex vivo reaction conditions. This work presents the modular design of PHA scaffolds and several streamlined manufacturing processes to the production of task-specific designer PHAs. Introducing the concept of modularity to the PHA particle technology enabled better control of particle uniformity, reproducibility, and immobilized protein density while remaining functional. These concepts should be broadly applicable to the design and manufacture of advanced functional materials for industrial applications.
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    Single palladium sites supported on carbon capsules : synthesis, structure, and catalysis : a thesis presented in partial fulfilment of the requirements of the degree of Masters of Science in Chemistry at Massey University, Manawatu, New Zealand
    (Massey University, 2019) Olive, Nicholas; Symon, Nicholas
    This work investigates the impregnation of palladium into hollow carbon capsules through a novel synthesis method. This work investigates the feasibility of the method, improves on the method and suggests further improvements. The formation of palladium nanoparticles in hollow carbon capsules is investigated by varying the loading of palladium. This is further investigated by demonstrating the effect of other synthesis variables. The synthesized single palladium sites supported on hollow carbon capsules are then investigated for catalytic activity. These catalysts were found to be catalytically active for the Suzuki coupling reaction.