School of Chemistry - Theses

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    Transport, bioaccumulation, and risk of per- and polyfluroalkyl substances (PFASs) in birds from south-east Australia
    Szabo, Drew ( 2022)
    Over six million per- and polyfluoroalkyl substances (PFASs) have been identified with a broad range of uses, including commercial and industrial products such as aqueous-film-forming foam (AFFF), mist suppressant, food contact materials, cosmetics, and therapeutic drugs. Some classes of PFASs have been termed “forever chemicals” due to the strong carbon-fluorine bond that resists metabolism and degradation. To help inform key stakeholders of the potential risks involved in the exposure to these compounds the occurrence, transport, and fate of legacy and emerging PFASs within the Southeast Australian environment, this thesis aims to describe the exposure pathways and bioaccumulation in native avian species. Wastewater treatment plants (WWTPs) are a common source of PFASs to the environment and hourly variations in PFAS concentrations could have wide ranging implications for the estimation of discharge to the environment that determine risk-based human and environmental health policies. Optimised and novel sampling and analytical methodologies were developed to measure the concentrations of PFASs in biological matrices from avian species exposed to long-range and diffuse sources of PFASs in Australia, such as WWTPs. Exposure to PFASs derived from long-range transport in marine and freshwater species results in concentrations generally considered to be low risk. Conversely, a moderately impacted surface water body in Melbourne has revealed the relatively high exposure of PFASs, including novel substances, to a resident swan population that may serve as an important model for the distribution and bioaccumulation of the chemicals in Australian species for the first time. Due to the limited information regarding the occurrence, fate, and potential impact to avian species in Southeast Australia, monitoring and hypothesis-driven research is required to assess the risk of PFASs to animals and humans that may also be exposed to similar environments.
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    Applications and analysis of sulfoglycolysis pathways
    Arumapperuma Arachchige, Thimali Kalanika Ariyarathne ( 2022)
    Sulfoquinovose (SQ; 6-deoxy-6-sulfo-D-glucose) is an analogue of glucose with a 6-sulfonate group. It is a major species in the biogeochemical sulfur cycle and arises from the hydrolysis of various natural SQ glycosides, including sulfoquinovosyl diacylglycerol (SQDG), through the action of highly specific glycosidases termed sulfoquinovosidases (SQase). Five sulfoglycolysis pathways have been reported that enable the catabolism of SQ and all gene clusters encoding these pathways usually contain genes encoding SQases. Thus, SQases are considered a key gateway enzyme to allow SQ to enter every sulfoglycolysis pathway. These pathways also contain SQ importers with one system involving an SQ binding protein that captures SQ and delivers it to an ATP-binding cassette transporter. In Chapter 2, we report the first fluorogenic SQase substrate, 4-methylumbelliferyl alpha-D-sulfoquinovoside (MU-SQ), which we use to characterize several SQases, including a new SQase from Eubacterium rectale. Unexpectedly, compared to the established chromogenic substrate, p-nitrophenyl alpha-sulfoquinovoside (PNP-SQ), enzyme activity measured using MU-SQ was extremely low (rate constants 10^4-10^5-fold lower). We speculate that the difference arises because the bicyclic structure of MU is too bulky to easily bind to SQases as a result of their evolution to preferentially process substrates with slender aglycons like SQDG. While we initially considered developing new fluorogenic and histological substrates for the detection of SQase activity in complex natural samples, the poor SQase activity on MU-SQ led us to abort this aim as the proposed substrates included even bulkier aromatic systems. Chapter 3 presents a detailed sub-family classification for the Carbohydrate Active Enzyme family GH31, a grouping of which SQases are a member. In addition to hosting the SQases, family GH31 is one of the major glycoside hydrolase families, and more than 99% of its members remain uncharacterised. However, predictions of their activity are difficult as there are only 124 characterized enzymes that display fifteen different activities. We conducted a sub-family classification using sequence similarity networks (SSNs), hidden Markov models (HMMs) and the results were explored and validated using phylogenetic and structural analysis. Our classification created subfamilies with assigned members possessing usually just one activity, and provides improved predictive power for more than 75% of uncharacterized enzymes in the family. The new subfamily classification has been deployed to the CAZy database where is it undergoing internal assessment as part of their daily curation activities. Chapter 4 pursues an application of discoveries in the field of sulfoglycolysis for modern DNA biotechnology. A commonly used purification tag for heterologously-expressed proteins uses maltose-binding protein (MBP). However, purifications using MBP as a tag has a drawback: the crosslinked amylose column is degraded by amylases constitutively-expressed by the host. Therefore, we proposed a new expression and purification system using the SQ binding protein (SQBP) from Agrobacterium tumefaciens as an affinity tag. This chapter reports the synthesis of an ethylene-glycol-based linker equipped with SQ for conjugation to CNBr-activated Sepharose. Sepharose conjugated with SQ will, in future work, be used to explore the use of SQBP as an affinity purification tag for heterologously expressed proteins fused to SQBP. Collectively, this thesis provides new approaches to study SQases, new insights into how SQases sit within the broader sequence-based classification of sequence related glycosidases, and provides a potential new application for an SQ binding protein in recombinant protein purification. The study of sulfoglycolysis pathways continues to furnish new discoveries and potential new applications.
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    Total Synthesis of Alkyl Citrate Natural Products via Cyclobutene Diesters
    Chen, Zongjia ( 2022)
    The alkyl citrate natural family of products all possess a common citric acid moiety with a lipophilic polyketide sidechain at the C2 position. Many members of the alkyl citrate natural products are potent squalene synthase (SSase) inhibitors along with many other biological properties. The main challenges of alkyl citrate synthesis are the construction of the contiguous asymmetric centres and introduction of the triacid oxidation state. For the synthesis of this family of compounds, the main aim was a synthesis of a common citrate fragment with the requisite stereochemistry and correct oxidation state.
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    Synthesis and antioxidant capacity of chalcogen-containing furanose derivatives
    Velichenko, Yuliia ( 2021)
    Cardiovascular diseases are known to be a leading cause of death around the globe. Oxidative damage of endothelium plays a crucial role in development and progression of hypertension, atherosclerosis and other pathological cardiovascular conditions. Therefore, antioxidants that can effectively remove reactive oxygen species, represent promising therapeutic approaches. Sulfur, selenium and tellurium compounds act as effective oxidant scavengers due to their fast reaction rates with typical biological oxidants. Previous studies have shown that a novel selenofuranose derivative, specifically 1,4-anhydro-seleno-D-talitol, can modulate oxidative damage of biomolecules in plasma and exhibits wound healing activity. It should be noted tissue repair is extremely important in the treatment of vascular pathologies. Little is known about furanose analogues of seleno-D-talitol. Their antioxidant capacity and biological action were not investigated while knowledge of those could provide guidance for the development of novel selenosugar based therapeutics. In this thesis, approaches to the synthesis of selenium and tellurium furanose derivatives are described. Selenium and tellurium sugars were prepared from a range of different starting materials such as monosaccharides, lactones and sugar alcohols. Selenide and telluride moieties were inserted into the sugar core using sodium selenide and sodium telluride prepared in situ. Final furanose analogues were synthesised in up to 8 steps with good yields. Unlike selenium containing furanose derivatives, most of their tellurium counterparts were unstable light sensitive compounds presumably due to the larger chalcogen atom causing strain in the sugar ring. Additionally, thio-D-talitol and D-talitol with oxygen in the sugar ring were prepared for comparison in antioxidant studies. Antioxidant activity of the synthesised compounds was determined in Chapter 3. Cyclic voltammetry and linear sweep voltammetry were used for investigation of oxidation of chalcogen-containing selenofuranose derivatives. It was shown that the primary oxidation of the sugars is an irreversible process which, presumably, occurs through oxygen transfer reaction. The oxidation potentials were determined and the half-wave potentials for electrochemical oxidation of the chalcogen-containing sugars were calculated. In Chapter 4 the in vitro vascular studies were carried out to investigate the effectiveness of the synthesised chalcogen-containing furanose derivatives, toward the prevention of endothelial damage in mouse aorta under oxidative stress conditions. The in vitro studies revealed that the stereo configuration of the sugar core significantly influences the biological activity of the chalcogen-containing furanose analogues of seleno-D-talitol. In the range of selenofuranose derivatives, seleno-D-talitol was shown to prevent endothelial dysfunction more effectively than its analogues. Furthermore, the structural isomer, hexose sugar selenogalactitol demonstrated different effects on mouse aorta than the selenopentoses, by presumably inhibiting endothelial nitric oxide synthase. As expected, thio-D-talitol exhibited a lower ability to protect the endothelium in mouse aorta from oxidative stress, than its selenium counterpart, seleno-D-talitol. Telluro-D-talitol appeared to be toxic to cells in mouse aorta.
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    Total Synthesis of the Viridiofungins and Structural Elucidation of 8,13-Deoxynargenicin
    Atkin, Liselle May ( 2022)
    A fourteen step total synthesis of alkyl citrate natural products viridiofungin A, B, A2 and NA808 and thirteen step synthesis of viridiofungin Z2 is described. The stereochemistry of the citrate core of these natural products is set up via a diastereoselective formal [2+2] cycloaddition followed by a HF-mediated rearrangement to afford a bicyclic lactone. A key step of this synthesis is a cross metathesis reaction of a hindered disubstituted alkene beta lactone with the alkene side chain, whereby a benzoquinone additive is used to suppress unwanted alkene isomerisation of the starting material. The next step in the synthetic route is the novel formation of an amide via the nucleophilic ring opening of a beta lactone with an amino acid ester. Deprotection afforded either viridiofungin A, B, A2 and NA808. Removal of the tert-butyl esters and concomitant hydrolysis of the beta lactone of viridiofungin Z2 tri-tert-butyl ester afforded viridiofungin Z2. The structural elucidation of NarN knockout metabolite and proposed biosynthetic precursor of antibiotic macrolide nargenicin A1, 8,13-deoxynargenicin, is described. A combination of 1H and 13C NMR spectroscopy, COSY, HSQC and HMBC 2D-NMR experiments were used to support the proposed structure of 8,13-deoxynargenicin. The relative stereochemistry of 8,13-deoxynargenicin was assigned from a combination of 1H-1H J coupling constants as well as 2D-NOESY NMR correlations.
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    Temperature Jump Spectroscopy Studies of Colloid Systems
    Tadgell, Benjamin David ( 2022)
    Temperature jump spectroscopy is a powerful method that has been used since its development in the 1960s to measure kinetics in chemical systems. It has very rarely been applied to colloids however, despite these systems being inherently complex and well-suited for relaxation studies. In this thesis we demonstrate that temperature jump spectroscopy is a fantastic asset to probe structural and morphological changes in colloid systems. We focus on a class of thermoresponsive core-shell microgels that undergo different types of reversible phase transitions. The first of these is a volume phase transition, where the gel network in the shell swells and deswells in response to temperature. The second is a reversible aggregation transition, which can be prompted by temperature and occurs under suitably high electrolyte conditions. The dynamics of these phase transitions are still largely unexplored. We first develop a scattering model that determines the relationship between the visible-light scattering cross-section and the morphology of microgels as they undergo swelling and deswelling in response to temperature. This enables us to correlate optical density changes observed upon relaxation of the system to specific structural changes. We then use temperature jump spectroscopy to characterise the reaction pathway undertaken by microgels as they transition between different volume phase states. Finally, we characterise aggregation/dissociation dynamics, which occurs at long time-scales following the temperature jump under certain conditions. This kinetic data will allow us to better understand how dynamic processes can be harnessed in microgels, and applied to applications like nanoparticle self-assembly, sensing and drug delivery. The general procedures developed throughout also demonstrate how temperature jump spectroscopy can be extended to other complex colloid systems.
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    Photocatalytic carbon dioxide reduction with water
    Agnihotri, Shruti ( 2021)
    Abstract New catalyst discovery to enhance photocatalytic reduction of CO2 with H2O is a materials space problem, where determining the ideal catalyst composition, catalyst processing conditions, and optimising the reaction conditions is a “wicked” problem. To examine more of the materials space, we need to develop new high throughput screening methods. A new continuous flow photocatalytic reactor with enhanced capabilities to discover robust photocatalyst for the photocatalytic reduction of CO2 is thus designed in this project. A key component in the new reactor is in-situ thermal monitoring of the activated catalyst. A more detailed analysis is made on selected catalysts that promote a greater temperature drop under constant illumination, that is more active catalysts will require more energy for this highly endothermic reaction. This reactor has the potential to accelerate the discovery/optimization process of required catalysts, when fully automated. Additionally, its continuous gas flow configuration, flexibility to test varied set of reaction parameters with precise control over input parameters makes it distinguished from conventionally used reactors. Validation of this custom-designed photocatalytic reactor setup, which is based on entirely new metric to identify reactivity of an active catalyst was commenced using benchmark catalyst material TiO2. Further, extended experiments using TiO2/C3N4 as photocatalysts confirmed the usefulness of in-situ temperature monitoring screening method, as detected enhanced CO2 reduction was linear to monitored drop in catalyst’s temperature. This newly built photocatalytic reactor set up was then used to explore photocatalytic CO2 reduction reactions over range of prepared catalysts. Catalyst designing was focussed to suppress recombination losses during photocatalytic reaction, which is reported as key responsible factor of low obtained product yields in the field. For this, nanoparticle – nanocomposites of C3N4 with various transition metal complexes were synthesized in this work and subsequently tested as photocatalysts. C3N4 based composite catalysts were found to be effective in enhancing photocatalytic CO2 reduction reaction, when compared to only single catalyst systems. Also, controlled syngas formation was made possible when modified C3N4 was combined with cobalt phosphate using layer by layer assembly method. Obtained results were also exemplifying that composite photocatalyst’s performance is also sensitive to used catalyst preparation method, which relates to provisioning more active sites over catalyst surface to enhance photocatalytic reaction rates. In addition to C3N4, another low-cost semiconductor option- FexOy has also been explored as photocatalyst for CO2 reduction reaction. Low conduction band edge energy of Fe2O3 was addressed by structural and surface modifications, where electrospinning method was used for fibrous catalyst preparation with additional doped metal cations. These strategies were helpful in enhancing selective CO formation as CO2 reduction product, significantly. Structural and morphological parameters of explored nano composites effecting catalytic performance were investigated using X-ray absorption spectroscopy and Electron microscopy.
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    Spectroelectrochemistry of Semiconductor Nanocrystals
    Ashokan, Arun ( 2021)
    Semiconductor nanocrystals exhibit well-known, size-dependent optical and electronic properties. Control over the charge carriers in semiconductor nanocrystals enables the possibility to tune the optical response. One way to achieve this is through electrochemistry. Carrier modulation through electrochemical methods allows more precise control over electron transfer compared to methods such as photocharging and chemical redox reactions. By combining electrochemistry with spectroscopic techniques, the charged states in semiconductor nanocrystals can be studied in detail. A spectroelectrochemical setup has been developed to study the charging of semiconductor nanocrystals in solution and its influence on absorption and photoluminescence (PL). A negative trion state can be generated in CdSe quantum dots (QDs) and stabilised for hours under an applied cathodic potential. By monitoring both the absorbance and fluorescence changes, one can determine whether charge carriers are free or trapped. The total number of electrons injected into the QDs can be estimated from current and coulometry measurements. Hole injection into CdSe QDs induces corrosion of the lattice, whereas injection into nanocrystals shelled with CdS induces bleaching. Coupling the spectroelectrochemical setup with time-resolved PL measurements reveals the trion lifetime of CdSe/CdS QDs as a function of shell thickness. In the last section of the thesis, the effects of charge injection on CdSe nanoplatelets (NPLs) is explored. In contrast to QDs, hole injection into the NPLs enhances the photoluminescence.
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    Amphiphilic Block Copolymers for Morphological Control in Bulk Heterojunction Solar Cells
    Ahluwalia, Gagandeep ( 2021)
    Organic solar cell (OSC) is a type of solar cell that utilise a solution-processable organic semiconductor material as a photoactive component. The use of less toxic, flexible organic semiconductors in solar cells leads to a formation of a lightweight device with a short energy payback time. Along with this, it is easy to fabricate organic solar cells on a large scale by roll-to-roll printing, which is the driving force for industrialisation. The recent efforts on organic materials such as small molecules or polymers have pushed the OSCs towards a milestone efficiency of more than 18 %. However, achieving the desired control over the morphology by blending of the donor (electron-rich) and acceptor (electron-deficient) materials and reproducibility for industrial scope has remained a challenge, based on the fact that often deposition techniques used in the laboratory are different to those in continuous operation, i.e. spin coating compared to slot die deposition. Moreover, the use of chlorinated solvents for processing restricts OSCs large-scale manufacturing scope. In order to increase the commercial applicability of OSCs, a bi-continuous interpenetrating network of the donor and acceptor block is required, where donor and acceptor materials should have 10-20 nm domain sizes with continuous interfaces to promote the charge generation/separation process. Also, the photoactive component should show solubility in non-chlorinated or industrial relevant solvents. Fully conjugated block copolymers, where a conjugated donor and acceptor block are covalently linked with each other, have an ability to attain a defined morphology by manipulating the Flory–Huggins segment–segment interaction parameter. The BCP materials could self-assemble into a thermodynamically favoured morphology and offers continuous interface, control over domain size, long term stability, and reproducibility. However, the BCP’s have failed to deliver a high performing OSC so far. The primary reason is the difficulty of achieving a clean phase separation in BCP’s due to the high inter-block interactions parameter between donor and acceptor block, which enhances the charge recombination over charge separation process. Moreover, developing a fully conjugated block copolymer with a specific molecular weight, block ratio, and high purity is lacking behind due to the unavailability of the synthetic approach. The synthesis of BCP via a well-known step-growth polymerisation usually ends-up containing a mixture of the desired BCP along with a significant number of polymer contaminants, which impacts device performance. Furthermore, the BCP’s reported in the literature usually require chlorinated solvents for the processing, which limits its industrial scope. For industrial adoption of OSCs, we have developed a strategy to control the synthesis of an amphiphilic di-block copolymer containing high performing push-pull donor and acceptor blocks to achieve a clean phase separation and solubility in non-chlorinated solvents. In order to obtain control synthesis of a block copolymer, firstly, we have developed a strategy to control the molecular weight/ end-group functionality of homopolymers. The strategy involves designing and synthesising of asymmetric functionalised push-pull monomers that undergo a Suzuki or a Stille pseudo-living polymerisation. Herein, studies on four different homopolymers, i.e., p(BDT-BT), p(BDT1-BT), p(IID-TT), p(NDI-TT), were performed and control over the p(BDT-BT), p(BDT1-BT) polymer via Suzuki catalyst transfer polymerisation and p(NDI-TT) via Stille catalyst transfer polymerisation was achieved. Two fully conjugated amphiphilic di-block copolymers with a specific molecular weight and block ratio (1:1) were synthesised via a stepwise or one-pot procedure. In a stepwise method, TfO-p(NDI-TT) was initially synthesised using a pseudo-living Stille polymerisation with a single triflate (OTf) end group and specific molecular weight. Subsequently, TfO-p(NDI-TT) was used as a macro-initiator to grow an amphiphilic di-block copolymer (BCP1) via a grafting-into approach, where the donor polymer block was grown using a pseudo-living Suzuki polymerisation. Moreover, the one-pot synthesis of an amphiphilic di-block copolymer (BCP2) with the sequential addition of donor and acceptor monomer was performed utilising similar optimised conditions developed for stepwise block copolymer synthesis. Furthermore, the preliminary morphological behaviour of BCP1 and BCP2 was investigated using X-ray scattering techniques. At last, a device containing a BCP1 as an active layer achieved an efficiency of 3.2 %, whereas BCP2 showing a maximum efficiency of 2.7 % was reported. This work has demonstrated a potential route of utilising asymmetrically functionalised push-pull monomers to achieve control over di-block copolymer synthesis containing high performing donor and acceptor polymer.
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    Spectral Engineering of QD-organic Hybrid Systems
    Wu, Na ( 2021)
    Colloidal semiconductor nanoparticles, which are commonly referred to as quantum dots (QDs), are inorganic crystals with sizes in the nanometre regime. QDs have been intensively studied because of their potential applications in diverse fields including light harvesting systems, light emitting devices, optoelectronics, sensing, and biological applications. Colloidal QDs consist of an inorganic core which is coated with an organic shell layer for stabilization. The inorganic core exhibits typical size-, shape-, and composition-dependent optoelectronic properties, while the organic surface ligands control the physical and chemical properties. The hybrid organic-inorganic structure makes them multidimensional materials which can be further functionalised by covalent attachment of molecules to the nanocrystal surface. This thesis aims to advance our understanding of this surface functionalization and how it can be used for spectral engineering. By combining QDs and functionalized organic molecules, the resulting hybrid systems have unique optical properties and are of great interest for applications in solar energy conversion and photosynthetic light harvesting. This thesis consists of the following sections: Firstly, blue emitting QDs were used as down-shifting materials for UV LEDs to afford targeted, narrow and stable, blue light sources. The solid-state QD-polymer composites were fabricated by blue-emitting alloyed CdZnSeS/ZnS and CdZnS/ZnS QDs in poly(methyl methacrylate) (PMMA) films. Functionalized PMMA molecules were employed as surface ligands, which could improve the compatibility of QDs with PMMA matrix. The photophysical properties of QD-PMMA composite films were studied with the controlling of polymer ligands, including functional group and polymer ligand binding ratio. The thiol group-based polymer ligands (SH-PMMA) quenched the photophysical properties of QDs in composites due to hole trapping by the thiol groups. Conversely, the carboxylic acid group-based poly(methyl methactylate-co-methacrylic acid) (P(MMA-co-MAA)) improved the dispersion of QDs in PMMA without altering the photophysical properties. The new ligands enable excellent solubility of QDs in a PMMA matrix. The photostability of CdZnS/ZnS QDs in PMMA was studied under UV light irradiation. QDs exhibited quenched PL intensity due to photooxidation of the semiconductor lattice catalysed by oxygen in the film. By using air-free CdZnS/ZnS QDs and appropriate encapsulation methods with a UV epoxy based polymer, the lifetime of QDs under UV light illumination was significantly extended. These results demonstrated that UV epoxy encapsulated air-free CdZnS/ZnS QD-PMMA film is extremely photostable, which is promising for down-shifting UV light to afford bright and narrow blue light. Then the investigation of QDs in light harvesting was performed by the fabrication of QD-organic fluorophore hybrid materials in PMMA film based on efficient surface functionalization. Three different emitting QDs were used as energy donors with the addition of two perylene diimide (PDI) dyes, bPDI3 and LR305, as energy acceptors to form QD-bPDI3-LR305 three-chromophore hybrid system in PMMA. The Forster resonance energy transfer (FRET) process was studied in these hybrid systems with three different emitting QDs. By tuning the concentration of bPDI-3, a two-step FRET process was identified with energy flowing from the QDs to LR305 via bPDI-3 in the PMMA film. This was the dominant energy transfer pathway in these three-chromophore systems. The photoluminescence quantum yield (PLQY) of QD-based films was significantly increased with the presence of efficient energy transfer process under UV light excitation. In this case, the UV light harvesting was broadened with the introduction of blue emitting QDs in organic hybrid system and exhibited bright red light emission. Regarding their light harvesting performance, the internal quantum efficiency of QD-bPDI3-LR305 LSC devices was quite close to that of bPDI3-LR305 LSC devices. This is attributed to the efficient energy transfer process and near unity PLQY of hybrid systems. These results indicated that the QD-organic hybrid system provides a promising way for broadening the light harvesting range, and the spectral engineering of QDs in solid-state was successfully achieved with near unity two-step FRET process. Finally, the interaction between QDs and surface ligands was studied with the fabrication of QD-organic fluorophore composites in solution. PDI derivatives, containing amine and carboxylic acid anchoring groups and two different anchoring chain lengths, have been designed and synthesized. In QD-PDI composites, PDI derivatives were used as energy acceptor with CdZnS/ZnS QDs as the energy donor. The effects of molecular geometry on both PDI binding and the energy transfer behaviour have been investigated in the composites. It was observed that stable carboxylic acid binding and longer anchoring chain length were essential to achieve high PDIs loading ratios on the QD surface. In addition, the FRET process was also closely related to the anchoring group and side chain length in QD-PDI composites. The colloidal stability of QD-PDI composites was investigated. Desorption of PDIs from the QD surface occurred and the FRET process efficiency decreased with increasing donor-acceptor distance. Due to the bulky structure of the PDI derivatives, oleic acid molecules could displace them on the QD surface and this exchange process slowed down QDs aggregate formation in solution. Among these composites, the QD-PDI-C11-COOH composites exhibited the best colloidal stability. These results demonstrated that both strong ligand binding and long anchoring chain length are essential to achieve good FRET-efficient and colloidally stable QD-PDI composites. Based on the results presented here, the understanding of QDs surface chemistry is advanced and the development of QD-based light conversion systems with minimum energy loss is further broadened.