Aromatic donor-acceptor interactions have been utilized by the Iverson group in the development of abiotic molecules, called aedamers, that achieve new folding motifs, intermolecular association in heteroduplexes, and new material properties. These molecules exploit the interaction between the electron-rich 1,5-dialkoxynapthalene (DAN) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) units in a face-centered stacking geometry in aqueous solution. This dissertation describes the use of DAN-NDI interactions in the realm of peptides and proteins to expand the scope for applications of this interaction. This work specifically focuses on three areas of aromatic donor-acceptor interactions: achieving protein behavior with abiotic molecules, introducing the interaction into natural peptides, and utilizing the interaction in the intermolecular association of an abiotic molecule and a natural peptide. Chapter 2 refines the model of aggregation of an amphiphilic aedamer, which forms a hydrogel upon heating. The aedamer behaves similarly to proteins called amlyoids, which form fibrils and plaques in vivo which have been implicated in a variety of diseases, including Alzheimer's. Chapter 3 describes the synthesis of [alpha]-amino acids with DAN- and NDI-containing side chains. These amino acids can be used in a peptide model of [beta]-hairpin secondary structure. The model system can determine whether aromatic donor-acceptor interactions are useful in stabilizing peptide and protein structure. Chapter 4 describes the study of the Anchored Periplasmic Expression System (APEx) for use in screening random peptide libraries. A random peptide library is used to determine the sequence of a natural peptide, potentially containing electron-rich aromatic residues, which could bind an NDI oligomer with high affinity for use as a protein expression tag. Chapter 5 describes work toward the use of cyclic NDI bisintercalators for binding both the major and minor grooves of a specific sequence of DNA simultaneously, in addition to the use of cyclic NDI and DAN molecules for the further study of NDI-DAN interactions in abiotic intermolecular assembiles. Overall, this work has advanced the application of aromatic donor-acceptor interactions in peptides and should serve as a foundation for the future study of this interaction in protein folding and behavior in biological systems. / text

Thesis (Ph.D.) - James Cook University, 2005. / Journal publications by the author contained on CD-ROM. Typescript (photocopy) Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Florida, 1981. / Description based on print version record. Typescript. Vita. Includes bibliographical references (leaves 204-213).

Thesis (Ph.D.)--University of Hong Kong, 2000. / Includes bibliographical references (leaves 338-377) Also available in print.

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

M.Sc. / The main objective of the work presented in this dissertation was to investigate the application of the phosphorus atom as a probe to evaluate stereo-electronic effects in arylphosphines. Traditionally, electronic effects are described as having inductive or resonance origins. In addition to the aforementioned mechanisms, the possibility of an additional field effect pathway was also investigated. For this purpose, a series of ortho, meta and para mono-substituted triaryl phosphines, i.e. Ph2(C6H4-X), were synthesised using a lithium-halogen exchange pathway. This series included a selection of electron-withdrawing and electron-donating substituents (X = F, CN, COOtBu, Me, OMe, NMe2) as well as combinations of these. Most of these ligands are crystalline which allowed analysis of their electronic nature by means of X-ray crystallography. From these ligands a representative range of electron-donating and electron-withdrawing aryl substituted phosphines was chosen to collect high-resolution (d=0.5 Å) data. An aspherical multipole refinement was carried out on each of the high-resolution data sets by employing the Hansen Coppens multipole formalism. This was followed by an experimental charge density analysis of each phosphine by employing the principles of QTAIM employed in WinXD. From topological analysis of the Laplacian of the electron density, properties at the (3,-3) lone pair critical points were evaluated. Similarly, the density properties at the (3,-1) bond critical points of the P-Cipso bond were evaluated by analysis of the topology of the electron density. In addition, several integrated properties including the volume, charge and electron population of the phosphorus atom were evaluated. All of the above properties showed very good linear correlations with the infrared CO stretching frequencies of the Rh-Vaska-type complexes corresponding to these phosphines. Furthermore, computational chemistry was employed as a complementary investigation tool to the X-ray crystallographic study. A theoretical charge density study was conducted for the complete range of phosphines described above in paragraph 1 of this Synopsis by employing the principles of QTAIM employed in AIMAll. All of the properties mentioned in the above paragraph were also calculated. In addition, the calculated molecular electrostatic potential properties of the phosphorus lone pair (Vmin and dcp), the integrated substituent bond dipole and NBO (Natural bond orbital) analysis was used to evaluate substituent electronic effects. All of the calculated properties (with the exception of the charge and electron population of the phosphorus atom calculated from NBO analysis) showed good linear correlations with the infrared CO stretching frequencies of the Vaska-type complexes corresponding to these phosphines within a particular electron-withdrawing/electron-donating or ortho/meta and para series. In addition, very ii good linear correlations were obtained between the experimental and theoretical properties within a particular electron-withdrawing/electron-donating or ortho/meta and para series. As additional investigation tools, the ligands were characterised by several techniques including infrared CO stretching frequency measurements performed on Rh Vaska-type compounds derived from the synthesised ligands, 31P NMR chemical shift measurements as well as 103Rh-31P coupling constant measurements to evaluate the effect of various substituents on the electron density at the phosphorus lone pair. In conclusion, it was found that the phosphorus atom is a sensitive probe of substituent electronic effects. Furthermore, it was found that high-resolution X-ray crystallography, computational chemistry, 31P NMR and infrared spectroscopy are all excellent techniques that can be employed to obtain a better understanding of the nature and transmission of substituent effects. From this study, it appeared that the electronic effects in phosphine ligands could not be rationalised by an inductive mechanism alone, but seemingly more correctly by an additional field effect mechanism.

Microbial electrochemical technologies (MET) exploit the bioelectrocatalytic activity of microorganisms, with a main focus on waste-to-resource recovery. Electromethanogenesis, a type of MET, describes the process of CO2 reduction specifically to methane, catalyzed by methanogens that utilize the cathode directly as an electron donor or through H2 evolving from the cathode surface. Applications are mainly in the direction of bioelectrochemical power-to-gas, as well as biogas upgrading and carbon capture and utilization. As the cathode and its associated microbial consortia are key to the process, larger scale applications require improvements especially in terms of optimal operational parameters, cathode materials and the dynamics of the effect of electron transfer within the cathodic biofilm. The focus of this dissertation is to improve the understanding of the dynamics and function of methaneproducing biofilms grown on cathodes in electromethanogenic reactors in the presence of two different electron donors: the cathode and the H2 evolving from the cathode surface. The spatial homogeneity of the microbial communities across the area of the cathode was demonstrated, which is relevant for large scale applications where reproducibility is required for predictable engineered systems. Metagenomic and metatranscriptomic methods were applied to elucidate the short-term changes in the actively transcribed methanogenesis and central carbon assimilation pathways in response to varying the availability of electrons by changing the set cathode potential in a novel Methanobacterium species enriched from electromethanogenic biocathodes. Although changes in functional performance were evident with varying potential, no significant differential expression was observed and genes from the methanogenesis and carbon assimilation pathways were highly expressed throughout. Indium tin oxide (ITO) as a potentially hydrogen evolution reaction (HER) – inert cathode material was evaluated using the mixotrophic Methanosarcina barkeri in an attempt to develop a simplified material-science driven approach to future electron transfer studies. It was found to be electrochemically unstable under the tested conditions, losing its conductivity over time. Overall, the findings from these studies provide new knowledge on the effects of electron donor availability on the functional performance and the biocathode community dynamics. The understandings derived from the study are relevant to methanogenic processes and should aid in system scaleup design.

The principle calcium regulator in the muscle cell is the calcium ion release channel (RyR). Improper calcium homeostasis in the muscle cell is the foundation of many pathological states and has been targeted as a contributing factor to ventricular tachycardia, which is known to precede sudden cardiac arrest. Numerous endogenous and exogenous compounds can affect the way RyR regulates calcium. In this study the anthocyanidin Pelargonidin (Pg), an important natural colorant and dietary antioxidant, is evaluated for its effect on regulating the transport of calcium through the RyR1 of skeletal muscle sarcoplasmic reticulum. Pelargonidin undergoes time dependent structural changes in aqueous solutions at physiological pH and a mixture of up to seven forms of Pelargonidin are present in solution simultaneously. Pelargonidin is a unique RyR1 modulator. It can both stimulate and inhibit the RyR1 depending on the experimental conditions. In addition, when Pelargonidin is irradiated with white light, its inhibition properties on the RyR1 are essentially nullified. Proposed mechanisms include excited state charge shift within RyR1-Pg complexes.

We initially studied the treatment of acid rock drainage using a sulfate-reducing bioreactor with zero-valent iron as the electron donor. The results demonstrate that this electron donor can serve as the sole exogenous slow-release electron donor to drive sulfate reduction over 400 operational days at short HRTs (1-3 days). The synthetic acid rock drainage contained high heavy metal concentrations (up to 50 mg/L of copper) and pH values ranging from 3.0 to 7.0. Treatment of this acid rock drainage efficiently removed Cu, Cd and Pb (>99.7%) and increased pH to circumneutral values (7.3-7.7). Elemental analysis indicated that formation of insoluble metal sulfides was responsible for the effective metal removal in the zero valent iron columns. In the second study, three inoculated columns containing anaerobic granular sludge were fed a synthetic medium containing H₂SO₄ and Cu²⁺ during the experimental period of 4 months. Algae biomass promoted 80% of sulfate removal (12.7 mg SO₄²⁻ d-1), enabling near complete Cu removal (>99.5 %), and alkalinity generation, raising the effluent pH to 6.5. In the algae amended columns Cu²⁺ was precipitated with biogenic H2S produced by sulfate reduction. Whole cell algae and lipid extracted algae biomasses were both shown to be effective e-donors in driving sulfate reduction of ARD, thus enabling the precipitation and removal of Cu²⁺. The precipitate retained in the columns was composed mostly of insoluble copper sulfide formed from the biogenic sulfide, as shown by sequential extraction and X-ray diffraction. In the third study, several pretreatments, i.e., thermal, chemical, sonication and combinations thereof, that enhance anaerobic biodegradability of Chlorella protothecoides biomass were evaluated. The results demonstrate that anaerobic digestion of pretreated Chlorella protothecoides biomass generates energy-rich methane and recovers nitrogen nutrients. Sonication of algal biomass under optimized conditions provided a significant increase in the methane yield (327 mL STP CH₄ g⁻¹ VS) compared to untreated algae (146 mL STP CH₄ g⁻¹ VS), as demonstrated in anaerobic digestion experiments incubated for 41 days. In contrast, thermal pretreatment provided only a moderate increase of the methane yield and alkaline treatment led to a decrease of the methane yield compared to the untreated algal biomass. Additionally, sonication treatment provided a 4.1-fold increase in the release of ammonia nitrogen during anaerobic digestion of the algal biomass. In the fourth study, the nutrient recovery and biogas generation from the anaerobic digestion of waste biomass from algal biofuel production was investigated. Anaerobic digestion of whole cell and lipid extracted Chlorella sorokiniana-1412 released 48.1 and 61.5% of the total algal nitrogen as NH₄⁺-N, and 87.7 and 93.6% of the total algal P as soluble P, respectively. The biochemical methane potential, quantified through the methane yield of whole cell algae and lipid extracted algae, was 0.298 and 0.253 L methane/g algal volatile solids, respectively. The conversion of lipid extracted algae and whole cell algae biomasses to methane was very similar (38 and 41% on a COD basis, respectively), indicating that the energy yield was not significantly lowered by extraction of the lipid fraction (which accounted for 9% of algal dry weight). Sonication improved the access of hydrolytic enzymes to algal biopolymers, compensating in part for the energy lost due to lipid extraction. The above results demonstrate that algal waste from the biodiesel industry has the potential to be recycled through anaerobic digestion into valuable nutrients and energy. These studies indicate that zero valent iron and algae biomass are promising reactive materials for the treatment of acid rock drainage in sulfate-reducing permeable reactive barrier systems. Additionally, to promote algae cultivation for the biodiesel industry, the anaerobic digestion of algae residues can generate nutrients and energy, making algae cultivation more fiscally attractive.