Non-covalent interactions are of great interest to chemists and biologists who study the molecular structure and function of biological systems, as well as those who seek to control, undo, or improve upon the efficiency of these systems with man-made chemical tools. The Iverson group has specifically applied noncovalent aromatic donor-acceptor interactions to biotic and abiotic aqueous systems through the use of the electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) moieties. Chapter 1 introduces and reviews the current state of self-assembly research, especially work conducted in aqueous media. Chapter 2 delineates the design and synthesis of a molecule that can self-assemble and form disulfide bonds, with the goal of creating higher-order structure. Chapter 3 comprises the design and synthesis of a series of pendant-NDI bisintercalators of DNA that are distinct from the backbone-incorporated intercalators previously employed in our laboratory. Chapter 4 contextualizes the term of art “pi-stacking,” reviewing the current state of knowledge of specific contributions to this effect and commenting on the putative uniqueness of the interaction. Theoretical and experimental work in the field is summarized. The work discussed in this dissertation serves to expand the scope of programmability of our DNA intercalators, to probe the higher-order assembly behavior of our donor-acceptor pair, and to clarify the term “pi-stacking,” lately overused, that imperfectly describes the interaction that gives both these systems their compelling binding properties. / text

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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.

Photoinduced electron transfer in self-assembled via axial coordination porphyrin-fullerene dyads is investigated. Fullerene functionalized with imidazole and fullerenes functionalized with pyridine are chosen as electron acceptors, while zinc pophyrin derivatives are utilized as electron donors. The electron withdrawing ability of halogen atoms make the porphyrin ring electrophilic, which explained the binding of (F20TPP)Zn with fullerene derivatives having the highest binding constant around 105M-1. Another important observation is that the fullerene imidazole binding to zinc pophyrin had higher stability than fullerene pyridine-porphyrin dyad. Computational DFT B3LYP-21G(*) calculations are used to study the geometric and electronic structures. The HOMO and LUMO was found to be located on the porphyrin and fullerene entities, respectively. Photoinduced electron transfer is investigated by the steady-state absorption and emission, differential pulse voltammetry, and nanosecond and femtosecond transient absorption studies. The measurements provided the same conclusion that the increasing number of the halogen atoms on the porphyrin ring leads to the higher binding of porphyrin-fullerene supramolecular dyads and efficient charge separation and charge recombination processes.