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

The pi-electron oligomers: Their synthesis and properties This diploma thesis is focused on the synthesis of p-oligophenyleneethynylene rods (dimer and trimer) containing laterally attached naphtalenediimide units as electron acceptor groups. These functionalised short oligomers are intended to serve as model oligodentate acceptors in the study on multiple interactions with electron rich molecules. The oligomers were assembled from building blocks such as aryl iodides and aryl alkynes bearing a naphthalenediimide unit. The functionalised monomers were combined in a stepwise way by using Sonogashira reaction to form the target p-oligophenyleneethynylene oligomers. The introductory UV-VIS spectroscopic studies on charge transfer complexes between electron donor (pyrene) and electron acceptor (a naphthalenediimide derivative) were performed. In addition, multiple noncovalent interaction between the electron acceptor dimer containing two naphthalenedimide moieties and the electron donor dimer containing two pyrene moieties were investigated by using 1 H NMR titration. The resulting oligomers and their precursors were characterized by using 1 H NMR, 13 C NMR, MS and IR spectroscopy.