Chemistry Theses and Dissertations
https://scholarsbank.uoregon.edu/xmlui/handle/1794/2046
2024-03-29T09:58:26ZCONFORMATIONAL DYNAMICS OF DNA AND PROTEIN-DNA COMPLEXES AT SINGLE-STRANDED-DOUBLE-STRANDED DNA JUNCTIONS
https://scholarsbank.uoregon.edu/xmlui/handle/1794/29293
CONFORMATIONAL DYNAMICS OF DNA AND PROTEIN-DNA COMPLEXES AT SINGLE-STRANDED-DOUBLE-STRANDED DNA JUNCTIONS
Maurer, Jack
Most biological systems, particularly protein-DNA complexes, leverage a dynamic evolution of their structure to perform a myriad of functions within the context of the cell. Decades of detailed biophysical research have established that the intricacies of such systems stem heavily from their dynamic evolution, abandoning the previous notion of a purely static ‘structure-function’ relationship. This dissertation introduces a new polarization-sensitive methodology for studying the dynamic evolution of local conformation in single-molecules of dsDNA containing an i(Cy3)2 dimer. The methodology developed during this dissertation is applied to DNA under a variety of experimental conditions as well as protein-DNA complexes. A massively parallel computational pipeline was developed in the course of this work to aid the optimization of kinetic network models, which forms the basis for all current analyses of single-molecule data in the Marcus and von Hippel lab. The primary discovery of this work is the persistence of four relevant conformational macrostates in DNA only systems and five relevant conformational macrostates in the protein-DNA systems examined. The thermodynamic and mechanical stability of these systems is analyzed in detail and structural mechanisms are proposed to merge the observed dynamics with hypothesized local conformations during the dynamic evolution of these ubiquitous biological systems.
2024-03-25T00:00:00ZThe Design, Synthesis, and Properties of Strained Alkyne Cycloparaphenylenes.
https://scholarsbank.uoregon.edu/xmlui/handle/1794/29290
The Design, Synthesis, and Properties of Strained Alkyne Cycloparaphenylenes.
Fehr, Julia
Strained molecules possess the potential energy required to do work in the form of further chemical transformations. Strained alkynes in particular are an attractive handle for such applications as they can undergo the metal-free strain-promoted azide-alkyne cycloaddition (SPAAC). Beyond heightening reactivity, imparting strain also affects other properties, as has been shown in the study of strained conjugated molecules. In this context, strain modulates the electronics of the molecules and typically heightens their conductivity and solubility. These ideas are described in detail in Chapter 1. This work includes published and unpublished coauthored material that highlights both of these applications by focusing on the design and study of strained alkyne-containing carbon nanohoops (also known as [n+1] cycloparaphenylenes or [n+1]CPPs). Carbon nanohoops are highly strained conjugated macrocycles composed primarily of para-substituted phenylene units. Incorporation of an alkyne into the backbone of these molecules provides a handle for controlled strain-promoted reactivity. Modulating the topology and electronics of [n+1]CPPs to in turn alter reactivity towards the SPAAC reaction is the focus of Chapter 2 of this work. Chapter 3 focuses on exploring other types of strain-promoted reactivity, in particular alkyne cyclotrimerization resulting in the formation of pinwheel-shaped large molecules. Finally, early efforts to modulate the emission color of a [n+1]CPP, to synthesize a thermally-activated delayed fluorescence nanohoop, and to synthesize a di-alkyne carbon nanohoop are described in Chapter 4.
2024-03-25T00:00:00ZThe Active Template Approach to Mechanically Interlocked Nanocarbons
https://scholarsbank.uoregon.edu/xmlui/handle/1794/29285
The Active Template Approach to Mechanically Interlocked Nanocarbons
May, James
Graphitic carbon nanomaterials hold tremendous promise for a variety of applications. The realization of this potential, however, has been hampered by the lack of synthetic methods by which we can prepare such materials in a selective manner. On the other hand, through organic synthesis we can construct small molecule analogues of these materials, a.k.a. molecular nanocarbons, in which the structure and composition can be precisely controlled. In doing so, we uncover the fundamental properties associated with these materials at the molecular size regime and begin to fill the gap between molecular and material properties. Furthermore, with organic synthesis we can begin to create nanocarbon structures with exotic topologies that do naturally occur in extended materials. In doing so, the structural landscape available to explore is limited only by the creativity of the pursuer and the synthetic methods available to them. With this in mind, the incorporation of molecular nanocarbons into mechanically interlocked architectures represents an exciting yet underexplored venture in the context of carbon nanoscience. In this dissertation I describe the development of active-metal template methods to incorporate [n]cycloparaphenylenes ([n]CPPs) into mechanically interlocked molecules (MIMs).
2024-03-25T00:00:00ZEnhancing the Antiaromaticity of s-Indacenes Through Heterocycle Fusion
https://scholarsbank.uoregon.edu/xmlui/handle/1794/29278
Enhancing the Antiaromaticity of s-Indacenes Through Heterocycle Fusion
Warren, Gabrielle
Antiaromaticity, while associated with instability, imparts beneficial properties such as decreased HOMO-LUMO energy gaps. Compounds containing antiaromatic subunits are not only of fundamental interest, but of interest as components in organic electronics. Since antiaromatic compounds are generally unstable, various strategies for isolating these compounds, such as annulation of aromatic subunits, have been developed. While this strategy stabilizes the antiaromatic subunit, it generally decreases the degree of antiaromaticity. Thus, methods to stabilize yet maintain or increase the degree of antiaromaticity are desirable. Recently, we found that fusion of aromatic heterocycles to s-indacene, a known antiaromatic molecule, yields isolable compounds with increased antiaromaticity in the s-indacene core. In this dissertation I will discuss the background of s-indacene and an overview of tuning the antiaromaticity of s-indacene, how fusion of naphthothiophene units increases the antiaromaticity of s-indacene and the development a computational understanding for the effect of heterocycle fusion on s-indacene.Chapter I is an overview of the literature about s-indacene followed by a discussion of the methods used to tune the antiaromaticity of s-indacene by the Haley group. Chapter II describes the synthesis of four naphthothiophene-fused s-indacenes, one of which increased the antiaromaticity of the s-indacene core above unsubstituted s-indacene. Chapter III extends the work of Chapter II further developing the synthesis of naphthothiophene-fused s-indacenes, varying the aryl substituents, and providing a detailed comparison of the properties of all isomers. Finally, Chapter IV explores fourteen different benzoheterocycle-fused s-indacenes through a variety of computational techniques to understand the effect of the heteroatom on the antiaromaticity of the s-indacene core.
This dissertation includes previously published and unpublished co-authored material.
2024-03-25T00:00:00Z