The study of ferritin includes a rich history of discoveries and scientific progress. Initially, the composition of ferritin was determined. Soon, it was shown that ferritin is a spherical, hollow protein. Eventually, over several decades of research, the structure and some function of this interesting protein was elucidated. However, the ferritin field was not completely satisfied. Today, for example, researchers are interested in refining the details of ferritin function, in discovering the role of ferritin in a variety of diseases, and in using ferritin for materials chemistry applications. The work presented in this dissertation highlights the progress that we have made in each of these three areas: 1) Mechanistic studies: The buffer used during horse spleen ferritin iron loading significantly influences the mineralization process and the quantity of iron deposited in ferritin. The ferrihydrite core of ferritin is crystalline and ordered when iron is loaded into ferritin in the presence of imidazole buffer. On the other hand, when iron is loaded into ferritin in the presence of MOPS buffer, the ferrihydrite core is less crystalline and less ordered, and a smaller amount of total iron is loaded in ferritin. We also show that iron can be released from the ferritin core in a non-reductive manner. The rate of Fe3+ release from horse spleen ferritin was measured using the Fe3+-specific chelator desferoxamine. We show that iron release occurs by three kinetic events. 2) Disease studies: In order to better understand iron disruption during disease states, we performed in vitro assays that mimicked chronic kidney disease. We tested the hypothesis that elevated levels of serum phosphate interrupted normal iron binding by transferrin and ferritin. Results show that phosphate competes for iron, forming an iron(III)-phosphate complex that is inaccessible to either transferrin or ferritin. Ferritin samples separated from the iron(III)-phosphate complex shows that as the phosphate concentration increases, iron loading into ferritin decreases. 3) Materials chemistry studies: Anion sequestration during ferritin core reduction was studied. When the core of horse spleen ferritin is fully reduced using formamidine sulfinic acid, a variety of anions, including halides and oxoanions, cross the protein shell and enter the ferritin interior. Efforts have been made to use ferritin to control the concentration of anions for reactions. In addition, the native ferrihydrite mineral core of ferritin is a semi-conductor capable of catalyzing oxidation/reduction reactions. Light can photo-reduce AuCl4- to form gold nanoparticles (AuNPs) with ferritin as a photocatalyst. The mechanism of AuNP formation using ferritin as a photocatalyst was examined. From this work, we propose that the ferrihydrite core of ferritin photo-reduces; the mineral core dissolves into a soluble iron(II) mineral. The iron(II) then re-oxidizes, and a new mineral forms that appears to be the new photocatalyst, as the lag phase is significantly decreased with this new mineral form of ferritin.

<p dir="ltr">Methods of protein engineering and mutation to achieve selective and designed enzymatic function are often challenged by issues with foldamer stability. Molecular nanocages present an exciting new opportunity for biomimetic-defined cavities capable of biomolecule recognition and catalysis. While many different types of molecular cages exist, covalent organic molecular cages offer great flexibility and control over the design of the cage. Furthermore, the covalent linkages provide a robust framework resistant to degradation and stable in many chemical environments. Lastly, covalent organic cages may be designed for the precise placement of functional groups, including group placement inside the cage cavity for molecular recognition and binding. I report our recent advances in developing new synthetic methods for robust organic molecular cages with well-defined cavities and tunable functions for artificial enzyme catalysis and recognition. The basic design philosophy for such protein-mimetic structures will be introduced for the scalable synthesis of these macromolecules. Herein, we report two approaches to a [8+12] triazine-linked organic cage and a similar [8+12] triazine and boroxine-linked cage. While our first approach attempts a kinetically controlled tethered cage formation, our second method relies on the principles of dynamic covalent chemistry in the thermodynamically controlled self-assembly of the final cage structure.</p>

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Single walled carbon nanotubes have been attracting interest for their electronic, magnetic, chemical and mechanical properties. Moreover, since they are ideal nano-containers, the adsorption and absorption properties provide them to be used as Li/Li+ ion batteries. The capacity, rate capability and cycle life of the batteries are the important points which must be improved to have better results. In this thesis Li/Li+ ion doped carbon nano structures are investigated theoretically in order to contribute to the lithium battery technology. The present studied carbon nano structures are the fullerenes, single-walled carbon nanotubes, pristine and defected (Stone-Wales and mono-vacancy defected) carbon nanocapsules. The Li/Li+ interactions with these nano structures have been investigated using semi-empirical molecular orbital method at PM3 level, density functional theory method with B3LYP exchange-correlation functional using 3-21G or 6-31G basis sets. Furthermore, the systems have been investigated by molecular dynamics simulations in which Tersoff potential and an empirical many-body potential have been used to define the various interactions. In this thesis the optimized geometries, thermodynamical quantities, interfrontier molecular orbital eigenvalues and dipole moments of the studied systems have been reported.

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