Dissertation made openly available per email from author, 6/8/2016.

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Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (p. [83]-91).

Thesis (Ph.D.) OGI School of Science & Engineering at OHSU, October 2007. / Includes bibliographical references (leaves 132-158).

Ph.D. / Biochemistry and Molecular Biology / Selenocysteine-containing mutants of human copper chaperone for superoxide dismutase (hCCS) were constructed using intein-mediated peptide ligation. These mutants were studied with respect to their ability to transfer Cu to E,Zn superoxide dismutase (SOD1) and their Cu-binding and X-ray absorption spectroscopic (XAS) properties. Previous studies have shown that three functionally distinct polypeptide domains are present in CCS: the N-terminal domain 1 (D1, residues 1-85) contains the copper-binding MXCXXC motif, domain 2 (D2, residues 86-234) has sequence homology to residues associated with the native SOD1 dimer interface, and the C-terminal domain 3 (D3, residues 235-274) contains a CXC motif. Recent results suggest the formation of a D3- D3 cluster within a dimeric or tetrameric protein and suggest that this cluster may be an important element of the copper transfer machinery. D3 cysteine-to-selenocysteine mutants of wild-type and D1 mutants of hCCS were constructed to investigate the D3 copper cluster in more detail. These mutants display similar activity to wild-type protein. The structure of the Cu centers of selenocysteine-containing mutants as shown by Cu EXAFS is similar to that of wild-type protein, with clear indications of a Cu cluster. Cu and Se EXAFS of these constructs reveal a unique adamantane-like cluster formed between two molecules of CCS at the D3-D3 interface. These results confirm the existence of a D3-D3 copper cluster in hCCS and suggest that a unique copper cluster may exist in this protein.

Chemical vapor deposition (CVD) has been the main method for synthesizing diamond thin films on hetero substrate materials since 1980s. It has been well acknowledged that both nucleation and growth of diamond on non-diamond surfaces without pre-treatment are very difficult and slow. Furthermore, the weak adhesion between the diamond thin films and substrates has been a major problem for widespread application of diamond thin films. Up to now, Si has been the most frequently used substrate for the study of diamond thin films and various methods, including bias and diamond powder scratching, have been applied to enhance diamond nucleation density. In the present study, nucleation and growth of diamond thin films on Ti3SiC2, a newly developed ceramic-metallic material, using Microwave Plasma Enhanced (MPE) and Hot-Filament (HF) CVD reactors were carried out. In addition, synchrotron-based Near Edge Extended X-Ray Absorption Fine Structure Spectroscopy (NEXAFS) was used to identify the electronic and chemical structures of various NCD films. The results from MPECVD showed that a much higher diamond nucleation density and a much higher film growth rate can be obtained on Ti3SiC2 compared with on Si. Consequently, nanocrystalline diamond (NCD) thin films were feasibly synthesized on Ti3SiC2 under the typical conditions for microcrystalline diamond film synthesis. Furthermore, the diamond films on Ti3SiC2 exhibited better adhesion than on Si. The early stage growth of diamond thin films on Ti3SiC2 by HFCVD indicated that a nanowhisker-like diamond-graphite composite layer, different from diamond nucleation on Si, initially formed on the surface of Ti3SiC2, which resulted in high diamond nucleation density. These results indicate that Ti3SiC2 has great potentials to be used both as substrates and interlayers on metals for diamond thin film deposition and application. This research may greatly expand the tribological application of both Ti3SiC2 and diamond thin films. The results demonstrated that NEXAFS is a reliable and powerful tool to identify NCD films.

Chemical vapor deposition (CVD) has been the main method for synthesizing diamond thin films on hetero substrate materials since 1980s. It has been well acknowledged that both nucleation and growth of diamond on non-diamond surfaces without pre-treatment are very difficult and slow. Furthermore, the weak adhesion between the diamond thin films and substrates has been a major problem for widespread application of diamond thin films. Up to now, Si has been the most frequently used substrate for the study of diamond thin films and various methods, including bias and diamond powder scratching, have been applied to enhance diamond nucleation density. In the present study, nucleation and growth of diamond thin films on Ti3SiC2, a newly developed ceramic-metallic material, using Microwave Plasma Enhanced (MPE) and Hot-Filament (HF) CVD reactors were carried out. In addition, synchrotron-based Near Edge Extended X-Ray Absorption Fine Structure Spectroscopy (NEXAFS) was used to identify the electronic and chemical structures of various NCD films. The results from MPECVD showed that a much higher diamond nucleation density and a much higher film growth rate can be obtained on Ti3SiC2 compared with on Si. Consequently, nanocrystalline diamond (NCD) thin films were feasibly synthesized on Ti3SiC2 under the typical conditions for microcrystalline diamond film synthesis. Furthermore, the diamond films on Ti3SiC2 exhibited better adhesion than on Si. The early stage growth of diamond thin films on Ti3SiC2 by HFCVD indicated that a nanowhisker-like diamond-graphite composite layer, different from diamond nucleation on Si, initially formed on the surface of Ti3SiC2, which resulted in high diamond nucleation density. These results indicate that Ti3SiC2 has great potentials to be used both as substrates and interlayers on metals for diamond thin film deposition and application. This research may greatly expand the tribological application of both Ti3SiC2 and diamond thin films. The results demonstrated that NEXAFS is a reliable and powerful tool to identify NCD films.

This work describes the synthesis of dendrimer-encapsulated nanoparticles (DENs) and the expansion of the characterization ability for these materials. The dendrimer-template method for the synthesis of nanoparticles allows precise control over the size, composition and structure of nanoparticles in the 40-250 atom range. In this size regime, the surface structure of the nanoparticles dominates their catalytic properties. The long term goal of this research is to correlate the structure of these nanoparticles to their catalytic activity, improving the ability to predict superior catalysts a priori. As a prerequisite for this analysis, the precise structure of the catalytically active nanoparticle must be determined. Characterization of nanoparticles in the 1-2 nm region is significantly more difficult than more commonly used nanoparticles of 3-5 nm diameter or larger. Typical characterization of these nanoparticles involves UV-vis spectroscopy for Mie absorbance and transmission electron microscopy for size analysis. This work involves the use of extended X-ray absorption-fine structure (EXAFS) to determine the local structure of the nanoparticles. For monometallic Pt DENs, EXAFS was combined with UV-vis, TEM, X-ray photoelectron spectroscopy (XPS) and electrochemistry to determine that the Pt system is not simply nanoparticles but a more complex, bimodal state. EXAFS has also been used to differentiate between different bimetallic structures. For PdAu DENs, there are two synthetic methods used. When both metals are reduced simultaneously, the resulting nanoparticles have a quasi-random alloy structure. These nanoparticles were then extracted from the dendrimer into an organic solvent by use of alkanethiols. The extraction process changed the alloy structure into Au-core/Pd-shell. When Pd and Au were reduced in sequence, the DENs were formed as a Au-core/Pd-shell material, regardless of the order of the reduction of the metals. The Au-core/Pd-shell structure was also present after extraction. In addition to structural analysis to determine the result of different synthetic methods, EXAFS was also used in situ to measure the structure of Pt DENs during the oxidation of absorbed CO. These in situ measurements are important for determining the structure of the actual catalyst rather than the precursor nanoparticle. In this case, the Pt DENs changed from a bimodal distribution into fully reduced nanoparticles by the application of a reducing potential. The binding of CO to the Pt DENs and subsequent oxidation did not cause measurable agglomeration of the nanoparticles. This reduction of the Pt system by electrochemical means was also explored as a synthetic method. The Pt-dendrimer complex was placed on a TEM grid for electrochemical treatment. A potential step was shown to reduce some of the Pt-dendrimer complexes into Pt nanoparticles of the expected size. However, most of the complexes were not reduced. Therefore, only the standard chemical reduction followed by electrochemical treatment is sufficient to fully reduce the nanoparticle samples. This work has explored additional synthetic methods for the synthesis of monometallic and bimetallic DENs. The use of EXAFS, as well as other advanced characterization techniques, has advanced knowledge of the structure of various DENs. Both the characterization toolset and the synthetic methods will provide a basis for investigations of catalytically active materials. / text

In the present thesis the electronic properties of two organic molecules were studied by means of density functional theory (DFT) in connection to their possible applications in organic photovoltaics and molecular spintronics respectively. The first analysed system is the C60 derivative PCBM extensively used in polymer solar cells for the charge separation process. Since fullerenes have been shown to undergo modifications as a result of light exposure, investigating their electronic structure is the first step in elucidating the photodegradation process. The electronic excitations from core levels to unoccupied molecular orbitals reveal not only the empty level structure of the molecule, but provide additional information related to the chemical bonds involving a specific atom type. In this way, they represent a means of determining the chemical changes that the molecule might withstand. The electronic transitions from carbon 1s core levels to unoccupied states are explained for the unmodified PCBM by a joint theoretical (DFT) and experimental study using the near edge x-ray absorption fine structure (NEXAFS) spectroscopy. The second investigated system is the transition metal phthalocyanine with a manganese atom as the metal center. Manganese phthalocyanine (MnPc) is a single molecular magnet in which the spin switch process can be triggered by various methods. It has been shown, for instance, that the adsorption of hydrogen to the Mn center changes the spin state of the molecule from 3/2 to 1. More interestingly, the process is reversible and can be controlled, opening up the possibility of using MnPc as a quantum bit in magnetic memory devices. Up to this date, the d orbital occupation in MnPc has been under a long debate, both theoretical and experimental studies revealing different configurations. In this thesis the electronic structure of the phthalocyanine is thoroughly analysed by means of DFT and the calculated results are compared to photoelectron spectroscopy measurements. The combination of theoretical and experimental tools reveals that in gas phase at high temepratures the molecule exhibits a mixed electronic configuration. In this light, the possible control of the specific electronic state of the central metal represents an interesting prospect for molecular spintronics.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (p. [151]-156).