<p>Silicon ceramics are popular in both commercial applications and material research. The purpose of this thesis is to present measurements and analysis of four different silicon ceramics: á, â and ã phases of silicon nitride and silicon oxynitride using soft x-ray spectroscopy, which analyses the electronic structure of materials by measuring the absorption and emission of x-ray radiation. Absorption and emission spectra of these materials are presented, many of which have not be previously documented. The results are compared to model spectra and together they provide information about the electronic structure of the material.</p><p>Assignments of emission features to element, orbital, and site symmetry are performed for each material. Combinations of silicon and nitrogen emission spectra provide insight into the strained bonding structure of nitrogen. It is concluded that p-dð interaction plays a role in the bonding arrangement of nitrogen and oxygen sites within these structures. The emission features of non-equivalent silicon sites within ã-Si3N4 are identified, which represents some of the first analysis of same element, non-equivalent sites in a material.</p><p>Silicon absorption and emission spectra were plotted on the same energy scale to facilitate measurement of the band gap. Since previously measured band gaps are not well represented in literature, the measured band gaps were compared to values predicted using DFT calculations. The band gap values are in reasonable agreement to calculated values, but do not vary as widely as predicted.</p>

Analysis of the electronic structures of nitrogen-doped, amorphous carbon samples and of nanodiamond films are carried out in order to determine their sp2 bonding concentration. The amorphous carbon samples under consideration are deposited onto polytetrafluoroethylene (PTFE) polymer substrates by hot wire plasma sputtering of graphite in varying nitrogen concentration atmospheres. The deposition or modification of the substrates surface may lend itself to increasing hardness and wear resistance. Eventually these polymer substrates may be used for applications in the field of biomaterials, focusing on cardiovascular surgery, where a low blood/surface interaction is important. The primary technique used in this study is x-ray absorption spectroscopy, measured at the Advanced Light Source synchrotron at the Lawrence Berkeley National Laboratory, Berkeley, USA. A method of analyzing these spectra was then developed to determine the sp2 bonding concentrations in carbon films. Through this newly developed analysis method, the sp2 bonding concentrations in these samples increases from 74 to 93% with growing nitrogen doping. The diamond films presented here are deposited on silicon wafer substrates in a methane atmosphere by microwave plasma deposition. Various deposition conditions, such as bias voltage and methane atmosphere concentration, affect the purity of the diamond film. This analysis reveals sp2 bonding concentrations in these samples from, typically, a few percent to 25%.

Analysis of the electronic structures of nitrogen-doped, amorphous carbon samples and of nanodiamond films are carried out in order to determine their sp2 bonding concentration. The amorphous carbon samples under consideration are deposited onto polytetrafluoroethylene (PTFE) polymer substrates by hot wire plasma sputtering of graphite in varying nitrogen concentration atmospheres. The deposition or modification of the substrates surface may lend itself to increasing hardness and wear resistance. Eventually these polymer substrates may be used for applications in the field of biomaterials, focusing on cardiovascular surgery, where a low blood/surface interaction is important. The primary technique used in this study is x-ray absorption spectroscopy, measured at the Advanced Light Source synchrotron at the Lawrence Berkeley National Laboratory, Berkeley, USA. A method of analyzing these spectra was then developed to determine the sp2 bonding concentrations in carbon films. Through this newly developed analysis method, the sp2 bonding concentrations in these samples increases from 74 to 93% with growing nitrogen doping. The diamond films presented here are deposited on silicon wafer substrates in a methane atmosphere by microwave plasma deposition. Various deposition conditions, such as bias voltage and methane atmosphere concentration, affect the purity of the diamond film. This analysis reveals sp2 bonding concentrations in these samples from, typically, a few percent to 25%.

<p>Silicon ceramics are popular in both commercial applications and material research. The purpose of this thesis is to present measurements and analysis of four different silicon ceramics: á, â and ã phases of silicon nitride and silicon oxynitride using soft x-ray spectroscopy, which analyses the electronic structure of materials by measuring the absorption and emission of x-ray radiation. Absorption and emission spectra of these materials are presented, many of which have not be previously documented. The results are compared to model spectra and together they provide information about the electronic structure of the material.</p><p>Assignments of emission features to element, orbital, and site symmetry are performed for each material. Combinations of silicon and nitrogen emission spectra provide insight into the strained bonding structure of nitrogen. It is concluded that p-dð interaction plays a role in the bonding arrangement of nitrogen and oxygen sites within these structures. The emission features of non-equivalent silicon sites within ã-Si3N4 are identified, which represents some of the first analysis of same element, non-equivalent sites in a material.</p><p>Silicon absorption and emission spectra were plotted on the same energy scale to facilitate measurement of the band gap. Since previously measured band gaps are not well represented in literature, the measured band gaps were compared to values predicted using DFT calculations. The band gap values are in reasonable agreement to calculated values, but do not vary as widely as predicted.</p>

Nowadays, material, energy and information technologies are three pillar industries. The materials that have close relation with our life have also been the foundation for the development of energy and information technologies. As the new member of the material family, functional molecular materials have become increasingly important for many applications, for which the design and characterization by the theoretical modeling have played the vital role. In this thesis, three different categories of functional molecular materials, the endohedral fullerenes, the fullerene derivatives and the self-assembled monolayers (SAMs), have been studied by means of first principles methods. The non-metal endohedral fullerene N@C60 is a special endohedral fullerene that is believed to be relevant to the construction of future quantum computer. The energy landscape inside the N@C60 has been carefully explored by density functional theory (DFT) calculations. The most energy favorable potential energysurfaces (PESs) for the N atom to move within the cavity have been identified. The effect of the charging on the PESs has also been examined. It is found that the inclusion of dispersion force is essential in determining the equilibriumstructure of N@C60. Furthermore, the performance of several commonly useddensity functionals with or without dispersion correction has been verified for ten different endohedral fullerenes A@C60 with the atom A being either reactive nonmetal or nobel gases elements. It shows that the inclusion of the dispersion forcedoes provide better description for the binding energy (BE), however, none ofthem could correctly describe the energy landscape inside all the ten endohedral fullerenes exclusively. It thus calls for the further improvement of current density functionals for weak interacting systems. Soft X-ray spectroscopy is a powerful tool for studying the chemical and electronic structures of functional molecular materials. Theoretical calculations have been proven to be extremely useful for providing correct assignments for spectraof large systems. In this thesis, we have performed first principles simulations forthe near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of fullerene derivatives and aminothiolates SAMs. Our calculatedspectra can accurately reproduce experimental results available for all the systemsunder investigations, and identify the species or structures that are responsible for those unexpected spectral features observed in experiments. We have suggested a modified building block (MBB) approach that allows to calculate NEXAFS spectraof a large number of fullerene derivatives with very small computational cost, and resolved the long standing puzzle around the experimental XPS and NEXAFS spectra of SAMs with aminothiolates. / <p>QC 20120523</p>

This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio. The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics. Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage. Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules. / QC 20110404