<p> We have studied the pyrolysis of aromatic combustion intermediates using an array of detection techniques. The molecules investigated include cyclic aromatic molecules with hydrocarbon substituents (ethylbenzene, n-propylbenzene, isopropylbenzene, and styrene), oxygen-containing substituents (anisole and phenol), resonance stabilized radicals (benzyl radical and tropyl radical) and phenyl radical. At the exit of a resistively heated micro-reactor (1 mm inner diameter, 3 cm long), the pyrolysis fragments are detected using photoionization mass spectrometry (PIMS), matrix isolation vibrational spectroscopy, microwave spectroscopy, tunable VUV synchrotron-based PIMS, and tabletop VUV PIMS with photoelectron photoion coincidence spectroscopy (PEPICO). This array of detection methods allows for the identification of all possible fragments including metastables, radicals, and atoms. The findings allow for detailed mechanistic information regarding which pathways are active at different pyrolysis temperatures and can also be used to help identify products and individual isomers that are formed during the gas-phase thermal decomposition of aromatic systems. By providing direct experimental pyrolysis data, models for fuel decomposition and soot formation can be improved to help understand current combustion systems and eventually aid in the design of superior fuel sources in the near future.</p>

<p> One process that has the potential of efficiently harvesting solar energy is singlet fission (SF), a process by which one photon of light can produce two excited states. Investigations of three different series of bistetracene (BT) were used to explore the effect of symmetry on the rate and driving force of SF, as well as the electronic coupling. A dimer and the corresponding monomer were used to build a synthetic infrastructure and explore preliminary photophysics. All of the dimers were connected by one to three norbornyl bridges and exhibit various amounts of electronic coupling.</p><p> The first section of this dissertation will discuss a series of cofacial BT dimers with C_2v symmetry that have one (BT1) to three (BT3) norbornyl bridges linking the two tetracene chromophores. Density functional theory calculations of BT1-BT3 were used to explore the SF driving force and the change in through-space versus through-bond contributions to the electronic coupling. The C_2v symmetry was found to be unprofitable to SF, but vibrations accessible to the ground state would break the C_2v symmetry. The thorough synthetic investigation of the monomeric tetracene-norbornyl bridge was developed to build a synthetic library that aided the synthesis of BT1, the first rigid SF dimer. Preliminary photophysics of BT1 and its monomer will also be described.</p><p> In the second portion of this work, the SF driving force, electronic coupling will be calculated for the second and third series of BT dimers, which are symmetry adaptations of BT1-BT3. In the second series, the orbital overlap of the norbornyl bridge and tetracene arms will be exploited by changing how the bridge and arms are connected to make dimers of C₂ and C_s symmetry. In the final series, a heteroatom substitution of BT1 creates a series of C₂ and C_s dimers that can be built using the synthetic infrastructure developed above. Both symmetry adapted series of BT dimers were found to lead to an increase in electronic coupling, which is expected to be productive for SF.</p>

<p> Electrospray ionization (ESI) is a premier method for volatilizing and ionizing biological analytes for mass spectrometry. In conventional mass spectrometry (MS), the spectrum of mass-to-charge ratio (<i>m/z</i>) for an ensemble of ions is measured. ESI produces a distribution of charges for each ionized species, and the mass of each species is determined by assigning a charge state to each peak in the <i>m/z</i> spectrum. These peaks are difficult to resolve for species above the 100-kDa range because of peak broadening and shifting due to salt adducts, incomplete desolvation, and intrinsic heterogeneity. Without resolved charge states, the mass cannot be determined. Charge detection mass spectrometry (CDMS) offers a solution to this problem. </p><p> In CDMS, both the <i>m/z</i> and the charge are measured simultaneously for individual ions. Multiplying those measurements for each ion yields the mass. Thus, there is no need for charge state resolution in an m/z spectrum. CDMS can therefore be used to measure the masses of extremely heavy and heterogeneous analytes far beyond the capabilities of conventional MS. This comes at the cost of efficiency, since single ions are measured serially, and resolution, since the charge measurement historically has been imprecise in CDMS. </p><p> Here we report a nearly perfect charge measurement in CDMS by analyzing each ion for 3 s in an electrostatic ion trap and implementing a novel analysis method. Then we discuss spontaneous mass and charge losses of trapped ions. Finally, we discuss multiple applications of CDMS to bacteriophage P22. P22 capsids assemble into <i>T = 7</i> &lsquo;procapsids&rsquo; with the assistance of a distribution of scaffolding proteins; we report the typical width of that distribution. Next we report our observation of mass loss in P22 procapsids over the course of weeks due to precipitation of scaffolding proteins. Then we discuss how the charge on electrosprayed P22 capsids allows us to distinguish morphologies of P22 capsids. Finally, we report an accurate mass measurement of the infectious P22 phage, a >50 MDa particle containing nucleic acid and nine kinds of protein.</p>

<p> Enzymes play a crucial role in modern biotechnology, industry, food processing and medical applications. Since their first discovered industrial use, man has attempted to discover new enzymes from Nature to catalyze different chemical reactions. In modern times, with the advent of computational methods, protein structure solutions, protein sequencing and DNA synthesis methods, we now have the tools to enable new approaches to rational enzyme engineering. With an enzyme structure in hand, a researcher may run an <i>in silico</i> experiment to sample different amino acids in the active site in order to identify new combinations which likely stabilize a transition-state-enzyme model. A suggested mutation can then be encoded into the desired enzyme gene, ordered, synthesized and tested. Although this truly astonishing feat of engineering and modern biotechnology allows the redesign of existing enzymes to acquire a new substrate specificity, it still requires a large amount of time, capital and technical capabilities. </p><p> Concurrently, while making strides in computational protein design, the cost of sequencing DNA plummeted after the turn of the century. With the reduced cost of sequencing, the number of sequences in public databases of naturally occurring proteins has grown exponentially. This new, large source of information can be utilized to enable rational enzyme design, as long as it can be coupled with accurate modeling of the protein sequences. </p><p> This work first describes a novel approach to reengineering enzymes (Genome Enzyme Orthologue Mining; GEO) that utilizes the vast amount of protein sequences in modern databases along with extensive computation modeling and achieves comparable results to the state-of-the-art rational enzyme design methods. Then, inspired by the success of this new method and aware of it's reliance on the accuracy of the protein models, we created a computational benchmark to both measure the accuracy of our models as well as improve it by encoding additional information about the structure, derived from mechanistic studies (Catalytic Geometry constraints; CG). Lastly, we use the improved accuracy method to automatically model hundreds of <i>putative</i> enzymes sequences and dock substrates into them to extract important features that are then used to inform experiments and design. This is used to reengineer a ribonucleotide reductase to catalyze a aldehyde deformylating oxygenase reaction. </p><p> These chapters advance the field of rational enzyme engineering, by providing a novel technique that may enable efficient routes to rationally design enzymes for reactions of interest. These chapters also advance the field of homology modeling, in the specific domain in which the researcher is modeling an enzyme with a known chemical reaction. Lastly, these chapters and techniques lead to an example which utilizes highly accurate computational models to create features which can help guide the rational design of enzyme catalysts.</p><p>

<p> Colloidal metal nanoparticles are renowned for their ability to strongly scatter and absorb light due to size- and environment-dependent plasmon modes. Active areas of research focus on using both single and collections of nanoparticles to control the shape of electromagnetic fields on the nanoscale. The excitation of plasmon modes in the nanoparticles confines the energy from incident fields to sub-wavelength scales with distributions controlled by the morphology of the particles, and multiple particles arranged in the near-field can extend the excitation into a collective mode. The excitation of plasmon modes can create enhancements of the field intensity, which have been leveraged for enhancing radiative rates of light-emitting particles and molecules and increasing molecular sensing signals. However, many of these applications rely on electric field enhancements in the near field and using static nanoparticle arrangements. We present extensions to this paradigm, first by exploring the excitation of collective plasmon modes in optically-patterned linear nanoparticle arrays with separations on the order of the wavelength of light, demonstrating new mechanisms for coupling beyond the well-known near-field interactions. The collective excitation over the intermediate-scale arrays is also shown to redirect the scattered light perpendicular to the expected forward scattering. Next, we demonstrate that self-arranged optically bound linear arrays act as optical cavities for co-trapped single-photon emitters, modifying the local density of electromagnetic states in the vicinty of the nanoparticle system. Finally, we probe optically 'dark' modes in a core-satellite nanostructure by exciting magnetic responses separately from electric modes with structured excitation light.</p><p>

<p> Since its discovery in 1985, buckminsterfullerene (C₆₀) has been extensively studied due to its unique properties and it's now being produced in multi-ton quantities. The ability to form stable aqueous C₆₀ colloids (known as nano-C₆₀ or <i>n</i>C₆₀) and the availability of these in natural systems at environmentally-relevant concentrations led to significant interest concerning the environmental health and safety of these colloidal aggregates. Addressing two issues with regard to this material's environmental health and safety concerns we have looked at the oxidative mechanism of these <i>n</i>C₆₀ colloidal aggregates and their thermal stability. For making accurate kinetics and measurements on oxidation caused by aqueous-<i>n</i>C₆₀ colloidal dispersions, we have developed experimental methods utilizing dihydrorhodamine 123 (DHR123) as a sacrificial probe molecule to monitor oxidation by fluorescence spectroscopy and kinetic models to explain observed oxidation. Evaluation of the oxidative behavior of fullerene colloids has been determined using the oxidation rate as a function of <i>n</i>C₆₀ concentration, <i> n</i>C₆₀ surface area, number of colloidal particles and C₆₀O content, operating where necessary under inert atmosphere and oxygen rich conditions. The effect of temperature on these colloids plays a significant role in both their synthesis and reactivity. Given that the colloids are mainly composed of C₆₀ and C₆₀O, C₆₀O might play a significant role in stabilizing the colloid, hence increasing the temperature might cause thermally-activated reactions with C₆₀O. Thermal stability of these colloids prepared by all four primary <i>n</i>C₆₀ synthesis methods has been investigated. Incorporation of C₆₀ into polymers is of potential interest for applications, for sequestration to address potential environmental health and safety issues, and as a component in novel architectures. A new composite material was developed by encapsulating C₆₀ into cross-linked polymer network formed by &gamma;-cyclodextrin. A simple synthesis route to achieve composite membranes of intercalated C₆₀ in the polymer network is presented.</p>

<p> Atomic Layer Deposition (ALD) is a an excellent technique for depositing conformal thin films on complex geometries in layer by layer fashion. The mechanisms of depositing TiO₂, platinum, and ethoxysilane molecules were probed with <i>in situ</i> Fourier transform infrared (FTIR) in order to better understand and improve the process. Each of these studies involves TiO₂. </p><p> There are many uses for thin films of titanium dioxide, a semiconductor and high dielectric material. Current Atomic Layer Deposition (ALD) of TiO₂ generally involves water or ozone, which can oxidize and corrode some substrates of interest. Ritala et al. successfully deposited an assortment of metal oxides using no water, but instead, metal alkoxides and metal halides as precursors. Presented is a study of ALD of titanium dioxide using titanium tetrachloride (TiCl₄) and titanium tetraisopropoxide (TTIP). In situ Fourier transform infrared (FTIR) studies revealed that the mechanism for TiO₂ ALD using titanium tetrachloride and titanium tetraisopropoxide changed with temperature. At temperatures between 250 and 300&deg;, the isopropoxide species after TTIP exposures quickly underwent &beta;-hydride elimination to produce TiOH species on the surface. The observation of propene by quadrupole mass spectrometry supported the &beta;-hydride elimination reaction pathway. Deposition was investigated between 150 and 300&deg; on substrates including zirconia, alumina, and silica. Quartz crystal microbalance results and X-ray reflectivity showed that the system grew 0.5&ndash;0.6 &Aring;/cycle at 250&deg; X-Ray photoelectron studies also confirmed TiO₂ film growth. </p><p> In another aspect of ALD use, self-limiting chemistry assisted with terminating a surface with alkoxysilanes. Tire rubber contains additives such as carbon black or silica particles to provide strength. Although in theory Kevlar fibers would provide strength while lowering the density and increasing car fuel efficiency, in practice Kevlar fibers disperse only very poorly in the rubber, leading to inhomogeneity. In order the increase the mixing likelihood between rubber and Kevlar, the reactions of some sulfurous siloxanes were examined on both aluminum oxide and titanium oxide. The titanium oxide adhesion layer allowed the deposition of molecules on the surface that looked promising for improving mixing with rubber and decreasing the weight of tires. </p><p> Atomic layer deposition offers the possibility of more precision in platinum deposition. In a platinum deposition study, the nucleation and growth of non-conformal platinum on TiO₂ and WO_x powder using Pt(hfac)₂ and formalin was examined with in-situ FTIR and transmission electron microscopy (TEM). Interest in substitution of Pt/C as the oxidation reduction reaction catalyst in polymer electrolyte membrane fuel cells (PEMFCs) led to the ALD synthesis of Pt/WO_x and Pt/TiO₂. A nucleation period on the order of 100 cycles was observed, after which, platinum loading and particle size measurably increased with increasing cycle number. The adsorption of the hfac ligand on the metal oxide substrate effectively inhibits nanoparticle coalescence during the growth phase, which led to further investigation of its use as a site-blocking agent. The results showed that Pt particle distance could be increased with the use of hfacH.</p>

Thesis (Ph. D.)--Indiana University, Dept. of Chemistry, 2008. / Title from PDF t.p. (viewed Oct. 7, 2009). Source: Dissertation Abstracts International, Volume: 70-02, Section: B, page: 1022. Advisers: Mu-Hyun Baik; Kenneth G. Caulton.

<p> Oligonucleotides, short nucleic acids of &ap; 100 bases and under, are therapeutics of great interest because of their ability to regulate gene expression and improve outcomes in diseases like cancer and atherosclerosis. However, they are vulnerable to degradation by enzymes in the body that can limit their effectiveness. Encapsulating oligonucleotides inside core-corona structures called polyelectrolyte complex micelles can be accomplished by mixing them with a block copolymer containing one neutral, hydrophilic block and one charged block. Using a micelle as a vehicle is a powerful way of protecting oligonucleotides while enabling their targeted delivery to a disease site via the attachment of targeting molecules to the micelle corona. Understanding how oligonucleotides interact with charged polymers, and how the polymers themselves affect micelle shape, size, and internal structure, are of fundamental importance to the process of efficiently and intelligently designing these micelles. By combining multiple physical characterization techniques including optical microscopy, FRET, circular dichroism, and FTIR, we can characterize bulk complexes of oligonucleotides with cationic homopolymers. By combining small-angle X-ray scattering, light scattering, and cryogenic transmission electron microscopy (cryo-TEM) we can characterize structures formed when oligonucleotides complex with oppositely charged block copolymers. These multimodal characterization schemes will increase the rigor of our investigations and our confidence in their results. Our main goals are to characterize bulk complexes of oligonucleotides and peptides to gain insight into the fundamentals of oligonucleotide interactions, and to determine what factors control the shape, size, and internal structure of oligonucleotide-polyelectrolyte complex micelles. </p><p>

<p> A novel concept to provide position-sensitivity to a microchannel plate (MCP) is described. While several designs exist to make MCPs position sensitive, all these designs are based upon collection of the electrons. In contrast, this approach utilizes an induced signal as the electron cloud emanates from an MCP and passes a wire plane. We demonstrate the validity of the concept by constructing a device that provides single electron detection with 98 &mu;m position resolution (FWHM) over an area of 50 mm &times; 50 mm. The characteristics of the detector are described through both bench-top tests and simulation. After characterization of the detector, the sense wire detector was utilized for slow-neutron radiography. Furthermore, we utilized our knowledge of position-sensitive techniques to realize a beam-imaging MCP detector useful for radioactive beam facilities.</p><p>