Different gel matrices were explored to extend the use of two dimensional (2D) gel electrophoresis for peptide analysis. Excellent separations of peptides labeled with the fluorescent dye Cascade Yellow were achieved in one dimension on two gel media: traditional polyacrylamide and reversible liquid crystalline gels of Pluronic F127. Separations on both media depended primarily on size to charge ratio, excepting a few peptides strongly retained by Pluronic F127. A unique 2D gel electrophoresis system for peptide separation coupled with MALDI-TOF mass spectrometry for identification was developed. Cascade Yellow succinimidyl ester, an amine-reactive dye, labels the amino-terminus of peptides and the å-amino group of lysines at pH 7-9. Occasional labeling of tyrosine residues was also observed. Specific amino-terminal labeling was achieved at alkaline pH (pH >10) due to the base-lability of the å-amino and the tyrosine adducts. The 2D system utilized 15% polyacrylamide with the basic (pH 8.3) Laemmli buffer system (without SDS) in the first dimension. Pluronic F127 (24%) was used in the second dimension with acidic Tris-ClCH2COOH buffer (pH 3.0). The second dimension in Pluronic F127 was done horizontally with a thin overlayer of buffer to provide direct access to the separated peptides. Due to its semi-fluid nature, Pluronic F127 provided a good interface between the two dimensions so that the peptides migrated smoothly from the first dimension to the second. The peak capacity of the 2D mini-gel system (8x10 cm) was approximately 500. Larger gels are expected to yield a peak capacity of about 2000, competitive with many 2D HPLC methods. MALDI-TOF MS was used to identify peptides in spots directly sipped from gels. Peptide samples with concentrations > 0.5 ìg/ml were directly spotted on MALDI targets and identified without further purification. Small polymer chains contaminating Pluronic F127 started to interfere with the detection of peptides at concentrations 10) due to the base-lability of the å-amino and the tyrosine adducts. The 2D system utilized 15% polyacrylamide with the basic (pH 8.3) Laemmli buffer system (without SDS) in the first dimension. Pluronic F127 (24%) was used in the second dimension with acidic Tris-ClCH2COOH buffer (pH 3.0). The second dimension in Pluronic F127 was done horizontally with a thin overlayer of buffer to provide direct access to the separated peptides. Due to its semi-fluid nature, Pluronic F127 provided a good interface between the two dimensions so that the peptides migrated smoothly from the first dimension to the second. The peak capacity of the 2D mini-gel system (8x10 cm) was approximately 500. Larger gels are expected to yield a peak capacity of about 2000, competitive with many 2D HPLC methods. MALDI-TOF MS was used to identify peptides in spots directly sipped from gels. Peptide samples with concentrations > 0.5 ìg/ml were directly spotted on MALDI targets and identified without further purification. Small polymer chains contaminating Pluronic F127 started to interfere with the detection of peptides at concentrations 0.5 ìg/ml were directly spotted on MALDI targets and identified without further purification. Small polymer chains contaminating Pluronic F127 started to interfere with the detection of peptides at concentrations / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Fall semester, 2004. / Date of Defense: October 27, 2004. / Cascade yellow, peptidomics, proteomics, gel electrophoresis, pluronic F127, mass spectrometry / Includes bibliographical references. / Randolph L. Rill, Professor Directing Dissertation; David H. Van Winkle, Outside Committee Member; John G. Dorsey, Committee Member; Joseph B. Schlenoff, Committee Member.

Polymers are a group of materials composed of molecules which have long sequences of atoms linked to each other by covalent bonds. They have existed in natural forms since life began; however, in 1910 Leo Baekeland produced bakelite, a phenolformaldehyde resin, which became the first commercialized fully-synthetic polymer. Nevertheless, it took another decade for scientists to truly accept the unusual properties of polymers as well as the forces that accompany them. The attractive forces between polymer chains play a large part in determining the polymer's properties. Because polymer chains are so long, these inter-chain forces are amplified far beyond the attractions between conventional molecules. In addition, the more entangled and elongated the chains are, the more amorphous is the polymer. Polymer chain length can be attributed to the monomer content within its structure. If the monomer is able to polymerize with a crosslinking agent, then this new macromolecule can be referred to as a gel. The gel is a semi-rigid mass of a lyophilic sol in which all the dispersion medium has penetrated into the sol particles. A particular class of gels, hydrogels, are hydrophilic polymer networks, which can take up large volumes of water and swell while retaining their shape. These materials are usually formed by radical polymerization of hydrophilic monomers and cross-linkers that dissolve in aqueous medium. The cross-linker can be a bifunctional monomer forming a network during polymerization. Depending on the particular chemical structure, these swollen networks display different properties due to external stimulation. The goal of this dissertation is the preparation of poly [N-(2-hydroxypropyl) methacrylamide] (PHPMA) hydrogels in which the typically random polymer network is altered to arrays of parallel channels. One particular application is to use the PHPMA hydrogels as templates for nerve cells. Ideally, the diameter of these channels should match the archetypal diameter of neuronal cell bodies or axons in order to provide a maximal internal surface area. With that aim in mind, we devised and optimized an experimental technique in which a modified HPMA-pregel solution is polymerized and cross-linked in the presence of an externally applied electric field. In addition, the effects of the porogen, polyethylene glycol, on the efficacy of channel formation, swelling dynamics, and the mechanical and structural characteristics of the resulting material are investigated. In conjunction with the aforementioned goal, we also functionalized the PHPMA hydrogels by incorporating Poly-L-Lysine into the polymer matrix. Poly-L-Lysine, a highly positively charged amino acid chain, is commonly used as a coating agent to promote cell adhesion in culture. Poly-L-Lysine will be used as a subbing solution in the biocompatible scaffolds that will serve as a host for mammalian olfactory bulb neurons. The research outlined above represents the major focus of this dissertation. The long-term goal was to enhance prosthetics in the area of biomedical engineering. Moreover, the dissertation is complemented by the description of two minor projects that (a) describe the creation of a mesoporous silica monolith containing oriented macroporous channels and (b) document light-scattering measurements of Belousov-Zhabotinsky(BZ) solutions in sodium bis (2-ethylhexyl) sulfosuccinate(AOT) water-in-oil microemulsions. The latter data should be helpful for understanding non-equilibrium Turing patterns in BZ-AOT systems. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Summer Semester, 2007. / Date of Defense: April 23, 2007. / Hydrogel, Polymer, Spinal Cord, Nerve Conduits / Includes bibliographical references. / Oliver Steinbock, Professor Directing Dissertation; Paul Q. Trombley, Outside Committee Member; Robert L. Fulton, Committee Member; Albert E. Stiegman, Committee Member.

Zeolite structures consist of a negatively charged, porous, aluminosilicate framework with the ability to ion exchange its charge balancing cations. However, problems associated with traditional methods of aqueous ion exchange can adversely affect the behavior and the industrial quality of these zeolites. In this work, an alternative to traditional ion exchange media was explored. Poly ethylene glycol (PEG) oligomers are known to dissolve and transport cations; therefore it was theorized that these solvents could be used to mobilize and exchange ions into zeolite structures. The theory was first tested with the ion exchange of Li+ for Na+ into hydrated and dehydrated sodalite using a series of PEG oligomers with different chain lengths and end groups. The outstanding results from this phase of work, with over 90% Li ion exchange, prompted its continuation with the exchange of catalytically active transition metal ions (Mn2+, Fe2+, and Co2+) into hydrated and dehydrated Zeolite X. Use of these oligomer solvents helped maintain the zeolite structure and allowed for a maximum of 91% ion exchange under hydrated conditions. Although more extensive oligomer incorporation under dehydrated conditions allowed for only 6% exchange, the catalytic activity of these samples was vastly improved over traditionally exchanged samples. The maximum turnover frequency of dehydrated Mn oligomer exchanged samples toward decomposition of NO was 2.37 x 10-2 s-1, whereas that of hydrated Mn aqueous exchanged samples was 9.67 x 10-4 s-1. Parallel ion exchange experiments involving luminescent rare earth metals (Nd3+ and Er3+) gave similar positive results. In addition, data from Raman spectroscopy indicated that while the aqueous exchange method promoted rare earth framework substitution, the oligomer solvents maintained exchange into the zeolite cages. The optimal conditions provided by the oligomer exchange method allowed for improved luminescence of the RE ions. Given its success, this method has been extended to the ion exchange of layered oxides, such as perovskites and cobaltates. Although this work has just begun, promising initial data indicate the possibility of continuing this work far into the future. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Fall Semester, 2009. / Date of Defense: October 12, 2009. / Poly(Ethylene Glycol) Oligomers, Ion Exchange, Layered Oxides, Porous Oxides, Zeolites / Includes bibliographical references. / Susan E. Latturner, Professor Directing Dissertation; Bruce R. Locke, University Representative; Albert E. Stiegman, Committee Member; Naresh Dalal, Committee Member.

The Baldwin rules provide a robust guideline for predicting the favorability of ring closure of reactive intermediates based upon stereoelectronic considerations. Our group was intrigued by the lack of examples of 5-endo-dig cyclizations with carbon-centered radicals, particularly because these reactions were suggested to be favorable according to the Baldwin rules and to our previous computational investigations using density functional analysis. We therefore set out to fill the gap in the arsenal of radical C-C bond forming processes by using computational data to design a new radical process. The first part of this thesis describes our studies aimed at the discovery of the first efficient 5-endo-dig cyclization of a carbon-centered radical. This is followed by experimental design and synthesis of substrates and finally reaction conditions which yield products through this novel mode of cyclization. The second part of this thesis explores the synthetic utility of the cyclized cyclopentene bromosulfone products. First, background information for the preparation and utility of vinyl sulfones is provided. This is followed by our results for derivatization of the bromide functional group of our cyclopentene bromosulfone products. Proper design of substrates and reaction conditions has allowed the 5-endo-dig radical cyclizations to finally become an experimental reality after more than forty years since the original prediction. The cyclized products which are enriched with functionality have been transformed into a variety of other products, emphasizing the importance of this discovery. / A Dissertation submitted to the Department of Chemistry & Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Fall Semester, 2009. / Date of Defense: July 22, 2009. / Cyclization, Endo, Dig, Radical, 5-Endo-Dig / Includes bibliographical references. / Igor Alabugin, Professor Directing Dissertation; William Landing, University Representative; Gregory Dudley, Committee Member; Brian Miller, Committee Member.

Liquid chromatography, particularly reversed-phase liquid chromatography (RPLC), is a ubiquitous analytical method throughout various industries. It has proven vital to the regulatory framework of agencies worldwide to ensure product quality and safety. With traditional RPLC, organic modifiers (e.g. acetonitrile, methanol, tetrahydrofuran) are generally used in conjunction with water to form a mobile phase with sufficient eluotropic strength to elute analytes of interest from the chromatographic stationary phase to the detector employed for the liquid chromatography system. The organic modifiers used are costly as the analyst must pay not only to procure them but also to safely dispose of them. Additionally, the organic modifiers are usually toxic and flammable. The use of 100% water as a chromatographic mobile phase would present an attractive alternative, however, ambient water is far too polar in most instances to be of much use as a mobile phase for RPLC. Subcritical water, considered in the present work to be water at a temperature greater than 100°C with sufficient pressure applied to keep it within the liquid state (but still below the supercritical point), has been proposed as an alternative to traditional organic modifiers due to the apparent similarities in polarity between subcritical water and traditional organic modifiers. The present work explores the differences between RPLC using subcritical water and traditional organic modifiers. Thermodynamic data presented indicates that there are differences in the analyte retention process between the two systems. Retention in subcritical water is characterized by large, favorable enthalpy of transfer values and unfavorable entropic constributions to retention. Traditional RPLC shows favorable (to a lesser degree) enthalpic contributions to retention with negligible or not as unfavorable entropic contributions to retention. From the thermodynamic data, as well as subsequent linear solvation energy relationship analysis, the differences are attributed primarily to a large disruption in the hydrogen bonding network in water at elevated temperature, as well as the lack of sorbed organic modifier in the stationary phase (increasing dispersive interactions of the analyte with the stationary phase) when using 100% subcritical water as a mobile phase. Selectivity for a shape-constrained analytes is also shown to decrease when using subcritical water mobile phases, likely due to a decrease in conformational ordering of the stationary phase at elevated temperatures. Reduced ordering of the stationary phase coupled with an unfavorable entropy change upon retention also strongly suggests that a significant amount of disordering occurs in the pure water mobile phase at elevated temperatures. Later studies were aimed at estimating the retention factor in pure water, k'w, using a high temperature to low temperature extrapolation. Analysis of the results of this study revealed such an extrapolation is not comparable to the more traditional organic modifier fraction extrapolation to 100% water due to an underestimation of the hydrogen bond donating ability of the subcritical water system during the extrapolation. Finally, subcritical water as an extractions solvent with subsequent analyte focusing is explored. It is shown that it is feasible to re-focus a chromatographic peak using the unique properties of subcritical water with very modest instrumentation. Additionally, differences in effective selectivity were demonstrated resulting from on-column migration of the focused peak. Potential applications of this technique are also discussed. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Fall Semester, 2010. / Date of Defense: August 17, 2010. / Lipophilicity, Octanol/Water Partitioning, Shape Selectivity, Hot Water Chromatography, Superheated Water, Subcritical Water, Retention Thermodynamics, Liquid Chromatography / Includes bibliographical references. / John G. Dorsey, Professor Directing Dissertation; Shridhar Sathe, University Representative; André M. Striegel, Committee Member; Michael G. Roper, Committee Member; Oliver Steinbock, Committee Member.

Arginine kinase buffers cellular ATP levels by catalyzing reversible phosphoryl transfer between ATP and arginine. A conserved cysteine has long been thought important in catalysis. Here, cysteine 271 of horseshoe crab arginine kinase has been mutated to serine, alanine, asparagine, or aspartate. Catalytic turnover rates were 0.02-1.0% of wild type, but the activity of uncharged mutations could be partially rescued with chloride. Steady state binding constants were slightly increased, more so for phospho-L-arginine than ADP. Substrate binding synergy observed in many phosphagen kinases was reduced or eliminated in mutant enzymes. The crystallographic structure of the alanine mutant at 2.3Å resolution, determined as a transition state analog complex with arginine, nitrate, and MgADP, was nearly identical to wild-type. Enzyme–substrate interactions are maintained as in wild-type, and substrates remain at least roughly aligned for in-line phosphoryl transfer. Homology models with serine, asparagine, or aspartate replacing the active site cysteine similarly show only minor structural changes. Most striking, however, is the presence in the C271A mutant crystallographic structure of a chloride ion within 3.5Å of the non-reactive Nη substrate nitrogen, approximating the position of the sulfur in the wild-type's cysteine. Together the results contradict prevailing speculation that the cysteine mediates a substrate-induced conformational change, confirm that it is the thiolate form that is relevant to catalysis, and suggest that one of its roles is to help enhance the catalytic rate through electrostatic stabilization of the transition state. / A Dissertation submitted to The Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Degree Awarded: Summer Semester, 2004. / Date of Defense: April 5, 2004. / Includes bibliographical references. / Michael Chapman, Professor Directing Dissertation; W. Ross Ellington, Outside Committee Member; Michael Blaber, Committee Member; Timothy Cross, Committee Member; Alan Marshall, Committee Member.

Single-walled carbon nanotubes and graphene are tunable for chemical sensors and field effect transistors (FETs). In order to tune the electronic, structural, and optical properties of these nanomaterials, covalent and noncovalent functionalization has been effective. Covalent functionalization of graphene and carbon nanotubes have many advantages but may greatly compromise the organized rc-electron network within their honey-comb lattice structures. On the other hand, noncovalent functionalization affords the opportunity to maintain the sp2-hybridized planar network of carbons with extended % conjugation, which makes it an ideal material for electronics applications, even though significant impact on the electronics of these systems may not be achieved. This work features theoretical investigations of both covalent and noncovalent interactions between chemicals and the surfaces of carbon nanotubes and graphene. Both experimental and theoretical investigations have shown that metallic singlewalled carbon nanotubes (SWNTs) have strong interactions with large aromatic molecules, such as pyrene, via tt-ti; stacking. However, pyrene molecules are not effective as dopants of graphene and carbon nanotubes. Polar derivatives of pyrene, however, have been demonstrated to both bind and modulate the properties of graphene. This is a particularly useful tool in biomimetics research. Also, because as-prepared carbon nanotubes are found in 2:1 bundles of metallic to semiconducting tubes, it is crucial that they are separated into tubes of similar type in order to better serve their functions in electronics applications. Experimental studies have shown that pyrene-azo compounds can selectively differentiate between carbon nanotube by (n,m) chirality and type. This project uses first-principles density-functional calculations to investigate mechanisms of interactions between these pyrene compounds and carbon nanomaterials, which will help to further elucidate binding mechanisms. The binding of radical groups such as hydrogen or fluorine to the surface of graphene, leads to covalent bond formation and the subsequent changing of orbital hybridization from trigonal (sp2) to tetragonal (sp3). Such a transformation drastically modifies graphene's electronic properties, which leads to the opening of a band gap through the removal of the bands near the Fermi level of pristine graphene. A similar phenomenon occurs as a result of covalent functionalization of carbon nanotubes, which has many electronics applications. Using first-principles density-functional calculations, we have investigated the structural and electronic properties of fluorinated graphene as well as carbon nanotubes treated with fluorinated olefins in order to better understand their reaction mechanisms and comparisons to previous experimental work are provided.

As green technology advances, the need for cheaper, stronger permanent magnets becomes more and more vital everyday. Electric motors, like those used in wind turbines and electric cars, rely heavily on Dy doped Nd2Fe14B in order to achieve the required efficiencies to be successful, however both Nd and Dy are expensive rare-earth elements that the field is trying to move away from relying on. In order to approach this issue, many are trying to combine these powerful permanent magnets with cheaper and more abundant soft magnetic materials in order to create exchange-spring magnets. While exchange coupling behavior has been studied for several decades now, there are major issues with controlling the uniformity in the generated materials leading to a limited understanding of the properties of these assemblies. In order to address both of these issues at the same time, we devised an approach to create a hard magnetic nanoparticle of fcc-FePt, which was then shelled with the soft magnet Co. In order to gain the desired control of the final core@shell particles, a mix and round bottom and microwave heating was utilized, the synthetic details of which are laid out in Chapter 2. Chapter 3 lays out the results from applying a layer-by-layer shell of Co onto a constant 5 nm FePt particle. From this shelling, the transition from hard-exchange to exchange-spring to decoupling of the core@shell system can be observed. The limit of these regions were found to be very small, with the hard-exchange regime only being in the case of shell sizes smaller than 1.4 nm and decoupling occurring in the materials with >2nm of Co shelled on. This limited range is due to cobalt’s short range coupling, which can not support strong coupling beyond 3-4 layers of Co. / A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester 2017. / November 20, 2017. / Exchange-spring, Materials Synthesis, Nanomaterials / Includes bibliographical references. / Michael Shatruk, Professor Co-Directing Dissertation; Geoffrey F. Strouse, Professor Co-Directing Dissertation; Peng Xiong, University Representative; Joseph Schlenoff, Committee Member.

Organic semiconductors such as polypyrrole, polyalkylthiophenes and polyanilines are being used as alternatives to current materials for electromagnetic interference (EMI) technology. Their production, processability, lightweight construction and cost compare very favourably with those of materials in more established technologies. The project involves the synthesis and purification of the conducting polymers, and the selective use of dopant additives to alter the local structure of the polymer chain, termed as 'doping' in order to produce desired interactions with electromagnetic radiation. Conducting polymers are effectively a new class of microwave absorbing material, and in order to optimise the use of such materials, correlations have been made between the structural variables (e.g. molecular weight, crystal structure, counter-ion size, side-group functionality), the electrical properties ([sigma][sub]dc, [epsilon]*) and the magnetic properties ([mu]*) Polythiophenes and polypyrroles were synthesised using both chemical and electrochemical methods; however, it was found that the chemical methods were more effective, as more processable, soluble and therefore lower molecular weight materials were produced as opposed to the brittle insoluble high molecular weight materials. This allows the manipulation of subtle properties of the conducting polymer such as [epsilon]', [epsilon]", [mu]' or [mu]" in order to enhance the lossy behaviour. These materials were doped to a wide range of conductivities, ranging from the undoped insulating state usually associated with polymers, through a semiconducting up to a metallic state, with conductivities comparable to that of copper. As the conductivity changed, it was found that the electromagnetic radiation could either be transmitted through the polymer material in the insulating state, or be reflected from the material in the conducting state. The intermediate semiconducting form had a maximum absorption of the electromagnetic radiation. The real and imaginary dielectric and magnetic constants of the conducting polymer were measured at microwave frequencies, using a vector network analyser. These conducting polymers were also arranged in a sandwich structure, together with other components with the aim of providing a lightweight, durable and portable device that may be switched 'on' or 'off' under the potentiostatic control, providing a method of controlling the radiation throughout of the device at optical and microwave frequencies. The rate of switching the reflective and transmissive states more conventionally known as the doped and undoped states respectively was controlled by the ionic volume of the dopant ions. The ionic value of dopant ions was determined to be < 1.8x10[sup]-27m[sup]3 based on using a variety of dopant ion volumes and measuring the diffusion coefficients. This device was constructed using a variety of techniques to determine which arrangement would confer the fastest switching time and give the best 'radiation absorbing characteristics'. A variety of conducting polymers, electrode and electrolyte combinations were used in order to fabricate a lightweight and portable device that could be made to interact with the incident electromagnetic radiation. This project investigates the effect of electromagnetic absorption with paramagnetic metal ion complexation to conducting polymers. Current electromagnetic absorption technology addresses either the electric component or the magnetic component of the electromagnetic wave. It has been established that an oscillating electromagnetic field is absorbed to some extent by conducting polymers by the excitation of the mid-gap states at intermediate doping levels. However, this addresses only the electric component of the electromagnetic wave. By complexing paramagnetic ions within the polymer chain, it is expected that this will provide additional electromagnetic absorption. With the electrochromic properties of conducting polymers being well understood, it is also the aim of this project to use the complexed conducting polymer to switch between the conducting and insulating state under the user's control. It is therefore of interest to find the limiting factors affecting the rate of switching. It was found that the complexation of magnetic ions into the polymer contributed to electromagnetic absorption by providing additional loss mechanisms for the incident radiation. Low conductivity materials that were doped to 3-5 mol% and were governed by DC conduction processes were the best absorbers of the electromagnetic radiation.

Over the past number of years, polymers with delocalised [pi]-orbitals have been of interest due to their electrical conducting properties. Exposing these polymers to electron donating or accepting dopants, remarkably alters the nature of these materials. In this project it was planned to synthesise and investigate the physical and chemical and electrochemical properties the "polyquinoxaline" family of materials. In order to investigate these materials, synthesis of 5,14-dihydro-5,7,12,14-tetraazapentacene(L5H[sub]2),7,16-dihydro-5,7,9,14,16,18-hexaazaheptacene (L7H[sub]2),7,20-dihydro-5,7,9,11,16,18,20,22-octaazanonacene (L9H[sub]2) and "Polyquinoxaline" (poly[1,6-dihydropyrazino(2,3 -g)-quinoxaline-2,3,8-triyl-7(2H)-ylidene-7,8-dimethylidene was carried out. A number of techniques such as FTIR, solid state NMR, Ultraviolet-Visible spectroscopy have been used in characterising these compounds. Thermogravimetric Analysis and annealing studies of the oligomers were carried out in order to establish optimum crystals growth conditions to aid crystallographic studies. The oligomers (L5H[sub]2) and (L7H[sub]2) were vacuum evaporated on ITO glass substrate. Studies using cyclic voltammetry (CV), and in-situ spectroelectrochemical techniques were used to measure the electrochromic changes and diffusion kinetics in the oligomers upon doping. A comparison with phenazine (L3) has been made where possible in order to complete the available series.