This research had the specific goal of synthesizing a monomer for the development of polymers with unique physical properties. The expected physical property to be pursued is that of an innate elasticity within the monomer itself. As such, bis-1,10-((6-azidohexyl)oxy)bicyclo[8.8.8]hexacosane (target 1) was synthesized with the expectation that the bicyclic core would have the freedom of movement necessary to provide such elasticity. The addition of the azide functional groups to the target molecule may be used in the well known Huisgen 1,3-cycloaddition reaction to form a polytriazole polymer when matched with another monomer containing the requisite terminal alkyne. For this purpose, and further study of the elasticity of the bicyclo[8.8.8]hexacosane core, bis-1,4-((5-hexynyl)oxy)benzene (target 4) was synthesized for the formation of the polytriazole, and bis-1,4-((6-azidohexyl)oxy)benzene (target 5) was synthesized to form a polytriazole analog without the elastic bicycle in the polymeric repeating units.

Students' learning in inquiry-based investigations has drawn considerable attention of the science education community. Inquiry activities can be viewed as knowledge construction processes in which students are expected to develop conceptual understanding and critical thinking abilities. Our study aimed to explore the effect of experiments with different levels of inquiry on students' interactions in the laboratory setting, as well as on students' written arguments and reflections. Our results are based on direct observations of group work in college general chemistry laboratories and analysis of associated written lab reports. The analysis of students' interactions in the laboratory was approached from three major analytic dimensions: Functional analysis,; cognitive processing,; and social processing. According to our results, higher levels of inquiry were associated with an increase in the relative frequency of episodes where students were engaged in proposing ideas versus asking and answering each others' questions. Higher levels of inquiry also favored episodes in which experimental work was approached in a more exploratory (versus procedural) manner. However, no major changes were observed in the extent to which students were engaged in either interpretive discussions of central scientific concepts and ideas. As part of our study we were also interested in characterizing the effects of experiments involving different levels of inquiry on the structure and adequacy of university general chemistry students' written arguments, as well as on the nature of their reflections about laboratory work. Our findings indicate that the level of inquiry of the observed experiments had no significant impact on the structure or adequacy of arguments generated by students. However, the level of inquiry of the experiments seemed to have a major impact on several areas of students' written reflections about laboratory work.In general, our results elicit trends and highlight issues that can help instructors and curriculum developers identify strategies to better support and scaffold productive engagement in the laboratory. Our results suggest that careful design and implementation of instructional interventions may be needed to maximize the learning effects of the more open-ended inquiry activities at the college level.

Rhamnolipids are rhamnose-based glycolipids with strong biosurfactant properties. Because they are naturally occurring surfactants found in Gram-negative bacterial walls, rhamnolipids are biodegradable, low in toxicity and have the potential for bioremediation. However, rhamnolipids are biosynthesized as a large mixture of congeners, making purification poor and scalability difficult. The "green" properties of the compound make it a highly desirable alternative for the many carcinogenic and toxic synthetic surfactants on the market. A method for synthesizing rhamnolipids cost-effectively and at a large scale is highly desirable in a competitive surfactant industry. There is a large amount of literature for glycolipid synthesis, as well as literature for small-scale libraries of rhamnolipid congeners. However, many syntheses involve expensive reagents, dangerous procedures and low-yielding reactions. Therefore, many modifications are made in this dissertation in order to eliminate these problems and limitations. Modifications include standard reduction reactions, easily removable protecting groups and glycosylations utilizing minimally competent Lewis acid promoters. Other techniques involve enantiomer-to-diastereomer conversion for attaining all stereoisomers of the rhamnolipid congeners for comparison and analysis in an efficient manner. A general, cost-effective synthesis for monorhamnolipids is achieved and discussed in the following dissertation. The generality allows for synthesis of glycolipids with different carbohydrates and a variety of primary and secondary lipid alcohols, with varying hydrocarbon chain lengths. Additionally, the synthesis utilizes enantiomer-to-diastereomer conversion via glycosylation for the synthesis and purification of all rhamnolipid diastereomers in a single synthesis. This makes it possible to analyze surface properties and structure-activity relationships of the different congeners and their respective stereochemistry. The synthesis minimizes reaction steps, cost and time required of previously published rhamnolipid syntheses and is general for utilization in the future synthesis of rhamnose- and non-rhamnose-based derivatives, dirhamnolipids, and rhamnolipid polymers.

The modifications of transparent conductive oxides (TCOs) have been studied using an electrochemical evaluation technique (cyclic voltammetry (CV)). Substituted ferrocenes were chemically adsorbed onto the surface of indium tin oxide (ITO) and indium zinc oxide (IZO). The electroactive surface coverage, the redox potential, and the charge transfer rate of the adsorbed modifiers were evaluated using CV. The highest electroactive surface coverage was produced by ferrocene phosphonic acid while ferrocene acetic acid showed the fastest charge transfer rate. The charge transfers with the modified electrodes were evaluated in the presence of a solution electroactive probe. The charge transfer rate of the solution probe was enhanced with the modified electrodes compared to the charge transfer rate measured with unmodified electrodes. Even though the cause of the enhancement in the charge transfer rate is not clear, the results suggest that the modification of TCO may improve the charge collection efficiency of TCO, which is desirable for the application of TCO in devices such as organic photovoltaic cells.

This dissertation focuses on the electrical, structural, and compositional characterization of atomic layer deposited ZnO, and the structural characterization of modified titanyl (TiOPc 6 and TiOPc 9) and copper phthalocyanines (Pc 5). All materials studied have application in organic photovoltaic devices, either as an interlayer (ALD ZnO) or as part of the active layer (TiOPcs and Pc 5). The goals of this research are to advance the understanding of defect chemistry and electronic properties of ALD ZnO after exposure to oxygen plasma, Ar+ sputtering, and aryl phosphonic acid modifications, and to understand the relationship between the chemical structure of modified phthalocyanines and their molecular organization.Based on X-ray photoelectron spectroscopy and photoluminescence, it was determined that the predominant defects in as-received ALD ZnO are zinc vacancies mostly located in the top layer of the ZnO film. Oxygen plasma treatment of as-received ALD ZnO changed the predominant defects to oxygen interstitials, which migrated out of the sample when left exposed in air. Phosphonic acid modification of oxygen plasma treated ALD ZnO was found to suppress the migration of oxygen interstitials from the ALD ZnO sample.Ultraviolet photoelectron spectroscopy was used to study the electronic properties of ALD ZnO. It was determined that surface chemistry strongly influences the work function of ALD ZnO. Oxygen plasma treated ALD ZnO showed the highest work function and as-received ALD ZnO the lowest work function. The phosphonic acid modification of ALD ZnO decreased the work function and surface free energy when compared to oxygen plasma treated ALD ZnO. Near edge X-ray absorption fine structure spectroscopy results showed planes of benzyl rings in aryl phosphonic acid modifiers tilted at approximately 30 - 38° with respect to the surface normal.X-ray diffraction studies on modified phthalocyanines powders and thin films were performed to correlate their chemical composition with their crystal structure. It was determined that strong interactions between molecules lead to higher-order lattices (monoclinic or triclinic). However, upon annealing at higher temperatures, higher-order lattices were transformed to columnar phases because of the side chains incorporated into the modified phthalocyanines.

Solar energy conversion is accomplished by multilayered devices consisting of various conducting and semiconducting materials. Because the layers are only 10s - 100s of nm thick, device behavior is governed primarily by interfacial molecular dynamics that often differ from the bulk behavior of these materials. The thermodynamics and kinetics of the interfacial interactions are particularly interesting, as interfacial electron transfer strongly influence the efficiency of photovoltaics and devices used in solar hydrogen production. This work focuses specifically on interfacial charge transfer processes occurring at three interfaces relevant to thin film organic/inorganic solar energy conversion devices. i) A potential-step polymer electrochemical deposition and doping procedure was developed and used to create poly(3-hexylthiophene) (e-P3HT) interlayer films for organic photovoltaics. Photoelectron spectroscopies suggest that an interface dipole forms spontaneously at the polymer donor/fullerene acceptor interface through partial interfacial charge transfer prior to photoexcitation; this doping-dependent interfacial dipole was correlated to the electrical properties of these critical heterojunctions. ii) Potential-modulated fluorescence spectroscopy (PMF) was developed and used examine the kinetics of the reversible oxidation of the (e-P3HT) films in attempt to elucidate the ITO/e-P3HT charge transfer rates. However, the optical switching increased linearly as the polymer film decreased, indicating that the molecular-level process probed by PMF was rate-limited by counter-ion movement into and out of the polymer film. iii) Potential-modulated attenuated total reflectance spectroscopy (PM-ATR) was used to examine the reversible reduction of CdSe semiconductor nanocrystals tethered to indium tin oxide electrodes as well as the surface-coverage dependent bleaching of these nanocrystals. A new equivalent circuit model describing the CdSe/ITO electrode is proposed, and a PM-ATR simulation program was used to quantify Faradiac resistances to interfacial charge transfer that trend with the magnitude of overpotential. The insights gained through these experiments add to a growing understanding of the fundamental, molecular-level competition between photoinduced charge generation and parasitic charge recombination at these critical interfaces.

The purpose of the research reported in this dissertation is to expand the general knowledge of the chemical properties of monorhamnolipids (produced by P. aeruginosa ATCC 9027) and monorhamnolipid-metal complexes in solution and at interfaces in order to advance the application of these biosurfactants in a variety of applications.The speciation and fragmentation behavior of monorhamnolipids (mRLs) using mass spectrometry at low and high resolution in positive ion mode was investigated as a function of pH, which has yet to be fully discussed to date in the literature. This study laid the groundwork for the speciation and fragmentation behavior of mRLs with two environmentally-relevant heavy metals, Pb²⁺ and UO₂²⁺. It was determined that mRLs form 1:1 and 2:1 mRL-metal complexes with both metal cations across the pH range investigated (pH 4.0, 6.0 and 8.0). mRL-metal complexes were found to fragment differently than free mRLs suggesting coordination of the metal cation in a binding pocket comprised of the mRL carboxylic acid moiety and the rhamnose sugar hydroxyls. This coordination environment was further verified as a function of solution pH using infrared spectroscopy (IR), nuclear magnetic resonance spectrometry (NMR) and hydrogen-deuterium exchange (HDX) mass spectrometry. Adsorption isotherms for mRLs and mRL-metal complexes on two soil components, silica and goethite, were characterized as a function of solution pH using ATR-FTIR and successfully fit to the Frumkin-Fowler-Guggenhiem isotherm to extract relevant thermodynamic adsorption parameters. These studies showed that at low pH, mRLs form bilayers on these surfaces, but the adsorption affinity of the mRLs is dictated by the molecular interactions these species have with the specific oxide surface. At neutral and basic pH values, mRLs were found to adsorb to silica despite the fact that both the surface and the mRLs are negatively charged. The Lewis acid/base interactions of mRLs with goethite at neutral and basic pH values results in multilayer adsorption. Adsorption of mRL-metal complexes on silica and goethite suggests that the interactions between these complexes and soil surfaces may have a direct impact on metal ion remediation efficiencies using mRLs. The adsorption affinity of mRL-Pb²⁺ complexes to silica is greater than that of mRL-UO₂²⁺ complexes; however, mRL-UO₂²⁺ complexes precipitate at the interface. The adsorption affinity of mRL-metal complexes on goethite is not significantly lower than for free mRLs; however, the surface coverage decreases.

This dissertation is focused on the elucidation of the reaction chemistry that governs the low work function metal/organic interface found in organic photovoltaics (OPVs). To this end Raman spectroscopy was used in ultra-high vacuum to study Ag, Mg, Ca, and Al metal vapor deposition on pyridine, C₆₀, and graphene. In an effort to understand the interfacial reaction chemistry of complex organic molecules with metal an approach of systematic deconstruction is used where by small molecules, in this case pyridine can be used to gain insight into the chemistry of various chemical functionalities with minimal spectral complication. In the Ag/pyridine system no reaction was observed and the integrity of the film was preserved with spectral enhancement being the only result. This enhancement is achieved via a weak Ag--N bonding interaction. For the other three metals (Mg, Ca, and Al) a great deal of fascinating reaction chemistry can be observed initiated in each case by metal-to-organic electron transfer resulting in the formation of pyridyl radical anions. Once radicals are formed the reaction pathways for each metal diverge resulting in different specific reaction products. In the case of Mg the pyridyl radicals undergo reductive dimerization and yield 4,4'-bipyridine. For Ca the pyridyl radicals follow two pathways either losing a hydride to form the diradical pyridyne or through a pathway of ring opening degrade into amorphous carbon. These results highlight the vast differences possible for reaction chemistry between metals and organics even for simple molecules. Buckminsterfullerene (C₆₀) and fullerene derivatives are ubiquitous to the field of OPVs, thus an understanding of their metal/organic interfacial chemistry is of critical importance to unlocking the full potential of devices. In a similar manner to what can be observed for Ag/pyridine systems the Ag/C₆₀ system shows little more than surface enhancement effects due to a lack of any substantial reactivity and Mg, Ca, and Al exhibit metal-to-organic charge transfer forming C60 anion radicals. These anion radical react to form an as of yet unidentified reaction product in the case of all three reactive metals and in the case of Al these reaction products further degrade forming amorphous carbon. The understanding of this chemistry can be directly correlated to device data found in the literature and provides insight into the formation of interfacial gape states at the metal/organic interface of OPVs. Due to its unique electrical properties and high degree of mechanical stability graphene is starting to play a significant role in the development of OPVs. Because graphene is being used in contact with vapor deposited metal it is of relevance to understand the chemistry that occurs at this interface. While deposition of Ag onto graphene again shows no reaction and only enhancement the enhancement leads to the identification of unique defects in the graphene lattice namely carbon vacancies and C--C bond rotations which lead to Stone-Wales defects which are likely a result of the graphene growth method. Mg, Ca, and Al show strong evidence for n-type doping of electrons into the graphene film due to their work functions being lower than graphene. This data highlight the stability of graphene showing that even though it undergoes a similar metal-to-organic electron transfer as seen with C₆₀ and pyridine there is no further compromise of the films molecular structure.

<p>In the last two decades, bacterial infections have reemerged as a serious public health threat. In the United States, nosocomial infections alone cost several billion dollars and are responsible for 100,000 deaths annually.3 Of particular concern is the emergence of bacteria with single and multidrug resistance. Infection by such bacteria can be difficult, if not impossible, to treat and cure. In recent years, methicillin-resistant Staphylococcus aureus (MRSA) has emerged as one of the most threatening resistant strains. MRSA infections are now responsible for more deaths each year than AIDS in the United States.4 Due to the multidrug resistance of these "superbugs", new antibiotics with novel mechanisms of action are urgently needed.5</p><p> Unfortunately, although novel antibiotics are needed to stem the resistance crisis, the pipeline for novel antibiotics has narrowed considerably in recent decades.3,6,7 In the last thirty years, only the oxazolidinones and cyclic lipopeptides have been developed as novel antibiotic classes.7 One novel cyclic lipodepsipeptide antibiotic in the clinical pipeline is WAP-8294A2. WAP-8294A2 (Figure 1.0.4) was isolated from the soil bacteria Lysobacter staphylocidin (FERM BP-4900) in Japan in 1997. It is the major component of a mixture of eighteen related compounds, all of which showed antibiotic activity.13 WAP-8294A2 showed strong in vitro antibiotic activity against Gram-positive bacteria including vancomycin-resistant Enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) (Table 1.1).14,15 In vivo assays also showed that WAP-8294A2 has strong activity against known MRSA strains.13 We were interested in gaining synthetic access to WAP-8294A2 and analogs to establish a system for structure-activity relationship (SAR) studies. We also sought to further characterize the proposed mechanism of action and identify and characterize the biosynthetic machinery.</p><p>We developed a solid-phase strategy for the development of WAP-8294A2 and analogs with on-resin cyclization based on molecular modeling studies. We chose a macrocyclization site between Glu8 and Asn9 to take advantage of a predicted turn element and used the carboxylate side chain of glutamic acid as a convenient handle for resin attachment. We describe three analogs that were synthesized and analyzed for their biological and mechanistic profiles, providing evidence that the N-acyl fatty acid tail and the depsipeptide ester bond are required for antibiotic activity, but not for binding to the membrane phospholipid cardiolipin. </p><p> Additionally, we developed a method to improve the production, isolation, and purification of the WAP-8294A antibiotic complex highly enriched in the A2 fraction. The antibiotic complex was analyzed for antibiotic activity and was found to be equally active to the reported values for the A2 fraction. Basic mechanism of action studies with cardiolipin confirmed the ability of the WAP-8294A mixture to bind to cardiolipin and also suggested that the binding is mediated through interactions with the phosphate groups in the polar headgroup of cardiolipin.</p><p>Finally, we sequenced the genome of L. staphylocidin and inspected it for the WAP-8294A biosynthetic machinery. We successfully identified the WAP-8294A NRPS biosynthetic gene cluster in L. staphylocidin. It is composed of two large open reading frames (ORFs) that encode NRPS machinery made up of 44 domains organized into 12 modules. The organization of the gene cluster argues for a co-linear assembly of the peptide template. We also identified the genes flanking the large NRPS ORFs, which encode for a redox enzyme and several host regulation and preservation proteins. </p><p>In the course of examining the L. staphylocidin genome for the WAP-8294A biosynthetic gene cluster, we discovered a single module hybrid PKS/NRPS with high homology to heat-stable antifungal factor (HSAF). HSAF has been identified in two strains of L. enzymogenes, but was previously unknown in L. staphylocidin. We identified the genes in this cluster and compared them to the previously known HSAF biosynthetic gene clusters noting important similarities and differences between them.</p> / Dissertation

This research project focused on the investigation and identification of various niobium(V) complexes containing selected O,Oâ-bidentate ligands that could potentially be used for the selective separation of niobium from tantalum. Emphasis was placed on acetylacetone (acacH) type of ligands due to the ease of varying their electronic and steric properties. The crystallographic characterization of three novel complexes, (acetylacetonato-κ2- O,Oâ)chloridotrimethoxidoniobium(V) (1), the âcageâ-like structure of tetrakis- (acetylacetonato-κ2-O,Oâ)octakis(etoxy)tetrakis(μ2-oxo)tetraniobium(V) (2) and the two structures that were obtained from the same crystal, (1-phenyl-1,3- butanedionato-κ2-O,Oâ)chloridotrimethoxidoniobium(V) (3a) and (1-phenyl-1,3- butanedionato-κ2-O,Oâ)dichloridodimethoxidoniobium(V) (3b), is discussed and compared to literature. Complex 1 crystallized in an orthorhombic crystal system and space group Pbca, while complexes 2, 3a and 3b all crystallized in a monoclinic crystal system and a space group P21/c, for all. In general it was observed that these mono substituted β-diketonato complexes of niobium(V) crystallized in a distorted octahedral coordination polyhedron. The average O-Nb-O bite angle and Nb-O bond distance for these complexes were determined as 80.5 (1) ° and 2.108 (2) Ã, respectively. A kinetic investigation was conducted to follow the formation of the (acetylacetonato- κ2-O,Oâ)chloridotrimethoxidoniobium(V) complex in methanol. The coordination mechanism is postulated for the two observed steps of acacH coordination, of which the initial coordination of the ligand takes place in the first step. The equilibrium constant, K1, was determined as 1975 (201) M-1 at 25.0 °C. The second, rate determining step is representative of the total reaction and includes the ring-closure of the acac ligand and yields K1 as 1403 (379) M-1. Within experimental error, this value is in good agreement with that of the first step. When comparing the rate constants, k1 and k2, it is found that the first reaction is roughly six orders of magnitude (106) faster than the slower, second reaction step. 93Nb NMR was successfully used in characterising the niobium(V) products synthesised and played an important role in the kinetic study of the project. With regards to the kinetic study; solvent coordination proceeded rapidly upon solvation of the dimeric starting material, [NbCl5]2, in methanol and the niobium(V) starting reagent was correctly determined as [NbCl2(OMe)3(MeOH)] through 93Nb NMR.