In low-resource areas of the world, accurate diagnosis of disease is especially challenging, as resources are limited and environmental conditions uncontrolled. Consequently, reliable low-resource diagnostics must be simple, cost effective, stable and sensitive. For diagnosis of malaria in low-resource settings, lateral-flow rapid diagnostic tests (RDTs) are commonly used. Unfortunately, RDTs lack sensitivity, leaving many low-level and asymptomatic infections untreated. In this work, new diagnostic strategies that are both stable and sensitive were developed for the malarial biomarker Plasmodium falciparum histidine-rich protein II (pfHRPII). Patient samples were analyzed to gain further insight into the properties of this biomarker. Additionally, sample preparation techniques utilizing metal affinity ligands for capture of this histidine-rich biomarker were evaluated. These methods concentrated pfHRPII from a large sample volumes, allowing for greater biomarker presentation to the tests. Magnetic particles utilizing this this capture strategy were shown to lower detection limits of commercial RDTs to single-digit parasitemias. To eliminate the need for additional diagnostic components, cellulose membranes modified with metal affinity ligands were synthesized. This inexpensive method allowed for capture and detection of pfHRPII on the membrane. Additionally, detection strategies based upon signal amplification with porphyrin nanoparticles were developed. In these methods, the dissolution of each nanoparticle into tens of thousands of porphyrin molecules resulted in amplified detection of the biomarker. By using nanoparticles as the signal-generating moiety, stability of the detection method was increased relative to commonly used enzyme-based assays. A fluorescent assay was designed, where the inherent fluorescent signal of tetra(4-carboxyphenyl) porphyrin could easily be measured after nanoparticle dissolution. Additionally, a catalytic assay, which employed a second type of signal amplification through the catalytic turnover of a substrate by hemin (ferriprotoporphyrin IX chloride), was developed. These methods were shown to detect picomolar levels of malarial biomarkers from complex matrices. By combining the modified cellulose membranes with hemin nanoparticle detection, a flow-through diagnostic was constructed. This diagnostic was shown to detect asymptomatic levels of pfHRPII. Thus, this work produced sensitive and stable diagnostic strategies which show great promise for implementation in low-resource settings.

The native form of turkey liver fructose 1,6-bisphosphatase (FbPase) consists of four identical subunits, each of which contains one tryptophan residue. The fluorescence emission spectra of the tryptophan residues have been recorded as a function of changes in pH, substrate (fructose 1,6-bisphosphate) and inhibitor (adenosine-5’ monophosphate) binding, and the addition of the metal cofactors Mg+2, Mn+2 and Co+2 . Changes in the fluorescence emission spectra of the tryptophan residues indicate that conformational changes in the enzyme occur under the above conditions.

<p>Significant advances in understanding the fundamental photophysical behavior of single-walled carbon nanotubes (SWNTs) have been made possible by the development of ionic, conjugated aryleneethynylene polymers that helically wrap SWNTs with well-defined morphology. My contribution to this work was the design and synthesis of porphyrin-containing polymers and the photophysical investigation of the corresponding polymer-wrapped SWNTs. For these new constructs, the polymer acts as more than just a solubilization scaffold; such assemblies can provide benchmark data for evaluating spectroscopic signatures of energy and charge transfer events and lay the groundwork for further, rational development of polymers with precisely tuned redox properties and electronic coupling with the underlying SWNT. The first design to incorporate a zinc porphyrin into the polymer backbone, PNES-PZn, suffered from severe aggregation in solution and was redesigned to produce the porphyrin-containing polymer S-PBN-PZn. This polymer was utilized to helically wrap chirality-enriched (6,5) SWNTs, which resulted in significant quenching of the porphyrin-based fluorescence. Time-resolved spectroscopy revealed a simultaneous rise and decay of the porphyrin radical cation and SWNT electron polaron spectroscopic signatures indicative of photoinduced electron transfer. A new polymer, S-PBN(b)-Ph2PZn3, was then synthesized which incorporated a meso-ethyne linked zinc porphyrin trimer. By changing the absorption profile and electrochemical redox potentials of the polymer, the photophysical behavior of the corresponding polymer-wrapped (6,5)-SWNTs was dramatically changed, and the polymer-wrapped SWNTs no longer showed evidence for photoinduced electron transfer.</p> / Dissertation

<p>Transition metals such as iron and copper are valued in biology for their redox activities because they are able to access various oxidation states. However, these transition metals are also implicated in a number of human disease states and play a role in bacterial infections. The ability to manipulate and monitor metal ions has vast implications on the fields of biology and human health. As such, the research described here covers two related goals: to manipulate metals in specific biological circumstances and to visualize this disturbance in cellular metal homeostasis.</p><p>Antibiotic resistance necessitates the development of drugs that exploit new mechanisms of action such as the disruption of metal homeostasis. In order to manipulate metals at the site of bacterial infection, two prochelators were developed around a β-lactam core such that the active chelator is released in the presence of bacteria that produce the resistance-causing β-lactamase enzyme. Both prochelators display enhanced activity toward resistant bacteria compared to clinical antibiotics.</p><p>Fluorescent sensors are a powerful tool for detecting small concentrations of biological analytes. Two analogs of a ratiometric fluorescent sensor were designed and synthesized to monitor cellular concentrations of copper and iron. These sensors were found to operate as designed in vitro; however the fluorescence intensity necessary for quantification of cellular metal pools has not yet been achieved.</p> / Dissertation

<p>Aligned single-walled carbon nanotubes (SWNTs) synthesized by the chemical vapor deposition (CVD) method have exceptional potential for next-generation nanoelectronics. However, there are considerable challenges in the preparation of semiconducting (s-) SWNTs with controlled properties (e.g., density, selectivity, and diameter) for their application in solving real-world problems. This dissertation describes research that aims to overcome the limitations by novel synthesis strategies and post-growth treatment. The application of as-prepared SWNTs as functional devices is also demonstrated. The dissertation includes the following parts: 1) decoupling the conflict between density and selectivity of s-SWNTs in CVD growth; 2) investigating the importance of diameter control for the selective synthesis of s-SWNTs; 3) synthesizing highly conductive SWNT thin film by thiophene-assisted CVD method; 4) eliminating metallic pathways in SWNT crossbars by gate-free electrical breakdown method; 5) enhancing the density of SWNT arrays by strain-release method; 6) studying the sensing mechanism of SWNT crossbar chemical sensors.</p> / Dissertation

The process of photosynthesis has served as a natural solar energy conversion system in autotrophs for billions of years. This complex biological process provides inspiration and key machinery that may be utilized in developing novel, low cost solar-to-electricity platforms. Photosystem I (PSI) is a large photoactive protein that is easily extracted from green plants and interfaced with different materials to generate simple photoactive electrodes. In this dissertation, several advances were made to improve the photovoltaic performance of PSI-based devices. First, a novel conducting polymer-PSI composite was prepared through facile in situ electrochemical polymerization of aniline and PSI. These photoactive films were initially studied on gold electrodes, before later being grown on semiconducting substrates to act as the photosensitizing layer of solid-state biophotovoltaic devices. In other studies, controlling the orientation of PSI as assembled on metallic electrodes was explored. Here, a simple functionalization strategy was devised to selectively modify the protein during extraction and introduce a ligand for activated surface coupling. Self assembly of these modified PSI complexes yielded significant increases in photocurrent, derived from improved protein orientation. Additionally, a new type of low cost bioderived photovoltaic device was introduced featuring a solid-state polyviologen film that served as an electron transport layer between the PSI layer and anode. In a push to further drive down the cost of PSI-based devices, a streamlined PSI extraction procedure was developed that required minimal laboratory equipment and could be performed by a user with limited chemistry experience. Finally, enzymatic biosensors were prepared by coupling various oxidases with osmium hydrogel redox polymers. These redox active films were used to construct a multianalyte electrochemical biosensor platform capable of measuring changes in glucose, lactate, and glutamate over a high background of an electroactive interferent (i.e. acetaminophen). These biosensors represent a new system that can be interfaced online with an Organ-on-Chip system to make electrochemical measurements in real time for improved in vitro analyses.

This work describes three separate projects, for which Density Functional Theory (DFT) computations provide a unifying theme. The DFT approach gives a theoretically sound way to model the chemical and physical properties of a system based its electron density. Although the exact functional has been proven to exist, its form is not completely known and so all calculations are completed with various approximations, which sometimes seriously affect the results. Conventional functionals, for example, fail to account for dispersion corrections adequately, and consequently dispersion-corrected functionals were used extensively in this work. Cation-Ï interactions involve the largely noncovalent attraction of a cation with a ligand's p- electrons, which are often those of an arene or a heteroarene. These interactions incorporate electrostatic, inductive, and charge transfer effects, and in some cases, dispersion forces. Factors that could affect the strength of cation-p interactions were examined with the use of a simple geometric model. A chief finding was that the relationship between the strength of the interaction and the number of Ï-bonds involved is not linear. Asymmetric cation-Ï interactions (i.e., those in which the cations are not in line with the centers of Ï-electron density) were also examined; despite their relative weakness compared to more symmetric arrangements, they can contribute considerably to the total bonding energy in molecules. The Ï- and Ï-bonding in high-spin manganese(II) allyls was examined with the aid of DFT methods. Comparisons were made to structurally similar magnesium allyls, as neither of these similarly-sized cations (Mn2+/Mg2+) provide ligand field stability to their compounds. The structure and bonding of group 2 and 14 metallocenes were studied with dispersion- corrected functionals. Metallocene compounds of calcium, strontium, and barium commonly display non-linear Cp-M-Cp (Cp = cyclopentadienyl) angles. Of the various explanations for this phenomenon, dispersion interactions between the cyclopentadienyl rings are among the most difficult to model computationally. Presently available DFT methods are not able to provide unambiguous evidence for the source(s) of the non-linear structures.

<p> The optimal surface enhanced Raman scattering (SERS) intensity was correlated to the localized surface plasmon resonance (LSPR) of individual and aggregated gold core/silver shell (<i>Au@Ag</i>) nanoparticles (NPs) in titrations involving the addition of both SERS label (e.g., rhodamine 6G, R6G) and the non-SERS active aggregant (chemical species that triggers the aggregation of NPs) potassium chloride (KCl). Titrating NP solutions with pure SERS label has often resulted in highly non-linear calibrations. In some cases, addition of non-SERS active aggregating agents such as KCl has also resulted in a large increase in SERS signals. An order of initial addition was followed in this report to find any advantage from the initial addition between the SERS label or the aggregant KCl. Interactions between <i>Au@Ag</i> solution and the SERS labels of R6G, 4 mercaptopyridine (MPY) and 4 mercaptobenzoic acid (MBA) were followed using spectrophotometric titrations. Evaluations of the role of aggregation in NP solutions were conducted through the micro-titrations using a quartz cuvette and in two separate stages: (1) a single amount of KCl was followed by increasing amounts of SERS label, and (2) a single amount of SERS label was followed by increasing amounts of KCl. The present reports allowed to conclude that the graphs of SERS intensity (&lambda;_EX = 785nm, corrected for solution absorption) versus aggregate absorptions (&lambda;_AG = 830 nm) had a correlation between intense SERS and LSPR band extinctions.</p>

Lipids are loosely defined as a group of naturally occurring organic compounds which are hydrophobic or amphipathic in nature, but which are also readily soluble in organic solvents. These solubility features are present in an extremely heterogeneous collection of molecules such as fatty acids, phospholipids, eicosanoids, and sterols. The functions of various lipids are diverse and wide ranging, and many are considered essential for standard life functions. Despite their importance within biological processes, many lipids are also susceptible to free radical oxidation and degradation in the presence of reactive oxygen species. This lipid oxidation, commonly referred to as lipid peroxidation, can have extensive physiological consequences and can play a role in the progression of human disease states such as Parkinsonâs disease and atherosclerosis. The focus of this dissertation is centered around the free radical oxidation of polyunsaturated fatty acids (PUFAs). We present several kinetic studies probing the rates at which these reactions occur are reported for a wide variety of PUFAs and sterols. We also highlight physical studies involving isotopically reinforced polyunsaturated fatty acids and assess their ability to reduce levels of free radical oxidation both in solution and in biological systems.

<p>Mechanically induced chemical bond scission underlies the fracture and macroscopic failure of polymeric materials. Thus, the mechanical strength of scissile chemical bonds plays a role in material failure and in the mechanical initiation of cascade reactions, but quantitative measurements of mechanical strength are rare. This dissertation describes research that quantifies relative mechanical strengths of polymers that possess a variety of chemical and topological functionalities in order to assess the strength of putative "weak bonds" along their backbones. </p><p>First, relative mechanical strengths of "weak" bonds that break by homolytic scission were assessed: the carbon-nitrogen bond of an azobisdialkylnitrile (< 30 kcal mol-1), the sulfur-sulfur bond of a disulfide (54 kcal mol-1), and the carbon-oxygen bond of a benzylphenyl ether (52-54 kcal mol-1). The mechanical strengths were assessed in the context of chain scission triggered by pulsed sonication of polymer solutions, by using the competing non-scissile mechanochemical reaction of gem dichlorocyclopropane mechanophores as a gauge of the force required for chain scission. The relative mechanical strengths of the three weak bonds are found to be: azobisdialkylnitrile (weakest) < disulfide < benzylphenyl ether. The greater mechanical strength of the benzylphenyl ether relative to the disulfide is ascribed in part to poor mechanochemical coupling as a result of the rehybridization that accompanies carbon-oxygen bond scission. </p><p>Studies of bond scission were extended to include the effect of topology. The introduction of mechanical bonding in polymers can sufficiently affect physical properties, but experimental measurements of the relative strengths of topological bonding are rare. We studied the relative mechanical strengths of three bonding topologies formed from the same set of chemical functionalities: a catenane, a symmetrical macrocycle, and a linear construct. Mechanical strengths were obtained by analysis of molecular weight of polymers with embedded topological molecules after 4 h of pulsed sonication (M4h). The obtained M4h was converted to the length (L4h) using the calculated force free length of each monomer. The relative mechanical strengths of these topological molecules are nearly identical based on L4h, and we conclude that the mechanical strength of a mechanical bond (catenane) is as high as that of a linear analog.</p><p>Using these methods, the relative mechanical strengths of triazoles were also investigated. Random copolymers containing either 1,4-triazole, 1,5-triazole, or indole were synthesized via entropy driven ring opening metathesis co-polymerization. Solutions of those polymers were subjected to pulsed ultrasound for 4 hours and M4h measured was less than the M4h of poly(gDCC). Taken together, these results suggest that the introduction of these heterocycles does weaken the polymer main chain, but not through mechanically assisted cycloreversion. </p><p>As an extended study of mechanical strength of different molecular topologies, the sonochemistry of a polymeric trefoil knot was also investigated. A zinc-templated polymeric trefoil knot was subjected to pulsed ultrasound, to determine whether demetallation can be mechanically triggered by tightening the trefoil knot under high forces of tension. The products of sonication of the polymeric trefoil knot were analyzed by 1H NMR and by the color change of dithizone solution used to coordinate any released zinc. No evidence for mechanical demetallation or knot scission was obtained, suggesting that the presence of the zinc template in the trefoil knot can prevent knot tightening and subsequent weakening and scission.</p> / Dissertation