Chemistry Commons^™

Clustering, Reorientation Dynamics, And Proton Transfer In Glassy Oligomeric Solids, Jacob Allen Harvey

Open Access Dissertations

We have modelled structures and dynamics of hydrogen bond networks that form from imidazoles tethered to oligomeric aliphatic backbones in crystalline and glassy phases. We have studied the behavior of oligomers containing 5 or 10 imidazole groups. These systems have been simulated over the range 100-900 K with constantpressure molecular dynamics using the AMBER 94 force field, which was found to show good agreement with ab initio calculations on hydrogen bond strengths and imidazole rotational barriers. Hypothetical crystalline solids formed from packed 5-mers and 10-mers melt above 600 K, then form glassy solids upon cooling. Viewing hydrogen bond networks as …

Reactive Heterocycles For Examining Polyketide Biosynthesis, Gitanjeli Prasad

Open Access Dissertations

Polyketides are a class of natural products that exhibit remarkable structural and functionally diversity and are highly sought after due to their medicinally important activities. For many decades now, polyketide synthases (PKSs), the mega-enzymes responsible for biosynthesis of polyketides have been the focus of extensive investigation to make new polyketides by polyketide engineering strategies. While there are many established methods to investigate polyketide enzymes and biosynthesis mechanisms, they have substantial shortcomings that have limited the extent of success with polyketide engineering efforts.

This thesis focuses on developing simple, flexible yet powerful tools for examining polyketide biosynthesis by overcoming some deficiencies …

O2 Activation And Allosteric Zn(Ii) Binding On Hif-Prolyl Hydroxylase-2 (Phd2), Serap Pektas

Open Access Dissertations

Oxygen homeostasis is essential to the life of aerobes, which is regulated in humans by Hypoxia Inducible Factor-1α (HIF-1α). Under hypoxic conditions, HIF-1α transactivates over a hundred genes related angiogenesis, erythropoiesis, etc. HIF-1α level and function is regulated by four HIF hydroxylase enzymes: three isoforms of prolyl hydroxylase domain (PHD1, PHD2 and PHD3) and factor inhibiting HIF-1α (FIH). PHD2 is the focus of this research. PHD2 is a non-heme Fe(II) 2-oxoglutarate dependent dioxygenase, which controls HIF-1α levels by hydroxylating two proline residues within the ODD domain of HIF-1α, then the hydroxylated prolines are recognized by pVHL, which targets HIF-1α for …

Development Of Mass Spectrometry-Based Methods For Quantitation And Characterization Of Protein Drugs: Transferrin As A Model Drug Delivery Vehicle, Shunhai Wang

Open Access Dissertations

In the last two decades, protein drugs have enjoyed a rapid growth and achieved a tremendous success in treating human diseases. However, the presence of physiological barriers greatly impedes the efficient delivery of such unconventional large molecule drugs, and therefore limits their clinical utility. An elegant way to address this challenge takes advantage of certain endogenous transporter proteins, such as human transferrin (Tf), whose ability to traverse physiological barriers has been extensively exploited. However, methods to investigate Tf-based drug delivery remained insufficient and unsatisfactory until recent development of quantitative mass spectrometry (MS). Hereby, MS-based methods have been developed and validated …

Enhanced Detection Strategies Accomplished Through Metal Binding And Miniature Mass Spectrometry, Adam Graichen

Open Access Dissertations

A multiplexed method for performing MS/MS on multiple ions simultaneously in a miniature rectilinear ion trap (RIT) mass spectrometer has been developed. This method uses an ion encoding procedure that relies on the mass bias that exists when ions are externally injected into an RIT operated with only a single phase RF applied to one pair of electrodes. The ion injection profile under such conditions ions is Gaussian-like over a wide range of RF amplitudes, or low mass cutoff (LMCO) values, during ion accumulation. We show that this distribution is related to ion m/z and is likely caused by ions …

Investigation Of The Orientation Dependence On Chiroptical Properties Of Single Molecules, Austin Joseph Cyphersmith

Open Access Dissertations

Optical activity is the defining property of chiral materials that is essential for characterization in biology, chemistry, and physics. While a substantial body of research has provided a strong theoretical framework of the origin of optical activity, we still know very little by way of experiment about an individual molecule’s contribution to the bulk optical activity. The chiroptical response of a single molecule can depend on molecular orientation and local molecular environment, information which is lost in ensemble averaging.

This thesis focuses on establishing methods for a priori determination of chiral molecule orientations and refining measurements to probe the chiroptical …

Determination Of Arsenic In Water By Potentially Portable Methodology, Chengbei Li

Open Access Dissertations

Arsenic contamination in groundwater is a worldwide problem. The existing portable field test kits can not provide accurate results when the arsenic concentration is around 10 μg L-1 or lower. This research first was focused on the development and validation of methods in which portable instrumentation, such as electrochemistry instruments or quartz crystal microbalances, could be used to accurately determine arsenic concentrations in water even when the concentration is below 10 μg L-1. A modified anodic stripping voltammetry (ASV) and cathodic stripping voltammetry (CSV) method with measurement at a microarray electrode manufactured by TraceDetect Inc. was developed. When the ASV …

Assembly Of Surface Engineered Nanoparticles For Functional Materials, Xi Yu

Open Access Dissertations

Nanoparticles are regarded as exciting new building blocks for functional materials due to their fascinating physical properties because of the nano-confinement. Organizing nanoparticles into ordered hierarchical structures are highly desired for constructing novel optical and electrical artificial materials that are different from their isolated state or thermodynamics random ensembles. My research integrates the surface chemistry of nanoparticles, interfacial assembly and lithography techniques to construct nanoparticle based functional structures. We designed and synthesized tailor-made ligands for gold, semiconductor and magnetic nanoparticle, to modulate the assembly process and collective properties of the assembled structures, by controlling the key parameters such as particle-interface …

Development And Characterization Of Caspase Activatable Gfp And A Family Of Fluorescent Reporters, Samantha Elizabeth Bernard Nicholls

Open Access Dissertations

The cellular process of programmed cell death, or apoptosis, is critical in homeostasis and development. In addition it's misfunction is implicated in an array of disease states from cancer to neurodegeration, making it an attractive pathway for drug targeting. A family of proteases, known as caspases, plays a central role in the apoptotic cascade resulting in the ultimate destruction of the cell. We report a genetically encoded dark-to-bright reporter of caspase activity used in E.coli, mammalian cells, and whole organisms which can be used to monitor apoptosis. This reporter, caspase activatable green fluorescent protein (CA-GFP) consists of GFP fused through …

Breaking The Barriers Of All-Polymer Solar Cells: Solving Electron Transporter And Morphology Problems, Nagarjuna Gavvalapalli

Open Access Dissertations

All-polymer solar cells (APSC) are a class of organic solar cells in which hole and electron transporting phases are made of conjugated polymers. Unlike polymer/fullerene solar cell, photoactive material of APSC can be designed to have hole and electron transporting polymers with complementary absorption range and proper frontier energy level offset. However, the highest reported PCE of APSC is 5 times less than that of polymer/fullerene solar cell. The low PCE of APSC is mainly due to: i) low charge separation efficiency; and ii) lack of optimal morphology to facilitate charge transfer and transport; and iii) lack of control over …

Allosteric Regulation Of Caspase-6 Proteolytic Activity, Elih M. Velazquez-Delgado

Open Access Dissertations

Caspases are cysteine proteases best known for their controlling roles in apoptosis and inflammation. Caspase-6 has recently been shown to play a key role in the cleavage of neurodegenerative substrates that causes Huntington and Alzheimer's Disease, heightening interest in caspase-6 and making it a drug target. All thirteen human caspases have related specificities for binding and cleaving substrate, so achieving caspase-specific regulation at the active site has been extremely challenging if not impossible. We have determined the structures of four unliganded forms of caspase-6, which attain a novel helical structure not observed in any other caspases. In this conformation, rotation …

Studies In The Atomic Spectrometric Determination Of Selenium, Mercury, And Rare Earth Elements, Lindsay Rhae Harris

Open Access Dissertations

The field of analytical chemistry is very important to today's society as more and more regulations and legislations emerge regarding trace elements in food, consumer products, medicines, and the environment. Like many areas of science, the current goals of trace elemental measurements and speciation are to increase knowledge on the subject and to improve upon current techniques by enhancing the figures of merit, such as accuracy and reproducibility, meanwhile balancing with the cost and time of analysis.

The topics covered in this work were investigated primarily through the use of inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma …

Determination Of Metallic Constituents In Environmental And Biological Materials, Monique Erica Johnson

Open Access Dissertations

Studies of the interaction of the relevant metal, metalloid or nanoparticulate species with biological systems are underpinned by the provision of reliable information about chemical composition of the relevant materials. Often, no methods of chemical analysis are available. The work described in this dissertation centers on developing methods to help with studies for a variety of analytes and samples. A method was developed for the determination of 11 trace elements (As, Cd, Co, Cr, Cu, Fe, Mg, Mn, Pb, Ti, and Zn) in human breast milk and infant formulas by inductively coupled plasma optical emission spectrometry (ICP-OES) following microwave-assisted digestion. …

Determination And Speciation Of Arsenic In Environmental And Biological Samples, Tiffany Berg

Open Access Dissertations

A method was developed for the determination of total arsenic in rice grain by microwave-assisted digestion inductively coupled plasma mass spectrometry. Standard calibration solutions were matrix-matched with respect to acid concentration and carbon content post-digest. The importance of eliminating the drying step during sample preparation procedures was investigated. The method was validated with spikes containing standard arsenate solutions into the rice matrix, and with certified reference material SRM1568a (rice flour) from NIST. The method was successfully applied to a commercially available rice sample. Four arsenic species [arsenate (As(V)), arsenite (As(III)), dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA)] were extracted from …

Regulation Of Caspase-9 By Natural And Synthetic Inhibitors, Kristen L. Huber

Open Access Dissertations

Tight regulation of caspase-9, a key initiator of apoptosis, is required to uphold cellular homeostasis. Although it is controlled on a multifactorial level, misregulation of this process does occur, which is a characteristic of a variety of diseases from ischemic injury to cancer. Therefore it remains important to gain a detailed understanding of the mechanisms behind native caspase-9 regulatory pathways and harness these mechanisms for therapeutic purposes.

Based on known mechanisms, such as the unique inhibitory complex of caspase-9 and XIAP-BIR3, development of synthetic regulators can be envisioned, while other mechanisms such as zinc-mediated inhibition and CARD activation of caspse-9 …

Engineering Surface Functionality Of Gold Nanoparticles For Therapeutic Applications, Chaekyu Kim

Open Access Dissertations

Over the past few decades, tremendous efforts have been made to develop nanomaterials for biotechnological applications such as therapeutics. Understanding and engineering interfaces between biomacromolecules and nanomaterials is a key to the creation of successful therapeutic systems. My research has been oriented toward developing therapeutic systems using gold nanoparticles (AuNPs) incorporating material science, organic synthesis, and biology. For this purpose, mixed monolayer protected AuNPs (~2 nm core size) with various functional groups have been employed for triggering therapeutic effects. Several strategies have been accomplished using anticancer drugs that non-covalently and covalently incorporate onto AuNPs as a drug delivery carrier. Alternatively, …

Functional Polymers For Anhydrous Proton Transport, Nagamani Chikkannagari

Open Access Dissertations

Anhydrous proton conducting polymers are highly sought after for applications in high temperature polymer electrolyte membrane fuel cells (PEMFCs). N-heterocycles (eg. imidazole, triazole, and benzimidazole), owing to their amphoteric nature, have been widely studied to develop efficient anhydrous proton transporting polymers. The proton conductivity of N-heterocyclic polymers is influenced by several factors and the design and development of polymers with a delicate balance among various synergistic and competing factors to provide appreciable proton conductivities has been a challenging task. In this thesis, the proton transport (PT) characteristics of polymers functionalized with two diverse classes of functional groups - N-heterocycles and …

Organic Materials As Templates For The Formation Of Mesoporous Inorganic Materials And Ordered Inorganic Nanocomposites, Christopher Ryan Ziegler

Open Access Dissertations

Hierarchically structured inorganic materials are everywhere in nature. From unicellular aquatic algae such as diatoms to the bones and/or cartilage that comprise the skeletal systems of vertebrates. Complex mechanisms involving site-specific chemistries and precision kinetics are responsible for the formation of such structures. In the synthetic realm, reproduction of even the most basic hierarchical structure effortlessly produced in nature is difficult. However, through the utilization of self-assembling structures or "templates", such as polymers or amphiphilic surfactants, combined with some favorable interaction between a chosen inorganic, the potential exists to imprint an inorganic material with a morphology dictated via synthetic molecular …

Design Of Hybrid Conjugated Polymer Materials: 1) Novel Inorganic/Organic Hybrid Semiconductors And 2) Surface Modification Via Grafting Approaches, Joseph J. Peterson

Open Access Dissertations

The research presented in this dissertation focuses on the design and synthesis of novel hybrid conjugated polymer materials using two different approaches: 1) inorganic/organic hybrid semiconductors through the incorporation of carboranes into the polymer structure and 2) the modification of surfaces with conjugated polymers via grafting approaches. Hybrid conjugated polymeric materials, which are materials or systems in which conjugated polymers are chemically integrated with non-traditional structures or surfaces, have the potential to harness useful properties from both components of the material to help overcome hurdles in their practical realization in polymer-based devices. This work is centered around the synthetic challenges …

Effect Of Side Chains On Organic Donor (D) And Acceptor (A) Complexes And Photophysical Properties Of D-A Dyads, Amarnath Bheemaraju

Open Access Dissertations

This dissertation aims to understand the effect of incompatible side chains on the complexes of pi-conjugated electron-rich donors and electron-deficient acceptors in solution. The role of incompatible side chains were studied in simple mixtures of organic donor and acceptor molecules that form donor-acceptor complexes. The incompatible branched and linear alkane side chains on the acceptor and donor respectively prevented complex formation between naphthalene diimide acceptor and naphthalene ether donor. However, the incompatible hydrocarbon-fluorocarbon and polar-non polar side chain pairs did not affect complex formation between the donor and acceptor. In quaterthiophene-naphthalene diimide dyads, the incompatibility of the side chain on …

Selective Inhibition And Mechanistic Studies Of The Human O2 Sensor, Prolyl Hydroxylase Domain 2 (Phd2), Shannon Coates Flagg

Open Access Dissertations

Prolyl Hydroxylase Domain 2 (PHD2) has been identified as a key oxygen sensor in humans along with Factor Inhibiting Hypoxia Inducible Factor (FIH). As such PHD2 and FIH play critical roles in myriad pathways of medical relevance by hydroxylation of their target substrate hypoxia inducible factor (HIF), a transcription factor responsible for the regulation of over 100+ genes. With such critical roles in human physiology the ability to selectively regulate these two enzymes could potentially lead the way for novel therapeutic treatments of a vast array of disease states from cancer to myocardial infarction. We report on three classes of …

Controlled Oxygen Activation In Human Oxygen Sensor Fih, Evren Saban

Open Access Dissertations

One of the primary oxygen sensors in human cells, which controls gene expression by hydroxylating the hypoxia inducible transcription factor (HIFα) is the factor inhibiting HIF (FIH). As FIH is an alpha-ketoglutarate dependent non-heme iron dioxygenase, oxygen activation is thought to precede substrate hydroxylation. The coupling between oxygen activation and substrate hydroxylation was hypothesized to be very tight, in order for FIH to fulfill its function as a regulatory enzyme. Coupling was investigated by looking for reactive oxygen species production during turnover. Alkylsulfatase (AtsK), a metabolic bacterial enzyme with a related mechanism and similar turnover frequency, was used for comparison, …

Design And Synthesis Of A New Class Of Self-Cross-Linked Polymer Nanogels, Siriporn Jiwpanich

Open Access Dissertations

The design and engineering of nanoscopic drug delivery vehicles that stably encapsulate lipophilic drug molecules, transport their loaded cargo to specific target sites, and release their payload in a controlled manner are of great interest in therapeutic applications, especially for cancer chemotherapy. This dissertation focuses on chemically cross-linked, water-soluble polymer nanoparticles, termed nanogels, which constitute a promising scaffold and offer the potential to circumvent encapsulation stability issues. A facile synthetic method for a new class of self-cross-linked polymer nanogels, synthesized by an intra/intermolecular disulfide cross-linking reaction in aqueous media, is described here. This simple emulsion-free method affords noncovalent lipophilic guest …

Mutational Analysis Of Geopilin Function In Geobacter Sulfurreducens, Lubna V. Richter

Open Access Dissertations

Geobacter sulfurreducens possesses type IV pili that are considered to be conductive nanowires and a crucial structural element in biofilm formation, enabling electron transfer to insoluble metal oxides in anaerobic sediments and to graphite anodes in microbial fuel cells. The molecular mechanism by which electrons are transferred through the nanowires to the electron acceptor is not fully understood. Prior to the work described in this thesis, the gene (pilA) encoding the structural pilus subunit had been identified, but little was known about the functional translation start codon, the length of the mature secreted protein, or what renders the pili conductive. …

Molecular Designs For Organic Semiconductors: Design, Synthesis And Charge Transport Properties, Tejaswini Sharad Kale

Open Access Dissertations

Understanding structure-property relationship of molecules is imperative for designing efficient materials for organic semiconductors. Organic semiconductors are based on π-conjugated molecules, either small molecules or macromolecules such as dendrimers or polymers. Charge transport through organic materials is one of the most important processes that drive organic electronic devices. We have investigated the charge transport properties in various molecular designs based on dendrons, dendron-rod-coil molecular triads, and conjugated oligomers. The charge transport properties were studied using bottom contact field effect transistors, in which the material was deposited by spin coating.

In case of dendrons, their generation and density of charge transporting …

Colloidal Microcapsules: Surface Engineering Of Nanoparticles For Interfacial Assembly, Debabrata Patra

Open Access Dissertations

Colloidal Microcapsules (MCs), i.e. capsules stabilized by nano-/microparticle shells are highly modular inherently multi-scale constructs with applications in many areas of material and biological sciences e.g. drug delivery, encapsulation and microreactors. These MCs are fabricated by stabilizing emulsions via self-assembly of colloidal micro/nanoparticles at liquid-liquid interface. In these systems, colloidal particles serve as modular building blocks, allowing incorporation of the particle properties into the functional capabilities of the MCs. As an example, nanoparticles (NPs) can serve as appropriate antennae to induce response by external triggers (e.g. magnetic fields or laser) for controlled release of encapsulated materials. Additionally, the dynamic nature …

Caspase-7 Loop Conformations As A Means Of Allosteric Control, Witold Andrej Witkowski

Open Access Dissertations

The caspase family of proteins is critical to biological understanding, because they serve as the final arbiters of life and death, being the initiators and executioners of cell death. Specifically, caspase-7 plays a key role in apoptosis, however its full complement of targets within the cell has not yet been elucidated, nor has its function been targeted by drug design efforts. These factors stem from the lack of fundamental understanding of the structural dynamics of the protein, including the mobile loops that constitute the active site binding groove of caspase-7, and their ability to modulate the function of the protein. …

Engineering Nanoparticles Surface For Biosensing: "Chemical Noses" To Detect And Identify Proteins, Bacteria And Cancerous Cells, Oscar Ramon Miranda-Sanchez

Open Access Dissertations

Rapid and sensitive detection of biomolecules is an important issue in nanomedicine. Many disorders are manifested by changes in protein levels of serum and other biofluids. Rapid and effective differentiation between normal and cancerous cells is an important challenge for the diagnosis and treatment of tumor. Likewise, rapid and effective identification of pathogens is a key target in both biomedical and environmental monitoring. Most biological recognition processes occur via specific interactions. Gold nanoparticles (AuNPs) feature sizes commensurate with biomacromolecules, coupled with useful physical and optical properties. A key issue in the use of nanomaterials is controlling the interfacial interactions of …

Vibrational Spectroscopy Of Intermediates Of C-H Bond Activation By Transition Metal Oxide Cations, Gokhan Altinay

Open Access Dissertations

Direct, efficient oxidation of alkanes is a long-standing goal of catalysis. Gas phase FeO+ can convert methane to methanol and benzene to phenol under thermal conditions. Two key intermediates of these reactions are the [HO-Fe-R]+ insertion intermediate and Fe+(ROH) (R=CH3 or C6H5) exit channel complex. This work describes measurements of the vibrational spectra of these intermediates and electronic structure theory calculations of the potential energy surfaces for the reactions. They help to characterize the mechanism for these reactions. Chapter 1 describes previous studies of methane-to-methanol and benzene-to-phenol conversion by gas-phase transition metal oxide cations. Spectra of gas-phase reaction intermediates are …

Charge And Energy Transport In Single Quantum Dot/Organic Hybrid Nanostructures, Kevin Thomas Early

Open Access Dissertations

Hybrid quantum dot /organic semiconductor systems are of great interest in optoelectronic and photovoltaic applications, because they combine the robust and tunable optical properties of inorganic semiconductors with the processability of organic thin films. In particular, cadmium selenide (CdSe) quantum dots coordinated with oligo-(phenylene vinylene) ligands have displayed a number of hybrid optical properties that make them particularly well-suited to these applications. When probed on an individual particle level, these so-called CdSe-OPV nanostructures display a number of surprising photophysical characteristics, including strong quenching of fluorescence from coordinating ligands, enhanced emission from the CdSe quantum dot core, suppression of fluorescence intermittency, …