Chemistry Commons^™

An Experimental And Numerical Investigation Of Flow Accelerated Flibe Corrosion, David B. Weitzel

Nuclear Engineering ETDs

Renewed interest in molten salt reactor technology has brought to light the need for a better understanding of FLiBe corrosion. To this end a flowing FLiBe corrosion test loop was designed to test the flow effects of FLiBe corrosion. The loop consists of a pump, melt tank, and stainless-steel tubing assembly that heats the molten salt to high temperatures and circulates it over test specimens. The experiment has been constructed and has completed initial shakedown testing.

To support the flowing FLiBe experiment, a numerical corrosion model that couples FLiBe electrochemistry, solid metal diffusion, and mass transport was implemented. The model …

Development Of Copper-Catalyzed Suzuki-Miyaura Coupling Using Alkylboron Reagents And Nickel-Catalyzed Alkene Dicarbofunctionalization Reactions, Prakash Basnet

Chemistry and Chemical Biology ETDs

This thesis is divided into two parts. The first part deals with the development of copper-catalyzed Suzuki-Miyaura coupling of alkylboron reagents for the first time. In the second part, we will discuss the development of novel nickel-catalyzed alkene dicarbofunctionalization reactions.

Part I. Cross-coupling reactions are versatile tools to form new carbon-carbon bonds and are widely used in the synthesis of various drug molecules, natural products and materials. However, these reactions are typically catalyzed by palladium, an expensive and rare metal which makes the reaction unsustainable in long-terms. Additionally, palladium-catalyzed cross-coupling reactions with alkylorganometallic reagents suffer from side reactions due to …

Development Of Functional Chemical Probes For The Study Of Viscosity, Fe(Ii), And Ferroptosis And Photo-Triggered Drug Delivery, Yongyi Wei

Chemistry and Chemical Biology ETDs

Small molecule probes are useful tools for the study of biology. In particular, the dye derived fluorescence probes enable to spatiotemporally monitor the events of analytes of interest. The noninvasive feature is particularly attractive for the biological studies in live cells. The challenge is to develop chemical probes capable of detection of the analyte of interest with high specificity.

Toward this end, my Ph. D. study centers on the development of novel chemical probes for the study and understanding of the alternation of important cellar contents and substances and their functions and relationship between normal and disease states. In the …

Synthesis, Characterization And Application Of Structurally Diverse Poly(Chalcogenylene Vinylene)S, Zhen Zhang

Chemistry and Chemical Biology ETDs

Conjugated polymers have found widespread applications in flexible and printable electronic devices, among which poly(thienylene vinylene) (PTV) displays outstanding optoelectronic properties and promising applications. However, further studies of its structure-property-function relationship have been greatly impeded mainly due to the synthetic difficulty of generating new structures beyond its rudimentary form.

To further investigate this class of material, I have developed a facile methodology for the preparation of structurally diverse poly(chalcogenylene vinylene)s (PCVs) through a combination of acyclic diene metathesis (ADMET) polymerization and post-polymerization modification techniques. Specifically, a series of halogenated and cross-conjugated PCVs have been designed and synthesized, followed by complete …

Developing More Specific Mirna Biogenesis Inhibitors To Get Effective Regulation Of Mirnas, Umesh Bhattarai

Chemistry and Chemical Biology ETDs

MicroRNAs (miRNAs) are short (~ 22 nucleotides long) noncoding RNAs that regulate gene expression post-transcriptionally. They control the expression of various genes that are crucial for cellular function, development and human diseases. Tools to regulate the level and function of miRNAs facilitate the studies of their functions and have therapeutic applications. In my thesis, I developed a newly customizable miRNA biogenesis inhibitor to regulate miRNAs.

Antisense oligonucleotides (ASOs) have been used to regulate miRNA through controlling their production or function. Although commonly used due to the fact that they are easy to design, several limitations exist for ASOs including serious …

Regulating Mirna Biogenesis By Small Molecules, Hao Yan

Chemistry and Chemical Biology ETDs

MiRNAs are key cellular regulators and their dysregulation is associated with many human diseases. The development of miRNA inhibitors has significant implications for the therapy of diseases associated with aberrant miRNA expression. It also provides chemical tools for studying miRNA function. This dissertation focuses on the development of small-molecule based miRNA inhibitors targeting miRNA biogenesis.

The dissertation consists of four chapters. In Chapter 1, the biogenesis of miRNA was first introduced, followed by the explanation of miRNA function in health and disease. Then the approaches used for regulating miRNA were reviewed. Finally, the difficulties with miRNA regulation were summarized.

One …

Catalytic Functionalization Of Organoaluminum Reagents And Olefins By Cross-Coupling With Copper And Nickel, Bijay Shrestha

Chemistry and Chemical Biology ETDs

This thesis is divided into two parts. The first part focuses on the Cu-catalyzed cross-coupling of organoaluminum reagents with organohalides. One of the most powerful tools for the construction of C-C bonds is cross-coupling. But, this reaction is predominantly catalyzed by Pd, a rare and expensive transition metal, which inevitably makes the process unsustainable in the long-term. Furthermore, Pd-catalyzed cross-coupling also shows low tolerance for alkyl and heteroaryl substrates because of β-hydride elimination and catalyst deactivation, respectively. Although these issues remain largely solved by using sterically hindered and electron-rich ligands, however making these types of ligands is synthetically challenging and …

Development Of Mof@Polymer Composite Materials Through Bottom-Up Self-Assembly Techniques, Roberto C. Arbulu

Chemistry and Chemical Biology ETDs

MOF-based mixed matrix membranes (MMMs) are a promising new class of MOF/polymer composite materials. Currently, fabrication of MMMs is based on top-down methods with limited control over MOF positioning, integration, or morphology. This work focuses on the growth of well-defined one-dimensional (1-D) MOF nanostructures within the pores of a nanoporous polymer template, either commercially available or through the self-assembly of block co-polymers having tailor-designed surface functionalities. Studies were conducted using zeolitic imidazole framework-8 (ZIF-8) and polycarbonate track etched (PCTE) membranes, which demonstrated the feasibility of the outlined approach, and revealed the formation of distinct super- and nanostructures with controlled morphologies …

Copper-Catalyzed Direct And Tandem Couplings, And Mechanistic Studies, Surendra Thapa

Chemistry and Chemical Biology ETDs

Cross-coupling reactions are exceptionally powerful tools to construct carbon-carbon (C-C) bonds. These reactions are widely used to synthesize natural products, polymers, agrochemical, organic materials and pharmaceutical compounds. However, these reactions are typically catalyzed by Palladium. Although these reactions are widely utilized and well developed, the use of noble metals like Pd raises a question about its long-term sustainability. We believe copper can be one of the best alternatives to palladium as it is more abundant, less expensive and less toxic. In addition, Pd-catalyzed transformations usually suffer from β-hydride elimination to afford undesired olefin and rearranged products, when it comes …

Detection Of Salen-Type Tracers For Subterranean Fluid Flow Monitoring Using Surface-Enhanced Raman Spectroscopy, Jenny C. Sanchez

Chemistry and Chemical Biology ETDs

A series of hydrocarbon and aqueous soluble salen-type ligands have been synthesized and characterized by electronic and vibrational spectroscopy. Aqueous soluble salen-type ligands were complexed to a metal and investigated as potential underground fluid flow tracers using Surface-Enhanced Raman Spectroscopy (SERS) as the analytical technique. Vibrational spectra obtained from SERS was shown to have enhanced the spectral signal for these complexes in low concentrations though did not show significant differences between the free ligands and their metal complexes. This research has shown that, with some structural modifications, salen-type ligands can be effective candidates as subterranean fluid flow tracers when SERS …

Development Of New Useful Methods For Aldehyde Synthesis And Its Application In Synthesis, He Huang

Chemistry and Chemical Biology ETDs

Development of sustainable synthetic technologies for molecular construction is an important but formidably challenging task in modern organic synthesis. Aldehyde synthesis represents a long-standing interest in synthesis because of the synthetic utility. Classic methods for aldehyde synthesis have the drawbacks of the use of harsh reaction conditions, poor atom-economy and multi-step operation, and production of stoichiometric amount of chemical wastes. The state-of-the-art strategies employ transition metal complexes as catalysts to promote formylation reactions. The concerns of catalyst cost, operation complexity and poor functional group tolerance demands more efficient synthetic technologies. My Ph.D. study focuses on design of conceptually novel catalytic …

Bioinformatics- And Phylogenetics-Guided Approaches To Understanding Sequence-Function Relationships Of Type Ii Polyketide Biosynthetic Gene Clusters, Han Bich Nguyen

Chemistry and Chemical Biology ETDs

Type II polyketides (PK-II) has made up a class of natural products that are structurally diverse and are clinically useful due to their wide-range of bioactivity. The work described in this dissertation focuses on developing approaches to facilitate our understanding of sequence-function relationships of PK-II biosynthetic gene clusters (BGCs). We have systematically summarized the previous characterizations of enzymes involved in the core structure biosynthesis, which have set a foundation for our developments of approaches to discover organisms harboring novel enzymes responsible for novel PK-II molecules. We have successfully developed bioinformatics tools to globally mine the PK-II BGCs in the NCBI …

From Flasks To Applications: Design And Optimization Of Giant Quantum Dots Using Traditional And Automated Synthetic Methods, Christina J. Hanson

Nanoscience and Microsystems ETDs

Semiconducting nanocrystals, also known as quantum dots (QDs), that emit light with near-unity quantum yield and are extremely photostable are attractive options as down-conversion and direct electricity-to-light materials for a variety of applications including solid-state lighting, display technologies, bio-imaging and optical tracking. Standard QDs with a core/thin shell structure display fluorescence intermittency (blinking) and photobleaching when exposed to prolonged room temperature excitation for single dot measurements, as well as significant reabsorption and energy transfer when densely packed into polymers or at high solution concentrations.

We have developed thick shell “giant” QDs (gQDs), ultra-stable photon sources both at the ensemble and …

An Integrated Approach To Studying And Engineering Bacterial Type Ii Polyketide Core Structure Biosynthesis, Xuechen Zhu

Chemistry and Chemical Biology ETDs

Natural products including alkaloids, phenylpropanoids, polyketides, terpenoids and antibiotics provide abundant resources for drugs and drug leads. Type II polyketides (PK-IIs) are a large array of aromatic polyketides that have exhibited various bioactivities including anti-tumor, anti-cancer, anti-fungal and anti-bacteria. Based on the lengths of carbon chains and the cyclization patterns in their core structures, most bacterial PK-IIs have been classified into 6 typical classes: benzoisochromanequinone (BIQ), anthracycline (ANT), angucycline (ANG), tetracycline (TET), tetracenomycin (TCM) and pentangular (PEN). Bioengineering for diversification of PK-II core structures will generate libraries of bioactivities, which can serve the drug discovery in this family of compounds. …

Systematic Size Control In The Synthesis Of Zero-Valent Iron Nanoparticles, Grant C. Bleier

Chemistry and Chemical Biology ETDs

A novel synthetic method for the production of highly magnetic, low size-dispersity nanoparticles through reversible magnetic agglomeration is introduced and studied in detail. Initially, a weakly coordinating surfactant (3-octadecyl-2,4-pentanedione) is employed to produce a wide range of nanoparticle sizes ranging from 8 to 20 nm in diameter. The kinetics faced in these reactions by cheap and widely available iron complex precursors can be avoided in this method with the introduction of thermodynamic control, which occurs in the form of a magnetic precipitation event that essentially halts nanoparticle growth. Utilizing this synthetic method, the length of the alkyl chain on the …

Synthesis, Characterization, And Spectroscopy Of Donor-Acceptor Charge Transfer Complexes, Dominic K. Kersi

Chemistry and Chemical Biology ETDs

A series of square-planar metal (diimine)(dichalcogenolene) chromophoric complexes have been synthesized, characterized and studied spectroscopically. Studies conducted on diimineplatinum(II) dichalcogenolene complexes (LPtL’) using time resolved spectroscopic techniques such as transient absorption and emission, reveal a charge-separated excited state of the type dichalcogenolene → diimine charge-transfer (LL’CT) [(dichalcogenolene^•+)Pt(diimine^•-) with an open shell donor-acceptor biradical character. Long-live excited state lifetimes were observed for these complexes upon visible photoexcitation of the LL’CT or MMLL’CT band. A direct linear relationship is observed to exist between photoluminescence rates, calculated SOC matrix elements, and ¹³C-NMR chemical shifts.

A series of …

Hydrogeochemical Investigation Of Recharge Pathways To Intermediate And Regional Groundwater In Cañon De Valle And Technical Area 16, Los Alamos National Laboratory, Brendan W. Brady

Civil Engineering ETDs

In aquifers consisting of fractured or porous igneous rocks, as well as conglomerate and sandstone products of volcanic formations, silicate minerals actively dissolve and precipitate (Eby, 2004; Eriksson, 1985; Drever, 1982). Dissolution of hydrated volcanic glass is also known to influence the character of groundwater to which it is exposed (White et al., 1980). Hydrochemical evolution, within saturated zones of volcanic formations, is modeled here as a means to resolve the sources feeding a perched groundwater zone. By observation of solute mass balances in groundwater, together with rock chemistry, this study characterizes the chemical weathering processes active along recharge pathways …

Investigating Scalable Manufacturing Of High-Conductivity Wires And Coatings From Ultra-Long Carbon Nanotubes, Pouria Khanbolouki

Mechanical Engineering ETDs

Carbon nanotubes (CNTs) are a promising candidate for next generation of electrical wirings and electromagnetic interference (EMI) shielding materials due to their exceptional mechanical and electrical properties. Wires and coatings from ultralong nanotubes that are highly crystalline, well-aligned and densely packed can achieve this goal. High-performance CNT conductors will be relatively lightweight and resistant to harsh conditions and therefore can potentially replace current conductors in many industries including aerospace, automotive, gas and oil.

This thesis investigates a new manufacturing approach, based on conventional solution coating and wire drawing methods, to fabricate high conductivity wires and coatings from ultra-long carbon nanotubes. …

Formation Of Highly Functionalized Indole Through Carbon-Carbon Bond Cleavage, Ryan A. S. Pike

Chemistry and Chemical Biology ETDs

Indoles are one of the most abundant heterocycles found in nature and have a wide range of functions. There are a wide variety of indole synthesis methods known both in synthetic chemistry and through biosynthesis. Many of the known indole synthesis routes use a benzene derivative or cyclized ring structure derivative as a starting material. Here, we describe a novel synthetic method utilizing 1, 3-diketones and fumaronitrile with a catalytic amount of base to form a highly functionalized indole as our product. We have isolated and characterized 12 functionalized indoles.

Construction Of Synthetic Signal Pathways In Mammalian Cells Via Induced Protein Proximity, Guihua Zeng

Chemistry and Chemical Biology ETDs

Cell signaling translates extracellular signals into intracellular processes that carry out cellular functions. The introduction of artificial signaling networks using synthetic biology methods has facilitated the investigation of signaling mechanisms and the generation of novel cell functions. Several synthetic biology methods that are based on chemical controls have been developed to provide precise temporal regulation. In my dissertation, we constructed new synthetic biology engineering strategies to control tailored cellular events.

Described in Chapter 2, we developed a new chemical strategy to generate de novo signaling pathways that link a signaling molecule, H₂O₂, to different downstream cellular …

Novel Design Strategies For Platinum-Containing Conjugated Polymers And Small Molecules For Organic Solar Cells, Wenhan He

Chemistry and Chemical Biology ETDs

Current state-of-the-art organic solar cells (OSCs) adopt the strategy of using conjugated polymers or small molecules as donors and fullerene derivatives as acceptors in their active layers. Regarding to the donors of interest, the conjugated polymers and small molecules coupled with heavy metals have been less explored compared to their counterparts. Among various transition metal complexes applied, Pt(II) complexes are unique because of their intrinsic square planar geometries and ability to serve as building blocks for conjugated systems. Furthermore, the heavy metal Pt facilitates the formation of triplet excitons with longer life times through spin-orbital coupling which are of benefit …

An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao

Chemistry and Chemical Biology ETDs

Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs produced by these …

Comprehensive Silica Removal With Ferric Compounds For Industrial Wastewater Reuse, Ehren D. Baca

Civil Engineering ETDs

Cooling towers, integrated circuit (IC) manufacture and reverse osmosis (RO) generate copious amounts of wastewater high in colloidal and reactive silica inhibiting on-site or synergistic reuse. Silica present in cooling water can reach solubility limits via evaporation and form impervious scale on heat transfer surfaces that decreases efficiency. When water is treated by RO operating at high rejection, silica forms difficult-to-remove scale on the membrane feed side in the form of glassy patches and communities of aggregate particles, inhibiting aspirations for zero liquid discharge. Current methods for silica scale mitigation include abundant dosing with chemical antiscalents or complex operating schemes. …

Universal Disorder In Organic Semiconductors Due To Fluctuations In Space Charge, Tzucheng Wu

Physics & Astronomy ETDs

This thesis concerns the study of charge transport in organic semiconductors. These materials are widely used as thin-film photoconductors in copiers and laser printers, and for their electroluminescent properties in organic light-emitting diodes. Much contemporary research is directed towards improving the efficiency of organic photovoltaic devices, which is limited to a large extent by the spatial and energetic disorder that hinders the charge mobility. One contribution to energetic disorder arises from the strong Coulomb interactions between injected charges with one another, but to date this has been largely ignored. We present a mean-field model for the effect of mutual interactions …

Enediyne Derived Conjugated Polymers, Keda Hu

Chemistry and Chemical Biology ETDs

The advance of conjugated polymers (CPs) is largely relied on the development of new polymerization methods, the discovery of novel polymers that possess unique chemical and physical properties, and understanding of their structure-property relationship. We have employed a set of trans-enediynes (trans-EDYs) for the preparation of four series of CPs, polydiacetylenes (PDAs), platinum-segmented PDAs, polytriacetylenes (PTAs) and boron doped polyacetylenes (BPAs). The resulting polymers displayed interesting optical and electrochemical properties which could be fine-tuned by the attachment of various side chains on the EDY moieties.

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

Development And Application Of An Expanded Streptomyces Genetic Code, Jingxuan He

Chemistry and Chemical Biology ETDs

Actinobacteria, especially those of genus Streptomyces, are a prominent source of bioactive natural products. The ability to site-specifically incorporate unnatural amino acids (UAAs) into natural product biosynthetic enzymes and ribosomally derived peptides in these organisms would constitute a valuable tool for drug discovery and development. The work described in this dissertation focuses on development and application of an expanded Streptomyces genetic code, including development of UAA incorporation systems based on amber suppression and sense codon reassignment, structural diversification of the model thiopeptide natural product thiostrepton using UAAs, and mapping protein-protein interactions in type II polyketide biosynthetic enzymes using photocrosslinking …

Engineering Small Molecule Based Dimerization To Induce Translation And Provide Optogenetic Control, Catherine Wright

Chemistry and Chemical Biology ETDs

We wanted to develop a system that combines the spatial control of photoactivation and control of translation to build a tool to spatially control translation in neurons. This kind of tool could be used to investigate the role of spatially controlled translation of any protein in neural behavior. In this way the development and growth of neural processes could be studied to elucidate the mechanisms for spatially sensitive events such as pathfinding, repair, or long-term potentiation.

Chemically induced dimerization was used to install a switch into the activation of translation for specific genes. An abscisic acid (ABA) dependent dimerization of …

Molecular Tetrapods For Optoelectronic Applications, Jianzhong Yang

Chemistry and Chemical Biology ETDs

In this dissertation, several molecular tetrapods were synthesized for optoelectronic applications. In the first two sections, two tetrapodal breakwater-like small molecules: SO and SFBTD were synthesized and characterized. Absorption, X-ray scattering and differential scanning calorimetry experiments indicate crystalline nature of these compounds but slow crystallization kinetics. Solar cells employing SO or SFBTD and phenyl-C₆₁-butyric acid methyl ester (PCBM) were fabricated and evaluated. Relatively low performance was obtained mainly due to the lack of appropriate phase separation, which was caused by molecularly mixed blends with PCBM. The molecularly mixed blends is the result of slow crystallization …

Case Studies Of The Hot Dog-Fold And Acyl-Adenylate-Forming Superfamilies: Characterizing The Importance Of Functional Divergence In Cellular Metabolism, Lucas Zimney

Chemistry and Chemical Biology ETDs

Some of the biggest contributors to cellular respiration (and cellular metabolism in general) are acyl-CoA derivatives, a subclass of biological thioesters. Known to function in a variety of pathways, the regulation of their formation and breakdown are critical, carried about by acyl-CoA synthetases and thioesterases, respectively. The work reported within this dissertation will focus on functional divergence within two enzyme superfamilies -- the hot dog-fold and acyl-adenylate-forming superfamilies — and can be broken down into two main parts. Part one will look at tracking the functional divergence within the hot dog-fold superfamily thioesterases. A highly evolved thioesterase, flK, has been …