Chemistry Commons^™

Understanding The Role Of Atom Trapping In The Evolution Of Hydrocarbon Transformation Catalyst Morphology, Griffin Alexander Canning

Chemistry and Chemical Biology ETDs

Converting alkanes to other, more chemically and economically valuable molecules requires catalysts that can survive elevated temperatures and highly reducing environments. These environments can cause many metal-nanoparticle based catalysts to sinter rapidly, causing a loss of activity. They must also tolerate the coke formation, as well, since coke can restrict access to active sites by gas phase molecules, thus lowering catalytic activity. While there are routes to improve both the sinter and coke resistance of catalysts, an alternative strategy is to develop a protocol for regenerating the activity of the catalyst in question when coke formation or sintering becomes problematic. …

Atom Trapping And Its Role On The Nucleation & Growth Of Platinum Nanoparticles, Deepak Kunwar

Chemistry and Chemical Biology ETDs

Diesel oxidation catalysts deactivate due to Pt sintering, a major problem in automotive industries. To make sure they operate effectively throughout the lifetime of the vehicle, automotive industries are putting an excessive amount of Pt. There is a need to develop a catalyst that serves long term performance with minimal use of Pt. Jones et al^.1 demonstrated that ceria traps Pt atoms. His work generated some logical and valid questions such as what is the mechanism for the formation of anomalously large Pt particles? What is the upper limit of Pt metal loading in the form of single atoms …

Small Molecule Analog Studies Of Paramagnetic Dmso Reductase Enzyme Family Intermediates, Khadanand Kc

Chemistry and Chemical Biology ETDs

Pyranopterin molybdenum and tungsten enzymes are expressed in numerous organisms from all domains of life. These enzymes catalyze a variety of atom, hydride, and electron transfer reactions. The enzymes are of great importance in the biogeochemical cycles of nitrogen, carbon, and sulfur. In recent years, chemists have investigated applications for some of these enzymes as industrial biocatalysts. The dimethylsulfoxide reductase (DMSOr) enzyme family is the broadest family of pyranopterin Mo enzymes. The first coordination sphere of the Mo or W-containing active site for each member of this family is made up of 4 sulfur donors from the two pyranopterin dithiolenes …

Charge Transfer And Plasmon-Pumped Molecular Excitation Mechanisms In Surface Enhanced Photochemistry, Tefera Entele Tesema

Chemistry and Chemical Biology ETDs

Photochemistry that can be driven at low incident photon flux on optically excited plasmonic nanoparticles is attracting increasing research interest because plasmon-driven reactions offer new pathways for efficient conversion of the abundant solar energy into fuel. The confinement of the electromagnetic field by plasmonic metal nanoparticle and consequent field enhancement gives a dual advantage of ultrasensitive in situ and operando spectroscopic methods to monitor enhanced field-driven photochemical transformation. Charge carrier driven either via direct or indirect excitation mechanism are well-established pathways in plasmon-driven reactions to date. However, the excitation mechanism via plasmon-pumped electron transition from an occupied molecular orbital (HOMO) …

Design And Applications Of Charge-Separated Metal-Organic Frameworks, Sheela Thapa

Chemistry and Chemical Biology ETDs

Ionic tetrapodal ligands with colinear coordinating arms are very effective for designing hybrid porous materials with unusual structure and properties. The novelty of this research work lies in the utilization of a unique borate ligand that leads to charge-separated MOF structure with tailor designed properties. Borate ligands being tetrahedral afford 3D materials and the negative charge of borate anion can compensate the positive charge of metal ion in the framework. The borate ligands designed in this research consists of quaternary ammonium cation and anionic borate with four pyridine arms. These ligands upon coordination with Cu(I), Cu(II), Ag(I) and Co(II) metal …

Self-Assembly, Integration, Characterizations And Applications Of Plasmonic And Excitonic Nanomaterials, Bijesh Kafle

Chemistry and Chemical Biology ETDs

Plasmon on metal nanoparticles can efficiently confine, amplify light at the nanoscale. This property is beneficial for different applications such as harvesting energy of the broad solar spectrum, highly sensitive spectroscopy, photocatalysis, and many other optoelectronic applications. For plasmonic applications, it is necessary to understand the fundamental physical properties of the individual, coupled plasmonic nanomaterials, and their interaction with the surrounding environment, which is not fully understood yet. In this dissertation, the chemical and optical interaction in plasmonic interfaces has been investigated. Plasmon-enhanced photochemistry of p-aminothiophenol as a model molecule is investigated using highly sensitive surface-enhanced Raman spectroscopy (SERS). The …

Development Of Ni-Catalyzed Alkene Dicarbofunctionalization Reactions, Shekhar Kc

Chemistry and Chemical Biology ETDs

Alkenes serve as one of the most important feedstocks for organic synthesis, having two vicinal sites for bond formation. In alkenes, both vicinal sites can be functionalized with two reagents in a process commonly known as alkene difunctionalization, which results in the formation of two new bonds. A number of alkenes difunctionalization reactions, such as diamination, dioxygenation, carboamination and carbooxygenation, are known. However, difunctionalization of alkenes with two carbon-based entities, termed alkene dicarbofunctionalization, is relatively less common. Development of such a process could provide a powerful method to introduce two different carbon fragments across an alkene in a regioselective manner, …

Triplet Population Dynamics And Excited State Relaxation In Chalcogenophene Polymers, Benjamin D. Datko

Chemistry and Chemical Biology ETDs

The conventional understanding of intersystem crossing in multichromophoric conju- gated polymers is usually depicted via a pure electronic model, neglecting contributions of vibrations or conformational order. Obtaining accurate structure-function correlations on spin-conversion processes involving photogenerated singlet excitons to triplet excitons and the excited state dynamics requires sensitivity to the subtle conformational ordering within conjugated polymers. This dissertation seeks to understand the kinetics of multi-exciton singlet-triplet interactions and the excited state relaxation of chalcogen containing (S, Se) conjugated polymers. Utilizing single molecule modulation spectroscopy allows determi- nation of triplet formation of individual conjugated polymer chains and aggregates. This technique resolves triplet-induced …

Nanostructuring Organic/Inorganic Multicomponent Composites For Solution Processable Solar Cells, Brad W. Watson

Chemistry and Chemical Biology ETDs

The current state of organic photovoltaics is centered on systems of polymeric donors and some type of acceptor molecule (i.e. fullerene) formed into an active layer that adopts a bulk-heterojunction morphology. Although these devices have come a far way from where they were when they were first discovered in the 1980’s much work is still needed to make them a viable technology. Two of the limitations of this type of devices revolve around the relatively narrow absorption window of the components and lack of control over the morphology after the film is cast. To overcome these shortcomings there are several …

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 Christian 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 …

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 Kofi 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. This makes the low-energy ligand-to-ligand charge-transfer (LL’CT), or the mixed-metal ligand-to-ligand charge-transfer (MMLL’CT), transitions of diimineplatinum(II) dichalcogenolene complexes particularly interesting to us in facilitating our knowledge of biradical charge-separated states. Long-live excited state lifetimes were observed for these complexes upon visible photoexcitation …

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 …

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. We have applied acyclic EDY metathesis for the synthesis of PDAs, a class of CPs …

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 …

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 …