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Abstract: We describe the synthesis of C-5 indole-tagged pyrimidine and C-8 indole-tagged purine nucleoside phosphoramidites and their incorporation into double-stranded DNA 15 base pairs in length. Of the 23 sequence modifications tested, two induced the DNA duplex to adopt a Z-like left-handed conformation under physiological salt conditions, bypassing the specific sequences typically required for a left-handed Z-DNA structure. The impact of these modifications varied with the linker type: flexible propyl linkers exhibited distinct effects compared to rigid propargyl linkers. Notably, modifications positioned directly on or near a restriction site emphasized the pivotal role of linker rigidity in controlling DNA conformation. Specifically, the conformational change induced by the flexible linker impacted nuclease and restriction endonuclease cleavage, reducing sequence specificity. In contrast, the rigid linker suppressed this effect. Furthermore, our findings indicate that nucleic acid duplexes modified with indole-linked nucleotides using a flexible propyl linker have a pronounced tendency to form BZ or Z-like regions in longer DNA sequences. A higher density of modifications may even induce a full Z-like conformation throughout the duplex. These modified nucleotides hold potential for the development of novel antisense therapeutics and introducing valuable tools for in vitro screening of small molecules targeting distorted B-DNA, BZ-DNA, and Z-DNA structures.

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Abstract: Shortwave infrared (SWIR, 1000-1700 nm) and extended SWIR (ESWIR, 1700-2700 nm) absorbing materials are valuable for applications including fluorescence based biological imaging, photodetectors, and light emitting diodes. Currently, ESWIR absorbing materials are largely dominated by inorganic semiconductors which are often costly both in raw materials and manufacturing processes used to produce them. The development of ESWIR absorbing organic molecules is thus of interest due to the tunability, solution processability, and low cost of organic materials compared to their inorganic counterparts. Herein, through the combination of heterocyclic indolizine donors and an antiaromatic fluorene core, a series of organic chromophores with absorption maxima ranging from 1470-2088 nm (0.84-0.59 eV) and absorption onsets ranging from 1693-2596 nm (0.73-0.48 eV) are designed and synthesized. The photophysical and electrochemical properties of these chromophores, referred to as FluIndz herein, are described via absorption spectroscopy in 17 solvents, cyclic voltammetry, solution photostability, and transient absorption spectroscopy. Molecular orbital energies, predicted electronic transitions, and antiaromaticity are compared to higher energy absorbing chromophores using density functional theory. The presence of thermally accessible diradical states is demonstrated using density functional theory and EPR spectroscopy, while XRD crystallography confirms structural connectivity and existence as a single molecule. Overall, the FluIndz chromophore scaffold exhibits a rational means to access organic chromophores with extremely narrow optical gaps.

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Abstract: Ligand-based virtual screening (LBVS) has rarely been tested as a method for discovering new structural scaffolds for PET radioligand development. This study used LBVS to discover potential chemotype leads for developing radioligands for PET imaging of tauopathies. ZINC12, a free database of over 12 million commercially available compounds, was searched to discover novel scaffolds based on similarities to four query compounds. Thirteen high-ranking hits were purchased and assayed for their ability to compete against three tritiated radioligands at their distinct binding sites in Alzheimer’s disease brain tissue. Three hits were 2-substituted 6-methoxy naphthalenes. Synthetic elaboration of this new chemotype yielded three new ligands (25, 26, and 28) with high affinity for the [³H]6 (flortaucipur) neurofibrillary tangle binding site. Compound 28 showed remarkably high affinity (K_i, 7 nM) and other desirable properties for a candidate PET radioligand, including low topological polar surface area, moderate computed log D, and amenability for labeling with carbon-11. LBVS appears to be uniquely valuable for discovering new chemotypes for candidate PET radioligands.

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Abstract: Diarylethenes (DAEs) are an important class ofphotoswitchable compounds that typically undergo reversiblephotochemical conversions between the open and closed cyclizedforms upon treatment with UV light or visible light. In this study,we introduced thioacid functional groups to several photochromicdithienylethene (DTE) derivatives and established a method thatcan be used to prepare these photoswitchable thioacids. Fourthioacid-functionalized diarylethene derivatives were synthesizedthrough the activation of carboxylic acids with N-hydroxysuccini-mide, followed by reactions with sodium hydrosulfide with yields over 90%. These derivatives exhibited reversible photoswitchingand photochromic properties upon treatment with ultraviolet (UV) and visible lights. The thioacid groups on these compounds canact as reaction sites for attaching other desirable functionalities. The photochromic properties of these new derivatives werecharacterized by using ultraviolet?visible (UV?vis) spectroscopy. The photocyclizations of one of the derivatives and its potassiumsalt were also characterized by using nuclear magnetic resonance (NMR) spectroscopy. The anions of the thioacid formed water-soluble photochromic systems, and their applications as colorimetric sensors in agarose hydrogels were demonstrated.

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Abstract: This thesis highlights strategies for fiinctionalizing carbon nanomaterials with reactive metaspecies for applications in chemical sensing and electrocatalysis. In Chapter 1, we begin with anintroduction of chemiresistive sensing using functionalized carbon nanotubes (CNTs). Thisintroduction summarizes the design, fabrication, characterization, and evaluation of carbonnanotube-based chemiresistive sensors. Potential strategies for optimizing sensitivity andselectivity are also discussed. Typical applications of'CNT-based chemiresistive sensing are alsosurveyed. In Chapter 2, we report the synthesis of Pentiptycene Polymer/Single-Walled CarbonNanotube Complexes and their applications in the selective detection of benzene, toluene, and o.xylene using chemiresistive and quartz crystal microbalance-based methods. In Chapter 3. wereport a method to efiectively immobilize transition metal selectors in close proximity to theS WCN'T surface using pentiptycene polymers containing metal-chelating backbone structures. Wehave identified sensitive, selective, and robust copper-based chemiresistive ammonia sensorsdisplaying low parts per billion detection limits. We have added these hybrid materials into theresonant radio firequency circuits of commercial near-field communication (NFC) tags to achievewireless detection ofammonia at physiologically relevant levels, offering a non-invasive and cost.efiective approach for early detection and monitoring of chronic kidney diseases. In Chapter 4we report that iptycene-containing poly(arylene ether)s (PAEs) show to limit the palladiumnanoparticles (Pd NPs) growth and stabilize the Pd NPs dispersion. SWCNT-based chemiresistorsand graphene field-efect transistors (GFETs)using these PAE-supported small Pd NPs aresensitive, selective, and robust sensory materials for hydrogen gas under ambient conditions. InChapter 5, we describe chemiresistors based on SWCNTs containing small and highly reactivecopper-based nanoparticles in sulfonated pentiptycene poly(arylene ether)s (PAEs). The sensorsshow exceptional sensitivity to trace hydrogen sulfide in wet air with a low-ppb detection limithigh selectivity over a wide range of interferants, and month-long stability under ambientconditions. In Chapter 6, we report a SWCNT-based chemiresistor catalyst combination that candetect ppb levels of' ethylene in air, driven by the chemoselectivity ofthe catalytic transformationThe utility of this ethylene sensor is demonstrated in the monitoring of senescence in red carnationsand purple lisianthus flowers.In Chapter 7, we report SWCNT-based chemiresistive sensorsbased on a catalytic system comprising a copper complex and TEMPO cocatalyst, enabling thesensitive, selective, and robust detection of trace ethanol in air. In Chapter 8, we report thesynthesis of carbon-nanomaterial-based metal chelates that enable effective electronic coupling toelectrocatalytic transition metals. The defined ligands on the graphene surfaces enable theformation of structurally precise heterogeneous molecular catalysts. We demonstrate that thedensely functionalized metal-chelated carbon nanomaterials are eliective heterogeneous catalystsin the oxygen evolution reaction with low overpotentials and tunable catalytic activity.

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Abstract: The reorganization energy (λ) for interfacial electron transfer (ET) and proton-coupled ET (PCET) from a conductive metal oxide (In2O3:Sn, ITO) to a surface-bound H2O oxidation catalyst was extracted from kinetic data measured as a function of the thermodn. driving force. Visible light excitation resulted in rapid excited-state injection (kinj > 108 s-1) to the ITO, which photo-initiated the two interfacial reactions of interest. The rate constants for both reactions increased with the driving force, -ΔG°, to a saturating limit, kmax, with rate constants consistently larger for ET than for PCET. Marcus-Gerischer anal. of the kinetic data provided the reorganization energy for interfacial PCET (0.90 ± 0.02 eV) and ET (0.40 ± 0.02 eV), resp. The magnitude of kmax for PCET decreases with pH, behavior that was absent for ET. Both the decrease in kmax and the larger reorganization energy for an unwanted competing PCET reaction from the ITO to the oxidized catalyst showcases a significant kinetic advantage for driving solar H2O oxidation at high pH. Computational anal. revealed a larger inner-sphere reorganization energy contribution for PCET than for ET arising from a more significant change in the Ru-O bond length for the PCET reaction. Extending the Marcus-Gerischer theory to PCET by including the excited electron-proton vibronic states and the proton donor-acceptor motion provided an apparent reorganization energy of 1.01 eV. The Marcus-Gerischer theory initially developed for ET can be reliably extended to PCET for quantifying and interpreting reorganization energies observed exptl.

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Abstract: Reactive oxygen species (ROS) are a heterogeneous group of highly reactive ions and molecules derived from molecular oxygen (O 2), which can cause DNA damage and lead to skin cancer. High levels of ROS can promote cancer development, cancer cell survival, and resistance to chemotherapeutics. NADPH oxidase (NOX) is a significant producer of ROS in the cell. NOX1 generates two superoxide molecules by reducing NADPH. This only occurs when the membrane-bound NOX cytochrome p450 alpha chain (CYBA) binds to the organizer subunit NOXO1 from the cytosolic portions of the holoenzyme on the cell surface. We propose that stopping NOX1 complex subunits from coming together at this CYBA-NOXO1 junction is a potential way to prevent ROS production in human skin cells when exposed to ultraviolet rays. This dissertation investigates potential small-molecule inhibitors of the crucial NOX1 holoenzyme to solve these issues. We designed and synthesized NOX1 specific Inhibitor 1 using a diapocyin backbone structure. Computational docking studies were used to optimize inhibitor design and evaluate the NOXO1 protein subunit specificity. Due to increased binding interaction with NOXO1 protein and to improve solubility of solution preparation for further physical binding studies, we modified Inhibitor 1 and synthesized Inhibitor 2 by adding the NHS-ester Biotin polyethylene glycol chain to the piperidine ring. Both inhibitors were found to be non-toxic in human keratinocyte cells. The Inhibitor 2 reduced the cyclobutene pyrimidine dimer (CPD) DNA mutation in a human skin explant model. Finally, the isothermal calorimetric (ITC) binding assay and MALDI-TOF mass spectrometry were used for physical binding studies to evaluate the critical molecular interaction, leading to the decreased binding affinity of Inhibitor 1, Inhibitor 2, resulting in additional modifications seen in Inhibitor 3 and Inhibitor 4. The results demonstrate that Inhibitor 2 and Inhibitor 3 reduced the binding affinity between NOXO1 protein and CYBA membrane peptide because of a higher binding interaction of the inhibitors with NOXO1 protein, due to the interaction of the polyethylene glycol chain. In the second section of the project, we computationally design and synthesize NOX1-specific inhibitors using the sequence of CYBA peptides as a modeling tool. Through docking studies, we demonstrated inhibitor interference with NOX1 complexes. Several molecules were designed computationally, and three candidate compounds were tested in vitro and demonstrated a reduction of UVR damage in keratinocyte cells. Biophysical studies, like ITC, were performed to identify interactions. Through these studies, an understanding of protein-protein interactions was gained that are essential for discovering and validating inhibitor candidates, along with information for future inhibitor design. To determine the optimum strategy to utilize the biological features of the small molecule NM-166, a structure-activity relationship analysis was performed.