Chemistry Commons^™

Rational Design Of Small Molecule Disruptors Of Protein-Protein Interactions: Pd-1/Pd-L1; C-Myc, Arid4b, Samuel Ofori

Theses and Dissertations--Chemistry

Protein-protein interactions (PPIs) are vital to many biological processes, including gene expression, and immune reactions to pathogens. There are approximately 650,000 PPIs in humans with pertinent physiological functions. Aberrant expression of PPIs lead to improper function and contribute to a plethora of disease conditions including cancer. Thus, PPIs represent an enormous target space for drug discovery and chemical probes. Direct targeting of clinically relevant PPIs with small molecules remains an unmet medical need. Development of small-molecule inhibitors of PPIs is a challenging enterprise and in most cases considered undruggable due to large protein surfaces, lack of deep binding pockets and …

Investigation Of Multidrug Efflux Transporter Acrb In Escherichia Coli: Assembly, Degradation And Dynamics, Prasangi Irosha Rajapaksha

Theses and Dissertations--Chemistry

The Resistant Nodulation Division (RND) super family member, tripartite AcrA-AcrB-TolC efflux pump, is a major contributor in conferring multidrug-resistance in Escherichia coli. The structure of the pump complex, and drug translocation by functional rotation mechanism have been widely studied. Despite of all these data, the dynamics of the assembly process of the pump and AcrB during functional rotation in the process of drug efflux remains poorly understood. My thesis focuses on understanding the pump assembly process, dynamics of AcrB in functional rotation mechanism, and also investigate the mechanism of degradation of AcrB facilitated by a C-terminal ssrA tag.

In the …

Design, Synthesis, And Anticancer Properties Of Ru(Ii) Complexes With Organometallic, “Expanded” Bipyridine, And O,O’-Chelating Ligands, Raphael Ryan

Theses and Dissertations--Chemistry

Cancer is a worldwide public health crisis that requires new and improved drugs to be developed to extend survival rates and improve quality of life for the patient. Platinum-based drugs are used in approximately 50% of cancer treatment regimens. These drugs are highly effective in many kinds of cancer; however, cancers can develop platinum resistance and these drugs have troubling side effects that reduced their use and efficacy. To overcome these disadvantages, many other metals have been studied for their anticancer properties. Notably, the anticancer properties of ruthenium-based agents have drawn considerable attention with multiple ruthenium complexes entering clinical trials. …

Synthesis Of Dual Small Molecule Hybrids To Probe The Synergy Between Dna Repair Enzymes And Ido1, Nathaniel George

Theses and Dissertations--Chemistry

Indoleamine 2 3-dioxygenase (IDO) has recently been highlighted as a promising target for small molecule based immunotherapy. IDO is often coopted by various cancer cells to promote an immune-suppressive environment around tumors. DNA damage repair (DDR) enzymes have recently been targeted for inhibition to promote genetic instability and bolster immune recognition. DDR enzymes such as PARP and POLγ are common inhibition targets due to their direct effects on cellular function. In the process of designing conjugate inhibitors of IDO and DDR enzymes, novel synthetic methodology was developed for the mild deprotection of N-Tert-butyloxycarbonyl (N-BOC) group from various amines. Conjugate …

Determining Material Structures And Surface Chemistry By Genetic Algorithms And Quantum Chemical Simulations, Josiah Jesse Roberts

Theses and Dissertations--Chemistry

With the advent of modern computing, the use of simulation in chemistry has become just as important as experiment. Simulations were originally only applicable to small molecules, but modern techniques, such as density functional theory (DFT) allow extension to materials science. While there are many valuable techniques for synthesis and characterization in chemistry laboratories, there are far more materials possible than can be synthesized, each with an entire host of surfaces. This wealth of chemical space to explore begs the use of computational chemistry to mimic synthesis and experimental characterization. In this work, genetic algorithms (GA), for the former, and …

Synthesis, Crystal Engineering, And Material Properties Of Small-Molecule Organic Semiconductors, Emma Holland

Theses and Dissertations--Chemistry

Small-molecule organic materials are of increasing interest for electronic and photonic devices due to their solution processability and tunability, allowing devices to be fabricated at low temperature on flexible substrates and offering utility in specialized applications. This tunability is the result of functionalization through careful synthetic strategy to influence both material properties and solid-state arrangement, both crucial variables in device applications. Functionalization of a core molecule with various substituents allows the fine-tuning of optical and electronic properties, and functionalization with solubilizing groups allows some degree of control over the solid- state order, or crystal packing. These combinations of core chromophores …

Developing Synthetic Strategies For Multifaceted Applications Of Stable Gold-Based Complexes, Randall Tyler Mertens

Theses and Dissertations--Chemistry

Development of stable gold-based complexes has been a rapidly advancing field due to the popularity of gold complexes, particularly for use in biomedical research and catalytic transformations. Given that auranofin, a gold(I) complex with FDA approval for the treatment of rheumatoid arthritis is used in the clinic, the development of stable gold-based molecules of clinical relevance is urgently needed. Herein are reported, synthetic strategies used for the development of new classes of gold(I) and gold(III) complexes for advancement in mitochondrial modulation for use as chemotherapeutics as well as application to gold catalysis due to the unique geometry of complexes presented …

Computational Insights On Medicinal Chemistry Targeting Cyp450s, Alexander D. Fenton

Theses and Dissertations--Chemistry

Modern-day medicinal chemistry has provided researchers with a wide variety of tools to not only gather greater insight from their data, but also to generate data in new ways. One such tool is the construction of computational protein models from crystallographic datasets, and their subsequent use to understand the structure-activity relationships of protein-ligand complexes. These models can be utilized for their predictive power to inform the synthesis of, and improvement of, lead compounds. It is the goal of this work to employ such models to the CYP450 enzyme system such that potent and selective inhibitors can be designed, evaluated biologically, …

Plasmon Enhanced Single Molecule Fluorescence In Zero Mode Waveguides (Zmws), Abdullah Masud

Theses and Dissertations--Chemistry

Plasmonic nanostructures are an extensive research focus due to their ability to modify the photophysical properties of nearby fluorophores. Surface plasmons (SP), defined as the collective oscillation of delocalized electrons, are the fundamental characteristic primarily responsible for altering those photophysical properties. Studying fluorophores at the single-molecule level has received significant attention since more specific information can be extracted from single molecule-based studies, which otherwise could be obscured in ensemble studies. However, single-molecule studies are inherently challenging because the signal from a single molecule is usually dim, making it difficult to detect. The situation is even worse in a crowded environment …

Mass Spectrometry Method Development For The Discovery And Characterization Of Secondary Metabolites, Zachary Kelley

Theses and Dissertations--Chemistry

Secondary metabolites are organic compounds produced by an organism for reasons other than growth and development. In plants, secondary metabolites generally act as defense agents produced to deter predators and inhibit other competitive species. For humans, these compounds can often have a beneficial effect and are pursued and utilized as natural pharmaceuticals. The development of sensitive, high-throughput analytical screening methods for plant derived metabolites is crucial for natural pharmaceutical product discovery and plant metabolomic profiling. Here, metabolomic profiling methods were developed using a microfluidic capillary zone electrophoresis device and evaluated against traditional separation approaches. An alkaloid screening assay was constructed …

Flavin Modification And Redox Tuning In The Bifurcating Electron Transfer Flavoprotein From Rhodopseudomonas Palustris: Two Arginines With Different Roles, Nishya Mohamed-Raseek

Theses and Dissertations--Chemistry

Electron bifurcation is considered as a third fundamental mode of energy conservation mechanism in addition to two well-known mechanisms, substrate level phosphorylation and Oxidative phosphorylation, in electron bifurcation endergonic and exergonic redox reactions are coupled. The newly discovered flavin based electron bifurcation in electron transfer flavoproteins (ETFs) helps to reduce low potential ferredoxin, which provides electrons to drive biologically demanding reactions such as atmospheric dinitrogen fixation in diazotroph and methane production in methanogens.

Current research demonstrates the capacity for electron bifurcation in the Rhodopseudomonas palustris ETF (RpalETF) system. RpalETF contains two chemically identical but functionally different FADs: …

Predicting Material Properties: Applications Of Multi-Scale Multiphysics Numerical Modeling To Transport Problems In Biochemical Systems And Chemical Process Engineering, Tom Pace

Theses and Dissertations--Physics and Astronomy

Material properties are used in a wide variety of theoretical models of material behavior. Descriptive properties quantify the nature, structure, or composition of the material. Behavioral properties quantify the response of the material to an imposed condition. The central question of this work concerns the prediction of behavioral properties from previously determined descriptive properties through hierarchical multi-scale, multiphysics models implemented as numerical simulations. Applications covered focus on mass transport models, including sequential enzyme-catalyzed reactions in systems biology, and an industrial chemical process in a common reaction medium.

An Overview Of The Effect Of Bioaerosol Size In Coronavirus Disease 2019 Transmission, Marcelo I. Guzman

Chemistry Faculty Publications

The fast spread of coronavirus disease 2019 (COVID-19) constitutes a worldwide challenge to the public health, educational and trade systems, affecting the overall well-being of human societies. The high transmission and mortality rates of this virus, and the unavailability of a vaccine or treatment, resulted in the decision of multiple governments to enact measures of social distancing. Such measures can reduce the exposure to bioaerosols, which can result in pathogen deposition in the respiratory tract of the host causing disease and an immunological response. Thus, it is important to consider the validity of the proposal for keeping a distance of …

Dark Iron-Catalyzed Reactions In Acidic And Viscous Aerosol Systems Efficiently Form Secondary Brown Carbon, Hind A. Al-Abadleh, Md Sohel Rana, Wisam Mohammed, Marcelo I. Guzman

Chemistry Faculty Publications

Iron-driven secondary brown carbon formation reactions from water-soluble organics in cloud droplets and aerosols create insoluble and soluble products of emerging atmospheric importance. This work shows, for the first time, results on dark iron-catalyzed polymerization of catechol forming insoluble black polycatechol particles and colored water-soluble oligomers under conditions characteristic of viscous multicomponent aerosol systems with relatively high ionic strength (I = 1–12 m) and acidic pH (∼2). These systems contain ammonium sulfate (AS)/nitrate (AN) and C3–C5 dicarboxylic acids, namely, malonic, malic, succinic, and glutaric acids. Using dynamic light scattering (DLS) and ultra high pressure liquid chromatography-mass spectrometry (UHPLC-MS), …

Application Of A Small Unmanned Aerial System To Measure Ammonia Emissions From A Pilot Amine-Co2 Capture System, Travis J. Schuyler, Bradley Irvin, Keemia Abad, Jesse G. Thompson, Kunlei Liu, Marcelo I. Guzman

Chemistry Faculty Publications

The quantification of atmospheric gases with small unmanned aerial systems (sUAS) is expanding the ability to safely perform environmental monitoring tasks and quickly evaluate the impact of technologies. In this work, a calibrated sUAS is used to quantify the emissions of ammonia (NH₃) gas from the exit stack a 0.1 MWth pilot-scale carbon capture system (CCS) employing a 5 M monoethanolamine (MEA) solvent to scrub CO₂ from coal combustion flue gas. A comparison of the results using the sUAS against the ion chromatography technique with the EPA CTM-027 method for the standard emission sampling of NH_{3 …}

Synthesis, Characterization, And Antiproliferative Activity Of Novel Chiral [Quinoxp*Aucl2]+ Complexes, Adedamola S. Arojojoye, R. Tyler Mertens, Samuel Ofori, Sean R. Parkin, Samuel G. Awuah

Chemistry Faculty Publications

Herein is reported the synthesis of two Au(III) complexes bearing the (R,R)-(–)-2,3-Bis(tert-butylmethylphosphino)quinoxaline (R,R-QuinoxP*) or (S,S)-(+)-2,3-Bis(tert-butylmethylphosphino)quinoxaline (S,S-QuinoxP*) ligands. By reacting two stoichiometric equivalents of HAuCl₄.3H₂O to one equivalent of the corresponding QuinoxP* ligand, (R,R)-(–)-2,3-Bis(tert-butylmethylphosphino)quinoxalinedichlorogold(III) tetrachloroaurates(III) (1) and (S,S)-(+)-2,3-Bis(tert-butylmethylphosphino)quinoxalinedichlorogold(III) tetrachloroaurates(III) (2) were formed, respectively, in moderate yields. The structure of (S,S)-(+)-2,3-Bis(tert-butylmethylphosphino)quinoxalinedichlorogold(III) tetrachloroaurates(III) (2) was further confirmed by X-ray crystallography. The antiproliferative activities of the two compounds were evaluated in a panel of cell lines and exhibited promising results comparable to auranofin and cisplatin with …

1,9,10-Substituted Phenothiazine Derivatives With Strained Radical Cations And Use Thereof, Susan A. Odom, Chad Risko, Matthew D. Casselman, Corrine F. Elliott, Nuwan Harsha Attanayake, Subrahmanyam Modekrutti

Chemistry Faculty Patents

Compounds for use in a rechargeable battery are provided, including a compound according to the formula: (see patent for the formula)

wherein R₁ and R₉ are independently selected from the group consisting of H, alkyl, aryl, perfluoroaryl, perfluoroalkyl, alkylaryl, alkoxyaryl, alkylcarboxyl, aryl carbonyl, haloalkyl, perfluoroalkyl, glycols, haloaryl, a negative electrolyte, and a polymer, so long as when R₁ is H, R₉ is not H; and R₁₀ is selected from the group consisting of methyl, alkyl, aryl, alkylaryl, alkoxyaryl, alkylcarboxyl, aryl carbonyl, haloalkyl, perfluoroalkyl, perfluoroaryl, glycols, haloaryl, an oligomer, and a polymer.

Atmospheric Measurements With Unmanned Aerial Systems (Uas), Marcelo I. Guzman

Chemistry Faculty Publications

This Special Issue provides the first literature collection focused on the development and implementation of unmanned aircraft systems (UAS) and their integration with sensors for atmospheric measurements on Earth. The research covered in the Special Issue combines chemical, physical, and meteorological measurements performed in field campaigns as well as conceptual and laboratory work. Useful examples for the development of platforms and autonomous systems for environmental studies are provided, which demonstrate how careful the operation of sensors aboard UAS must be to gather information for remote sensing in the atmosphere. The work serves as a key collection of articles to introduce …

Oxidation Of Phenolic Aldehydes By Ozone And Hydroxyl Radicals At The Air-Water Interface, Md Sohel Rana, Marcelo I. Guzman

Chemistry Faculty Publications

Biomass burning releases highly reactive methoxyphenols into the atmosphere, which can undergo heterogeneous oxidation and act as precursors for secondary organic aerosol (SOA) formation. Understanding the reactivity of such methoxyphenols at the air–water interface is a matter of major atmospheric interest. Online electrospray ionization mass spectrometry (OESI-MS) is used here to study the oxidation of two methoxyphenols among three phenolic aldehydes, 4-hydroxybenzaldehyde, vanillin, and syringaldehyde, on the surface of water. The OESI-MS results together with cyclic voltammetry measurements at variable pH are integrated into a mechanism describing the heterogeneous oxidative processing of methoxyphenols by gaseous ozone (O₃) and …

Mitochondrial Oxidative And Nitrosative Stress And Alzheimer Disease, D. Allan Butterfield, Debra Boyd-Kimball

Chemistry Faculty Publications

Oxidative and nitrosative stress are widely recognized as critical factors in the pathogenesis and progression of Alzheimer disease (AD) and its earlier stage, amnestic mild cognitive impairment (MCI). A major source of free radicals that lead to oxidative and nitrosative damage is mitochondria. This review paper discusses oxidative and nitrosative stress and markers thereof in the brain, along with redox proteomics, which are techniques that have been pioneered in the Butterfield laboratory. Selected biological alterations in—and oxidative and nitrosative modifications of—mitochondria in AD and MCI and systems of relevance thereof also are presented. The review article concludes with a section …

The Bach1/Nrf2 Axis In Brain In Down Syndrome And Transition To Alzheimer Disease-Like Neuropathology And Dementia, Marzia Perluigi, Antonella Tramutola, Sara Pagnotta, Eugenio Barone, D. Allan Butterfield

Chemistry Faculty Publications

Down syndrome (DS) is the most common genetic cause of intellectual disability that is associated with an increased risk to develop early-onset Alzheimer-like dementia (AD). The brain neuropathological features include alteration of redox homeostasis, mitochondrial deficits, inflammation, accumulation of both amyloid beta-peptide oligomers and senile plaques, as well as aggregated hyperphosphorylated tau protein-containing neurofibrillary tangles, among others. It is worth mentioning that some of the triplicated genes encoded are likely to cause increased oxidative stress (OS) conditions that are also associated with reduced cellular responses. Published studies from our laboratories propose that increased oxidative damage occurs early in life in …

Near Simultaneous Laser Scanning Confocal And Atomic Force Microscopy (Conpokal) On Live Cells, Joree N. Sandin, Surya P. Aryal, Thomas E. Wilkop, Christopher I. Richards, Martha E. Grady

Physiology Faculty Publications

Techniques available for micro- and nano-scale mechanical characterization have exploded in the last few decades. From further development of the scanning and transmission electron microscope, to the invention of atomic force microscopy, and advances in fluorescent imaging, there have been substantial gains in technologies that enable the study of small materials. Conpokal is a portmanteau that combines confocal microscopy with atomic force microscopy (AFM), where a probe "pokes" the surface. Although each technique is extremely effective for the qualitative and/or quantitative image collection on their own, Conpokal provides the capability to test with blended fluorescence imaging and mechanical characterization. Designed …

University Of Kentucky Measurements Of Wind, Temperature, Pressure And Humidity In Support Of Lapse-Rate Using Multisite Fixed-Wing And Rotorcraft Unmanned Aerial Systems, Sean C. C. Bailey, Michael P. Sama, Caleb A. Canter, Luis Felipe Pampolini, Zachary S. Lippay, Travis J. Schuyler, Jonathan D. Hamilton, Sean B. Macphee, Isaac S. Rowe, Christopher D. Sanders, Virginia G. Smith, Christina N. Vezzi, Harrison M. Wight, Jesse B. Hoagg, Marcelo I. Guzman, Suzanne Weaver Smith

Mechanical Engineering Faculty Publications

In July 2018, unmanned aerial systems (UASs) were deployed to measure the properties of the lower atmosphere within the San Luis Valley, an elevated valley in Colorado, USA, as part of the Lower Atmospheric Profiling Studies at Elevation – a Remotely-piloted Aircraft Team Experiment (LAPSE-RATE). Measurement objectives included detailing boundary layer transition, canyon cold-air drainage and convection initiation within the valley. Details of the contribution to LAPSE-RATE made by the University of Kentucky are provided here, which include measurements by seven different fixed-wing and rotorcraft UASs totaling over 178 flights with validated data. The data from these coordinated UAS flights …

Nanoceria Distribution And Effects Are Mouse-Strain Dependent, Robert A. Yokel, Michael T. Tseng, D. Allan Butterfield, Matthew L. Hancock, Eric A. Grulke, Jason M. Unrine, Arnold J. Stromberg, Alan K. Dozier, Uschi M. Graham

Pharmaceutical Sciences Faculty Publications

Prior studies showed nanoparticle clearance was different in C57BL/6 versus BALB/c mice, strains prone to Th1 and Th2 immune responses, respectively. Objective: Assess nanoceria (cerium oxide, CeO₂ nanoparticle) uptake time course and organ distribution, cellular and oxidative stress, and bioprocessing as a function of mouse strain. Methods: C57BL/6 and BALB/c female mice were i.p. injected with 10 mg/kg nanoceria or vehicle and terminated 0.5 to 24 h later. Organs were collected for cerium analysis; light and electron microscopy with elemental mapping; and protein carbonyl, IL-1β, and caspase-1 determination. Results: Peripheral organ cerium significantly increased, generally more …

Plasma And Serum Proteins Bound To Nanoceria: Insights Into Pathways By Which Nanoceria May Exert Its Beneficial And Deleterious Effects In Vivo, D. Allan Butterfield, Binghui Wang, Peng Wu, Sarita S. Hardas, Jason M. Unrine, Eric A. Grulke, Jian Cai, Jon B. Klein, William M. Pierce, Robert A. Yokel, Rukhsana Sultana

Chemistry Faculty Publications

Nanoceria (CeO2, cerium oxide nanoparticles) is proposed as a therapeutic for multiple disorders. In blood, nanoceria becomes protein-coated, changing its surface properties to yield a different presentation to cells. There is little information on the interaction of nanoceria with blood proteins. The current study is the first to report the proteomics identification of plasma and serum proteins adsorbed to nanoceria. The results identify a number of plasma and serum proteins interacting with nanoceria, proteins whose normal activities regulate numerous cell functions: antioxidant/detoxification, energy regulation, lipoproteins, signaling, complement, immune function, coagulation, iron homeostasis, proteolysis, inflammation, protein folding, protease inhibition, adhesion, protein/RNA …

Conversion Between Triplet Pair States Is Controlled By Molecular Coupling In Pentadithiophene Thin Films, Natalie A. Pace, Brandon K. Rugg, Christopher H. Chang, Obadiah G. Reid, Karl J. Thorley, Sean Parkin, John E. Anthony, Justin C. Johnson

Chemistry Faculty Publications

In singlet fission (SF) the initially formed correlated triplet pair state, ¹(TT), may evolve toward independent triplet excitons or higher spin states of the (TT) species. The latter result is often considered undesirable from a light harvesting perspective but may be attractive for quantum information sciences (QIS) applications, as the final exciton pair can be spin-entangled and magnetically active with relatively long room temperature decoherence times. In this study we use ultrafast transient absorption (TA) and time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy to monitor SF and triplet pair evolution in a series of alkyl silyl-functionalized pentadithiophene (PDT) thin films …

Correlating The Physicochemical Properties Of Magnesium Stearate With Tablet Dissolution And Lubrication, Julie L. Calahan

Theses and Dissertations--Pharmacy

Magnesium stearate (MgSt) is the most commonly used pharmaceutical excipient and is present in over half the tablet formulations on the market. In spite of its popularity as an effective lubricant, it has been repeatedly recognized that there is significant variability between MgSt samples, which can cause inconsistent lubrication between batches of MgSt. The hypothesis of this research is that the batch-to-batch variability in tablet lubrication and dissolution observed in tablet formulations containing different MgSt samples can be correlated with differences in MgSt physicochemical properties (fatty acid salt composition, crystal hydrate form, particle size and surface area). Developing correlations between …

Carbon Oxidation At The Atomic Level: A Computational Study On Oxidative Graphene Etching And Pitting Of Graphitic Carbon Surfaces, Simon Schmitt

Theses and Dissertations--Mechanical and Aerospace Engineering

In order to understand the oxidation of solid carbon materials by oxygen-containing gases, carbon oxidation has to be studied on the atomic level where the surface reactions occur. Graphene and graphite are etched by oxygen to form characteristic pits that are scattered across the material surface, and pitting in turn leads to microstructural changes that determine the macroscopic oxidation behavior. While this is a well-documented phenomenon, it is heretofore poorly understood due to the notorious difficulty of experiments and a lack of comprehensive computational studies. The main objective of the present work is the development of a computational framework from …

Mild Deprotection Of The N-Tert-Butyloxycarbonyl (N-Boc) Group Using Oxalyl Chloride, Nathaniel George, Samuel Ofori, Sean R. Parkin, Samuel G. Awuah

Chemistry Faculty Publications

We report a mild method for the selective deprotection of the N-Boc group from a structurally diverse set of compounds, encompassing aliphatic, aromatic, and heterocyclic substrates by using oxalyl chloride in methanol. The reactions take place under room temperature conditions for 1–4 h with yields up to 90%. This mild procedure was applied to a hybrid, medicinally active compound FC1, which is a novel dual inhibitor of IDO1 and DNA Pol gamma. A broader mechanism involving the electrophilic character of oxalyl chloride is postulated for this deprotection strategy.

A Biophysical Investigation Of Stability, Ligand Binding, And Iron State Of Cyp102a1, Catherine A. Denning-Jannace

Theses and Dissertations--Chemistry

Cytochrome P450s (CYPs) are cysteine ligated Fe-heme monooxygenases that are found in all domains of life. In mammals, they have a role in xenobiotic metabolism and steroid synthesis, making them a fundamental requirement for survival. In addition, their ability to perform a variety of chemical reactions on an array of substrates makes CYPs highly sought for biotechnical applications such as wastewater remediation, production of potential drug candidates, and creation of drug metabolites. By mutating specific amino acids, these enzymes can be engineered to change their substrate binding profiles and achieve stereo- and regio-specific chemistry. While these mutations are essential to …