Physical Sciences and Mathematics Commons^™

Studies Of Oxidopyrylium Ylide Dimers And Their Utility In The Synthesis Of Densely Functionalized Troponoids, Daniel V. Schiavone

Dissertations, Theses, and Capstone Projects

Herein, we describe our efforts to investigate mechanistic considerations of oxidopyrylium ylides and their use in cycloadditions to form complex bicyclic structures and the advancement of these cycloadducts to the synthesis of densely functionalized tropolones. This work also describes applications of tropolones as biologically relevant structures and dynamic fluorophores.

In Chapter 1, we expand upon previous studies done in the Murelli Lab describing the ability of 3-hydroxy-4-pyrone derived oxidopyrylium dimers to revert back to ylides in situ and as result can be used as a clean oxidopyrylium ylide source in accessing oxabicyclic compounds. Intermolecular cycloadditions of these ylides can be …

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

Stereospecific Cross-Coupling Reactions Of Vinyl Triflates And An Investigation Of The Synthesis And Reactivity Of Activated Alkyltricyclohexylstannanes, Pejman Ghaemimohammadi

Dissertations, Theses, and Capstone Projects

Organic chemistry exists in all aspects of everyday life from polymers to pharmaceutics. Formation of carbon-carbon bonds is essential for the synthesis of complex organic compounds. This goal can be achieved by using transition metal catalysts. Second-row transition metals such as Pd, Pt, Rh, and Ir have shown remarkable efficacy in these reactions. Metal-catalyzed cross-coupling reactions form carbon-carbon bonds between electrophiles and nucleophiles using transition metal catalysts. Pd is mainly used in this reaction.

Transition metal-catalyzed cross-coupling reactions that form a bond between two C(sp²) carbons have been widely studied over the past decades. C(sp²)-C(sp^{3 …}

Evaluating The Reliability And Accuracy Of Alchemical Binding Free Energy Methods And Calculations, Fnu Sheenam

Dissertations, Theses, and Capstone Projects

Molecular recognition plays a crucial role in various biological processes, such as enzymatic reactions, signal transduction, and genetic information processing. Investigating how proteins selectively bind to their partners is an active research area, but there is a lack of experimental details on protein structures and interactions in molecular complexes. Computational techniques based on macromolecular structures offer a way to predict protein-ligand interactions and explore their recognition mechanisms. Estimating binding affinities, particularly through alchemical binding free energy calculations, has become valuable in supporting drug discovery. This work introduces new methodologies, utilizing the Alchemical Transfer Method, to address issues like poor convergence …

Disordered Protein Aggregates Are Linked To Changes In The Histone Post-Translational Modification Landscape In Disease And Non-Disease Models, Samantha Cobos

Dissertations, Theses, and Capstone Projects

Proper protein folding is a delicate balance that is crucial for normal biological function. In mammals, protein misfolding and aggregation leads to loss of function of the original protein while in many cases being associated with neurodegenerative diseases, eventually leading to death of the organism. In yeast however, the aggregated prion state is associated with positive cellular outcomes, and cells can switch between the [PRION+] and [prion-] states. Understanding the factors that lead to changes in prion state conformation in yeast could lead to novel insight into the conditions controlling misfolding by neurodegenerative proteinopathies. We believe that by studying the …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Kinetics Of Photochemical And Mechanochemical Organic Reactions On Surface, Yerzhan Zholdassov

Dissertations, Theses, and Capstone Projects

Solvents used in traditional chemical processes account for a large percentage of reaction mass and waste and can pose significant environmental and health risks. The environmentally friendly nature of mechanochemistry, in addition to other benefits, makes it a promising approach for sustainable chemistry over traditional solvent-based methods. However, it is still not a widely adopted method for performing chemical reactions on an industrial scale. This is partially due to the significant challenge associated with understanding the reaction kinetics under mechanochemical conditions. Many variations of scanning probe lithography (SPL) techniques are able to manipulate the organic molecules with precise control over …

Quantifying Temperature-, Pressure-, And Nuclear Quantum Effects On Hydrophobic And Hydrophilic Water-Mediated Interactions, Justin T. Engstler

Dissertations, Theses, and Capstone Projects

Water-mediated interactions (WMIs) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure, and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic–hydrophilic) interactions have been mostly overlooked. Here, we study the role of T and P on the WMI between nanoscale (i) hydrophobic–hydrophobic, (ii) hydrophilic–hydrophilic, and (iii) hydrophilic–hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic, and hybrid interactions are all sensitive to …

Stereospecific Cross-Coupling Reactions With Enantioenriched Electrophiles, Iv Kraja

Dissertations, Theses, and Capstone Projects

We have developed a novel palladium-catalyzed stereospecific C(sp³)–C(sp³) Stille cross-coupling reaction between carbastannatrane nucleophiles and α-(trifluoromethyl) benzylic tosylates. This constitutes the first example of a stereospecific C(sp³)–C(sp³) cross-coupling reaction using an enantioenriched electrophile and an alkyltin nucleophile. This system has the potential to be extended to cross-coupling reactions using configurationally stable enantioenriched nucleophiles, thus enabling stereochemical control of two newly formed contiguous stereocenters. Generating enantioenriched α-(trifluoromethyl) benzylic compounds also has importance in pharmaceutical and agrochemical industries.

Through the development of this reaction, our findings show that the addition …

Synthesis Of Biologically Active Tropolones And Stereochemically Rich Compounds Via Cross-Coupling Reactions, Nana B. Agyemang

Dissertations, Theses, and Capstone Projects

Over the past years the Murelli lab has established research based on the synthesis and biological evaluations of alpha-hydroxytropolones (alpha-HTs). These seven-membered aromatic rings have three contiguous oxygen atoms that chelates to metals, thus, biologically having the ability to bind dinuclear metalloenzymes and promoting inhibition. Synthetic routes to alpha-HT’s are scarce and therefore has been the main driving force in developing efficient and general synthetic methods to obtain variations in alpha-HTs, enabling SAR studies. The Murelli lab have therefore developed an oxidopyrylium cycloaddition/ring-opening strategy that is able to generate polysubstituted alpha-HTs starting from kojic acid, a cheap and readily available …

Analysis Of Polymer-Coated Bullets Using Spectroscopic Methods, Liana R. Albano

Student Theses

Polymer-coated bullets have gained popularity because they can reduce the user’s exposure to heavy metals in the ammunition. The synthetic jacket, which surrounds the lead core, is advantageous because it prevents metal-on-metal contact between the bullet and the bore. A challenge for firearms identification is that polymer-coated bullets do not retain unique markings that can be used to identify the gun, the way standard metal-coated bullets do. However, metal-coated bullets will result in a similar challenge if the bullet is too deformed once it is recovered. Another issue is that the composition of the polymer coating was never disclosed by …

Identification Of Different Hair Dyes In Dyed Hair Using Attenuated Total Reflectance (Atr Ft-Ir), Surface Enhancing Raman Spectroscopy (Sers) Techniques, Nicholas Lovera

Student Theses

This investigation compares the ability of Attenuated Total Reflection Fourier Transfer Infrared Spectroscopy (ATR FT-IR) and Surface Enhance Raman Spectroscopy (SERS) to identify and differentiate different hair dye brands on dyed hair samples. Hair is a common type of trace evidence found at crime scenes and can provide numerous information through forensic hair analysis. Cosmetic hair treatment such as dying the hair different colors has grown and became popular, thus it can be a very common type of trace evidence. This study can provide a forensic scientist an additional method for analyzing dyed hair samples. The goal was to compare …

The Development Of Novel Radioimmunoconjugates For The Pet Imaging And Radioimmunotherapy Of Cancer, Samantha M. Sarrett

Dissertations, Theses, and Capstone Projects

Antibodies have long played a vital role in nuclear medicine for both the diagnosis and therapy of various malignancies. The role and development of antibodies in nuclear medicine can be broadly separated into three different categories: 1) bioconjugation strategies, 2) immunoPET imaging, and 3) radioimmunotherapy. This dissertation will attempt to comprehensively cover each of these categories through a series of studies, protocols, and reviews. For the bioconjugation strategies, we will describe the development of a novel site-selective bioconjugation strategy using an innovative lysine-targeting reagent, PFP-bisN₃, to prepare [⁸⁹Zr]Zr-^SSKDFO-pertuzumab for visualizing HER2+ breast cancer. Further, …

A Typological And Chemical Analysis Of Roman Oil Lamps From Poggio Del Molino, Brandon Tejo

Dissertations, Theses, and Capstone Projects

Terracotta lamps, known to the Romans as lucernae, are small, handheld, often decorated objects which provided ancient people light. To modern researchers, they serve as tools for dating stratigraphy and iconographic studies. Beyond their immediately apparent aesthetic and symbolic value, the chemical compositions of the clay of these lamps reflect their origin. This study complements archaeological typologies with chemometric analyses to describe 16 Late Republican and Imperial Roman lamps recovered from the villa at Poggio del Molino (PdM), Tuscany. These finds were recovered from the 2021 and 2022 PdM excavations. The combined approach of typology with X-ray Diffraction (XRD) …

Sers For The Detection Of Trace Materials, Omari Kirkland

Dissertations, Theses, and Capstone Projects

In this dissertation are presented three projects that contribute to the body of research on SERS in the forensic, heritage, and semiconductor fields. The first project, Charge-Transfer mapping on GaN/Ag, a silver-decorated nanopillar semiconductor substrate fabricated from the GaN is used with the Raman probe Rhodamine 6 G (R6G) to map the effect of the nanofeatures on the CT resonance. The second project, in collaboration with Marco Leona from the Metropolitan Museum of Art, explores the use of AgNIFs to identify colorants used on textile fiber samples from four 19th century works of Japanese art. The final project analyzes the …

Design, Synthesis, And Kinetic Study Of The First Generation Phenyloxadiazole Compounds And The Second Generation Phenyloxadiazole Compounds And Highly Selective Hydroboration Of Alkenes, Ketones And Aldehydes Catalyzed By A Well-Defined Manganese Complex, Haisu Zeng

Dissertations, Theses, and Capstone Projects

This thesis focuses on two projects. In the first project, my goal was to discover a new variant of phenyloxadiazole compounds that could exhibit increased thiol-reactivity during bioconjugation processes. To achieve this, I synthesized several phenyloxadiazole derivatives and subjected them to NMR kinetic studies to assess their reactivity with a model thiol. Based on the results, I was able to identify a phenyloxadiazole analog that demonstrated enhanced reactivity, which included a chlorine atom located in the meta-position of the phenyl ring.

I provided a detailed description of the synthesis and characterization of the newly discovered phenyloxadiazole analog and demonstrate its …

Synthesis And Biomedical Applications Of Hollow Iron Oxide Nanoparticles, Aloka S. Paragoda Arachchilage

Dissertations, Theses, and Capstone Projects

Nano-scale materials have gained much attention during the past few decades due to the stark differences in their properties compared to bulk material. Thus, they are being studied for a myriad of applications ranging from harnessing solar energy to diagnostics. This thesis focuses on the synthesis of hollow iron oxide nanoparticles using Galvanic replacement reactions and their application in drug delivery. Moreover, the use of a peptide precursor for the enhancement of exosomes is also discussed.

Chapter 1 discusses a simple and economical Galvanic approach used for the synthesis of hollow one-dimensional iron oxide nanotubes. In the initial reaction, the …

Nanoscale Imaging Of Electrocatalytic Nanomaterials By High-Resolution Scanning Electrochemical Microscopy, Xiang Wang

Dissertations, Theses, and Capstone Projects

Numerous insights of the structure–electrochemical activity relationship of nanocatalysts have been obtained by using macroscopic electrochemical measurements over the last several decades. However, signals measured by large electrodes are inevitably averaged out of many nanocatalysts, non-uniformed sizes, uneven morphologies, and multiple crystallographic facets. Over the last ten years, Scanning Electrochemical Microscopy (SECM) has advanced electrochemical measurements toward micro- to nanoscale level at a high spatial resolution. The advantages of using nanoelectrode in SECM include fast mass transfer of reactive species, dominated radial diffusion pattern, small double layer capacitance and small RC constant. In this thesis, high-resolution SECM is applied to …

Optimized Peptide Nanomaterials As Delivery Vehicles For Hydrophobic Metal-Based Anticancer Agents, Yaron Marciano

Dissertations, Theses, and Capstone Projects

Enzyme-responsive materials have been well explored, particularly as therapeutic and diagnostic agents. In this thesis we demonstrate that anionic self-assembling peptides can be utilized as delivery vehicles for metal-based hydrophobic payloads. The tunability of the system is highlighted as well as the increase in cytotoxicity and selectivity in vitro. The rapid degradation of peptides in cell media may lead to the formation of new peptide-drug bioconjugates with increased activity and selectivity. The physiological stability of these peptide delivery vehicles has been optimized by capping the N-terminus with an acetyl group. This simple backbone modification was shown to not prevent self-assembly, …

Synthesis And Analysis Of Novel Troponoid-Based Chemical Probes, Alex Berkowitz

Dissertations, Theses, and Capstone Projects

Troponoids are a class of non-benzenoid aromatic species featuring a cycloheptatrienone ring and varying degrees of oxygenation. These scaffolds have proven ubiquitous amongst natural products, and have displayed promise as therapeutic agents against a variety of diseases. Herein, we will describe our efforts towards furthering troponoids as potential pharmaceuticals. In Chapter 1, we outline a kojic acid-derived oxidopyrylium cycloaddition/ring-opening method developed in our lab to generate ahydroxytropolones (aHTs). This route was successfully adapted to synthesize a small library of lipophilic aHTs that were proven to be effective against herpes simplex virus-1 (HSV-1) replication, while providing further insight into the mechanism …

The Water, Ji Kim

Open Educational Resources

Water is everywhere, thus, we tend to take it for granted. However, access to clean water has been inequitable; climate change is threatening the sea water level, causing the acidification of ocean water. In this project, we will investigate the environmental and social issues related to clean water and its impacts on our life by reading articles, watching videos, and exploring activities.

Microstructural Origin Of The High-Energy Storage Performance In Epitaxial Lead-Free Ba(Zr 0.2 Ti 0.8 )O 3 Thick Films, Jun Ouyang, Xianke Wang, Changtao Shao, Hongbo Cheng, Hanfei Zhu, Yuhang Ren

Publications and Research

In our previous work, epitaxial Ba(Zr 0.2 Ti 0.8 )O 3 thick films (~1–2 μ m) showed an excellent energy storage performance with a large recyclable energy density (~58 J/cc) and a high energy efficiency (~92%), which was attributed to a nanoscale entangled heterophase polydomain structure. Here, we propose a detailed analysis of the structure–property relationship in these film materials, using an annealing process to illustrate the effect of nanodomain entanglement on the energy storage performance. It is revealed that an annealing-induced stress relaxation led to the segregation of the nanodomains (via detailed XRD analyses), and a degraded energy storage …

Markovnikov Alcohols Via Epoxide Hydroboration By Molecular Alkali Metal Catalysts, Guoqi Zhang, Haisu Zeng, Shengping Zheng, Michelle C. Neary, Los Alamos National Laboratory

Publications and Research

Summary

Sensitized Photooxidation Of Prenylated Compounds: Mechanisms Of Downstream Dark Effects And Phototoxicity Priming, Shakeela Jabeen

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters as detailed below.

Chapter 1 discusses a singlet oxygen priming mechanism. Airborne singlet oxygen derived from photosensitization of triplet dioxygen is shown to react with an alkene surfactant (8-methylnon-7-ene-1 sulfonate) leading to ‘ene’ hydroperoxides that in the dark inactivate planktonic E. coli. The ‘ene’ hydroperoxide photoproducts are not toxic on their own, but they become toxic after the bacteria are pretreated with singlet oxygen. The total quenching rate constant (k_T) of singlet oxygen of the alkene surfactant was measured to be 1.1 × 10⁶ M⁻¹ s^{− …}

Visible Light Photocatalysis Of Organic Reactions In H2o, Sankarsan Biswas

Dissertations, Theses, and Capstone Projects

Visible-light photocatalysis in H₂O provides an attractive, green alternative to typical organic synthesis, which often involves toxic solvents, metal catalysts, and large energy demands. Hence, there is a growing need for an efficient photocatalytic methods that use either aqueous media as a solvent or can proceed solvent-free. However, commercially available photocatalysts do not work well for aqueous photocatalysis. Supramolecular systems in particular have been explored recently to address these issues associated with aqueous photocatalysis. Chapter 1 will review recent advances in aqueous supramolecular photocatalysis with examples of different supramolecular systems and how they have addressed some of the …

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

Engineering Rare-Earth Based Color Centers In Wide Bandgap Semiconductors For Quantum And Nanoscale Applications, Gabriel I. López-Morales

Dissertations, Theses, and Capstone Projects

For many years, atomic point-defects have been readily used to tune the bulk properties of solid-state crystalline materials, for instance, through the inclusion of elemental impurities (doping) during growth, or post-processing treatments such as ion bombardment or high-energy irradiation. Such atomic point-defects introduce local ‘incompatible’ chemical interactions with the periodic atomic arrangement that makes up the crystal, resulting for example in localized electronic states due to dangling bonds or excess of electrons. When present in sufficient concentrations, the defects interact collectively to alter the overall bulk properties of the host material. In the low concentration limit, however, point-defects can serve …

Growth, Optimization, And Characterization Of Topological Insulator Nanostructures By Molecular Beam Epitaxy, Ido Levy

Dissertations, Theses, and Capstone Projects

Topological insulators (TIs) have been the subject of much research since their discovery in 2009. The unique band structure of the TIs makes them attractive in research of exotic physical phenomena, such as the realization of the quantum anomalous Hall effect, as well as novel applications, including quantum computing, spintronics, and more. From a crystal growth perspective, their van-der-Waals structure also provides new opportunities, for example, by enabling the growth on a large selection of substrates. This thesis presents the growth of three-dimensional TI layers, heterostructures and magnetic TIs by molecular beam epitaxy (MBE). First, we show the improvement of …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

A Comparison Of Methods Used For The Elimination Of Organics From Soil Prior To Analysis By Ftir-Atr And Sem-Eds, Argeliz Pomales

Student Theses

This project suggests improvements to the treatment methods utilized for the sample preparation and evaluation of minerals in soil samples encountered in forensic science casework and research. The evaluation of pre-treated and post-treated soil samples were performed using Fourier-Transform Infrared Spectroscopy with Attenuated Total Reflection (FTIR-ATR) and Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS). Because soil samples contain a significant amount of organic matter and water which interfere with examination of these minerals while using these instruments, pretreatment methods are necessary to isolate the mineral fraction for examination and analysis.

Soil samples were first sieved with various size stainless steel mesh …