Physical Sciences and Mathematics Commons^™

Development Of Stochastic And Time-Dependent Quantum Chemical Methods For Accurate Description Of Light-Matter Interactions With Applications In Photoionization And Inverse Photoemission In Nanomaterials, Nicole Spanedda

Dissertations - ALL

There are three main focuses of this work. First, the theoretical details of the Stratified Stochastic Enumeration of Molecular Orbitals (SSE-MO) method is presented, along with its application for calculating ionization potentials (IPs) of quantum dots. The SSE-MO method can readily be applied for the purpose of efficiently and accurately calculating ionization potentials, by constructing the frequency-dependent self-energy operator and then subsequently, solving the associated Dyson equation. Constructing the frequency-dependent self-energy operator is challenging because the scaling of the computational cost with respect to system size, becomes prohibitive for large systems, such as quantum dots. This is due to the …

Synthetic Studies On Ship Modulators, Hif-2Α Antagonists, And New Rhodium Carboxylate Catalysts, Angela Pacherille

Dissertations - ALL

The PI3K pathway is a major cell signaling axis in eukaryotic cells. This pathway employs the second messenger, inositol phospholipid PI(3,4,5)P3, which is responsible for activating Akt and other kinases creating a cascade of signals. The enzyme, SH2-containing inositol-5’-phosphatase (SHIP), plays a key role in this pathway by maintaining the delicate balance of PI(3,4,5)P3. Modulation of SHIP activity through the use of small molecule inhibitors may be utilized for the treatment of certain types of cancer, Alzheimer’s disease, and diabetes. A high-throughput screen identified the small molecule SHIP1 inhibitor, NSC23922, a mixture of 3α- and 3β-aminocholestane. These diastereomers were synthesized …

The Design, Synthesis, And Investigation Into Small Molecule Modulators Of The Src Homology 2 Domain-Containing Inositol 5’-Phosphatase (Ship), Shea Thomas Meyer

Dissertations - ALL

The PI3K pathway is a major cell signaling pathway that influences survival and longevity in eukaryotic cells. Abnormal signaling of this pathway has been implicated in a number of disorders, including Alzheimer's disease and cancer. The PI3K pathway utilizes the inositolphospholipid PI(3,4,5)P3 as a key secondary messenger in the transmission of signals from outside the cell to the nucleus. The SRC Homology 2 containing Inositol 5’-Phosphatase (SHIP) also plays a key role in the PI3K pathway, mediating hydrolysis of the inositol phospholipid PI(3,4,5)P3 to PI(3,4)P2. Early testing has shown modulation of SHIP activity through the use of small molecule modulators …

Exploring The Biomedical Applications Of Polyurethane-Based Foams, Films, And Hydrogels, Anand Utpal Vakil

Dissertations - ALL

Shape memory polymers (SMPs) are a class of smart materials that can be temporarily stored in a deformed shape and can actively recover their original shape upon exposure to an external stimulus, such as heat, magnetic field, moisture, pH, light, or electric field. The ability of SMPs to change shape when required can be used for a wide range of applications, especially in the case of minimally invasive biomedical applications. In this work, polyurethane-based SMPs were explored for their use in tissue engineering, drug delivery, and wound healing applications.

In the second chapter, low density porous foams with tunable degradability …

Evaluation Of The Energetic Factors In Crystalline Pharmaceuticals Using Solid-State Density Functional Theory And Low-Frequency Vibrational Spectroscopy, Margaret P. Davis

Dissertations - ALL

Due to the importance of maintaining stable and effective pharmaceutical solid doses, it is critical to study the variety of solid forms that active pharmaceutical ingredients can adopt including polymorphs, hydrates, and cocrystals. In this work, low-frequency vibrational spectroscopies and rigorous quantum mechanical simulations are combined to provide a new technique for characterizing and investigating pharmaceutically relevant polymorphs, hydrates, and cocrystals as well as a series of model cocrystals. Low-frequency spectra in the sub-200 cm-1 range provide not only unique and characteristic spectra for all of the systems explored here but, along with X-ray structural parameters, they offer a way …

A New Class Of Antibiotic That Prevents Drug Tolerance, Persistence, And Resistance By Controlling Emergence Of Phenotypes., Pankaj Dinkar Patil

Dissertations - ALL

The fight against bacterial infections and innovations in antibiotic therapy has never halted throughout human history. However, bacteria have evolved smartly and resistance against practically all conventional antibiotics has been developed. Furthermore, bacteria can form biofilms, which are surface-attached multicellular colonies. Biofilms shield bacteria against antibiotics and makes it harder to entirely eradicate infections . Under antibiotics stress, bacteria evolve into different phenotypes like hyper motile, hyper adherent and hyper virulent which are tolerant and persistent to antibiotic treatment. The use of antibiotic therapy to combat such resilient bacterial phenotypes is extremely tough. As a result, the scientific community is …

Trichloroacetimidates As Outstanding Electrophiles For The Carbon-Nitrogen, Carbon-Oxygen And Carbon-Carbon Bonds Formation And Synthetic Studies Of Protein Phosphatase-5 (Pp5) Small Molecule Inhibitors, Nilamber Mate

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Trichloroacetimidates have been previously used for glycosidic bond formation in carbohydrate chemistry and in Friedel-Craft reactions. Traditionally, trichloroacetimidates had be synthesized using an alcohol and strongly basic conditions, but in recent years milder preparation methods have been reported. Given the ease of preparation of these versatile reagents, their chemistry has been explored intensely in recent years. While few reported methods suggest they can react under promoter free conditions, activation by Lewis or Brønsted acid leads to a formation of a carbocation from benzylic trichloroacetimidates. Work described herein makes use of these convenient carbocation precursors for new reactions.Isatin is an ambidentate …

Monitoring Bacteria Cultures Using Near Infrared (Nir) Binary Spectronephelometry (Bsn), Raman Spectra And Principal Component Analysis (Pca), Steven Ortiz

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Current noninvasive methods cannot continuously and simultaneously monitor the concentrations of cells and media components that define the state of native bacterial cultures, because of changing turbidity. A new technique, binary spectronephelometry (BSN) has the same or better sensitivity and precision for population monitoring as optical density at 600nm (OD600), while simultaneously measuring metabolic processes. The BSN algorithm uses laser induced emission to probe mildly turbid media i.e., propagation of light occurs in the single scattering regime. A BSN "training set" associates a grid of elastic emission measurements, comprising Rayleigh and Mie scattering, and inelastic emission measurements, comprising fluorescence and …

Synthesis, Characterization And Cellular Uptake Of Magnesium Complexes Of Pyrones And Amino Acids, Derek Robert Case

Dissertations - ALL

This thesis focuses on the treatment of micronutrient deficiency, specifically hypomagnesemia, through the synthesis and solution- and solid-state characterization of "pharma grade", biorelevant magnesium complexes (nutraceuticals) utilizing short-chain peptides (di- and tri-), pyrones, and amino acids. There is further emphasis placed on determining the in vitro uptake of all produced complexes. This work aims to mitigate the shortcomings of current magnesium supplements and better illustrate an understanding of the factors impacting magnesium uptake. Specifically, 1) There is a paucity of information regarding the coordination of biorelevant ligands to magnesium, most of which was investigated between the 1950s and 1980s, and …

The Phase Behavior Of Ubqln Proteins And Implications For Protein Quality Control, Yiran Yang

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The ubiquitin-proteasome system (UPS) and autophagy are essential pathways for maintaining protein quality control (PQC) in cells. Misfolded proteins and large aggregates are cleared by UPS and autophagy signaled by ubiquitin (Ub) or polyubiquitin (polyUb) chains. Shuttle proteins facilitate cargo transporting by interacting with both ubiquitin and degradation machineries. Previously, our lab discovered that the shuttle protein Ubiquilin-2 (UBQLN2) is recruited to stress granules in cells and undergoes liquid-liquid phase separation (LLPS) in vitro. LLPS is a biophysical process by which proteins separate themselves from the surrounding aqueous solution by forming protein-rich droplets. The overarching goals of this work are …

Exploration Of Carbon-Oxygen And Carbon-Nitrogen Bond Formation Utilizing Trichloroacetimidates And Investigations Of New Reactions Mediated By Oxoammonium Salts, Rowan Meador

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Mono-O-alkylated 1,1′-bi-2-naphthols (BINOLs) are often used as the source of chirality for catalysts or ligand systems that are employed in asymmetric organic transformations. However, these BINOLs can be hard to synthesize. The O-alkylation of BINOL can be accomplished with primary and secondary alkyl halides or under Mitsunobu conditions, the yields of these alkylations with tertiary halides or alcohols are very low. A new protocol was developed utilizing trichloroacetamide electrophiles to install bulky groups onto one of the phenolic oxygens. Trichloroacetimidates are also shown to be useful reactions for the synthesis of esters. These reagents proceeded through a symbiotic activation pathway. …

Design And Development Of 2d Functional Semiconductor Nanocrystals, Andrew Hunter Davis

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Anisotropic nanocrystals (NCs) have become of keen interest in recent years, especially for applications in optoelectronic devices due to their directionally oriented emissions, narrow emission spectra, and suitable morphologies for device integration. Of the desired anisotropic NCs, two-dimensional (2D) NCs are of profound interest, due to their impressive optical and electronic properties as well as their prospective advantages towards applications in layered optoelectronic devices, such as solar cells. However, 2D NCs face many challenges, including limited synthetic derivation, as well as decreased stability and optical response, due to their large surface-to-volume ratio and reactive planar surface increasing surface defect state …

Computational Methodologies For The Simulation And Analysis Of Low-Frequency Vibrations In Molecular Crystals, Sara Jean Dampf

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Quantum mechanical models are used to calculate a host of physical phenomena in molecular solids ranging from mechanical elasticity to the energetic stability ordering of polymorphs. However, with the many software packages and methodologies available, it can be difficult to select the most suitable model for the problem at hand without prior knowledge. A promising approach for evaluating the performance of solid-state models is the comparison of the simulations to experimentally measured low-frequency (sub-200 cm-1) vibrational spectra. As this region is dominated by weak intermolecular forces and shallow potential energy surfaces, even slight miscalculations in the solid-state packing arrangements can …

Peptide Corrination For The Mitigation Of Nausea And Emesis In The Treatment Of Type 2 Diabetes, Ian Tinsley

Dissertations - ALL

This thesis addresses several questions focused on the activation of receptors expressed withinthe area postrema (AP) and the nucleus tractus solitarius (NTS), regions known to influence nausea and emesis. Prevention of such effects were achieved via corrination, covalent attachment to vitamin B12 (B12) or other corrin constructs, of GLP glucagon-like peptide-one (GLP-1) receptor (GLP-1R) agonists or via the use of GRASP a growth differentiation factor 15 (GDF15) glial derived neurotropic family receptor α-like (GFRAL) complex antagonist.

Effects Of Air Pollution, Temperature And Moisture Content On Copper And Silver Corrosions And The Reliability Of Data Center Equipment, Rui Zhang

Dissertations - ALL

The effects of moisture content, temperature, and pollutant mixture on atmospheric corrosion of copper and silver were investigated by exposing test specimens to different environmental conditions, followed by surface characterization using the coulometric reduction, Scanning Electron Microscopy, and Energy Dispersive Spectrometry (SEM/EDS). Printed circuit board test cards (PCBs) with bare copper were also used to investigate the effects of voltage bias on the PCBs on the corrosion rate. The test specimens were exposed to mixed flowing gases (MFG) environment with eight different combinations of the following five pollutants at the fixed concentration levels: 60 ppb O3, 80 ppb NO2, 40 …

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …

Carbonate Paleothermometry In Fayetteville Green Lake, New York, Micah Wiesner

Theses - ALL

Lacustrine carbonates are important paleoclimate archives, but unknowns in the seasonal timing and depth of precipitation obscure the interpretation of temperatures associated with them. The clumped isotope paleothermometer records the formation temperature T(D47) of carbonates. This study examines a set of lacustrine carbonates formed in the water column, in addition to carbonate from a sediment core, to better understand the depth and seasonality of carbonate formation in a lacustrine setting. We test that, regardless of season and formation temperature, lacustrine carbonates form in isotopic equilibrium with respect to D47 and d18O fractionation. Further, we account for the effect of our …

Effects Of Air Pollution, Temperature And Moisture Content On Copper And Silver Corrosions And The Reliability Of Data Center Equipment, Rui Zhang

Dissertations - ALL

The effects of moisture content, temperature, and pollutant mixture on atmospheric corrosion of copper and silver were investigated by exposing test specimens to different environmental conditions, followed by surface characterization using the coulometric reduction, Scanning Electron Microscopy, and Energy Dispersive Spectrometry (SEM/EDS). Printed circuit board test cards (PCBs) with bare copper were also used to investigate the effects of voltage bias on the PCBs on the corrosion rate. The test specimens were exposed to mixed flowing gases (MFG) environment with eight different combinations of the following five pollutants at the fixed concentration levels: 60 ppb O3, 80 ppb NO2, 40 …

Carbonate Paleothermometry In Fayetteville Green Lake, New York, Micah Wiesner

Theses - ALL

Lacustrine carbonates are important paleoclimate archives, but unknowns in the seasonal timing and depth of precipitation obscure the interpretation of temperatures associated with them. The clumped isotope paleothermometer records the formation temperature T(D47) of carbonates. This study examines a set of lacustrine carbonates formed in the water column, in addition to carbonate from a sediment core, to better understand the depth and seasonality of carbonate formation in a lacustrine setting. We test that, regardless of season and formation temperature, lacustrine carbonates form in isotopic equilibrium with respect to D47 and d18O fractionation. Further, we account for the effect of our …

Dom Control Of Mercury Methylation In The Water Column Of A Meromictic Lake, Madalyn Bozinski

Honors Capstone Projects - All

The trophic transfer and bioaccumulation of methyl mercury (MeHg) in aquatic ecosystems is a substantial concern, resulting in fish consumption advisories worldwide. Aquatic ecosystems have been identified as the critical environments that breed production of MeHg and low levels of initial accumulation in biota. MeHg production is a microbially-mediated process, occurring primarily at the transition between oxic and anoxic environments. This research aimed to assess the extent to which dissolved organic matter (DOM) affects methylation of mercury in the oligotrophic meromictic lake, Green Lake, in Fayetteville, NY and the warm monomictic lake, Seneca Lake, in Geneva, NY. General physical parameters …

A Closer Look At The Synthesis And Characterization Of Alkaline Earth Metal Tetraarylborates And Heteroleptic Tetraarylborate Pyrazolates, Ashley Clements

Honors Capstone Projects - All

Compounds containing s-block metals are highly sought after as precursor materials for the Metal Organic Chemical Vapor Deposition (MOCVD) process with applications for novel and improved electronic materials. Previous work in the Ruhlandt Group has been focused on the synthesis and characterization of novel homoleptic alkaline earth (Ae) metal pyrazolate and tetraarylborate complexes, while understanding the importance of secondary interactions such as M- in the isolation of these compounds. More recently, it was further proposed that the pyrazolate and tetraarylborate ligand systems combined with an Ae silyl amide via transamination may very well result in an improved heteroleptic MOCVD potential …

Investigating The Effects Of Environmental Solutes On The Reaction Environment In Ice And At Ice Surfaces, Philip Malley

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The reaction environments present in water, ice, and at ice surfaces are physically distinct from one another and studies have shown that photolytic reactions can take place at different rates in the different media. Kinetics of reactions in frozen media are measured in snow and ice prepared from deionized water. This reduces experimental artifacts, but is not relevant to snow in the environment, which contains solutes. We have monitored the effect of nonchromophoric (will not absorb sunlight) organic matter on the photolytic fate of the polycyclic aromatic hydrocarbons (PAHs) phenanthrene, pyrene, and anthracene in ice and at ice surfaces. Nonchromophoric …

Studies Towards The Synthesis Of (-)-Centrolobine Via The Carbonyl Ene Reaction Of Exocyclic Enol Ethers, Brianna Shores

Honors Capstone Projects - All

The goal of this study is the synthesis of centrolobine 7, a naturally-occuring compound that exhibits anti-parasitic and anti-inflammatory activity.

The strategy is to utilize the carbonyl ene reaction to form the 2,6-disubstituted framework of centrolobine 7 from exocyclic enol ether 110 and aldehyde 111. Exocyclic enol ether 110 would be synthesized via literature procedures starting from commercially available glutaric anhydride 11 and anisole 114.

The work completed to date optimizing the following reactions: Friedel-Crafts acylation of glutaric anhydride 11 and anisole 114, the reduction of alcohol 116, and cyclization of alcohol 116 to lactone …

Synthesis Of Substituted Tetrahydropyrans Using Metal-Catalyzed Coupling Reaction, Amanda Lieu

Honors Capstone Projects - All

The purpose of this research is to explore the use of cobalt- and iron-catalyzed cross coupling reactions of alkyl iodides containing beta-tetrahydropyran groups to develop a general method to synthesize substituted tetrahydropyrans. Substituted tetrahydropyrans can be used towards the total syntheses of biologically active natural products. The starting iodide compounds underwent sp3-sp3 and sp3-sp2 cobalt- and iron-catalyzed cross-coupling reactions with different Grignard reagents. It was expected that the formation of the coupled product would be faster than the formation of the side products (elimination and homocoupling) and thus yield the desired substituted tetrahydropyrans. The results of this study showed that …

Structural Variations Involving S-Block Metal Pyrazolates, Joshua Woods

Honors Capstone Projects - All

Alkali and alkaline earth metal organometallics have been sought after for a variety of applications such as in electronic devices produced by novel metal organic chemical vapor deposition precursors, catalysts and as synthetic reagents. Despite significant advances in synthetic techniques, the chemistry of the highly reactive s-block metals is still relatively unexplored. It is difficult to predict properties, structure and binding modes of these compounds due to a number of factors including enhanced reactivity and tendency to aggregation due to the large metal diameter. On the other hand, many of the s-block metals are earth abundant and environmentally friendly, …

Investigation Of The Tandem Alkylation-Cyclization Of Endocyclic Enol Ethers For The Preparation Of Unusual Oxygen Heterocycles, Sarah Mehdi

Honors Capstone Projects - All

The purpose of this research is to study the alkylation and subsequent cyclization reaction of endocyclic enol ethers such as 2H-dihydropyran. This sequence is expected to yield oxygen heterocycles whose structures represent unique scaffolds with promising functionality.

A series of trichloroacetimidates were selected for the direct alkylation of 2H-dihydropyran. Following the alkylation, the addition of acid was expected to induce an intramolecular cyclization reaction that would yield the desired oxygen heterocycles. This stepwise scheme would then be converted into a tandem process in which the reaction would be expected to proceed in a single pot.

Studies showed that the alkylation …

Ruthenium Hydride Catalyzed Silylvinylation Of Terminal And Internal Alkynes And Synthesis Of Poly(Trimethylenecarbonate) And Poly(Dimethylacrylamide) Block Copolymer, Alec Beaton Jr.

Honors Capstone Projects - All

Various propargyl alcohols were synthesized via Grignard reactions. These alkynic alcohols are tethered with dimethyl and biphenyl silicon tethers. These terminal alkyne substrates are reacted with RuHCl(CO)(H₂IMes)(PPh₃) as a catalyst under high pressure (80 psi) ethylene atmosphere to afford the 5-exo-dig trans-silylvinylation product in poor yield. Internal alkyne substrates are found to be much more efficiently transformed into the silylvinylation product, favoring one cycloisomer product over the other.

The Use Of Shape Memory Polymers As A Tool To Study Human Fibrosarcoma And Murine Mesenchymal Stem Cell Migration, Justin N. Elkhechen

Honors Capstone Projects - All

Shape memory polymers (SMPs) are a class of “smart” materials that can transform between two distinct conformations through external stimuli, such as heat or electricity. Their usage in bioengineering has led to a promising field of research that lies at the interface of cell and mechanobiology, potentially providing insight into cancer therapies and tissue development—two processes that exist in dynamic environments in vivo. The present work involves creating new, shape changing, scaffolds for studies to analyze cell migration upon changes to the environmental topography. Specifically, this Capstone has been primarily focused on the development of a “half and half” fibrous …

Electrostatic Assembly Of Gold Nanoparticles Mediated By Polyoxomolybdates, Shannon M. Walter

Honors Capstone Projects - All

The electrostatic assembly of cationic gold nanoparticles (AuNPs) with core diameters of approximately 1.5 nm and 4.5 nm and the anionic sphere and wheel polyoxomolybdates (Mo-132a), (Mo‑132b), and (Mo‑154) was investigated. The AuNPs were capped with a trimethylammonium terminated ligand. Zeta potential and UV-Vis studies supported the successful assembly of the oppositely charged species. The ratio at which the precipitation of aggregates from solution occurred was consistent with the point of electroneutrality observed in the zeta potential results. The UV-Vis studies showed the loss of the surface plasmon resonance (SPR) band as this point of electroneutrality was approached.

In a …

Theoretical Investigation Of The Quantum-Confined Stark Effect, Christopher Jon Blanton

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The two main objectives of this dissertation are the systematic development of explicitly correlated electron-hole wave function based methods and the application of these methods to chemical systems with an

emphasis on nanoparticles.

The understanding of the basic physics of excited electronic states is an important consideration when developing new methods and applications. In this dissertation, excited electronic states were studied using the electron-hole quasiparticle representation. Theoretical treatment of electronic excitation in large quantum dots and nanoparticles is challenging because of the large number of electrons in the system. The quasiparticle representation provides an alternative representation that can partially alleviate …