Chemistry Commons^™

Using Student Interests To Explore Inclusion In Undergraduate Chemistry, Sonja Hoversten

CSB and SJU Distinguished Thesis

For students who are not chemistry majors, but who are on a career track requiring four chemistry courses, taking the final reactivity chemistry course (CHEM 251) for pre-health students can be daunting. For this reason, this research is focused on the CHEM 251 course at The College of Saint Benedict and Saint John’s University (CSBSJU) which is one of the four required chemistry courses for pre-medicine and some pre-physician assistant students, and all chemistry and biochemistry majors. Student perception of inclusion in the course increased through the implementation of group assignments including prompts for individual application of the material. The …

Photodynamic Treatment Of Staphylococcus Aureus With Non-Iron Hemin Analogs In The Presence Of Hydrogen Peroxide, Badhu Prashanthika Sivasubramaniam, Benjamin M. Washer, Yuichiro Watanabe, Kathryn E. Ragheb, J. Paul Robinson, Alexander Wei

Department of Chemistry Faculty Publications

Bacteria subjected to antiseptic or antibiotic stress often develop tolerance, a trait that can lead to permanent resistance. To determine whether photodynamic agents could be used to counter tolerance, we evaluated three non-iron hemin analogs (M-PpIX; M = Al, Ga, In) as targeted photosensitizers for antimicrobial photodynamic inactivation (aPDI) following exposure to sublethal H2O2. Al-PpIX is an active producer of ROS whereas Ga- and In-PpIX are more efficient at generating singlet oxygen. Al- and Ga-PpIX are highly potent aPDI agents against S. aureus and methicillin-resistant strains (MRSA) with antimicrobial activity (3 log reduction in colony-forming units) at nanomolar concentrations. The …

Design, Synthesis, Self-Assembly, And Applications Of Functional Bottlebrush Architectures Through Ring-Opening Metathesis Polymerization, Yipei Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Shear-thinning hydrogels are a class of materials with unique rheological properties that enable them to undergo a reversible reduction in viscosity under shear stress, which allows for easy injection. The injectability of shear-thinning hydrogels is particularly important when considering their use in biomedical applications, such as drug delivery, tissue engineering, and wound healing. However, before advancing to these applications, it is crucial to evaluate the “injectability” of new shear-thinning hydrogels to avoid clogging of the needle for injection. Injectability is typically associated with determining suitable viscosity, storage/loss moduli, and other factors, such as injection force (e.g., needle length and gauge …

Outlining The Hidden Curriculum: Perspectives On Successfully Navigating Scientific Conferences, Eduardo J. Caro-Diaz, Marcy J. Balunas, Lesley Ann Giddings, Sandra Loesgen, Brian T. Murphy, C. Benjamin Naman, Christine E. Salomon, Kevin J. Tidgewell, Jaclyn M. Winter

Chemistry: Faculty Publications

Scientific conferences and meetings are valuable opportunities for researchers to network, communicate, and develop knowledge. For early career scientists, conferences can also be intimidating, confusing, and overwhelming, especially without having adequate preparation or experience. In this Perspective, we provide advice based on previous experiences navigating scientific meetings and conferences. These guidelines outline parts of the hidden curriculum around preparing for and attending meetings, navigating conference sessions, networking with other scientists, and participating in social activities while upholding a recommended code of conduct.

Incorporating Solvent Effects In Dft: Insights From Cation Exchange In Faujasites, An T. Ta, Ayoub Daouli, R. Seaton Ullberg, Eric Fonseca, Vanessa Proust, Agnès Grandjean, Richard G. Hennig, Hans Conrad Zur Loye, Michael Badawi, Simon R. Phillpot

Faculty Publications

Zeolites are versatile materials renowned for their extra-framework cation exchange capabilities, with applications spanning diverse fields, including nuclear waste treatment. While detailed experimental characterization offers valuable insight, density functional theory (DFT) proves particularly adept at investigating ion exchange in zeolites, owing to its atomic and electronic resolution. However, the prevalent occurrence of zeolitic ion exchange in aqueous environments poses a challenge to conventional DFT modeling, traditionally conducted in a vacuum. This study seeks to enhance zeolite modeling by systematically evaluating predictive differences across varying degrees of aqueous solvent inclusion. Specifically focusing on monovalent cation exchange in Na-X zeolites, we explore …

Investigation Of Lignin Solubilization Using Quantum Chemical Calculations In Constrained Media, Leo Sanzone

Arts & Sciences Undergraduate Showcase

Lignin is a common, yet complex polymer found in a majority of vascular plants. The polymer can easily be functionalized, and it is a readily available and renewable source of carbon-based material without a petrol source. There are various methods to allow for the dissolution of lignin, one of which involves the use of H₂O and CO₂ in supercritical conditions. This particular solution bends the normal solvation rules and allows for multiple instances of H-bonding interactions.

By using Density Functional theory, this study aims to identify the molecular interactions of guaiacol (the most basic fragment of lignin) …

Outlining The Hidden Curriculum: Perspectives On Successfully Navigating Scientific Conferences, Eduardo J. Caro-Diaz, Marcy J. Balunas, Lesley Ann Giddings, Sandra Loesgen, Brian T. Murphy, C. Benjamin Naman, Christine E. Salomon, Kevin J. Tidgewell, Jaclyn M. Winter

Chemistry: Faculty Publications

Scientific conferences and meetings are valuable opportunities for researchers to network, communicate, and develop knowledge. For early career scientists, conferences can also be intimidating, confusing, and overwhelming, especially without having adequate preparation or experience. In this Perspective, we provide advice based on previous experiences navigating scientific meetings and conferences. These guidelines outline parts of the hidden curriculum around preparing for and attending meetings, navigating conference sessions, networking with other scientists, and participating in social activities while upholding a recommended code of conduct.

Zeolitic Imidazolate Framework-8 Encapsulated With Mo-Based Polyoxometalates As Surfaces With Antibacterial Activity Against Escherichia Coli, Mariam M. Abdelkhalek, Aya M. Mohamed, Rehab Z. Abdallah, Ghada E. Khedr, Rania Siam, Nageh K. Allam

Faculty Journal Articles

Bacterial infections represent a major global health concern, causing millions of deaths and a significant economic burden. The development of antibacterial nanoporous surfaces with potential mechano-bactericidal effects can revolutionize infection control practices. In this study, a hybrid material of zeolitic imidazolate framework-8 (ZIF-8) doped with phosphomolybdic acid (PMA) was synthesized and characterized by field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and N2 sorption isotherms. PMA@ZIF-8 performance as an antibacterial agent against E. coli was superior to that of its individual constituents, suggesting a synergistic effect of PMA and ZIF-8. The …

Anodic Cyclizations To Form Alkaloid Ring Systems And The Role Of The Second Oxidation Step, Zachary Tyler Medcalf

Arts & Sciences Graduate Student Theses and Dissertations

In chapter 1 we will explore the essential background on electrochemistry and anodic cyclization reactions, laying the foundation for understanding the subsequent chapters. In chapter 2, we will explore the mechanistic model established for anodic olefin coupling reactions and the importance of the second oxidation step in the success of these reactions. We showed how a fast second oxidation step can be used to push an anodic cyclization down a kinetic pathway. We will also explore how this step impacts the generation of product in photoelectron-transfer initiated radical cation reactions. It is evident that a fast second oxidation step alone …

Peace With Painful Memories, Mona Muzammil, Muzammil Arshad, Washain Muzammil

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

This Book helps you identify and heal from childhood emotional neglect so you can be more connected and emotionally present in your life.

Do you sometimes feel like you’re just going through the motions in life? Do you often act like you’re fine when you secretly feel lonely and disconnected? Perhaps you have a good life and yet somehow, it’s not enough to make you happy. Or perhaps you drink too much, eat too much, or risk too much to feel something good. If so, you are not alone and you may be suffering from emotional neglect.

Are you one …

Enabling More Efficient Solar Thermal Energy Production And Storage, Allan Wilson

Poster Presentations

Concentrated Solar Power (CSP) stores & transfers energy using a Thermal Energy Storage Fluid (EIA AEO 2022)

Formation Of Diazirine Functionality For Propellant Applications, Abby Mock

Poster Presentations

Overall, this research focuses on a cost-effective approach which minimizes synthetic overhead when assembling compounds with diazirine functionality. The goals are to prevent the surplus use of ammonia in the formation of the diaziridines and use electrochemistry to perform the oxidation of diaziridines. In addition, this project will evaluate the efficiency of different diazirine molecules as propellants.

The Effects Of Free Volume And Processing On The Development Of Gas Separation Membranes, Jacob Schekman

Dissertations

Structure, thermal, mechanical, gas transport, and free volume properties of thiol-ene based systems are investigated and discussed. In the pursuit of generating low energy-cost polymer membranes for gas separation, it became apparent that UV-curing of thiol-ene materials presented several routes toward achieving this goal. Network structure plays a vital role in determining the gas transport properties of membrane materials. UV photopolymerization techniques provide a means to rapidly vitrify network morphologies which can be tuned depending on choice of monomer. Thiol-ene monomers offer a broad range of precursor materials from which to choose for the design of functional membrane materials.

Chapter …

Synthesis Of Poly-N-Methylated Peptides Against Malaria, Kaitlyn Watson

Theses & Dissertations

Malaria, a life-threatening global health concern, is primarily targeted by mainstream treatments such as artemisinin-based combination therapies, focusing on the blood stage of the disease. Primaquine, one of the few drugs active against the liver stage, faces challenges with reports of resistance in Plasmodium vivax strains and relapsing infections. With the scarcity of liver-stage-targeting drugs and increasing cases of drug-resistant malaria, the World Health Organization emphasizes the urgent need for novel therapeutic agents. Marine organisms are a rich source of new bioactive compounds, and extracts from the Antarctic Sea sponge Inflatella coelosphaeroides revealed new N-methylated peptides exhibiting promising antimalarial activity, …

Enabling High-Rate Thermoplastic Composite Manufacturing Through Structure-Processing-Property Relationships Of Polyphenylene Sulfide, Lina Ghanbari

Dissertations

In this dissertation, relationships between polyphenylene sulfide (PPS) chain structure and melt processing parameters are linked to thermoplastic composite (TPC) properties and mechanical performance. Deviations from linear PPS structure and the formation of branching/crosslinked moieties upon exposure to TPC manufacturing steps presents an opportunity to systematically uncover the interdependencies of melt-state thermal history on polymer rheology, crystallization, crystal structure, and translate these properties to the continuum level. This work first explores unreinforced PPS and how the formation of non-linear chain architectures yield altered rheological states when held at melt processing temperatures. These hindered chains exhibit unconventional crystallization behavior and non-uniform …

Development Of An Enhanced Sampling Workflow To Accelerate Molecular Docking With Sparse Biophysical Information, Zachary Stichter

Masters Theses & Specialist Projects

Rapid docking of flexible biological macromolecules remains a significant open challenge in protein structure determination. While rigid docking is relatively simple with toolkits such as TagDock, a key obstacle to rapid flexible docking is the complexity and roughness of the free energy surface associated with protein conformational motion (often termed the many-minima problem), meaning conventional molecular dynamics methods do not effectively sample protein conformations near the interaction complex in accessible timescales. Methods such as metadynamics and replica exchange molecular dynamics exist to ameliorate this obstacle, yet these methods use nonphysical biases or random swaps to enhance sampling. In contrast, high …

Development Of Novel Immobilized Copper–Ligand Complex For Click Chemistry Of Biomolecules, Rene Kandler, Yomal Benaragama, Manoranjan Bera, Caroline Wang, Rasheda Aktar Samiha, W.M.C. Sameera, Samir Das, Arundhati Nag

Chemistry

Copper-catalyzed azide–alkyne cycloaddition click (CuAAC) reaction is widely used to synthesize drug candidates and other biomolecule classes. Homogeneous catalysts, which consist of copper coordinated to a ligand framework, have been optimized for high yield and specificity of the CuAAC reaction, but CuAAC reaction with these catalysts requires the addition of a reducing agent and basic conditions, which can complicate some of the desired syntheses. Additionally, removing copper from the synthesized CuAAC-containing biomolecule is necessary for biological applications but inconvenient and requires additional purification steps. We describe here the design and synthesis of a PNN-type pincer ligand complex with copper (I) …

Assessment Of Culture Media Conditions For Bacteria/Macrophages Co-Cultures, Sage M. Luebbert

Chemistry & Biochemistry Undergraduate Honors Theses

Co-cultures are utilized as a tool in biology to measure immune responses to pathogens. This method involves a coordinated reaction between two populations, a bacterial biofilm of S.aureus and macrophages derived from THP-1 cells. The current state of the art prevents the continuous supply of nutrients and removal of waste products which causes macrophage death. This limits the time to collect samples and therefore the ability to measure proteins within the innate immune response. The time constraint is a major issue for long term co-culturing. This thesis aims to optimize the co-culturing process by developing a two-pump system to …

Modification, Transport, And Sources Of Hydrocarbon Oxidation Products From Groundwater At Crude Oil And Diesel Spill Sites In Minnesota: Unveiling Common “Theems” Via Spectroscopy & Chromatography, Eduardo E. Turcios Valle

LSU New Orleans Theses and Dissertations

In this thesis, petroleum-contaminated groundwater from three spill-affected Minnesota sites—two contaminated with crude oil; one with diesel—is investigated to elucidate whether differences in degradation products from different parent oils exist. After spill events, parent molecules from the leaked oil seep underground and undergo microbial degradation over time, transforming into hydrocarbon oxidation products (HOPs), water-soluble contaminants that infiltrate groundwater aquifers, flowing into nearby environments and towns while exhibiting environmental persistence, toxicity to aquatic biota, and potential risks to humans that become exposed. Spectroscopic and chromatographic study of the structural themes and spatial distributions of HOPs reveals preferential degradation of aliphatic (biolabile) …

N-Methylation Of Amphetamine By Phenylethanolamine N- Methyltransferase: Implications For Chronic Therapeutic Use, Mackenzie Pavlik

Master's Theses

In current forensic analysis, the presence of methamphetamine in a sample is routinely presumed to reflect methamphetamine abuse. This is due to the expectation that individuals either abusing, or receiving amphetamine for therapeutic purposes (e.g. as treatment for ADHD) will not generate any significant levels of methamphetamine as a product of metabolism. We have hypothesized however, that because amphetamine can serve as a substrate for methylation by phenylethanolamine n-methyltransferase (PNMT), (which will be in equilibrium with the reverse demethylation reaction) some individuals chronically taking amphetamine for therapeutic purposes may generate low levels of methamphetamine that would show up on a …

Tpm^Ph Derivative Of Tungsten; Hydrogen-Bonding In 7-Coordinate Cation Complex, Olivia Ryon Simcox

Undergraduate Honors Thesis Collection

Tpm^Ph, or tris(3-phenylpyrazolyl)methane reacts with tungsten hexacarbonyl to form the ligand-metal complex tris(3-phenylpyrazolyl)methane tungsten tricarbonyl, or Tpm^PhW(CO)3. The further complexes of Tpm^PhW(CO)3 and Tpm^PhMo(CO)3 are not known. This project aims to explore how the addition of a phenyl substituent to the pyrazole ring on Tpm impacts the synthesis of [Tpm^PhW(CO)3I]+X– and [Tpm^PhW(CO)3H]+X–. The inclusion of this phenyl substituent may impact the possible hydrogen bonding of then hydrogen contained in the carbon-hydrogen bond. This work aims to explore the extent of hydrogen-bonding of the carbon-hydrogen bond of the Tpm^Ph ligand in cationic metal complexes.

A Copper-Selective Sensor And Its Inhibition Of Copper-Amyloid Beta Aggregation, Ngoc Kim Nguyen, Bella Poduska, Mia Franks, Manoranjan Bera, Ian Maccormack, Guoxing Lin, Alexander P. Petroff, Samir Das, Arundhati Nag

Chemistry

Copper is an essential trace metal for biological processes in humans and animals. A low level of copper detection at physiological pH using fluorescent probes is very important for in vitro applications, such as the detection of copper in water or urine, and in vivo applications, such as tracking the dynamic copper concentrations inside cells. Copper homeostasis is disrupted in neurological diseases like Alzheimer’s disease, and copper forms aggregates with amyloid beta (Ab42) peptide, resulting in senile plaques in Alzheimer’s brains. Therefore, a selective copper detector probe that can detect amyloid beta peptide-copper aggregates and decrease the aggregate size has …

Optimization Of Xrf Experimental Protocol For Bruker Picofox, Tyler Ashcraft

Undergraduate Honors Theses

The research performed was to improve the precision and accuracy of sample measurements made with the Bruker Picofox X-ray fluorescence spectrometer. The initial method of sample preparation using a 10 μL drop spotted onto an acrylic plate and then drying in an oven at 80˚C produced inconsistent results even when processing replicates or the same sample multiples times. Multiple experiments were conducted to determine the effects of different sample preparation conditions on the resulting accuracy. The conditions tested were drop size, plate composition, and drying temperature. For each experiment an internal standard (gallium) was used at concentrations similar to that …

Determining The Time Since Deposition Of Bloodstains Based On Vibrational Spectroscopy For Forensic Purposes, Alexis Renee Weber

Legacy Theses & Dissertations (2009 - 2024)

At the scene of violent crimes, bloodstain evidence is one of the most frequently found and valuable types of evidence. Blood traces discovered at crime scenes can provide crucial information to an investigation. By obtaining a DNA profile from the bloodstain, the profile can be used to link someone to a crime scene, which can corroborate or dispute a witness's statement. However, the current analysis of bloodstains is still not able to answer a key question for investigators: how much time has passed since the criminal event occurred? In addition, an equally important aspect of crime reconstruction is the ability …

Exploring Nucleic Acid Modifications For Rna-Based Therapeutics: Insights From Molecular Dynamics Simulations, Samantha Biaesch

Legacy Theses & Dissertations (2009 - 2024)

Nucleic acid modifications are pivotal in biological processes due to their multifaceted roles. They regulate gene expression by modulating transcription, with modifications in the nucleic acid, sugar group, or in its phosphate backbone. In our investigation, we explore the use of molecular dynamics simulations to study nucleic acid modifications for potential applications in RNA-based therapeutics. These modifications introduce nonstandard atoms, such as selenium, and new parameterizations must be performed to properly simulate in GROMACS. These parameters govern bonded (strength of bonds, angles and dihedrals) and non-bonded (size and charges) interactions for each of the atoms in the modification. The first …

Argonaute 2 Binding Affinity To Determine Repression Of Mirna-Mrna Pairs, Christina M. S. Karadiakos

ALL - Honors Theses

MicroRNAs (miRNA) are a class of small non-coding RNAs that play a key role in gene silencing. miRNAs form an RNA-induced silencing complex (RISC) with the argonaute 2 (AGO2) protein in order to control gene expression through silencing messenger RNAs (mRNA). The ability for a miRNA-mRNA complex to fit into AGO2 and form the RISC is based on the location and characteristics of a central bulge, but the mechanism and interactions that lead to a functional RISC remain unknown. Using available experimental data, we modeled complexes composed of a miRNA (miR-34a) and different mRNA sequences inside of AGO2. The resulting …

Conversion Of Microcrystalline Cellulose To Hexane Using Hydrogenated Metal Oxides At Low Temperature And Pressure, Mubarak Osman

Electronic Theses and Dissertations

Increasing global energy demand and environmental concerns have fueled the exploration of sustainable and efficient methods for renewable fuel production. The conversion of cellulosic waste to hydrocarbon fuels using hydrogenated metal oxides presents a novel and eco-friendly approach to sustainably address energy demand. In this study, hydrogenated metal oxides were used as catalysts in a relatively low-temperature and atmospheric-pressure environment to facilitate the conversion of cellulosic waste into hydrocarbon fuels. Hydrogenated metal oxides have been introduced as potential hydrogen transfer catalysts. The expected result is the selective conversion of cellulose to hexane at relatively low temperatures, which significantly reduces energy …

Advancement Of Iterative Optimization Technology Algorithms Toward Calibration-Free Process Analytical Technology Applications, Adam Rish

Electronic Theses and Dissertations

The expansion of spectroscopic process analytical technology (PAT) tools within the pharmaceutical industry has the potential to elevate the current state-of-the-art of pharmaceutical manufacturing by offering opportunities for reduced quality testing times, enhanced process control, and greater production flexibility. Spectroscopic PAT tools are dependent on multivariate models to extract the relevant information from the spectral outputs. However, there is a substantial calibration burden for developing and maintaining these multivariate models that discourages the application of PAT, despite the encouragement from regulators. This has led to an interest in calibration-free methods such as iterative optimization technology (IOT) for spectroscopic PAT that …

Using Ion Mobility Mass Spectrometry In Conjuction With Derivatization Methods To Enhance The Separation Of Different Steroid Isomers, Shadrack Lucas

All Theses

One of the major problems facing analytical chemistry challenge is the isomers separation, due to their closely related molecular structures and physicochemical properties. Therefore, in this thesis, we have performed the separation of steroid isomers through the use of ion mobility mass spectrometry, using various chemical approaches. Ion mobility is an effective high-resolution separation techniques that utilizes the mobility of ions in the gas-phase environment. A useful tool for isomeric analysis due to the ability to separate different isomeric classes of steroids according to their varied collision cross-sections, which is achieved by taking advantage of differences in ion mobility.

Moreover, …

A Revised Synthesis Of The Cationic Lipids Dmri And Mlri, Benjamin A. Kostic

College of Arts & Sciences Senior Theses

Lipid nanoparticles (LNPs) are an increasingly utilized method of intracellular delivery for nucleic acids. The COVID-19 vaccines from Moderna and Pfizer-BioNTech have used LNP technology to combat the recent global SARS-CoV-2 pandemic, saving millions of lives.^1,2 These vaccines consist of a lipid formulation that binds to the anionic phosphate groups of mRNAs and serves as an effective way to transport the nucleic acid across membranes into cells.⁹The mRNA encodes a viral protein. When introduced to cells, the viral protein is produced so that the immune system then can generate an appropriate antibody response.³ However, this approach …