Chemistry Commons^™

Synthesis And Evaluation Of Biologically Active Phosphorous Heterocycles And Lipid A Antagonist Compounds, Saroj Kafle

Dissertations

Cyclophostin and cyclipostins are naturally occurring organophosphates with common structural core units and different phosphate ester substituents. Cyclophostin is a cyclic phosphate triester with a chiral center at phosphorous and C-3a carbon atom while the cyclipostins have characteristic alkyl substituents with varying chain lengths at the phosphate center. Long-chain substituted monocyclic phosphate (2b) and phosphonate (2a) analogs of cyclophostin and cyclipostin are promising inhibitors against serine hydrolases acetylcholinesterase with an IC₅₀ in the nanomolar range.

Biologically active β-lactones and lactams owe their activity, in part, to ring strain. The ring opening of β-lactones and lactams …

Additivity Of Diene Substituent Gibbs Free Energy Contributions For Diels–Alder Reactions Between Me2c=Cme2 And Substituted Cyclopentadienes, Thomas M. Gilbert, Austin S. Flemming, Brendan C. Dutmer

Faculty Articles, Papers, and Other Scholarship

Systematic computational studies of pericyclic Diels–Alder reactions between (H3C)2C═C(CH3)2, 1, and all permutations of substituted cyclopentadienes c-C5R1R2R3R4R5aR5b (R = H, CH3, CF3, F) allowed isolation of substitutional effects on Gibbs free energy barrier heights and reaction Gibbs free energies. “Average Substitution Gibbs Free Energy Correction” ΔGASC#‡/ΔGASC# values for each substituent in each position appeared to be additive. Substituent effects on barriers showed interesting contrasts. Methyl substitution at positions 5a and 5b increased barriers significantly, while substitution at all other positions had essentially no impact. In contrast, fluoro substitution at positions 5a and 5b lowered barriers more than substitution at other …

Nanosecond Infrared Laser Ablation Dynamics, Achala Priyadarshani Deenamulla Kankanamalage

LSU Doctoral Dissertations

Laser ablation dynamics encompasses studies of fundamental physical processes of mid infrared laser ablation. Understanding the mechanisms of IR laser desorption and ionization can lead to improvements in laser ablation-based techniques and expansion of their applications. Control of material removal ensures both accuracy and precision of the laser ablation-based techniques. The laser ablation mechanism in the studied wavelength region, is a process of water vaporization and photothermal disruption of tissue. Glycerol was used as the ablation target to establish the methods. Experiments were first aimed at developing methods to monitor material removal during ablation using a 2.94 µm wavelength mid-IR …

Synthesis And Characterization Of Humic/Melanin-Like Compounds By Oxidative Polymerization Of Simple Aromatic Precursors, Nastaran Khademimoshgenani, Sarah A. Green

Michigan Tech Publications, Part 1

Dissolved organic matter (DOM) is a complex mixture of naturally occurring organic molecules originating from multiple marine and terrestrial sources. DOM plays a significant role in water quality by affecting the photochemistry, trace metal transport, and acidity in aquatic systems. Understanding the chemical composition of DOM helps interpret the links between its optical properties and molecular structures. Currently, the molecular origins of the optical properties of DOM are not well-defined. In this study, we oxidize and initiate the polymerization of melanin precursors 1,8-dihydroxy naphthalene and 5,6-dihydroxy indole by the addition of hydrogen peroxide and/or with ultraviolet irradiation. Our goal is …

Synthesis And Characterization Of Semi-Interpenetrating And Double Networks Of Sulfonimide- And Imidazolium-Containing Poly(Ionic Liquids), Jeremiah Coughlon, Seth Taylor, Jason Bara, Kevin Miller, Sourav Chatterjee

Scholars Week

In recent years, there has been increased research interest in creating electrically conductive polymer membranes with materials that are widely available and environmentally safe. Herein, we report how polymeric membranes comprised of unique combinations of ionenes and poly(ionic liquids), including a recently developed sulfonimide- and imidazolium-containing methacryloxy-based monomer, were produced via UV photopolymerization. These membranes were specifically tailored to exhibit both ionic conductivity and an affinity for carbon dioxide, which are both crucial characteristics in such applications as electron transport in lithium-ion batteries and gas sorbency in separation techniques. Monomers, such as the aforementioned methacryloxy-based ionic liquid (IL) and C4VIm, …

Synthesis And Properties Of Bio-Based 3d Printable Resins, Cameron Woods, Seth Taylor, Jeremiah Coughlon, Turner Perdue, Sourav Chatterjee, Jason E. Bara

Scholars Week

A photopolymer resin is a monomer that, when introduced to light of a certain wavelength, starts to polymerize into a solid. This has become a growing part of the 3D printing industry. There have been many advancements in the field of 3D printing, however, a lot of these resins are not environmentally friendly and even harmful if not handled in the correct manner. Plant based resins are becoming more and more popular because of their biodegradability and for the possibility of using renewable resources. Glycerol is a plant-based compound that is produced in excess in industry. Glycerol obtained from bioethanol …

Physiochemical Properties Of Urethane-Containing Ionic Liquids And Ionenes From A Non-Isocyanate Synthetic Approach, George Timmermann

Scholars Week

Ionic polymers that are designed to contain ionic liquids (ILs) in their backbones have been shown to exhibit a high degree of variability through changing the type of ionic character and the location of the ionic region within the molecule. This large amount of variability in both the structure and characteristics of ILs allows researchers to design task-specific ionic polymers and ILs for a variety of applications including gas separation membranes and solid polymer electrolytes. The synthesis of a specific class of ILs and ionenes through the incorporation of urethane groups with imidazolium rings by reacting carbonyl diimidazole with various …

Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable …

Optimization Of Adsorption Of Methylene Blue Dye On Activated Charcoal, Abigail Seputro

Research and Creativity Symposium

Methylene blue and crystal violet are cationic dyes of high intensity that are commonly discharged in wastewater. The colored compounds in this environment inhibit sunlight penetration in waterways, resulting in the destruction of aquatic ecosystems. Activated carbon offers an attractive option for the efficient removal of dyes from wastewater due its excellent adsorption ability, highly porous structure, and large thermal/chemical stability. This study was conducted in order to investigate the adsorption of methylene blue dye from aqueous solution by various types of activated charcoal using UV-Vis spectroscopy. The effects of temperature and adsorbent quantity were studied to optimize the efficiency …

Using Transition State Theory To Understand The Kinetics For The Gas-Phase Synthesis Of Ammonia, Chloe Boyd, Stephen Case, Abigail Seputro

Research and Creativity Symposium

To identify the rate-determining step and the most stable transition state for the Haber-Bosch synthesis of gas-phase ammonia, electronic structure calculations for the reactants (N2, H2, NNH2, H2NNH2, HNNH3), intermediates, and transition states were found using the program GAMESS and the basis sets 6-31G*, 6-311G**, and STO-3G (1). The basis set 6-31G* revealed N2(g) + 3H2(g) ⇌ TS1 ⇌ NNH2(g)+ 2H2(g) as the rate-determining step because it had the smallest equilibrium constant (Keq) of 4.2085*10-36. The reaction coordinate diagram showed the most stable transition state was TS4 from the step HNNH3(g) + H2(g) ⇌ TS4 ⇌ 2NH3(g), which had the …

The Coastal Monitor: Vol. 10 No. 1, John Tanacredi Ph.D.

The Coastal Monitor

New Year’s Day has always been, for me, a time to reflect and project into the near future. Nature’s influence on us all certainly tops my listing with several environmental concerns. For example, the frequency and intensity of hurricanes to Long Island. A decade has passed since Superstorm Sandy re-opened the “Old Inlet” on Long Island which now has mostly naturally closed. So, the new year immediately prompts me to assess the previous year’s Hurricane Ian, a Category 4 system, with winds exceeding 150 mph, which had considerable impact in Florida, and then proceeded north resulting in over 2 inches …

Stem Club, Rohan Tatineni, Kevin Prososki

Honors Program: Expanded Learning Clubs

The goal of STEM club is to teach the students various basic scientific principles and relate them to experiments and the real world. In addition, the scientific method will be taught and be a main focus of the club along with the engineering design process.

Synthesis And Characterization Of Terbium(Iii) Complexes: Can We Manipulate The Emission Signature?, Ryan Gagnon

[Archive] Belmont University Research Symposium (BURS)

Successful Lewis acid/base reactions of terbium(III) nitrate with 2,2’-bipyrdine (22’bpy), 1,10-phenanthroline (phen), and 2,6-pyridine dimethanol (pydm) have yielded the products: Tb(22’bpy)₂(NO₃)₃, Tb(phen)₂(NO₃)_3, and [Tb(pydm)₃](NO₃)₃, respectively. In accord with the well-known antenna-effect, the absorption spectrum of each complex is similar to the spectrum of the free ligand, while the emission spectrum of the complex is identical for the free terbium(III) ion. In contrast, the substitution of a ligand containing a third-row nonmetal strategically placed near the terbium may force interaction between the 3p nonmetal …

Crystal Structure Of Dihydrofolate Reductase From The Filarial Nematode W. Bancrofti In Complex With Nadph And Folate, Keith Lange, Kathleen M. Frey, Tyler Eck, Cheryl A. Janson, Ueli Gubler, Nina M. Goodey

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of …

Using Cyclic-Step Chronopotentiometry To Explore Electron Mobility In Dye-Sensitized Solar Cells, Jasmine Hopson, Ian Mcneil

Honors Projects

In this project, we are making dye-sensitized solar cells using titanium dioxide and the dye from raspberries. We are exploring how electrons diffuse through these systems. To do this, we perform cyclic chronopotentiometry where we cycle between periods of applying a voltage to achieve a certain current and periods where the current is stopped. We focus on the time-dependent decay of the voltage when the current is stopped and fit these decays with a bi-exponential model. We compare the results of devices with and without lithium perchlorate in the electrolyte solution since lithium lowers the energies of the acceptor states …

Investigation Of Cofactor Activities Of Endothelial Microparticle- Thrombomodulin With Liposomal Surrogate, Valentinas Gruzdys, Lin Wang, Dan Wang, Rachel Huang, Xue-Long Sun

Chemistry Faculty Publications

Thrombomodulin (TM) is a type I transmembrane glycoprotein mainly expressed on the endothelial cells, where it binds thrombin to form the thrombin-TM complex that can activate protein C and thrombin-activable fibrinolysis inhibitor (TAFI) and induce anticoagulant and anti-fibrinolytic reactions, respec-tively. Cell activation and injury often sheds microparticles that contain membrane TM, which circulate in biofluids like blood. However, the biological function of circulating microparticle-TM is still unknown even though it has been recognized as a biomarker of endothelial cell injury and damage. In comparison with cell membrane, different phospholipids are exposed on the microparticle surface due to cell membrane "flip-flop"upon …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Synthesis And Characterization Of Some Disubstituted Cyclopentadienyl Rhenium Complexes As Potential Candidates In Semiconductive Materials, Chloe Vernon

Senior Honors Theses

Since 2000, when the Nobel Prize in Chemistry as awarded for conductive polymer research few studies have been performed concerning the conductive capabilities of discrete organometallic compounds. For this project, organometallic compounds were formed specifically with a transition metal included in the structure. Through oxidation and reduction reactions, the variation in the electrical conductivity could allow for an analysis of whether this unique structure would allow for tunability. The goal of this research was to begin with aromatic substituted fulvenes and perform various multistep synthesis processes, utilizing thallium salt intermediates, to produce several disubstituted cyclopentadienyl rhenium complexes. In this project, …

Microscale Chemical Manipulation And Imaging Using Photoactive Molecules And Light, Uroob Haris

Chemistry Theses and Dissertations

Chemical manipulation with light has been an active and growing area of research with important implications in materials science, biotechnology, and environmental science. From early investigations of light sensitive materials for photography in the 19^th century, to printing billions of transistors on a semiconductor chip in present day, scientists have gained a deep understanding of photochemistry and the processes that allow us to harness light for everyday applications. In this work, we explore microscale fabrication and molecular imaging using light and photoactive molecules as foundational tools. We develop a visible-light mediated technique for high resolution microscale chemical lithography comprising …

Phenotypic And Target-Based Drug Discovery, Angelica Veronica Carmona

Theses & Dissertations

Batten Disease or Neuronal Ceroid Lipofuscinosis (NCL) is a group of rare, fatal, inherited pediatric neurodegenerative lysosomal storage disorders. NCLs are characterized by intracellular accumulation of an auto-fluorescent lipopigment called ceroid lipofuscin and neurodegeneration. Several forms of NCLs exist, some of which share some of the same features and symptoms but vary in severity and onset of symptoms with respect to age. Some common symptoms include progressive loss of vision, mental and motor deterioration, epileptic seizures, premature death, and in the rare adult-onset, dementia. Subtypes of NCLs occur when one of 13 different genes are mutated, and only two subtypes …

Development And Validation Of A Liquid Chromatography-Tandem Mass Spectrometry Method For The Determination Of Temozolomide In Mouse Brain Tissue, Raghavi Kakarla, Kimberly Yacoub, Rebecca L. Bearden, Aimin Zhou, Sanjib Mukherjee, Frank Y. Shan, Baochuan Guo

Chemistry Faculty Publications

Temozolomide is a Food and Drug Administration-approved anticancer drug that has poor drug delivery via oral or intravenous routes. A potential strategy to combat this problem is investigating alternative routes of administration, requiring quantitation of the drug in the brain tissues by liquid chromatography-mass spectrometry. However, current methods used to extract the drug from brain tissues resulted in poor recovery and substantial matrix effects. Herein, we reported a new two-step extraction method that involves the use of Proteinase K to lyse tumor tissues to efficiently release the drug, followed by ethanol protein precipitation. The extracts were then separated on a …

Simulating A Flexible Water Model As Rigid: Best Practices And Lessons Learned, Raymond Weldon, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model’s Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models …

Biophysical And X-Ray Crystallographic Characterizations On Complexes Of G-Quadruplexes With Small-Molecule Ligands, Ming Ye , '23

Senior Theses, Projects, and Awards

DNA can fold into G-quadruplexes (GQs), non-canonical secondary structures formed by stacking of G-tetrads. GQs are important in many biological processes, which makes them promising therapeutic targets for anticancer and antiviral drugs. Therefore, investigating the interaction between GQs and small-molecule ligands is important.

This thesis work surveyed the DNA-ligand interactions of over 20 GQ-ligand complexes via biophysical and X-ray crystallographic methods. Two sets of GQ-ligand complexes were characterized in detail. One set is a group of purine-only sequences, named GA, with a highly selective GQ ligand, N-methyl mesoporphyrin IX (NMM). The other set is a human telomeric sequence, Tel22, with …

Diffractive Imaging Of Laser Induced Molecular Reactions With Kiloelectron–Volt Ultrafast Electron Diffraction, Yanwei Xiong

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

Capturing the structural changes during a molecular reaction with ultrafast electron diffraction (UED) requires a high spatiotemporal resolution and sufficiently high signal-to-noise to record the signals with high fidelity. In this dissertation, I have focused on the development of a tabletop gas phase keV-UED setup with a femtosecond temporal resolution. A DC electron gun was employed to generate electron pulses with a high repetition rate of 5 kHz. The space charge effect in the electron pulse was ameliorated by compressing the 90 keV electron pulse longitudinally with a time varying electric field in an RF cavity. The velocity mismatch between …

Molecular Cluster Complex Of High-Valence Chromium Selenide Carbonyl As Effective Electrocatalyst For Water Oxidation, Ibrahim Munkaila Abdullahi, Manashi Nath

Chemistry Faculty Research & Creative Works

Developing Simple, Affordable, and Environmentally Friendly Water Oxidation Electrocatalysts with High Intrinsic Activity and Low overpotential Continues to Be an Area of Intense Research. in This Article, a Trichromium Diselenide Carbonyl Cluster Complex (Et₄N)₂[Se₂Cr₃(CO)₁₀], with a Unique Bonding Structure Comprising Bridging Se Groups, Has Been Identified as a Promising Electrocatalyst for Oxygen Evolution Reaction (OER). This Carbonyl Cluster Exhibits a Promising overpotential of 310 MV and a Low Tafel Slope of 82.0 MV Dec⁻¹ at 10 MAcm⁻², with Superior Durability in an Alkaline Medium, for a Prolonged …

Nitric Oxide As A Signaling Molecule For Biofilm Formation And Dispersal In Mediated Electron Transfer Microbial Electrochemical Systems, Kevin Beaver, Ashwini Dantanarayana, Ana Bonizol Zani, Danielle L. Lehto, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

With applications in bioremediation, biosensing, and bioenergy, microbial electrochemical systems are a rapidly growing, multidisciplinary field within biological, chemical, and materials science. Since these systems use living microorganisms as biocatalysts, it is important to understand how microbial physiology, namely biofilm formation, affects these electrochemical systems. Specifically, the literature lacks research that assesses the effects of biofilm on metabolic current output in mediated electron transfer systems. in this study, Rhodobacter capsulates and Pseudomonas putida GPo1 were used as model, nonpathogenic strains that facilitate electron transfer via diffusible redox mediators. Nitric oxide has gained attention in biomedicine as a gaseous signaling molecule, …

Exploring New Techniques For Precision Deuteration Of Alkenes And Alkynes, Zoua Pa Vang

Dissertations (1934 -)

Deuterium labeled compounds are often utilized in chemical research as internal standards in mass spectrometry, to study reaction mechanisms and in the pharmaceutical industry to slow the rate of metabolism. With the increase interest for deuterium labeled molecules, there is a renewed interest in selective methods for the installation of deuterium atoms into small organic molecules. However, current methods to incorporate deuterium atoms into organic molecules can lead to isotopic mixtures such as isotopologues and isotopomers. These isotopic species are indistinguishable due to their similar physical properties, leading to inseparable products by common purification techniques. Furthermore, common spectroscopic techniques to …

Using Caulobacter Crescentus As A Model To Probe The Environmental Reactivity Of Silver Nanoparticles, Madeline M. Farber , '23

Senior Theses, Projects, and Awards

Silver nanoparticles (AgNPs) are an increasingly common environmental pollutant with antimicrobial and antibacterial properties. The elucidation of their interaction with cellular membranes and subsequent mechanisms of toxicity are critical areas of research that need to be better understood in order to manage potential adverse environmental effects. This work investigates the interaction of AgNPs with large unilamellar vesicles (LUVs) as a model membrane system. Similar studies conducted by others in this field have largely been conducted with uncoated AgNPs, ignoring the effect of environmental conditions on the formation of an eco-corona on AgNPs. Thus, in this study, the spent medium (SM) …

Master Equation Modeling Of Prompt Dissociation Kinetics For Isoprene Derived Criegee Intermediates, Rory R. Schmidt , '23

Senior Theses, Projects, and Awards

Isoprene ozonolysis is a major atmospheric producer of atmospheric oxidizers and aerosols. This complex reaction pathway forms an exothermic cascade, where constant competition between bimolecular sinks, unimolecular isomerizations, and collisional relaxation dictate reactivity. This work focuses on two isoprene derived Criegee intermediates, methacrolein oxide (MACR oxide) and formaldehyde oxide (FO). While the potential energy surface of FO is well understood, the reactivity of energetically excited FO has not been explored in detail. MACR oxide isomerization and primary products have been adequately characterized and explored computationally and experimentally, but the potential energy surface beyond isopropenyl dioxirane has not received the same …

Exploring Protein Conformations And Functions Through Molecular Dynamics Simulations And Machine Learning, Hao Tian

Chemistry Theses and Dissertations

Proteins are essential biomacromolecules that perform a variety of critical functions in living organisms. The tertiary structure of a protein plays a crucial role in its biological activity as it determines how the protein interacts with other molecules. Consequently, understanding protein conformation and function is an important area of research with implications in medicine, biotechnology, and other fields.

The first part of this dissertation focuses on protein allostery, a process by which proteins transmit perturbations caused by binding at one site to a distal site, thereby regulating activity. With the development of computational methods like molecular dynamics simulations and machine …