Chemistry Commons^™

Design, Synthesis And Characterization Of Carbohydrate Based Macrocycles, Photo Responsive Derivatives, And Glycoconjugates Based Low Molecular Weight Gelators, Surya Bahadur Adhikari

Chemistry & Biochemistry Theses & Dissertations

Functional glycoconjugates are important classes of compounds with many applications in different research fields. Our lab has been studying the synthesis and applications of different classes of glycoconjugates ranging from macrocycles to sugar heterocycle derivatives. Due to the importance of these compounds, our research is based on development of synthetic methods for various carbohydrate derivatives. This dissertation includes introduction and overview of projects, followed by the synthesis and studies of several different series of glycomacrolactones. The second project focuses on two classes of photoresponsive molecules, the coumarins and diarylethenes. The third project involves the synthesis and self-assembling properties of isoxazole-based …

Identification Of Phosphorous Loading Point Source Facilities To 303(D) Listed Nutrient Impaired Waters Through Watershed Delineation Using Arcgis For Life Cycle Assessment Applications, John Zimmerman

Chemical Engineering Undergraduate Honors Theses

The work done for this project is part of a larger “life cycle assessment (LCA) of novel electrochemical phosphorus recovery technology at the wastewater treatment plant and U.S. watershed scales” (Morrissey 2019). The goal of that LCA is to determine “environmental impacts of implementing electrochemical struvite recovery at the wastewater treatment plant, U.S watershed, and global scales” (Morrissey 2019). This project’s goal is to identify locations deemed more sensitive to eutrophication impacts. The results will be used as part of the life cycle inventory (LCI) accounting for geographically explicit phosphorus flows. The waters identified as impaired were sourced from the …

Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants And Characterizing Their Photophysics Properties Towards Designing Fret Assays, Mamello Mohale

Graduate Theses and Dissertations

Human fibroblast growth factor one (hFGF1) belongs to a family of 22 FGF members produced by fibroblast cells. Cell signaling during physiological processes of angiogenesis and wound healing occurs when hFGF1 binds to its receptor (FGFR). However, when heterogenous homeostasis is not maintained, fibroblast cells exhibit excessive proliferation which can lead to a myriad of cancers. smFRET is an ultrasensitive distant dependent (1-10 nm) technique capable of resolving such heterogeneity in structural dynamics and binding affinities (Kd). Therefore, we successfully designed and characterized fluorescently labeled hFGF1 tracers which span the visible light region of the electromagnetic spectrum for use in …

Techniques For The Enantioselective Asymmetric Synthesis Of Benzyl Substituted Malonic Acid Esters, Madison Hansen

Honors Theses

A popular method for the enantioselective synthesis of substituted malonic half esters is hydrolysis via Pig Liver Esterase (PLE), however some substrates produce low enantiomeric excess, namely benzyl-substituted malonic esters. Presented here are alternative methods explored for this synthesis, the first being phase-transfer catalyzed hydrolysis via N-benzyl quaternary ammonium salts derived from cinchona alkaloids. The second method utilized chiral auxiliary directed benzylation with auxiliaries including menthol and oxazolidinones. Though unsuccessful, this research provided valuable groundwork in the investigation for the enantioselective asymmetric synthesis of benzyl-substituted malonic acid esters.

Keywords: Pig Liver Esterase, Enantioselectivity, Phase-Transfer Catalysis, Cinchona Alkaloids, Quaternary Ammonium …

Investigation Of N-Sulfonyliminium Ion Triggered Cyclizations For The Synthesis Of Piperidine Scaffolds, Kaitlyn Birkhoff

Honors Theses

In consideration of the on-going global pandemic, immediate access to Food and Drug Administration approved pharmaceutical medications and vaccines is a matter of utmost priority to our national healthcare system. One significant modality in managed care is the dispensation of prescription drugs for the prevention or treatment of illnesses and diseases. According to the Centers for Disease Control and Prevention, physicians order and provide over 2.9 billion prescriptions each year with analgesics, antihyperlipidemics, and dermatological agents being the most prescribed therapeutic classes. Within those classes exists a disparate variety of chemical structures that must be prepared on a metric ton …

Study Of The Cell Membrane And The Synthesis Of Chimeric Human Bacterial Phospholipids, Opeyemi O. Tade

Electronic Theses and Dissertations

Phospholipid bilayers are the principal component of the cell membrane. Membranes ensure the maintenance of processes required for cells’ survival by regulating the inflow and outflow of nutrients and other molecules using membrane proteins. However, studying the cell membrane is challenging because of its complexity and small size. In-vitro membrane models made of phospholipids are important tools for studying membranes. In this work, we aim to study the fluidity of phospholipid bilayers of different lipids using general polarization (GP) of the fluorescent probe Laurdan as a measure. We will focus on the relative importance of head groups and fatty acids …

Design, Synthesis, And Catalytic Application Of Crystalline Porous Nanomaterials, Zainab Abdullah Almansaf

Graduate Theses and Dissertations

Chapter 1: COFs (covalent organic frameworks) are a new type of microporous crystalline polymer connected by organic units via strong covalent bonds. Due to their well-defined crystalline structures and excellent chemical and thermal stabilities, COF materials are considered promising candidates in applications such as gas adsorption, catalysis, and energy storage.Chapter 2: A new covalent organic framework (COF) based on imine bonds was assembled from 2-(4-formylphenyl)-5-formylpyridine and 1,3,6,8-tetrakis(4-aminophenyl)pyrene, which showed an interesting dual-pore structure with high crystallinity. Postmetallation of the COF with Pt occurred selectively at the N donor (imine and pyridyl) in the larger pores. The metalated COF served as …

Preparation And Study Of Bacterial Membrane Models, Enoch Asimbisa

Electronic Theses and Dissertations

Fuel molecules are organic solvents that have disruptive effects on the bacterial membrane. This is a significant barrier in biofuel production, as it limits the fuel concentration that can be achieved through fermentation. One potential way of overcoming this barrier is to identify lipid compositions that can better withstand solvent stress, for which it is important to understand how organic solvents disrupt the membrane. Use of biophysical characterization techniques to quantify physical properties like fluidity and thickness will enable us to understand the mechanism by which solvents disrupt membranes. Native membranes are very complex, and we sought to develop in-vitro …

Synthesis Of Phosphatidylethanolamine Lipids For Model Studies Of The Cell Membrane, John Hayford G. Teye-Kau

Electronic Theses and Dissertations

Concerns about global warming have resulted in a surge of research into alternatives to fossil fuels. In recent years, biofuels have gained traction due to their low environmental impact. Biofuel production most commonly employs microorganisms to convert biomass to fuel for industrial and transportation applications. Compounds made in biofuel production, however, are toxic to cell membranes and disrupt their integrity, harming the microorganisms and limiting biofuel yield. A key to overcoming this challenge is understanding how fuels interact with microorganisms’ cell membranes, which perform a host of functions, including transport, cell recognition, transduction, and movement. Phospholipids are the cell membrane’s …

Synthesis Of Phytosulfokine Analogs As Probes For Studying Plant Signaling And Molecular Trafficking, Thomas Ntim

Electronic Theses and Dissertations

Plants are exposed to a wide range of biotic and abiotic stresses that hinder their growth and reduce crop productivity. In their adaptive response, plants use signaling molecules that are trafficked throughout the plant. This research focuses on the chemical synthesis and assessment of analogs of the plant signal phytosulfokine (PSK, a sulfated pentapeptide), its delivery to plants and its observation using a fiber-optic fluorescence microscope. PSK regulates growth, cell expansion, heat tolerance, and tissue longevity. Analogs of PSK were synthesized using solid-phase peptide synthesis. Pure PSK and TAMRA-labeled PSK were delivered into the wild-type Arabidopsis thaliana Col-0 and a …

Rapid Method For Consistency And Concentration Reporting Of Cannabidiol Using 1H-Nmr And Computer-Assisted Chemical Software, Michael A. Fernando

University Honors Theses

An integrated computational method was demonstrated with hemp-derived Cannabidiol for an assessment of its purity and concentration. The sample was structurally verified, high purity, and 2.98 mmol/L in dissolved DMSO. The method presented is a general approach to assessing purity and concentration for any small organic molecule in CMC-Assist.

Multifunctional Programmable Self-Assembled Nanoparticles In Nanomedicine, Yoshie Sakamaki

Graduate Theses and Dissertations

Developing methodologies to control the architecture of nanoparticles (NPs) at the atomic level prevents their inhomogeneity and leads to a variety of expected functions. Rationally designed nanoparticles can either be programmed or crystallized structures into pre-determined structures achieving tunable particle pore size and physiochemistry. In this dissertation, two broad classes of multifunctional nanoparticles are developed, metal-organic frameworks and DNA-NP aggregates.

Metal-organic frameworks are a novel class of highly porous crystalline materials built from organic linkers and metal cluster-based secondary building units. However, applications in bioremediation have not been developed very well especially in applications regarding drug delivery systems (DDS). The …

Catalytic Activity Of Molybdenum-Dioxo Complexes, Randy Tran

Graduate Theses and Dissertations

This dissertation details the development of rationally designed dioxomolybdenum catalyst active for deoxydehydration (DODH), the net reduction of diols and polyols into alkenes and dienes. Catalyst design involved variations on dioxomolybdenum(VI) supported by a dianionic meridional pincer ligand. Rational substrate scope was explored using aliphatic diols, aromatic diols, and biomass derived diols. Various reductants were tested for ability to catalyze the reaction. The substrate specific mechanism of DODH was explored utilizing NMR and in-situ infrared spectroscopy and important rate constants and rate determining steps were found to aid in the optimization of ideal reaction conditions. Catalytic activity was observed to …

Experimental And Computational Studies Of Electron Rich Alkenes, Alexa May

Graduate Theses and Dissertations

Thermal homolysis is one of the most fundamental reactions in organic chemistry. Free radical reactions are generally initiated by light or a radical initiator to generate the first radical, which can then propagate or terminate the reaction. Direct thermal homolysis requires no chemical initiators, just an increase in temperature depending on the homolysis energy.There are few studies of direct radical homolysis in complex systems or under mild conditions. The reactions involving C-N homolysis under mild conditions are reported in Chapter 1. Though the authors do not all propose a radical mechanism, we believe they can all be explained by a …

Designing Environmentally Responsible And Highly Effective Bioorthogonally Functionalized Chiral Mri Contrast Agents, Karley Breann Maier

Dissertations and Theses

Magnetic resonance imaging (MRI) revolutionized diagnostic imaging and modernized the characterization of numerous diseases. The clinical success of MRI is in large part due to the employment of gadolinium-based contrast agents (GBCAs). Due to sensitivity limitations, GBCAs are indicated at markedly high dosages (~1 g Gd³⁺ per exam). The routine use of such large quantities of gadolinium poses significant health and environmental risks. There are growing concerns over the effects of dechelation of the metal in vivo and the possible effect of resulting gadolinium deposition. Concurrently, there is a rising awareness of gadolinium anomalies borne by GBCAs which undergo …

Me3al-Mediated Domino Nucleophilic Addition/Intramolecular Cyclisation Of 2-(2-Oxo-2-Phenylethyl)Benzonitriles With Amines; A Convenient Approach For The Synthesis Of Substituted 1-Aminoisoquinolines, Krishna M. S. Adusumalli, Lakshmi N.S. Konidena, Hima B. Gandham, Krishnaiah Kumari, Krishan R. Valluru, Satya K.R. Nidasanametla, Venkateswara R. Battula, Hari K. Namballa

Publications and Research

A simple and efficient protocol for the construction of 1-aminoisoquinolines was achieved by treating 2-(2-oxo-2- phenylethyl)benzonitriles with amines in the presence of Me 3 Al. The reaction proceeds via a domino nucleophilic addition with subsequent intramolecular cyclisation. This method provides a wide variety of substituted 1-aminoisoquinolines with good func- tional group tolerance. Furthermore, the synthetic utility of this protocol was demonstrated in the successful synthesis of the anti- tumor agent CWJ-a-5 in gram scale.

New Methods For The Synthesis, Activation, And Application Of Thioglycosides, Samira Escopy

Dissertations

From their ubiquitous presence in Nature to their vital roles in biology and medicine, carbohydrates (sugars or glycans) are essential molecules of life, which are made and/or utilized by every living organism. Our cells are coated with sugars that are involved in almost every biological process and defensive mechanism in our body. To mention some of their crucial biological functions, carbohydrates are essential source of energy, they participate in blood coagulation, immune defense, cell growth, cell-cell interaction, and anti-inflammatory processes. Understanding of glycan functions and structure is crucial for the development of vaccines and therapeutics. Producing complex carbohydrates in sufficient …

Issue Of False Amphetamine Field Test Positives Caused By Sugar: Use Of Baeyer Test As A Secondary Test Solution, Reed A. Knutson, Jennah Duncan, Kara Peightal, Samuel Thomas

Department of Chemistry: Dissertations, Theses, and Student Research

The Marquis reagent is a well-established and widely used chemical presumptive test for 3,4-Methylenedioxymethamphetamine (MDMA) and methamphetamine. It is composed of concentrated sulfuric acid and 40% formaldehyde, which act upon alkaloids causing them to complex into larger molecules. This complexation causes a color change that can be visually interpreted as a positive or negative result. Almost any sugar molecule can be complexed in this way as well, due to their many OH groups. Experimentally it was found that the sugar molecules did complex with one another when the Marquis test was administered. The color produced by this reaction was brownish-red. …

Electro-Organic Synthesis Of Schiff-Bases And Azo-Schiff Bases By Electrochemical Reduction Of The Nitro Group Group In Different Media, Siba Naseef, Deep Bakair, Rushdi Mador

Hadhramout University Journal of Natural & Applied Sciences

In this research synthesized amino is derivative of Schiff-bases by using electrolysis cell. Electrochemical reduction of para-nitroaniline and electrocatalysed condensation have been carried out at zinc electrode and anode from coal in the presence of potassium chloride as supporting electrolyte in water/methanol solution, and in the application of 20V voltage, where interaction is in two stages: the first stage involves the electrochemical reduction of nitro group and get the amino and the second phase also, azo Schiff was synthesized between para-nitroaniline and metoxybenzealdehyde by electrolysis method, which was supplied with a zinc electrode as cathode to perform electrochemical reduction in …

Organic Synthesis, Kevin M. Shea, Libretext

Open Educational Resources: Textbooks

My goal in writing this text is to help advanced undergraduates and beginning graduate students learn key topics in organic chemistry that often don't come up in your Organic I and II classes. So, you can think about this as an Organic III text. My focus is on key reaction types that enable the construction of complex organic molecules: pericyclic reactions, transition metal catalyzed reactions, rearrangements, fragmentations, radical reactions, and carbene reactions. I hope that this text is a resource that helps you understand the mechanisms of these reactions and enables you to use these reactions in your own syntheses. …

Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig

Faculty Research, Scholarly, and Creative Activity

Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.

Developing Covalent-Organic Frameworks For Protecting Against Radiation, Megan J. Francis

Senior Theses

This research focuses on the development of lightweight, thermostable dual-function materials for secondary radiation protection and sensing by the integration of hydrogen-rich aliphatic chains inside the porous matrix of covalent-organic frameworks (COFs). The main aims of this project are the synthesis of organic linkers for forming a robust porous COF, synthesizing the porous COF through a condensation reaction, the development of hydrogen-rich aliphatic chains, and integration of aliphatic chains into COFs through click chemistry. This manuscript outlines the methodology and development of a novel self-assembled crystalline, porous material engineered to combine the functions of a shield and sensitive dosimeter. The …

Synthesis And Complexation Of Monotosylated 4-Aminopyridine With Nickel (Ii) And Iron (Ii) Ions, Kingsley John Orie, Remy Ukachukwu Duru, Raphael I-Oro Ngochindo

Makara Journal of Science

Tosylated 4-aminopyridine and other sulfonylated compounds of amines comprise a substantial class of pharmaceutical drugs used as antibiotics in the field of medicine. This research aimed at the synthesis of tosylated 4-aminopyridine and the complexation of the tosyated 4-aminopyridine with Ni(II) and Fe(II) ions. The sulfonamide was prepared by the action of tosyl chloride on 4-aminopyridine in an aqueous alkaline medium. The complexes were synthesized by the reaction of Ni(NO₃)_2.6H₂O /Fe(NO₃)_2.6H₂O with sulfonamide derivative. These compounds were characterized through Ultraviolet Visible spectroscopy (UV–Vis), Fourier Transform Infer-Red (FTIR) spectroscopy, …

Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNA^Phe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNA^Phe, despite these oxidized residues not …

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Enhanced Platinum (Ii) Drug Delivery For Anti-Cancer Therapy, Marek T. Wlodarczyk

Dissertations, Theses, and Capstone Projects

Over the years, anti-cancer therapies have improved the overall survival rate of patients. Nevertheless, the traditional free drug therapies still suffer from side effects and systemic toxicity, resulting in low drug dosages in the clinic. This often leads to suboptimal drug concentrations reaching cancer cells, contributing to treatment failure and drug resistance. Among available anti-cancer therapies, metallodrugs are of great interest. Platinum (II)-based agents are highly potent and are used to treat many cancers, including ovarian cancer (OC). Cisplatin (cis-diaminedichloroplatinum (II)) is the first Food and Drug Administration (FDA)-approved metallodrug for treatment of solid tumors, and its mechanism …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Immobilized-Enzyme Reactors Integrated Into Analytical Platforms: Recent Advances And Challenges, Bert Wouters Dr, Sinead Currivan, Noor Abdulhussain, T. Hankemeier, Peter J. Schoenmakers

Articles

Immobilized-enzyme reactors (IMERs) are flow-through devices containing enzymes that are physically confined or localized with retention of their catalytic activities. IMERs can be used repeatedly and continuously and have been applied for (bio)polymer degradation, proteomics, biomarker discovery, inhibitor screening, and detection. Online integration of IMERs with analytical instrumentation, such as high-performance liquid chromatography (HPLC) systems, reduces the time needed for multi-step workflows, reduces the need for sample handling, and enables automation. However, online integration can also be challenging, as reaching its full potential requires complex instrumental setups and experienced users. This review aims to provide an assessment of recent advances …

Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem

Computational and Data Sciences (MS) Theses

Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …