Chemistry Commons^™

Advanced Analytical Method Development: From Highly-Enrolled Classroom To Data-Intensive Proteomics, Laxmi Sinduri Vuppala

USF Tampa Graduate Theses and Dissertations

In analytical chemistry, method development is key to identifying, separating, and quantifying chemical components of interest systems. The chemical aspects are fundamental to understanding the subject of any analytical system, whether in academic research, industry, or government. These methodologies serve as a bridge between the classroom, where students are taught to be curious and enlightened, and research, where one strives to contribute. The Ph.D. dissertation integrates advanced methodologies in basic and applied research and advanced instrumentation, but the core criteria for validation remain the same. As part of chemical education curriculum development, a large cohort of undergraduates performed two gas …

Exchange Broadening Underlies The Enhancement Of Ide-Dependent Degradation Of Insulin By Anionic Membranes, Qiuchen Zheng, Bethany Lee, Micheal T. Kebede, Valerie A. Ivancic, Merc M. Kemeh, Henrique Lemos Brito, Donald E. Spratt, Noel D. Lazo

Chemistry

Insulin-degrading enzyme (IDE) is an evolutionarily conserved ubiquitous zinc metalloprotease implicated in the efficient degradation of insulin monomer. However, IDE also degrades monomers of amyloidogenic peptides associated with disease, complicating the development of IDE inhibitors. In this work, we investigated the effects of the lipid composition of membranes on the IDE-dependent degradation of insulin. Kinetic analysis based on chromatography and insulin's helical circular dichroic signal showed that the presence of anionic lipids in membranes enhances IDE's activity toward insulin. Using NMR spectroscopy, we discovered that exchange broadening underlies the enhancement of IDE's activity. These findings, together with the adverse effects …

Structure-Property Investigations In Urea Tethered Iodinated Triphenylamines, Muhammad Saddam Hossain, Fiaz Ahmed, Stavros G. Karakalos, Mark D. Smith, Namrata Pant, Sophya V. Garashchuk, Andrew B, Greytak, Pablo Docampo, Linda S. Shimizu

Faculty Publications

Herein, we report structural, computational, and conductivity studies on urea-directed self-assembled iodinated triphenylamine (TPA) derivatives. Despite numerous reports of conductive TPAs, the challenges of correlating their solid-state assembly with charge transport properties hinder the efficient design of new materials. In this work, we compare the assembled structures of a methylene urea bridged dimer of di-iodo TPA (1) and the corresponding methylene urea di-iodo TPA monomer (2) with a di-iodo mono aldehyde (3) control. These modifications lead to needle shaped crystals for 1 and 2 that are organized by urea hydrogen bonding, π⋯π stacking, I⋯I, and I⋯π interactions as determined by …

Development Of 1,2-Cis-Selective Glycosylation Protocols And Multistep Synthesis Of Glycans From Acinetobacter Baumannii., Dancan Kamau Njeri

LSU Doctoral Dissertations

Access to various oligosaccharides has been made possible by glycosylation reactions. This is mainly through chemical synthesis and enzymatic approaches. Herein, I talk about glycosylation through chemical synthesis. In general, glycosylation reactions lead to a mixture of 1,2-cis and 1,2-trans stereoisomers. Stereoselective access to 1,2-trans isomer is highly developed; it efficiently relies on neighboring group participation. However, efficient access to 1,2-cis selective glycosylation is still a work in progress. In Chapter 1, I highlight notable efforts developed so far that address the 1,2-cis selectivity challenge in glycosylation.

In Chapter 2, I demonstrate how I improved …

Computational, Synthetic And Spectroscopic Studies On Donor Acceptor Transition Metal Complexes, Ranjana Dangi

Chemistry and Chemical Biology ETDs

Fundamental advances in our ability to design and construct electronic components at the nanoscale will require new design paradigms. One proposed nanoscale electronic component is the molecular rectifier. Molecular and molecule-based electronic components are advantageous due to their ease of synthetic manipulation, and the fact that the size dimensions of molecules are inherently at the nanoscale (0.5 - 3nm). Our group has shown how the Donor-Bridge-Acceptor biradical approach can be used to derive key structure-property relationships that allow insight into the choice of bridge fragments for molecular rectification by using constitutional isomers of the donor-bridge-acceptor biradical (NN-Th-Py-SQ) (S=1/2 ortho-semiquinonate, …

Determining The 3d Structure And Dynamics Of Mouse Notch1 Epidermal Growth Factor-Like Repeat 26 Using Nuclear Magnetic Resonance Spectroscopy, Kendra D. Jenkins

LSU Doctoral Dissertations

NOTCH is a transmembrane protein that transmits signals between cells in direct contact and alters gene expression. The signaling pathway is important because it is involved in cell fate determination. The NOTCH1 extracellular domain has 36 epidermal growth factor-like (EGF) repeats that are responsible for ligand binding. Mutations in the EGF-like repeats cause various neurological and developmental disorders. NOTCH1 signaling initiates when DSL ligands bind to EGF11-12, the minimum Ligand Binding Domain (LBD). The Abruptex region of the NOTCH1 protein (EGF24-29) is a highly glycosylated, flexible region with calcium binding sites that regulates NOTCH1 signaling and binding by interacting with …

Nmr Analyses Of Flavored E-Cigarette Liquids Before And After Aerosolization, Paul Joseph Kerber

Dissertations and Theses

Electronic cigarettes (e-cigarettes) are the most commonly used tobacco products among adolescents with ~11 and ~3% of high school and middle school students reporting past 30 day use in 2021 according to the Centers for Disease Control and Prevention (CDC), respectively. Furthermore, greater than ~80% of high school and middle school e-cigarette consumers use flavored e-liquids. Consumers can be exposed to variable toxicant levels upon e-liquid aerosolization, depending on the composition of the e-liquid, type of e-cigarette, e-cigarette settings, and other customizations.

E-liquids are typically composed of a carrier solvent (propylene glycol (PG) and glycerol (GL)), flavorants, and nicotine. PG …

The Photoionization Dynamics, Electronic Spectroscopy, And Excited State Photochemistry Of Alco And Aloc, Vincent J. Esposito, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The high cosmic abundance of carbon monoxide (CO) and the ubiquitous nature of aluminum-coated dust grains sets the stage for the production of weakly bound triatomic molecules AlCO (X ²Π) and AlOC (X ²Π) in circumstellar envelopes of evolved stars. Following desorption of cold AlCO and AlOC from the dust grain surface, incoming stellar radiation in the 2–9 eV wavelength range (visible to vacuum ultraviolet) will drive various photochemical processes. Ionization to the singlet cation state will cause an immediate Al–X (X = C, O) bond dissociation to form Al⁺ (¹S) and CO (X ^{1 …}

Negative Photoresponse In Ti3C2TX Mxene Monolayers, Nataliia S. Vorobeva, Saman Bagheri, Angel Torres, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Two-dimensional transition metal carbides, nitrides, and carbonitrides, collectively known as MXenes, are finding numerous applications in many different areas, including optoelectronics and photonics, but there is limited information about their intrinsic photoresponse. In this study, we investigated the visible and near-infrared range photoresponse of Ti₃C₂T_x, the most popular MXene material to date. The electrical measurements were performed on devices based on individual monolayer Ti₃C₂T_x MXene flakes, which were characterized by a variety of microscopic and spectroscopic methods. For MXene devices with different electrode layouts, the current reproducibly decreased under …

Characterization Of Three-Dimensional Fractional Viscoelastic Models Through Complex Modulus Analysis And Polar Decomposition, Avradip Ghosh, Avinash Kumar Both, Chin Li Cheung

Department of Chemistry: Faculty Publications

Soft materials such as gels, elastomers, and biological tissues have diverse applications in nature and technology due to their viscoelastic nature. These soft materials often exhibit complex rheology and display elastic and viscous characteristics when undergoing deformation. In recent years, fractional calculus has emerged as a promising tool to explain the viscoelastic behavior of soft materials. Scalar constants are primarily used to quantify viscoelastic elements such as springs and dashpots. However, in three-dimensional (3D) space, not all materials show the same elastic or viscoelastic properties in all directions, especially under elastic/viscoelastic wave propagation (or anisotropy). Though previously reported studies on …

Integrating Conformational Dynamics And Perturbation-Based Network Modeling For Mutational Profiling Of Binding And Allostery In The Sars-Cov-2 Spike Variant Complexes With Antibodies: Balancing Local And Global Determinants Of Mutational Escape Mechanisms, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

n this study, we combined all-atom MD simulations, the ensemble-based mutational scanning of protein stability and binding, and perturbation-based network profiling of allosteric interactions in the SARS-CoV-2 spike complexes with a panel of cross-reactive and ultra-potent single antibodies (B1-182.1 and A23-58.1) as well as antibody combinations (A19-61.1/B1-182.1 and A19-46.1/B1-182.1). Using this approach, we quantify the local and global effects of mutations in the complexes, identify protein stability centers, characterize binding energy hotspots, and predict the allosteric control points of long-range interactions and communications. Conformational dynamics and distance fluctuation analysis revealed the antibody-specific signatures of protein stability and flexibility of the …

Multiplexed Monitoring Of Neurochemicals Via Electrografting- Enabled Site-Selective Functionalization Of Aptamers On Field-Effect Transistors, Zan Gao, Guangfu Wu, Yang Song, Huijie Li, Yuxuan Zhang, Michael J. Schneider, Yingqi Qiang, Jackson Kaszas, Zhengyan Weng, He Sun, Bryan D. Huey, Rebecca Lai, Yi Zhang

Department of Chemistry: Faculty Publications

Neurochemical corelease has received much attention in understanding brain activity and cognition. Despite many attempts, the multiplexed monitoring of coreleased neurochemicals with spatiotemporal precision and minimal crosstalk using existing methods remains challenging. Here, we report a soft neural probe for multiplexed neurochemical monitoring via the electrografting-assisted site-selective functionalization of aptamers on graphene field-effect transistors (G-FETs). The neural probes possess excellent flexibility, ultralight mass (28 mg), and a nearly cellular-scale dimension of 50 μm × 50 μm for each G-FET. As a demonstration, we show that G-FETs with electrochemically grafted molecular linkers (−COOH or −NH2) and specific aptamers can be used …

Quantifying Protein Quality To Understand Protein Homeostasis (Supplemental Data), Hsien-Jung Lavender Lin

ScholarsArchive Data

This data set includes the supplementary data for chpaters 3 and 4 in the dissertation Quantifying Protein Quality to Understand Protein Homeostasis. It includes various excel worksheets that were used to generate the data reported in the dissertation. We make this data available to the public so anyone who wants to reproduce the results has the resources and access to other perspectives that weren't discussed in depth in the dissertation. Chapter 3 used mass-spectrometry to quantify the surface accessibility differences in human serum albumin (HSA)between patients with and without rheumatoid arthritis (RA). We found certain residues are less reactive …

Kinetics, Products, And Brown Carbon Formation By Aqueous-Phase Reactions Of Glycolaldehyde With Atmospheric Amines And Ammonium Sulfate (Raw Data), David O. De Haan, Alyssa A. Rodriguez, Michael A. Rafla, Hannah G. Welsh, Elyse A. Pennington, Jason R. Casar, Lelia N. Hawkins, Natalie G. Jimenez, Alexia De Loera, Devoun R. Stewart, Antonio Rojas, Matthew-Khoa Tran, Peng Lin, Alexander Laskin, Paola Formenti, Mathieu Cazaunau, Edouard Pangui, Jean-François Doussin

Chemistry and Biochemistry: Faculty Scholarship

The zipped data files are in the following formats: Metadata: Word documents (.docx), Chamber data: Excel spreadsheets (.xlsx) and European Data Format files (.edf), organized by experiment number and instrumentation. “CAPS” files contain cavity attenuated phase shift (CAPS) extinction and scattering data; “SMPS” files contain scanning mobility particle sizing aerosol number and aerosol mass data.

Combination Of High Ph And An Antioxidant Improves Chemical Stability Of Two-Dimensional Transition-Metal Carbides And Carbonitrides (Mxenes) In Aqueous Colloidal Solutions, Shuohan Huang, Vadym Mochalin

Chemistry Faculty Research & Creative Works

MXenes, a large family of two-dimensional (2D) transition-metal carbides/nitrides, have attracted increased attention in recent years because of their excellent electronic, mechanical, thermal, and optical properties. Studying chemical properties of MXenes is important to prolong the shelf life of their colloids and provide robust performance of MXenes in devices and applications. While the role of MXene reactivity with the environment, including water and components of air, is becoming more recognized, less is known about the role of parameters influencing the reactivity. In this work, we investigate the individual and combined effects of the pH and antioxidant on chemical stability of …

Evaluation Of Silver Nanoparticles Attached To Methylene Blue As An Antimicrobial Agent And Its Cytotoxicity, Somon Hakimov

Masters Theses & Specialist Projects

Antibiotics resistance is considered as one of the greatest public health challenges of our time. In this work, we have synthesized silver nanoparticles (Ag NPs) using pulsed liquid ablation in different medium of growth and later combined with methylene blue (MB) to evaluate its potential as an effective photodynamic therapy agent. Ag NPs were synthesized by pulsed laser ablation technique in Polyvinylpyrrolidone (PVP), citrate, and Polyvinyl alcohol (PVA). The Ag NPs were characterized using transmission electron microscopy (TEM), UV-Visible (UV-Vis), and photoluminescence (PL) spectra. Next, Ag NPs were coupled with MB and used to deactivate the Gram-negative bacteria, Escherichia coli …

Can You Master This? : Initial Attempts At Specifications-Based Grading In Introductory Chemistry, Laura Kopff

Faculty Publications & Research

The Illinois Mathematics and Science Academy (IMSA) requires all incoming students to complete a one-semester introductory chemistry course in their sophomore year – Scientific Inquiries in Chemistry (SI-Chem). This course has historically been taught using a traditional grading/assessment model, however, in the Spring of 2021, a switch was made to a specification-based grading system. One motivating factor in this decision is an institutional shift to an equity-focused grading approach, and an analysis of our historical assessment model indicated areas for improvement.

Our initial foray into specifications grading was during the Spring of 2021 semester, when all of our courses were …

Synthesis And Characterization Of Biomimetic Co And Fe Complexes With Trispyrazolylborate Ligands, Praveen Kumar

Dissertations (1934 -)

Numerous reactions of biological and environmental significance are catalyzed by dioxygenases that incorporate both atoms of O2 into the substrate. These enzymes require a transition-metal cofactor for activity, typically a mononuclear nonheme iron center, although dioxygenases with first-row transition metal ions (Mn, Co, Ni) have been discovered. This dissertation focuses on synthetic studies based on mononuclear dioxygenases found in bacterial pathways for the breakdown and assimilation of inert organic compounds, including human-generated pollutants. Such enzymes are essential for bioremediation technologies used to restore contaminated soils and groundwaters. While crystallographic studies have revealed the active-site structures of various types of dioxygenases, …

Disinfection Byproducts In Wastewater, Swimming Pools, And Tea: Identification, Quantification, And Drivers Of Toxicity, Caroline O. Granger

Theses and Dissertations

Drinking water disinfection is considered one of the greatest scientific achievements of the 20th Century because it significantly reduced the number of deaths related to waterborne diseases. However, in 1974 J.J. Rook discovered that chlorine, a commonly used disinfectant, can react with natural organic matter to form disinfection byproducts (DBPs). Since then, more than 700 DBPs have been identified, with several epidemiological and toxicological studies linking DBPs to several adverse health effects such as bladder and colorectal cancer, adverse birth outcomes, and asthma. Due to their ubiquity in disinfected water and their adverse health effects, studying the formation and identifying …

Mass Spectrometric Investigation Of Removal/Transformation Of Emerging Contaminants For Safer Potable Wastewater Reuse, Kristin Cochran

Theses and Dissertations

Water scarcity is of increasing global concern as rising demand depletes current sources, so other sources such as potable wastewater reuse are being utilized. Advanced wastewater reuse removes pathogens and many contaminants, but there are concerns about resistant contaminants and the transformation products that are generated during the treatment process. This research focuses on several different contaminant classes, how well they are removed via advanced treatment processes, what transformation products arise from both advanced treatment and chlorination disinfection, and how those treated waters may impact health via toxicity and estrogen activity.

Contaminant classes considered are illicit drugs, pharmaceuticals such as …

Probing The Stability And Solution Processability Of Metal Chalcogenide Semiconducting Materials, Mengwen Yan

Legacy Theses & Dissertations (2009 - 2024)

Metal chalcogenide (MCh) semiconductors have long research history due to their earth abundance, easy synthesizability, and accessible band gap tunability. People have realized their functionality as p-type semiconductors that provide good hole mobility and conductivity within the materials. However, MChs have easier reaction pathway with gas molecules (H2O and O2) compared to other semiconductors such as metal oxides. Also, poor solution processability of all MChs make low-cost thin film fabrication methods hard to achieve. In this thesis, we target to understand both the chemical stability and solution processability of MCh materials. ZnSe based inorganic organic layered hybrids (LHs) were exfoliated …

Photocrosslinking Probes Proximity Of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates To Dna Holliday Junction, Shibani Basu, Keitel Cervantes-Salguero, Bernard Yurke, William B. Knowlton, Jeunghoon Lee, Olga A. Mass

Chemistry and Biochemistry Faculty Publications and Presentations

A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine …

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 …

Taking Action: Managing Inclusive Excellence In Academia, Lesley Ann Giddings, Christine Salomon

Chemistry: Faculty Publications

No abstract provided.

Properties And Behavior Of Tricarbonyl Manganese Scorpionate Complexes, Billy Shone

Master's Theses (2009 -)

Manganese tricarbonyl complexes have widely been studied for their ability to release carbon monoxide (CO) in the presence of light for potential applications in cancer therapy and in catalysis. Most studies focus on the kinetics and quantity of CO release and the overall impact on cell death. Far fewer studies identify the manganese intermediates and final products after decarbonylation. Identification of such products would be critical to improving reactivity and understanding potential (undesirable) side effects in future applications employing these CO releasing molecules (CORMs). Recently, nitrogen confused C-scorpionate ligands were introduced by the Gardinier group where a pyrazolyl ring is …

The Development Of A Monolithic Spatial Heterodyne Spectrometer For Extreme Environments, Arelis Michelle Colόn

Theses and Dissertations

This work describes improvements to a novel instrument, the monolithic spatial heterodyne Raman spectrometer (mSHRS), which has potential to be utilized in space exploration and deep-ocean marine sensing. In previous work, the spatial heterodyne Raman spectrometer (SHRS) was demonstrated, as a small, high resolution, wide field of view spectrometer, originally developed for space applications where small size and compactness is a key consideration or where a wide field of view is advantageous, such as in remote spectroscopy. The spatial heterodyne spectrometer (SHS) was then later utilized for remote Laser-Induced Breakdown Spectroscopy (LIBS). The high throughput, high spectral resolution, and large …

Pyridyl Bis-Urea Macrocycles As Supramolecular Synthons And The Design And Synthesis Of Small Molecule Pharmaceuticals Targeting Ly6k, Devan D. Buchanan

Theses and Dissertations

Assembled pyridyl bis-urea macrocycles have been utilized as 1D supramolecular synthons to construct hierarchical assemblies. These macrocycles have both urea and pyridyl functional groups and can form non-covalent interactions with hydrogen or halogen bond donors through symmetric, ditopic acceptor motifs. Bis-urea macrocycles offer interesting capabilities as synthons to organize donors into well-defined crystal structures. In part, this is due to the urea motifs’ propensity to assemble through hydrogen bonding. New, asymmetric pyridyl macrocycles were synthesized, crystallized, and experimentally probed to determine how symmetry affects their assembly and utility as supramolecular synthons.

The Uphadhyay group identified small molecules, including NSC11150, …

Developing A Rational Approach To Designing Recombinant Proteins For Peptide-Directed Nanoparticle Synthesis, Adithya Polasa, Imann Mosleh, James Losey, Alireza Abbaspourrad, Robert Beitle, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The controlled formation of nanoparticles with optimum characteristics and functional aspects has proven successful via peptide-mediated nanoparticle synthesis. However, the effects of the peptide sequence and binding motif on surface features and physicochemical properties of nanoparticles are not well-understood. In this study, we investigate in a comparative manner how a specific peptide known as Pd4 and its two known variants may form nanoparticles both in an isolated state and when attached to a green fluorescent protein (GFPuv). More importantly, we introduce a novel computational approach to predict the trend of the size and activity of the peptide-directed nanoparticles by estimating …

Improved Photodecarboxylation Properties In Zinc Photocages Constructed Using M‐Nitrophenylacetic Acid Variants, Austin K. Shigemoto, Avik Bhattacharjee, Erin E. Hickey, Hallee Jade Boyd, Theresa M. Mccormick, Shawn C. Burdette

Chemistry Faculty Publications and Presentations

The methoxy- and fluoro-derivatives of meta-nitrophenylacetic acid (mNPA) chromophores undergo photodecarboxylation with comparable quantum yields to unsubstituted mNPA, but uncage at red-shifted excitation wavelengths. This observation prompted us to investigate DPAdeCageOMe (2-[bis(pyridin-2-ylmethyl)amino]-2-(4-methoxy-3-nitrophenyl)acetic acid) and DPAdeCageF (2-[bis(pyridin-2-ylmethyl)amino]-2-(4-fluoro-3-nitrophenyl)acetic acid) as Zn2+ photocages. DPAdeCageOMe has a high quantum yield and exhibits other photophysical properties comparable to XDPAdeCage ({bis[(2-pyridyl)methyl]amino}(9-oxo-2-xanthenyl) acetic acid), the best perforiming Zn2+ photocage reported to date. Since the synthesis of DPAdeCageOMe is more straightforward than XDPACage, the new photocage will be a highly competitive tool for biological applications.

A Protein-Based Therapeutic Combination For The Treatment Of Hard-To-Heal Wounds, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Chronic wounds present many clinical challenges in relation to the successful treatment and closure of the damaged tissue. Most current treatment methods focused on one or two aspects to drive wound closure, while most chronic wounds are multifactorial environments with many of those dependencies relying on the termination of one another to effectively gain tissue construction, closure, and full skin thickness and composition. Natural wound healing processes allude to potential biologics that can impede the chronic breakdown of tissue, while restoring deposition of new tissue, and effectively leading to a healed wound. Proteases secreted by the body’s immune system lay …