Chemistry Commons^™

Changes In An Enzyme Ensemble During Catalysis Observed By High Resolution Xfel Crystallography, Nathan J. Smith, Medhanjali Dasgupta, David C. Wych, Cole Dolamore, Raymond G. Sierra, Stella Lisova, Darya Marchany-Rivera, Aina E. Cohen, Sébastien Boutet, Mark S. Hunter, Christopher Kupitz, Frédéric Poitevin, Frank R. Moss Iii, Aaron S. Brewster, Nicholas K. Sauter, Iris D. Young, Alexander M. Wolff, Virendra K. Tiwari, Nivesh Kumar, David B. Berkowitz, Ryan G. Hadt, Michael C. Thompson, Alec H. Follmer, Mark A. Wilson

Department of Chemistry: Faculty Publications

Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large …

On The Boundary Of The Cosmos, Daniel Linford

Department of Chemistry: Faculty Publications

Intuitively, the totality of physical reality – the Cosmos – has a beginning only if (i) all parts of the Cosmos agree on the direction of time (the Direction Condition) and (ii) there is a boundary to the past of all non-initial spacetime points such that there are no spacetime points to the past of the boundary (the Boundary Condition). Following a distinction previously introduced by J. Brian Pitts, the Boundary Condition can be conceived of in two distinct ways: either topologically, i.e., in terms of a closed boundary, or metrically, i.e., in terms of the Cosmos having a finite …

On The Chemistry Of Aqueous Ammonium Acetate Droplets During Native Electrospray Ionization Mass Spectrometry, Lars Konermann, Zeyuan Liu, Yousef Haidar, Methew J. Willians, Nicholas A. Bainbridge

Chemistry Publications

Ammonium acetate (NH₄Ac) is a widely used solvent additive in native electrospray ionization (ESI) mass spectrometry. NH₄Ac can undergo proton transfer to form ammonia and acetic acid (NH₄⁺ + Ac^- → NH₃ + HAc). The volatility of these products ensures that electrosprayed ions are free of undesired adducts. NH₄Ac dissolution in water yields pH 7, providing “physiological” conditions. However, NH₄Ac is not a buffer at pH 7 because NH₄⁺ and Ac^- are not a conjugate acid/base pair (L. Konermann, J. Am. Soc. Mass Spectrom. 2017 …

Novel Applications Of Enhanced Raman Spectroscopy For Drug Discovery, Mrna Vaccine Stability Assessment, And Forensic Purposes, Lamyaa M. Almehmadi

Legacy Theses & Dissertations (2009 - 2024)

The main focus of this dissertation was to apply enhanced Raman spectroscopy techniques to a variety of applications, ranging from drug discovery, mRNA vaccine stability, to forensic analysis. There are five chapters in this dissertation. The first chapter discusses the basics of enhanced Raman spectroscopy techniques and their relevance. The second chapter is focused on the use of surface-enhanced Raman spectroscopy (SERS) for drug discovery. The third chapter introduces the use of deep ultraviolet resonance Raman (DUVRR) spectroscopy for the detection of mRNA degradation in a mRNA vaccine model. The fourth chapter introduces the use of stand-off Raman spectroscopy in …

Integrating Sensor Development, Risk Assessment, And Community Engagement To Support Environmental Justice In The Rural Community Of El Tiple, Colombia, David Bahamon Pinzon

All Dissertations

In Colombia, ethnic communities have traditionally been responsible stewards of natural resources. They recognize the importance of these resources for their livelihood, as well as their ancestral and cultural heritage. El Tiple, a rural Afro-Colombian community, has been affected by the incursion of private corporations that promoted the expansion of sugarcane monocrops in their territory. Since the introduction of the monoculture industry, local freshwater sources have been depleted due to intensive water use for irrigation of the sugarcane crops. Additionally, the intensive usage of agrochemicals has been linked with loss of native flora, damages to family farms, and pollution of …

Inkjet-Printed Electrochemical Sensors For Lead Detection, Annatoma Arif

Open Access Theses & Dissertations

This PhD dissertation research has developed a simple, miniaturized, sensitive, selective, reproducible, and disposable 3D (inkjet printed – additive manufacturing technology) gold (Au) plated electrochemical sensor (ECS) on shape memory polymer (SMP) for aqueous lead detection. This technology has shown promising performance in the application of electrochemical sensing (lead (II) detection) due to increased effective electrode surface area (7.25 mm^2 ± 0.15 mm^2) despite miniaturizing lateral surface area (4.19 mm^2). The design, fabrication processes, optimization including bismuth functionalization, evaluation, uncertainty analysis, and cost analysis of the novel SMP based inkjet printed Au plated sensor have been delineated in this manuscript …

Removal Of Nonylphenols From Water And Wastewater Using Alginate-Activated Carbon Beads, Angelica Araly Chacon

Open Access Theses & Dissertations

The presence of contaminants of emerging concern (CECs) have been affecting water quality in recent years. The United States Environmental Protection Agency (U.S EPA) defines CECs as toxic chemicals without regulatory status and with adversely impact on the wildlife and people. Among the CECs, nonylphenols (NPs) are frequently found in all water systems and are categorized as endocrine-disrupting compounds (EDCs) due to their ability to mimic hormones causing reproductive and developmental effects in humans and animals. The main sources of discharge and distribution of NPs into the environment are wastewater treatment plants (WWTPs) which are not designed to remove them. …

A Low Cost, Compact Electrochemical Analyzer Based On An Open-Source Microcontroller, Michael Kofi Darko Addo

Electronic Theses and Dissertations

Compared to other instruments for chemical analyses, electrochemical analyzers are relatively simple, inexpensive, easy to miniaturize and require little-to-no maintenance. However, like all commercially available instruments, commercial electrochemical analyzers like potentiostats primarily operate as black boxes with manufacturers providing little or no information about internal circuitry and programming. This practice can limit a researcher’s ability to develop new techniques or adapt an instrument for applications outside its typical use. In contrast, creators of open-source instruments release all the necessary information for reproduction of the hardware and software – minimizing such barriers to innovation in chemical analyses. Here, we report a …

Differential Membrane Binding Of Α/Β-Peptide Foldamers: Implications For Cellular Delivery And Mitochondrial Targeting, Tzong-Hsien Lee, James W. Checco, Tess Malcolm, Chelcie H. Eller, Ronald T. Raines, Samuel H. Gellman, Erinna F. Lee, W. Douglas Fairlie, Marie-Isabel Aguilar

Department of Chemistry: Faculty Publications

The intrinsic pathway of apoptosis is regulated by the Bcl-2 family of proteins. Inhibition of the anti-apoptotic members represents a strategy to induce apoptotic cell death in cancer cells. We have measured the membrane binding properties of a series of peptides, including modified α/β-peptides, designed to exhibit enhanced membrane permeability to allow cell entry and improved access for engagement of Bcl-2 family members. The peptide cargo is based on the pro-apoptotic protein Bim, which interacts with all anti-apoptotic proteins to initiate apoptosis. The α/β-peptides contained cyclic β-amino acid residues designed to increase their stability and membrane-permeability. Dual polarisation interferometry was …

From Waste To Energy: The Electrochemical Reduction Of Co2 Using Recycled Nanostructured Catalysts, Ibrahim Badawy

Theses and Dissertations

The reduction of carbon dioxide (CO₂RR) using electrochemistry is a promising solution for the burgeoning global energy crisis. The overall vision of its implementation relies on renewable energy sources to power the reaction creating carbon neutral products and effectively closing the carbon cycle. Research in this field has come a long way since its inception in the mid-1900s. However, there remain significant hurdles and important considerations to overcome in order to reach full commercialization. Most electrocatalysts tested for CO₂RR have been designed solely for maximum performance while ignoring the environmental consequences if such a material were …

Temperature-Pressure Phase Diagram Of Confined Monolayer Water/Ice At First-Principles Accuracy With A Machine-Learning Force Field, Bo Lin, Jian Jiang, Xiao Cheng Zeng, Lei Li

Department of Chemistry: Faculty Publications

Understanding the phase behaviour of nanoconfined water films is of fundamental importance in broad fields of science and engineering. However, the phase behaviour of the thinnest water film – monolayer water – is still incompletely known. Here, we developed a machine-learning force field (MLFF) at first-principles accuracy to determine the phase diagram of monolayer water/ice in nanoconfinement with hydrophobic walls. We observed the spontaneous formation of two previously unreported high-density ices, namely, zigzag quasi-bilayer ice (ZZ-qBI) and branched-zigzag quasi-bilayer ice (bZZ-qBI). Unlike conventional bilayer ices, few inter-layer hydrogen bonds were observed in both quasi-bilayer ices. Notably, the bZZ-qBI entails a …

Long-Term Monitoring Of Clodronate In Equine Hair Using Liquid Chromatography-Tandem Mass Spectrometry, Heather K. Knych, D. S. Mckemie, S. Yim, S. D. Stanley, R. M. Arthur

UK CARES Faculty Publications

Given the potential for long-term inhibition of bone remodeling/healing and detrimental effects to horses in training, bisphosphonates are tightly regulated in horseracing. Hair has proven to be an effective matrix for detection of drug administration to horses and has been particularly effective in detecting drugs for a long period of time post administration. Thus, hair may prove to be a useful matrix for detection of administration of this class of drugs. The objective of the current study was to develop an assay and assess the usefulness of hair as a matrix for long-term detection of clodronate to horses. Seven horses …

Preface To The Special Issue On Interfactial Regulation And Electrochemical Sensors, Jing-Hong Li, Yang Tian, Yuan-Hong Xu, Li-Min Zhang

Journal of Electrochemistry

No abstract provided.

Colorful "Stars" In The Dark, Chao Jing, Yi-Tao Long

Journal of Electrochemistry

Plasmonic nanoparticles such as Au and Ag with localized surface plasmon resonance (LSPR) property exhibit unique scattering and absorption features. The plasmonic scattering and absorption bands are mainly located at visible light region which can be easily applied in visual detections. By modulating the size, shape, and composition of gold and silver colloid solutions, plenty of colorimetric methods have been constructed for the detection of metal ions, biomolecules, and environmental contaminants, etc. For many years, the LSPR-based measurements are implemented in reagent tubes. Since 2000, the plasmon resonance scattering (PRS) light of metal nanoparticles captured by dark-field microscopy enables the …

Recent Advances In Electrochemical Impedance Spectroscopy-Based Pathogenic Bacteria Sensing, Tao Chen, Yuan-Hong Xu, Jing-Hong Li

Journal of Electrochemistry

Pathogenic bacteria have been throwing great threat on human health for thousands of years. Their real-time monitoring is in urgent need as it could effectively halt the spread of pathogenic bacteria and thus reducing the risk to human health. Up till now, diverse technologies such as electrochemistry, optics, piezoelectricity and calorimetry have been developed for bacteria sensing. Therein, electrochemical impedance spectroscopy (EIS)-based sensors show great potential in point-of-care bacterial analysis because of their low-cost, short read-out time, good reproducibility, and portable equipment construction. In this review, we will primarily summarize the typical applications of electrochemical impedance technology in bacteria sensing …

Metal-Organic Frameworks For Electrochemical And Electrochemiluminescent Immunoassay, Xiao-Li Qin, Zi-Ying Zhan, Sara Jahanghiri, Kenneth Chu, Cong-Yang Zhang, Zhi-Feng Ding

Journal of Electrochemistry

Development of ultrasensitive, highly accurate and selective immunosensors is significant for the early diagnosis, screening, and monitoring of diseases. Electrochemical and electrochemiluminescent (ECL) immunoassays have both attracted great attention and become a current research hotspot due to their advantages such as good stability, high sensitivity and selectivity, wide linear range, and good controllability. Metal-organic frameworks (MOFs), as a new class of porous crystalline materials, have been widely applied in electrochemical and ECL immunosensors owing to their large specific surface area, good chemical stability, as well as adjustable pore size and nanoscale framework structures. Various MOF nanomaterials with different properties for …

Boronate Affinity-Assisted Electrochemically Controlled Atrp For Ultrasensitive Electrochemical Aptasensing Of Carcinoembryonic Antigen, Qiong Hu, Shi-Qi Li, Yi-Yi Liang, Wen-Xing Feng, Yi-Lin Luo, Xiao-Jing Cao, Li Niu

Journal of Electrochemistry

As an acidic glycoprotein, carcinoembryonic antigen (CEA) is of great value as a broad-spectrum tumor marker in the differential diagnosis and surveillance of malignant tumors. In this work, we report an electrochemical aptasensor for the ultrasensitive and highly selective detection of CEA, taking advantage of the dual amplification by the boronate affinity-assisted electrochemically controlled atom transfer radical polymerization (BA-eATRP). Specifically, the BA-eATRP-based electrochemical aptasensing of CEA involves the capture of target antigens by nucleic acid aptamers, the covalent crosslinking of ATRP initiators to CEA antigens via the selective interactions between the phenylboronic acid (PBA) group and the cis-diol group of …

N–((2–Acetylphenyl)Carbamothioyl)Benzamide: Synthesis, Crystal Structure Analysis, And Theoretical Studies, Akin Oztaslar, Hakan Arslan

Karbala International Journal of Modern Science

N–((2–Acetylphenyl)carbamothioyl)benzamide has been synthesized and characterized. The molecular conformation of the investigated compound is stabilized by C16–H16B⋅⋅⋅O2ⁱ (i: 1+x, y, z) intermolecular and C14–H14⋅⋅⋅S1, N2–H2⋅⋅⋅O2, and N2–H2⋅⋅⋅O1 intramolecular H–bonds. All DFT calculations have been implemented at the B3LYP level with the 6–311G(d,p) basis set. The optimized molecular structure parameters have been compared with the experimental one in the solid phase. The energy gap, global chemical reactivity descriptor parameters, MEP, Fukui functions, DoS, NLO, and NBO analysis were also computed and investigated. The intermolecular interactions and their energies are evaluated using Hirshfeld surface and energy framework analyses. To determine …

Investigating The Activity Of Alternative Warheads For Targeted Covalent Inhibition Of The Inhibitor Vertebrate Lysozyme Protein From Pseudomonas Aeruginosa, Katie Hambrick

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative bacterium that causes blood and lung infections in hospital environments due to its ability to survive on improperly sterilized medical equipment. P. aeruginosa has developed several multi-drug resistance mechanisms that make it very difficult to treat with current antibiotics.¹ This presents the need for a new class of antibiotics that cannot be overcome by P. aeruginosa’s mechanisms of resistance.

The primary goal of this project was to develop a small library of inhibitors that could later be incorporated into lead compounds for novel antibiotic drug discovery. One of P. …

Tio2 Crystallization At Room Temperature And Preparation Of Transparent Carbon Counter Electrode For Low-Cost Dye-Sensitized Solar Cells, Muhammad Iqbal Syauqi, Afiten Rahmin Sanjaya, Mohammad Jihad Madiabu, Munawar Khalil, Jarnuzi Gunlazuardi

Makara Journal of Science

We developed a low-cost dye-sensitized solar cell (DSSC) using TiO₂ fabricated via rapid breakdown anodization (RBA) and ultrafast room-temperature crystallization (URTC). The prepared TiO₂ was deposited on a self-made fluorine-doped tin oxide (FTO) conductive glass, and the FTO/TiO₂ system was sensitized using curcumin dye. The DSSC was constructed by sandwiching the FTO/TiO₂/curcumin electrode with an I⁻/I₂ electrolyte and a transparent carbon counter electrode prepared using a liquid–liquid interface system. The characterization results showed that the TiO₂ freshly prepared via URTC was transformed into an anatase crystalline phase, which exhibited a 3.10 …

Physicochemical Changes And Role Of Analytical Chemistry In Black Garlic (Allium Sativum L.) Processing, Surjani Wonorahardjo, Dian Puspita Sari, Arini Salsabila, Estiyawati Estiyawati, Dewi Yuliani, Anugrah Ricky Wijaya, Suharti Suharti, Irma Kartika Kusumaningrum, Chariztya Anggita Maharani, Thjiong Angelina Noviyanti

Makara Journal of Science

Black garlic is a traditional spice having potential of herbal medicine; however, continuous heating darkens its color and changes its taste due to chemical processes and new equilibrium in the system. In this study, fresh garlic was processed into black garlic at 60 °C for 24 days. Changes in physical and chemical parameters, such as browning and protein content, reducing sugar content, and antioxidative components were recorded. Protein content was measured by Kjeldahl method, brown color development was analyzed using a color reader, reducing sugar was examined using a dinitro salicylic DNS reagent, and antioxidative activities were studied with a …

Applications In Opioid Analysis With Faims Through Control Of Vapor Phase Solvent Modifiers, Nathan Grimes

USF Tampa Graduate Theses and Dissertations

Field Asymmetric Ion Mobility Spectrometry (FAIMS), often coupled with mass spectrometry (MS), offers rapid analytical ion filtration, useful in reducing matrix interference and differentiating isomeric compounds. This study focuses on augmenting FAIMS-MS analyses through the incorporation of gas phase solvents, or "modifiers," inducing dynamic microsolvation, a particularly potent method of analysis enhancement.

Initially, the research utilized a bubbler-based system, incorporating a humidity sensor, improving modifier concentration control when using water. Our application in opioid detection and differentiation revealed considerable advancements. Notably, an increased peak capacity in an opioid mixture and successful separation of the isobaric opioid pair, alfentanil and ortho-isopropyl …

Long-Term Degradation Mechanisms In Application-Implemented Radical Thin Films, Ewa Malgorzata Nowik-Boltyk, Tobias Junghoefer, Mathias Glaser, Erika Giangrisostomi, Ruslan Ovsyannikov, Shuyang Zhang, Chan Shu, Andrzej Rajca, Arrigo Calzolari, M. Benedetta Casu

Department of Chemistry: Faculty Publications

Blatter radical derivatives are very attractive due to their potential applications, ranging from batteries to quantum technologies. In this work, we focus on the latest insights regarding the fundamental mechanisms of radical thin film (long-term) degradation, by comparing two Blatter radical derivatives. We find that the interaction with different contaminants (such as atomic H, Ar, N, and O and molecular H₂, N₂, O₂, H₂O, and NH₂) affects the chemical and magnetic properties of the thin films upon air exposure. Also, the radical-specific site, where the contaminant interaction takes place, plays …

Stepwise Assembly Of Quinary Multivariate Metal−Organic Frameworks Via Diversified Linker Exchange And Installation, Yuchen Hu, Xin Zhang, Rebecca Shu Hui Khoo, Christian Fiankor, Xu Zhang, Jian Zhang

Department of Chemistry: Faculty Publications

Multivariate MOFs (MTV-MOFs) constructed from multiple components with atomistic precision hold the promise for many fascinating developments in both fundamental sciences and applications. Sequential linker installation can be an effective method to introduce different functional linkers into an MOF that contains coordinatively unsaturated metal sites. However, in many cases, these linkers must be installed according to a specific sequence and the complete synthetic flexibility and freedom is yet to be realized. Here, we rationally decreased the size of the primary ligand used in NPF-300, a Zr-MOF with scu topology (NPF = Nebraska Porous Framework), and synthesized its isostructure, NPF-320. NPF-320 …

Synthesis And Study Of High-Spin Stable Organic Radicals For Electrical Conductors And Mannosamine Nitroxide For Mri Contrast Agents, Shuyang Zhang

Department of Chemistry: Dissertations, Theses, and Student Research

In the first project, we describe the synthesis of an ambient stable high spin organic diradical 4 based on the Blatter moiety. The high-spin (S = 1) organic diradical 4, which consists of two Blatter radical moieties in a conjugated structure, exhibits a nearly exclusive population (88%) on triplet ground state at room temperature as a consequence of a large single-triplet energy gap (ΔEST = 0.5 kcal/mol). The target diradical molecule is synthesized over five steps with structural confirmation by single-crystal X-ray diffraction. The thermogravimetric analysis (TGA) shows the onset of decomposition at ~264 oC, indicating the diradical molecule has …

Identification Of Different Hair Dyes In Dyed Hair Using Attenuated Total Reflectance (Atr Ft-Ir), Surface Enhancing Raman Spectroscopy (Sers) Techniques, Nicholas Lovera

Student Theses

This investigation compares the ability of Attenuated Total Reflection Fourier Transfer Infrared Spectroscopy (ATR FT-IR) and Surface Enhance Raman Spectroscopy (SERS) to identify and differentiate different hair dye brands on dyed hair samples. Hair is a common type of trace evidence found at crime scenes and can provide numerous information through forensic hair analysis. Cosmetic hair treatment such as dying the hair different colors has grown and became popular, thus it can be a very common type of trace evidence. This study can provide a forensic scientist an additional method for analyzing dyed hair samples. The goal was to compare …

Sers For The Detection Of Trace Materials, Omari Kirkland

Dissertations, Theses, and Capstone Projects

In this dissertation are presented three projects that contribute to the body of research on SERS in the forensic, heritage, and semiconductor fields. The first project, Charge-Transfer mapping on GaN/Ag, a silver-decorated nanopillar semiconductor substrate fabricated from the GaN is used with the Raman probe Rhodamine 6 G (R6G) to map the effect of the nanofeatures on the CT resonance. The second project, in collaboration with Marco Leona from the Metropolitan Museum of Art, explores the use of AgNIFs to identify colorants used on textile fiber samples from four 19th century works of Japanese art. The final project analyzes the …

The Effect Of The Carbon Nanotubes’ Surface Area On The Morphology And Performance Of Cellulose Acetate Nanocomposite Membranes In Nanofiltration Applications, Nouran Elbadawi

Theses and Dissertations

Population increase and climate change have significantly affected the availability of fresh water for consumption. Studies by UNESCO showed that more than 28% of the world population didn’t have access to clean safe drinking water in 2020. This situation is expected to get more serious over the coming 30 years with the limited availability of natural fresh water sources. The need to find solutions from alternative non-freshwater resources for drinking or irrigation is becoming a necessity. Within the context of desalination technologies, thousands of investigations are conducted to find the cheapest most efficient way of water treatment aiming at expanding …

The Kappa Opioid Receptor Agonist 16-Bromo Salvinorin A Has Anti-Cocaine Effects Without Significant Effects On Locomotion, Food Reward, Learning And Memory, Or Anxiety And Depressive-Like Behaviors, Ross Van De Wetering, Amy Ewald, Susan Welsh, Lindsay Kornberger, Samuel E. Williamson, Bryan D. Mcelroy, Eduardo R. Butelman, Thomas E. Prisinzano, Bronwyn M. Kivell

Markey Cancer Center Faculty Publications

Kappa opioid receptor (KOR) agonists have preclinical antipsychostimulant effects; however, adverse side effects have limited their therapeutic development. In this preclinical study, conducted in Sprague Dawley rats, B6-SJL mice, and non-human primates (NHPs), we evaluated the G-protein-biased analogue of salvinorin A (SalA), 16-bromo salvinorin A (16-BrSalA), for its anticocaine effects, side effects, and activation of cellular signaling pathways. 16-BrSalA dose-dependently decreased the cocaine-primed reinstatement of drug-seeking behavior in a KOR-dependent manner. It also decreased cocaine-induced hyperactivity, but had no effect on responding for cocaine on a progressive ratio schedule. Compared to SalA, 16-BrSalA had an improved side effect profile, with …

Enhanced Methods In Forensic Mass Spectrometry For Targeted And Untargeted Drug Analysis, Dina M. Swanson

USF Tampa Graduate Theses and Dissertations

Forensic science has long used mass spectrometry for the analysis of drugsand metabolites. Traditionally, screening methods consisted of color tests or immunoassay and confirmation methods used gas chromatography with mass spectrometry, which was considered the gold standard for identification. In the last several decades, advances in liquid chromatography with mass spectrometry (LCMS) have brought this technology to the forefront of forensic drug identification. Drug identification in forensic drug chemistry and forensic toxicology has become increasingly challenging due to the rapid increase in illicit drug analogs including novel opioids such as fentanyl analogs. Traditional screening methodologies are often unable to identify …