Physical Sciences and Mathematics Commons^™

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 …

An Aptamer-Based Microelectrode With Tunable Linear Range For Monitoring Of K+ In The Living Mouse Brain, Yuan-Dong Liu, Jia-Run Li, Li-Min Zhang, Yang Tian

Journal of Electrochemistry

Potassium ion (K⁺) is widely involved in several physiopathological processes, and its abnormal changes are closely related to the occurrence of brain diseases of cerebral ischemia. In vivo acquirement of K⁺ variation is significant to understand the roles of K⁺ playing in brain functions. A microelectrode based on single-stranded DNA aptamers was developed for highly selective detection of K⁺ in brain, in which the aptamer probes were designed to contain an aptamer part for specific recognition of K⁺, an alkynyl group used for stable confinement of aptamer probe on the gold surface, and …

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 …

Eutectic Formation And Cutaneous Wound Healing By Binary Allantoin- Octadecenedioic Acid System, Syed Waqar Hussain Shah, Farah Ali, Iram Bibi, Kashif Ali, Neelam Pervaiz, Mariyum Yousaf

Karbala International Journal of Modern Science

Eutectic formation in allantoin-octadecenedioic acid system (AOM) has been studied. The binary phase diagram revealed the existence of eutectic at X_allantoin = 0.7. Dioic acid caused disruption of network in allantoin and induced defects, ultimately causing the reduction in crystallinity as shown by XRD and SEM analysis. The thermal stability in TGA graphs of allantoin was negligibly altered after mixture formation. Classical hydrogen bonding and alkyl interactions were predicted using software Avogadro and BIOVIA Discovery Studio. The functionalities involved in interactions taking place in the system were studied through in-depth FT-IR spectroscopy. The eutectic showed efficacy for cutaneous wound …

Structural Mapping Of The Base Stacks Containing Post-Transcriptionally Modified Bases In Rna, Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma

Chemistry and Biochemistry Publications

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis …

Structural Mapping Of The Base Stacks Containing Post-Transcriptionally Modified Bases In Rna, Zakir Ali, Sarabjeet Kaur, Teagan Kukhta, Abd Al-Aziz A Abu-Saleh, Ayush Jhunjhunwala, Abhijit Mitra, John F. Trant, Purshotam Sharma

Chemistry and Biochemistry Publications

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis …

Methods Of Magneto-Optical Spectroscopy And Analysis For Porphyrins And Polymer Thin-Films, Emigdio E. Turner

Chemistry and Chemical Biology ETDs

This dissertation describes the construction of two high precision magneto-polarimeters for performing Faraday rotation and Magnetic Circular Dichroism (MCD) measurements of polymer thin-films. There is a focus in materials science on the development of thin-film magneto-optically active materials. These materials could allow for the construction of a thin-film optical diode, an important device for next-generation photonic technology. Upon completion of the Faraday rotation spectrometer, two publications were generated from Faraday rotation measurements of novel polymer thin-film materials.

With growing interest by materials scientists in magneto-optically active transition-metal containing materials, an MCD spectrometer was constructed to study these materials. This spectrometer …

Skin Permeation Studies Of Chromium Species - Evaluation Of A Reconstructed Human Epidermis Model., L Hagvall, M Munem, M Hoang Philipsen, M Dowlatshahi Pour, Yolanda S. Hedberg, P Malmberg

Chemistry Publications

A reconstructed human epidermis (RHE) model, the EpiDerm, was investigated and compared to human skin ex vivo regarding tissue penetration and distribution of two chromium species, relevant in both occupational and general exposure in the population. Imaging mass spectrometry was used in analysis of the sectioned tissue. The RHE model gave similar results compared to human skin ex vivo for skin penetration of Cr

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 …

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 …

Study Of Antioxidant Activity Of The Derivatives Of Quinoline-4-Carboxylic Acids By The Modification Of Isatin Via Pfitzinger Reaction, Sakti Hidayati Fikriya, Antonius Herry Cahyana

Makara Journal of Science

In this study, a quinoline-4-carboxylic acid derivative was synthesized through Pfitzinger reaction. In this reaction, isatin is modified via its reaction with ketone and refluxed for 24 h to obtain quinoline-4-carboxylic acid. The presence of a carboxylic group was identified by Fourier Transform Infrared (FTIR) spectroscopy and ultraviolet–visible (UV-Vis) spectrophotometry. The results showed that the absorption peaks of C=O and O–H stretching’s were detected in the range of 1724–1708 and 3436–3242 cm⁻¹, respectively. In the UV-vis spectrum, a shift in the absorption peak was observed toward a larger wavelength, which is referred as a bathochromic shift. The formation …

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. …

Symbiotic Ucyn-A Strains Co-Occurred With El Niño, Relaxed Upwelling, And Varied Eukaryotes Over 10 Years Off Southern California, Colette Fletcher-Hoppe, Yi-Chun Yeh, Yubin Raut, J. L. Weissman, Jed A. Fuhrman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation, the conversion of N₂ gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon …

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 …

Synthesis, Characterization, And Separation Of Loaded Liposomes For Drug Delivery, Sandra Khalife

USF Tampa Graduate Theses and Dissertations

Liposomes are viable candidates for drug delivery vehicles due to their ability to protect loaded compounds, dampen side effects of drugs, and be delivered to target sites in the body. The amphipathic nature of these lipid vesicles makes them very customizable through careful selection of bilayer and aqueous core components as well as synthetic and downsizing methods. However, synthetic methods may result in unencapsulated compounds remaining present alongside loaded liposomes, which require removal before the liposome suspension can be used.

This work explores the use of model DOPC as well as DOPC and CHOL liposomes and the methods that were …

Investigation Of Challenging Transformations In Gold Catalysis, Qi Tang

USF Tampa Graduate Theses and Dissertations

This dissertation mainly contains three parts: 1) Divergent gold catalysis for alkyne trifunctionalization, encompassing three distinct modes to achieve the simultaneous formation of C-N, C-O, and C-C bonds in a single step 2) the study and development of a new method to synthesize azaborine derivatives; and 3) the construction of benzotriazole boranes (BTAB) as stable four-coordinate N-B heterocycles through gold-catalyzed alkyne hydroboration.

In the first part, alkyne trifunctionalization via divergent gold catalysis will be introduced. This novel approach involves a sequence of reactions that combine gold π-activation, vinyl gold nucleophilic addition, and gold (III) reductive elimination. By utilizing this methodology, …

Cationic Polymer Coating Increases The Catalytic Activity Of Gold Nanoparticles Toward Anionic Substrates, Nicholas Langer, Mason Legrand, Ofer Kedem

Chemistry Faculty Research and Publications

Organic coatings on catalytic metal nanoparticles (NPs) typically hinder their activity due to the blocking of active sites. Therefore, considerable effort is made to remove organic ligands when preparing supported NP catalytic materials. Here, cationic polyelectrolyte coatings are shown to increase the catalytic activity of partially embedded gold nanoislands (Au NIs) toward transfer hydrogenation and oxidation reactions with anionic substrates compared to the activity of identical but uncoated Au NIs. Any potential steric hindrance caused by the coating is countered by a decrease in the activation energy of the reaction by half, resulting in overall enhancement. The direct comparison to …

Gold-Catalyzed Diyne-Ene Cyclization: Synthesis Of Hetero Polyaromatic Hydrocarbons And 1,2-Dihydropyridines, Jingwen Wei

USF Tampa Graduate Theses and Dissertations

Homogeneous gold catalysts are known as a powerful tool for selectively activating alkynes and are well-developed in the construction of C-C, C-N, and C-O bonds to form complex compounds that are widely used in pharmaceuticals, industries, agriculture, etc. The investigation of gold(I) catalysis on conjugated diyne (compounds having two acetylene groups) enriches the complexity of the bond construction and allows the building of interesting skeletons in organic synthesis. One typical kind of substrate, diyne-ene, has both a conjugated diyne part and a 1,6- enyne part. We developed a new methodology to allow its divergent synthesis to heterocycles.

This dissertation mainly …

The Effect Of Solution Parameters On The Interfacial Chemical Dynamics Of Early-Stage Corrosion, Brianna K. Rector

Electronic Thesis and Dissertation Repository

Corrosion is a key long-term degradation process for metallic components in nuclear industry infrastructure. Accurately predicting the corrosion rate of a component in its service environment is considered a grand challenge in the corrosion community. Corrosion is a multi-step electrochemical process, with elementary steps involving mass transfer across more than one stage. Due to the multi-step, multi-phase nature of corrosion systems, predicting corrosion behaviour over time is complex. Existing corrosion models can describe electron transfer and mass transport steps independently, under narrow sets of conditions or over a specified duration but cannot account for the changes that occur over time …

Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of 3TEL-hlx-DARPin (SUMO) The solved structure used frames 1-1799 and has been deposited in the wwPDB under the PDB ID 7N2B. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of Batch 1 1TEL-AA-vWa (SUMO) The solved structure used frames 1-999 and has been deposited in the wwPDB under the PDB ID 7N1O. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

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

Chemistry Department: 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 …

Simulations Of Intruder-Free X-Ray Transient Absorption And Time-Resolved X-Ray Scattering For Probing Attosecond Electron Dynamics, Mengqi Yang

LSU Doctoral Dissertations

The motion of electrons plays a fundamental role in both physics and chemistry, and capturing such dynamics requires the ability to resolve changes at the attosecond timescale, which is enabled by the advent of ultrashort laser pulses. This dissertation aims to facilitate the interpretation of ultrafast electron dynamics and attosecond spectroscopy by real-time time-dependent density functional theory (RT-TDDFT) simulations. The first part of this dissertation focuses on improving the simulation of X-ray transient absorption spectra (XTAS) with Gaussian basis sets in RT-TDDFT by applying a filter to the transition dipole matrix. Due to the spatial limitation of atom-centered Gaussian functions, …

Supramolecular Architectures Generated By Self-Assembly Of Guanosine And Isoguanosine Derivatives, Mengjia Liu

USF Tampa Graduate Theses and Dissertations

This dissertation is primarily divided into three parts: 1) Anion, solvent-mediated, tunable self-assemblies of isoguanosine (isoG). 2) Post-assembly modification of the non-covalent isoG-pentaplex for Cesium extraction. 3) Supramolecular asymmetric amine catalysis.

The structural conformational design of the isoG decamer was employed for systematic investigations involving various substituted groups at the C8 position of purine and ribose. A series of isoG analogs with C8-phenyl substitutions were synthesized and utilized for Cesium coordination. The proximity between purine and ribose structures limited pentaplex formation for C8-phenyl substituted isoG derivatives. Based on this observation, a deoxy isoG derivative with a modified ribose was employed …

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

Chemistry Department: 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 …

Investigating The Structure Of The Oxide On Ni-Cr-Mo Alloys While Presenting A Method For Analysis Of Complex Oxides Using Quases, Adam M. Morgan, Jeffrey D. Henderson, Brad A. Kobe, Mark Biesinger, James J. Noel

Chemistry Publications

X-ray photoelectron spectroscopy (XPS) is a technique that is widely used to studythin oxide films because of its extremely high surface sensitivity. Utilizing theQUASES (Quantitative Analysis of Surfaces by Electron Spectroscopy) software pack-age developed by Sven Tougaard (University of Southern Denmark), a user canobtain additional information that is not extracted in conventional XPS analysis, spe-cifically the composition as a function of depth. Presented here is the QUASES analy-sis of four Ni-Cr-Mo alloys performed while testing various inelastic mean free path(IMFP) determination methods in the context of providing a framework for the analy-sis of complex oxides in QUASES. Ni-Cr-Mo alloys are …

Atomistic Assessment Of Drug-Phospholipid Interactions Consequent To Cancer Treatment: A Study Of Anthracycline Cardiotoxicity, Yara Elsayed Ahmed

Theses and Dissertations

Despite being one of the most effective chemotherapeutic agents developed to date, Anthracyclines are notorious for their cardiotoxicity. Their clinical use is frequently limited both in dosage and in prescription due to the severe cardiac damage they cause. The mechanism of anthracycline-induced cardiotoxicity is not yet fully understood. However, it is hypothesized that interactions with the myocardial membrane play an important role in imparting cardiotoxicity. In this study, we use molecular dynamics simulations and density functional theory calculations to study the anthracycline drug molecules and the interactions that they have with the myocardial membrane. We construct a myocardial membrane model …

Environmental Impact Assessment (Eia) Of As, Se, Sn, And Hg In Water And Sediments From The Egyptian Red Sea Ports, Lamiaa I. Mohamedein, Khalid M. El-Moselhy, Mohamed A. El-Sawy

Blue Economy

Background: Pollution monitoring is an important tool to protect the marine ecosystems where ports had been seen as a source of contamination affecting the public wellbeing. Methods: Therefore, in the present study, surface seawater and surficial sediment samples were collected from 19 stations covering six ports of the Egyptian Red Sea during summer 2017 and winter 2018. The concentrations of As, Se, Sn, and Hg were determined using the Hydride system MH10 coupled with atomic absorption spectrophotometer. Results: The obtained data revealed that mean values of AS, Se, Sn and Hg for water samples were ranged between …

Implementation And Assessment Of A Course-Based Undergraduate Research Experience (Cure) In General Chemistry, Alissa Potts

College of Science and Health Theses and Dissertations

Course-based undergraduate research experiences (CUREs) are growing in popularity in the chemistry community to replace traditional laboratory courses. This approach creates a research experience for a larger number of students than traditional research mentorship experiences offered at universities. CUREs can help students take ownership of projects, learn to design and troubleshoot experimental setups, problem-solve experiments that don’t have a “known answer”, and gain confidence in the laboratory. To assess the effectiveness of a general chemistry laboratory-based CURE course with DePaul students, the Experimental Design Ability Test (EDAT) and the Meaningful Learning in the Laboratory Instrument (MLLI) survey were given to …

Chemical And Genetic Composition Analysis Of Organic And Nonorganic Tortilla Chips, Aubrey White-Day

Honors Theses

The aim of this study was to explore the chemical and genetic differences between organic and nonorganic tortilla chips using GC-MS and PCR. Twenty chip brands were selected: 10 organic and 10 nonorganic. A survey on shopping preferences was created and distributed to compare results of public opinion to experimental data. It yielded 212 responses. All organic chip brands, and one out of ten nonorganic chip brands, tested negative for GMOs. This study concluded that there are minimal chemical differences based on Jaccard similarity indicies and stark genetic differences between organic and nonorganic tortilla chips. In comparing statistical analyses to …