Chemistry Commons^™

Integrated Computational Approaches: Elucidating Molecular Mechanisms Of Pathogenic Proteins And Designing Novel Inhibitors Against Mycobacterium Tuberculosis And Sars-Cov-2, Justin David Carbone

Theses and Dissertations

Chapter 1 introduces computational strategies in computer aided drug design (CADD), focusing on physics-based methodologies to enhance drug discovery. This chapter also discusses the theoretical foundations and practical applications of molecular dynamics (MD) simulations including free energy and stochastic kinetic analysis. In Chapter 2, CADD methods lead to development of inhibitors targeting the RNA Dependent RNA Polymerase (RdRP) of SARS-CoV-2. Inspired by the nucleotide inhibitor Molnupiravir, we aim to design a combinatorial library of 72 novel inhibitors capable of impeding a dual threat inhibition mechanism inducing lethal mutations along with stalling viral replication with specific selectivity to RdRp over Human …

Incorporating Oxygen Isotopes Of Oxidized Reactive Nitrogen In The Regional Atmospheric Chemistry Mechanism, Version 2 (Icoin-Racm2), Wendell W. Walter, Masayuki Takeuchi, Nga L. Ng, Meredith G. Hastings

Faculty Publications

The oxygen isotope anomaly (Δ¹⁷O = δ¹⁷O − 0.52 × δ¹⁸O > 0) has proven to be a robust tool for probing photochemical cycling and atmospheric formation pathways of oxidized reactive nitrogen (NO_y). Several studies have developed modeling techniques to implicitly model Δ¹⁷O of NO_y molecules based on numerous assumptions that may not always be valid. Thus, these models may be oversimplified and limit our ability to compare model Δ¹⁷O values of NO_y with observations. In this work, we introduce a novel method for explicitly tracking Δ …

Nanodysferlins Support Membrane Repair And Binding To Trim72/Mg53 But Do Not Localize To T-Tubules Or Stabilize Ca2+ Signaling, Joaquin Muriel, Valeriy Lukyanenko, Thomas A. Kwiatkowski, Yi Li, Sayak Bhattacharya, Kassidy K. Banford, Daniel Garman, Hannah R. Bulgart, Roger B. Sutton, Noah Weisleder, Robert J. Bloch

Chemistry Faculty Publications

Mutations in the DYSF gene, encoding the protein dysferlin, lead to several forms of muscular dystrophy. In healthy skeletal muscle, dysferlin concentrates in the transverse tubules and is involved in repairing the sarcolemma and stabilizing Ca2+ signaling after membrane disruption. The DYSF gene encodes 7-8 C2 domains, several Fer and Dysf domains, and a C-terminal transmembrane sequence. Because its coding sequence is too large to package in adeno-associated virus, the full-length sequence is not amenable to current gene delivery methods. Thus, we have examined smaller versions of dysferlin, termed "nanodysferlins," designed to eliminate several C2 domains, specifically C2 domains D, …

Clinically Proven Natural Products In Aid Of Treating Parkinson's Disease: A Comprehensive Review, Md Abul Hasan Roni, Md. Abu Bakar Siddique Jami, Sajidul Hoque, Md. Al Hasibuzzaman, Kazi Hamida Banu, Rozina, Farzana Ansari, Md Sohel, Md. Ashifuzzaman, Nazmul Huda

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Parkinson's disease (PD) is a neurodegenerative disorder that is caused by degeneration of nerve cells in the part of the brain called the substantia nigra, which controls movement. Although there is some considerable evidence with conventional drugs for PD, treating patients becomes increasingly difficult due to their short- and long-term adverse effects and other restrictions. This dire circumstance emphasizes the need for an innovative, strong alternative treatment for PD. Plants and natural products are considered one of the most important sources of bioactive molecules against a wide range of health disorders. With mechanistic insights, this systematic review explains the efficacy …

Zinc Oxide Nanostructures Synthesized By Hot Water Treatment For The Photocatalytic Degradation Of Organic Pollutants In Water, Ranjitha Kumarapuram Hariharalakshmanan

Theses and Dissertations

Photocatalysis using nanostructured semiconductors for the degradation of organic pollutants has received significant attention as an advanced water treatment method. A photocatalyst absorbs light with energy greater than or equal to its band gap and generates electron-hole pairs. These electrons and holes take part in redox reactions in water to generate reactive oxygen species, such as hydroxyl radicals and superoxide anions, which can break down organic contaminants. However, this method has some challenges, such as electron-hole recombination, which reduces the efficiency, high cost of nanostructure synthesis, and reduced durability of nanostructured photocatalysts in suspension form. The immobilization of photocatalyst nanostructures …

The Mrnacalc Webserver Accounts For The N1-Methylpseudouridine Hypochromicity To Enable Precise Nucleoside-Modified Mrna Quantification, Sarah E. Krul, Sean J. Hoehn, Carlos E. Crespo-Hernández

Faculty Scholarship

Nucleoside-modified messenger RNA (mRNA) technologies necessarily incorporate N1-methylpseudouridine into the mRNA molecules to prevent the over-stimulation of cytoplasmic RNA sensors. Despite this modification, mRNA concentrations remain mostly determined through the measurement of UV absorbance at 260 nm wavelength (A260). Herein, we report that the N1-methylpseudouridine absorbs approximately 40% less UV light at 260 nm than uridine, and its incorporation into mRNAs leads to the under-estimation of nucleoside-modified mRNA concentrations, with 5%–15% error, in an mRNA-sequence-dependent manner. We therefore examined the RNA quantification methods and developed the mRNACalc webserver. It accounts for the molar absorption coefficient of modified nucleotides at 260 …

Complete Genome Sequence Of Strain Jm503a, A Genetically Tractable Dental Abscess Clinical Isolate, Dustin L. Higashi, Anh Nguyen, Hua Qin, Christina Borland, Elizabeth A. Palmer, Nicolas Biais, Jens Kreth, Justin Merritt

Chemistry Faculty Publications and Presentations

Parvimonas micra is a pathobiont of humans that is often found in abundance at sites of mucosal inflammation as well as within malignant tumors. Here, we report the complete genome sequence of P. micra strain JM503A, which is a genetically tractable clinical isolate derived from a human odontogenic abscess specimen.

Heavy Metals Implications To Sediment Microbiome And Coral Response To Arsenic Dosing, Dimitrios G. Giarikos, Amy Hirons, Jose V. Lopez, Abigail Renegar, Jason Gershman

SECLER Data

No abstract provided.

Predicting Ph At In-Situ Temperature For Aquatic Environments, Sarah E. Bartoloni

USF Tampa Graduate Theses and Dissertations

pH is typically measured at a constant temperature and, as needed, converted to in-situ temperature using a system of thermodynamic equations. Using this equilibrium approach, adjustment of pH to in situ conditions requires two measured CO2 system parameters (pH, total alkalinity, dissolved inorganic carbon, or CO2 fugacity). Currently, when pH is the only measured CO2 system parameter, linear models are used to adjust the pH to in-situ temperature. Although many studies have attempted to optimize CO2 equilibrium constants (K1 and K2) for the CO2 system over a range of conditions, very little prior work has experimentally examined which CO2 system …

Production Of The Siderophore Lysochelin In Rich Media Through Maltose-Promoted High-Density Growth Of Lysobacter Sp. 3655, Fang Zhang, Jia Liu, Lin Jiang, Yongbiao Zheng, Lingjun Yu, Liangcheng Du

Department of Chemistry: Faculty Publications

Siderophores are produced by bacteria in iron-restricted conditions. However, we found maltose could induce the biosynthesis of the siderophore lysochelin in Lysobacter sp. 3655 in rich media that are not compatible with siderophore production. Maltose markedly promoted cell growth, with over 300% increase in cell density (OD₆₀₀) when LB medium was added with maltose (LBM). While lysochelin was not detectable when OD₆₀₀ in LBM was below 5.0, the siderophore was clearly produced when OD₆₀₀ reached 7.5 and dramatically increased when OD₆₀₀ was 15.0. Coincidently, the transcription of lysochelin biosynthesis genes was remarkably enhanced following the …

An Investigation Of The Mindset Context And Its Downstream Effects On Marginalized Student Outcomes In College Stem Courses, Ronia Naim Kattoum

Theses and Dissertations

Multiple national calls centered on critical thinking and social justice have been made to improve and reform higher education in science, technology, engineering, and mathematics (STEM) courses to increase the representation of students from marginalized groups in the STEM workforce and equip all students for success. To help answer this call, our project has two overarching goals: 1) Identify pathways to increase student success in STEM courses at a moderately selective metropolitan institution with a diverse population that can be generalized to similar institutions, and 2) determine how instructional practices influence perceptions of the learning environment, especially for marginalized students. …

A Speleogenetic History Of Novoafonskaya Cave In The Western Caucasus, Olga Chervyatsova, Sergey Potapov, Jonathan Baker, Dmitry Gavryushkin, Victor Polyak, Matt Heizler, Sergey Tokarev, Sergey Sadykov, Roman Dbar, Yuri Dublyansky

International Journal of Speleology

Speleogenesis in hypogene karst settings may be closely tied to regional tectonic dynamics and concomitant hydrochemical evolution of karst waters. However, placing temporal constraints on these processes can require a wider array of field observations and techniques than for typical karst systems. Herein, we present a comprehensive study of Novoafonskaya Cave (Western Caucasus, Abkhazia). The updated speleogenetic history of the cave comprises four stages: (1) the most ancient, a low-T hydrothermal (ca. 40–50°C) priming stage; (2) the main stage enabled by mixing of upwelling thermomineral and locally recharged common karst waters; (3) the late sulfuric-acid speleogenesis (SAS) stage, which left …

Designing Of Human Serum Albumin Nanoparticles For Drug Delivery: A Potential Use Of Anticancer Treatment, Ali Al-Ani, Rasha Alsahlanee

Karbala International Journal of Modern Science

Human serum albumin (HSA) nanoparticles have been widely used as versatile drug delivery systems for improving the efficiency and pharmaceutical properties of drugs. The present study aimed to design HSA nanoparticle encapsulated with the hydrophobic anticancer pyridine derivative (2-((2-([1,1'-biphenyl]-4-yl)imidazo[1,2-a]pyrimidin-3-yl)methylene)hydrazine-1-carbothioamide (BIPHC)). The synthesis of HSA-BIPHC nanoparticles was achieved using a desolvation process. Atomic force microscopy (AFM) analysis showed the average size of HSA-BIPHC nanoparticles was 80.21 nm. The percentages of entrapment efficacy, loading capacity and production yield were 98.11%, 9.77% and 91.29%, respectively. An In vitro release study revealed that HSA-BIPHC nanoparticles displayed fast dissolution at pH 7.4 compared to pH …

Modified Toulmin's Argumentation Model Based On Prior Experiences, Ali Hadi Hasan, Mohamad Ab. Saleh, Ahmed T. Sadiq

Karbala International Journal of Modern Science

Our work focuses on the usefulness of previously stored correct extracted results, which form a sort of stored knowledge got from previous experiences, from enhancing Toulmin's argument model that deals with drug conflict problems in therapeutic diagnostics. New patients are entered using friendly user interface to store in files and then they are matched with the records of previous results, patients’ symptoms and histories datasets which also contain the correct best drugs extracted results. If the new entered record of a patient is matching with any previous record then the correct result of drug will be found immediately and displayed. …

Produced Water Management From Production Sites In The State Of Kuwait, Feras Adel Alsalem

Thesis/ Dissertation Defenses

Crude oil extraction leads to the production of produced water (PW). PW is by far the most significant by-product in the process of extracting hydrocarbons from the subsurface. Consequently, handling PW has become a great concern to oil and gas producers. The increasing amounts of PW and more stringent environmental and safety regulations in regard to PW make more efficient treatment methods necessary, where sustainable long-term solutions for PW management need to be provided. The focus of this study is on PW from onshore operations as the majority of the oil and gas extraction operations (upstream processes) are conducted onshore, …

Design, Synthesis And Characterization Of Zinc And Gold-Based Metal-Organic Frameworks And Complexes For The Detection And Treatment Of Cancer, May Reda Mohamed

Thesis/ Dissertation Defenses

The early detection of cancer plays a pivotal role in improving patient outcomes, emphasizing the urgent need for highly sensitive and selective biosensing platforms. Metal-Organic Frameworks (MOFs) have emerged as promising candidates in this domain due to their tunable properties, large surface area, and high porosity. Herein, the utilization of zinc-based MOF as a sophisticated biosensing platform tailored for the precise detection of the HER2 cancer biomarker is presented. HER2, a critical protein marker in breast cancer diagnostics and treatment, demands highly selective and accurate detection methods for effective patient management. Simple hydrothermal synthesis methodology has been adopted to synthetize …

Mechanism Of Nitrone Formation By A Flavin-Dependent Monooxygenase, Sydney B. Johnson, Hao Li, Hannah Valentino, Pablo Sobrado

Chemistry Faculty Research & Creative Works

OxaD is a flavin-dependent monooxygenase (FMO) responsible for catalyzing the oxidation of an indole nitrogen atom, resulting in the formation of a nitrone. Nitrones serve as versatile intermediates in complex syntheses, including challenging reactions like cycloadditions. Traditional organic synthesis methods often yield limited results and involve environmentally harmful chemicals. Therefore, the enzymatic synthesis of nitrone-containing compounds holds promise for more sustainable industrial processes. In this study, we explored the catalytic mechanism of OxaD using a combination of steady-state and rapid-reaction kinetics, site-directed mutagenesis, spectroscopy, and structural modeling. Our investigations showed that OxaD catalyzes two oxidations of the indole nitrogen of …

Assigning The Ch Stretch Overtone Spectrum Of Benzene And Naphthalene With Extension To Anthracene And Tetracene Using 2- And 3-Quanta Anharmonic Quantum Chemical Computations, Vincent J. Esposito, Ryan C. Fortenberry, Christiaan Boersma, Louis J. Allamandola

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The CH stretch overtone region (5750–6300 cm⁻¹) of benzene and naphthalene is assigned herein using anharmonic quantum chemical computations, and the trend of how this extends to larger polycyclic aromatic hydrocarbons (PAHs) is established. The assignment of all experimental bands to specific vibrational states is performed for the first time. Resonance polyads and the inclusion of 3-quanta vibrational states are both needed to compute accurate vibrational frequencies with the proper density-of-states to match the experimental band shape. Hundreds of 3-quanta states produce the observed band structure in naphthalene, anthracene, and tetracene, and this number is expected to increase …

Dft Based Modeling Of The Heavy Atom Effect In Triplet Photosensitizers: From Fundamental Mechanics To Rational Design, Bret Andrew Steinkamp

Dissertations and Theses

Photochemistry is the study of how light interacts with molecules and includes both the absorption and release of light. This document focuses on triplet photosensitizers -- molecules that utilize the excited triplet state -- for a variety of applications including photodynamic therapy and photocatalysis. There are many factors that influence the design of triplet photosensitizers; in this work, we have developed and used a methodology for the rational design of triplet photosensitizers based on an approximation of the heavy atom effect (HAE) from density functional theory calculations and the experimentally measured singlet oxygen quantum yield (Ф_Δ).

As excited …

Nanoparticles As Antioxidant Agents: A Comprehensive Review, Sulyman Olalekan Ibrahim, Halimat Yusuf Lukman, Fatimat Ronke Abdulkadir, Monsurat Yemisi Bello, Yusuf Oloruntoyin Ayipo, Halimah Funmilayo Babamale, Marili Funmilayo Zubair, Olubunmi Atolani

Al-Bahir

This study seeks to provide a comprehensive overview of the latest progress in the antioxidant properties of nanoparticles. Nanoparticles (NPs) have emerged as a promising tool in several domains of science and industry, including their application as antioxidant agents. The main knowledge gaps seem to be in correctly identifying the make-up of the naturally occurring phytochemicals that give these nano-antioxidants their extraordinary pharmacology and drug-like properties. In many instances, that characterization is done using spectroscopy instrumentation such as fourier-transform Infrared (FT-IR), scanning electron microscope (SEM), and X-ray diffraction analysis (XRD). From literature appraisals, it was discovered that a lot of …

Herbicides, Department Of Primary Industries And Regional Development, Western Australia

Grains and other field crops factsheets

Herbicides play a vital role in integrated weed management programs. Knowledge of the mechanisms and activity of herbicides will improve the impact and sustainability of herbicides as a weed management tactic. This fact sheet is a guide to the types of herbicides available and when and how they should be used.

Spectroscopic Characterization, Dft Calculations, In Vitro Pharmacological Potentials, And Molecular Docking Studies Of N, N, O-Schiff Base And Its Trivalent Metal Complexes, Ikechukwu P. Ejidike, Amani Direm, Cemal Parlak, Adebayo A. Adeniyi, Mohammad Azam, Athar Ata, Michael O. Eze, Joshua W. Hollett, Hadley S. Clayton

Michigan Tech Publications

In this study, trivalent metal complexes of the category: [M(L)(H2O)nCly] obtained from the interaction of metal3+ ion salts with organic N, N, O-Schiff base (HL) (where: HL = 4-{(Z)-((2-{(E)-((2-hydroxyphenyl)methylidene)amino}ethyl)imino)methyl}-2-methoxyphenol; n, y = 1 or 2 and M = Ti(III), Fe(III), Ru(III), Cr(III) and Al(III)) were synthesized and characterized viz molar conductance, FT-IR, and UV–Vis spectroscopies, elemental analyses, thermal analyses (TGA and DTA), and UV–Vis spectroscopy, theoretical calculations. A distorted octahedral structure around the metal ions was proposed based on the obtained experimental and calculated data. Thermal examination of the complexes signposts the step-by-step disintegration to give the final decomposition product …

General Chemistry Ii: Chem 2134, Subha Pratihar

ATU Faculty OER Books and Materials

No abstract provided.

Hatt-Flow: Hierarchical Attention-Flow Mechanism For Group-Activity Scene Graph Generation In Videos, Naga Venkata Sai Raviteja Chappa, Pha Nguyen, Thi Hoang Ngan Le, Page Daniel Dobbs, Khoa Luu

Electrical Engineering and Computer Science Faculty Publications and Presentations

Group-activity scene graph (GASG) generation is a challenging task in computer vision, aiming to anticipate and describe relationships between subjects and objects in video sequences. Traditional video scene graph generation (VidSGG) methods focus on retrospective analysis, limiting their predictive capabilities. To enrich the scene-understanding capabilities, we introduced a GASG dataset extending the JRDB dataset with nuanced annotations involving appearance, interaction, position, relationship, and situation attributes. This work also introduces an innovative approach, a Hierarchical Attention–Flow (HAtt-Flow) mechanism, rooted in flow network theory to enhance GASG performance. Flow–attention incorporates flow conservation principles, fostering competition …

In Situ And 2d And 3d In Silico Redox Cycling Studies For Design Optimization Of Coplanar Arrays Of Microband Electrodes In A 70 Μm × 100 Μm Electroactive Footprint, Miguel Angel Abrego Tello, Mahsa Lotfi Marchoubeh, Ingrid Fritsch

Chemistry & Biochemistry Faculty Publications and Presentations

Optimization of redox-cycling currents was performed by adjusting the height (sidewalls, h), width (w), and length (l) of band electrodes and their spacing (w_gap) in coplanar arrays restricted to a small-electroactive window of 70 × 100 μm. These arrays can function in μL-volumes for chemical analysis (e.g., in-vivo dopamine detection using probes). Experiments were conducted with an array of five electrodes (NE = 5), w = 4.3 μm, w_gap = 3.7 μm, h = 0.150 μm, and l = 99.2 μm. Reasons for …

Simulation Of Linear And Cyclic Alkanes With Second-Order Møller–Plesset Perturbation Theory Through Adaptive Force Matching, Alexei Nikitin, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Predicting ensemble properties, such as density and heat of vaporization, of small hydrocarbons is challenging due to the dispersion-dominated weak interactions between these molecules. With the adaptive force matching (AFM) method, the bonded and short-range nonbonded interactions are fitted to second-order Møller–Plesset perturbation theory (MP2) references computed with the def2-TZVP basis set. The dispersion is modeled using symmetry adapted perturbation theory (SAPT) at MP4 accuracy using the def2-TZVPD basis set. A new charge matrix decomposition technique is described to obtain partial charges in AFM. Although the models developed do not have any empirical parameters, several properties of the resulting models …

Development Of Platinum(Iv)-Gold(I)-Based Anticancer Agents, Javier E. Lopez-Hernandez

Dissertations, Theses, and Capstone Projects

Heterometallic compounds have emerged as prospective multitarget anticancer drugs. These species may display improved efficacy and physicochemical properties compared to the individual metallic fragments, while helping combat drug resistance by exerting effects on multiple pathways. In this thesis we describe the synthesis of new bi- and tri-metallic compounds based on platinum(IV) compounds containing FDA-approved platinum agents, and gold(I) derivatives with known anticancer properties. We demonstrate their toxicity and selectivity against a small panel of renal, bladder, ovarian, and breast cancer cell lines, as well as their synergistic effects. We have selected a trinuclear PtAu₂compound containing the Pt(IV) core …

Positron Emission Tomography In Oncology And Environmental Science, Samantha Delaney

Dissertations, Theses, and Capstone Projects

The last half century has played witness to the onset of molecular imaging for the clinical assessment of physiological targets. While several medical imaging modalities allow for the visualization of the functional and anatomical properties of humans and living systems, few offer accurate quantitation and the ability to detect biochemical processes with low-administered drug mass doses. This limits how physicians and scientists may diagnose and treat medical issues, such as cancer, disease, and foreign agents.

A promising alternative to extant invasive procedures and suboptimal imaging modalities to assess the nature of a biological environment is the use of positron emission …

Modeling Hydroxide In Classical Proton Hopping Simulations And Amyloid Beta Membrane Pores, Ankita Dutta

Dissertations, Theses, and Capstone Projects

H3O+ and OH- ions display anomalously large diffusion coefficients, a property that is often attributed to their ability to perform structural diffusion which allow these ions to move through aqueous solutions by sequential proton transfers, also known as ‘Grotthuss hopping’. A rearrangement of the local solvation structure is known to be the prerequisite for proton transfer events via these ions. Studying this phenomenon using classical molecular dynamics simulations that do not allow bond rearrangements poses significant obstacles. Here we use a Monte Carlo augmented classical Molecular Dynamics method called the MOBHY algorithm which allows instantaneous changes in protonation states in …

Recombinant Bile Salt Hydrolase Enhances The Inhibition Efficiency Of Taurodeoxycholic Acid Against Clostridium Perfringens Virulence, Tahrir Alenezi, Bilal Alrubaye, Ying Fu, Janashrit Shrestha, Samar Algehani, Hong Wang, Rohana Liyanage, Xiaolun Sun

Chemistry & Biochemistry Faculty Publications and Presentations

Clostridium perfringens is the main pathogen of chicken necrotic enteritis (NE) causing huge economic losses in the poultry industry. Although dietary secondary bile acid deoxycholic acid (DCA) reduced chicken NE, the accumulation of conjugated tauro-DCA (TDCA) raised concerns regarding DCA efficacy. In this study, we aimed to deconjugate TDCA by bile salt hydrolase (BSH) to increase DCA efficacy against the NE pathogen C. perfringens. Assays were conducted to evaluate the inhibition of C. perfringens growth, hydrogen sulfide (H₂S) production, and virulence gene expression by TDCA and DCA. BSH activity and sequence alignment were conducted to select the …