Chemistry Commons^™

Protein And Water Modeling In Computer-Aided Drug Discovery, Mossa Ghattas

Dissertations, Theses, and Capstone Projects

The field of Computer-Aided Drug Design (CADD) is continuously evolving to improve protein modeling, a crucial step in the drug discovery process. However, limitations exist in how CADD accounts for the various configurations a protein can adopt due to different rotamer and protonation states of its residues. This thesis explores advancements in CADD to address this challenge, focusing on protein modeling and water interactions.

In Chapter 1, I introduce the drug discovery process with a brief overview of its history, the purpose of FDA clinical trials, and the cost and time duration for bringing a drug to the market. I …

Structural, Electronic And Magnetic Properties Of Vanadium Doped Transition Metal Dichalcogenides (Tmds), Qudsia Ashraf

Dissertations, Theses, and Capstone Projects

Magnetic semiconductors are a prerequisite for spintronic devices but their ferromagnetism disappears at room-temperature hindering application in room temperature electronic devices. Enormous research has been conducted on the room-temperature ferromagnetic order in monolayer form of bulk van der Waals materials but the few layer system has not been extensively explored.

Doping is an effective approach to modulate the structural, electronic and magnetic properties of two-dimensional (2D) Transition metal dichalcogenides (TMDs) and expand their application. The effect of vanadium dopant on structural, electronic and magnetic properties of Tungsten Diselenide (WSe₂) was studied by X-ray Photoelectron Spectroscopy (XPS), Atomic Force …

44ti/44sc Generator Development And Radiolabeling Optimization For Medical Applications, Christine E. Schmidt-Kennelty

Dissertations, Theses, and Capstone Projects

In recent years, there has been a growing interest in scandium-44 (⁴⁴Sc) for medical applications due to its favorable decay properties. With a relatively short half-life of 3.97 hours and high positron branching ratio of 94.3%, ⁴⁴Sc is an ideal candidate for positron emission tomography (PET) imaging. However, producing ⁴⁴Sc without an on-site cyclotron limits access, as its short half-life makes it impractical to ship to more remote locations.

To address this issue, ⁴⁴Ti/⁴⁴Sc generators have become a focal point of research, providing an onsite source of⁴⁴Sc. Despite their potential, current …

Synthesis Of C-Di- And C-Tri- Saccharides From Glycosyl Crotylating Agents, Steven Truong

Dissertations, Theses, and Capstone Projects

The involvement of carbohydrates in a plethora of fundamental biological pathways, including disease related processes, has created a demand for molecular probes for elucidating these mechanisms. Accordingly, synthesis of tailored and diverse carbohydrate-like molecules, commonly referred to as glycomimetics, is a very active area of research. Among the more popular classes of glycomimetics are C-glycosides, analogues in which the anomeric carbon of a parent sugar is attached to a carbon substituent. C-glycosides have attracted attention in the medicinal chemistry community as there are several naturally occurring examples with interesting pharmacologically activity. C-glycosides are also of interest because in …

Electrified Membrane For Water Treatment And Resource Recovery: Advancing Multiscale Strategies In Gas-Involving Reactions, Jianan Gao

Dissertations

Multifunctional, modular, and scalable water treatment technologies that operate without chemical additives are crucial for addressing global water pollution challenges. While traditional membrane-based separation processes are crucial for ensuring clean water supplies, they primarily focus on pollutant removal rather than on the upcycling of pollutants into valuable resources. Electrified membrane filtration presents a robust alternative, utilizing minimal or no chemical additives and harnessing electrical power to directly reduce contaminants or produce reactive oxidants or reductants on-site.

This dissertation is dedicated to the development of innovative electrochemically reactive membranes designed to address three major challenges: (1) the engineering of electrocatalysts with …

Antioxidant, Photoprotective, And Cytotoxic Activities Of Tristaniopsis Merguensis Leaf Fractions With Molecular Docking Study Of Potential Fraction, Boima Situmeang, Respati Tri Swasono, Tri Joko Raharjo

Karbala International Journal of Modern Science

Through experimental along with molecular docking techniques of potential fraction, this study intended to evaluate the essential phytochemical elements of Tristaniopsis merguensis leaflets as well as potential antioxidant, photoprotective, along with cytotoxic activities. The DPPH and ABTS tests were used to evaluate the antioxidant efficacy of the n-hexane (HPF), ethyl acetate (EPF), and methanol (MPF) fractions. Using an in-vitro solar protection factor (SPF) assessment, the photoprotective ability of T. merguensis components against UV damage was examined. Subsequently, invitro cytotoxic research were carried out against MCF-7 cell line (breast cancer line) assay. This was followed by molecular docking stimulation testing against …

A Dft Comparison Of C–C Reductive Coupling From Terminal Cyanido And Cyaphido Complexes Of Nickel, Roberto Escobar, Jessica Meza, Javier Pena, Abdurrahman Atesin, William D. Jones, Christian Müller, Tülay A. Ateşin

School of Integrative Biological & Chemical Sciences Faculty Publications

The density functional theory study of the thermal C–C reductive coupling from terminal cyanido and hypothetical cyaphido complexes of [Ni(dmpe)] (dmpe = 1,2-bis(dimethylphosphino)ethane) revealed the key reaction intermediate in the reductive C–CP coupling being a σ-CC complex unlike an η2-aryl complex in the Ni C–CN system, as already observed in our previous studies. The reaction in THF is endothermic by 4.9 kcal/mol for cyanido with a 32.0 kcal/mol activation barrier and exothermic by 28.5 kcal/mol for cyaphido with an 11.3 kcal/mol activation barrier. To compare our results with the existing experimental data, we chose mesityl as the aryl group and …

Rate Law For Photoelectrochemical Water Splitting Over Cuo, Bo-Yuan Gao, Wen-Hua Leng

Journal of Electrochemistry

Photocatalytic splitting of water over p-type semiconductors is a promising strategy for production of hydrogen. However, the determination of rate law is rarely reported. To this purpose, copper oxide (CuO) is selected as a model photocathode in this study, and the photogenerated surface charge density, interfacial charge transfer rate constant and their relation to the water reduction rate (in terms of photocurrent) were investigated by a combination of (photo)electrochemical techniques. The results showed that the charge transfer rate constant is exponential-dependent on the surface charge density, and that the photocurrent equals to the product of the charge transfer rate constant …

Winning Works From Journal Of Electrochemistry: The 2Nd Xiamen University Short Video Abstract Contest For Science And Technology Journal Papers, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Recent Advances On Ruthenium-Based Electrocatalysts For Lithium-Oxygen Batteries, Yu-Zhe Wang, Zhuo-Liang Jiang, Bo Wen, Yao-Hui Huang, Fu-Jun Li

Journal of Electrochemistry

Rechargeable lithium-oxygen (Li-O₂) batteries have attracted wide attention due to their high energy density. However, the sluggish cathode kinetics results in high overvoltage and poor cycling performance. Ruthenium (Ru)-based electrocatalysts have been demonstrated to be promising cathode catalysts to promote oxygen evolution reaction (OER). It facilitates decomposition of lithium peroxide (Li₂O₂) by adjusting Li₂O₂ morphologies, which is due to the strong interaction between Ru-based catalyst and superoxide anion (O₂^–) intermediate. In this review, the design strategies of Ru-based electrocatalysts are introduced to enhance their OER catalytic kinetics in …

Numerical Analysis Of Explosion Characteristics Of Vent Gas From 18650 Lifepo4 Batteries With Different States Of Charge, Shi-Lin Wang, Xu Gong, Li-Na Liu, Yi-Tong Li, Chen-Yu Zhang, Le-Jun Xu, Xu-Ning Feng, Huai-Bin Wang

Journal of Electrochemistry

The combustion and explosion characteristics of lithium-ion battery vent gas is a key factor in determining the fire hazard of lithium-ion batteries. Investigating the combustion and explosion hazards of lithium-ion batteries vent gas can provide guidance for rescue and protection in explosion accidents in energy storage stations and new energy vehicles, thereby promoting the application and development of lithium-ion batteries. Based on this understanding and combined with previous research on gas production from lithium-ion batteries, this article conducted a study on the combustion and explosion risks of vent gas from thermal runaway of 18650 LFP batteries with different states of …

Winning Results Of The 2Nd Xiamen University Short Video Abstract Contest For Science And Technology Papers, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

2024 "Electrochemical Research Paradigms" Summer School Successfully Held, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

2024 World Fuel Cell Conference Held In Ningbo, Zhejiang, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Upcoming Meeting-The 1St Young Investigator Symposium On Electrosynthesis, Chinese Chemical Society, Chinese Society Of Electrochemistry (Cse)

Journal of Electrochemistry

No abstract provided.

Generative A.I.-Assisted Organic Chemistry Tutoring, Ji Kim

Open Educational Resources

By utilizing tools like ChatGPT, the project aims to provide detailed explanations, answer student questions, and assist with problem-solving, thereby creating a more interactive and personalized learning experience. This approach will help students grasp complex topics more effectively and improve their overall performance in chemistry.

Improvement Of Single-Crystal Structures Of Very Heavy Element Compounds By Refining Anomalous Dispersion Parameters, Florian Meurer, Gregory Morrison, Birgit Hischa, Hans Conrad Zur Loye, Christoph Hennig, Michael Bodensteiner

Faculty Publications

Refining the anomalous dispersion parameters of the four uranium compounds NaUF5, NaU2F9, Cs2(UO2)TiO4, and Cs2(UO2)Ti2O6 gave insights into the crystallographic model improvement of very heavy atoms. We found that the values for the dispersive and absorptive parts, f′ and f″, closely followed the X-ray absorption spectra on their L3, L2, and L1 edges. The obtained values are sensitive to the chemical environment at each crystallographically independent position. An incorrect treatment of the anomalous dispersion correction can lead to a wrong crystallographic model. The above-mentioned, already published structures were improved by this process. General guidelines were given for the crystal structure …

Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2, John Vincent Mcguire

Electronic Theses and Dissertations

The SARS-CoV-2 virus was recently able to cause a global pandemic, largely due to the asymptomatic period that occurs during initial infection. During this period, patients are infectious but do not exhibit symptoms, resulting in the unintentional spread of the virus. This occurs because the virus effectively avoids detection by the immune system during the early stages of infection, and as symptoms are the result of immune system activation, they never manifest. Non-structural Protein 15 (Nsp15) is one of the tools the virus uses to remain undetected, via its degradation of Pathogen-Associated Molecular Patterns (PAMPs) that would otherwise be recognized …

On The Formation And Detectability Of H2Cncn And Its Progenitors, Ryan C. Fortenberry, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

New highly exothermic formation pathways incorporating both thermodynamic and kinetic control for the newly astronomically detected H₂CNCN molecule are paired with extremely accurate quantum chemical rovibrational spectroscopic computations. The reactions between astronomically known CH₂CN/CH₂CCH + HNCN follow effectively identical pathways and proceed through stable intermediates and over deeply submerged transition states to form H₂CNCN and HCN/HCCH coproducts. Similarly, the reaction between CHM₂CN and NCN⁻ can also form H₂CNCN, although this pathway first requires the initial formation of NCN⁻, which is currently undetected in space, via …

Carbon-Sulfur Bond Elongation As The Promoting Reaction Coordinate In The Efficient Sub-Nanosecond Intersystem Crossing In Thianaphthene Derivatives, Cameron Griffith, Erqian Mao, Sean J. Hoehn, Sarah E. Krul, Carlos E. Crespo-Hernández

Faculty Scholarship

Thiophene derivatives have become integral to OLEDs, photovoltaics, and photodynamic therapy research. A deeper understanding of their excited state dynamics and electronic relaxation mechanisms is expected to provide important physical insights of direct relevance for these applications. In this study, thianaphthene (TN), 2-methylbenzothiophene (2MBT), and 3-methylbenzothiophene (3MBT) are investigated using femtosecond broadband transient absorption and steady-state spectroscopy techniques along with time-dependent density functional calculations in cyclohexane and acetonitrile. The photophysical properties and electronic relaxation mechanisms of these derivatives are elucidated. Small fluorescence quantum yields ranging from 0.4 to 1.1% are measured. It is demonstrated that excitation of TN at 290 …

Investigating The Cellular Localization, Trafficking, And Biological Function Of Ghrelin O-Acyltransferase, Sadie Xiao Hua Novak

Dissertations - ALL

Ghrelin O-acyltransferase (GOAT) catalyzes the acylation and activation of ghrelin, a peptide hormone involved in a range of physiological pathways and therapeutic target for metabolism-linked diseases such as obesity and diabetes. GOAT was determined to be localized in the membrane of the endoplasmic reticulum (ER) in early cell-based studies, but recent patient studies detected this integral membrane enzyme in blood plasma and urine. These findings challenge the current understanding of GOAT’s cellular localization, and it may provide a potential mechanism for ghrelin re-acylation by plasma membrane-resident GOAT. The work described in this dissertation aimed to define the intracellular trafficking mechanism …

An Online Nanoinformatics Platform Empowering Computational Modeling Of Nanomaterials By Nanostructure Annotations And Machine Learning Toolkits., Tong Wang, Daniel P Russo, Philip Demokritou, Xuelian Jia, Heng Huang, Xinyu Yang, Hao Zhu

College of Science & Mathematics Departmental Research

Modern nanotechnology has generated numerous datasets from in vitro and in vivo studies on nanomaterials, with some available on nanoinformatics portals. However, these existing databases lack the digital data and tools suitable for machine learning studies. Here, we report a nanoinformatics platform that accurately annotates nanostructures into machine-readable data files and provides modeling toolkits. This platform, accessible to the public at https://vinas-toolbox.com/, has annotated nanostructures of 14 material types. The associated nanodescriptor data and assay test results are appropriate for modeling purposes. The modeling toolkits enable data standardization, data visualization, and machine learning model development to predict properties and bioactivities …

Application Of A Novel Plasma-Based Advanced Oxidation Process For Efficient And Cost-Effective Destruction Of Refractory Organics In Tertiary Effluents And Contaminated Groundwater, Itay Even-Ezra, Anat Mizrahi, Daniel Gerrity, Shane A. Snyder, Andrew Salveson, Ori Lahav

Civil and Environmental Engineering and Construction Faculty Research

Corona discharge is emerging as a promising advanced oxidation process (AOP) for the treatment of a variety of organic contaminants, including compounds that are not effectively destroyed by more common AOPs. This paper presents laboratory and field results describing the destruction of regulated and Contaminant Candidate List (CCL) compounds in tertiary treated wastewater effluent and contaminated groundwater during the operation of a novel hydro-non-thermal-plasma (HNTP) AOP system. The system generates a plasma discharge above the target water matrix, which emits an “electron wind”, ultraviolet (UV) irradiation, O_3(g) and hydroxyl radicals (•OH) into a relatively thin water layer. The synergism …

Molecular Docking, Pharmacological Profiling, And Molecular Dynamics Simulation Of Potential Antihyperuricemic Agent From Secondary Metabolites Of Dillenia Philippinensis Rolfe (Dilleniaceae), Louie Rince C. Suyo, John P. Paulin, Nicole Clarence Louise L. Gapaz, Markus Brent S. Arevalo, Vince Tyrell P. Yongco, Librado A. Santiago

Karbala International Journal of Modern Science

Crystal accumulation in the joints due to increased serum uric acid (sUA) may lead to an inflammatory condition called gout. Increased sUA is caused by the excessive reabsorption of the urate anion transporter-1 (URAT-1). Therefore, URAT-1 inhibition will promote uric acid excretion and reduce the risk of having gout. Dillenia philippinensis Rolfe, often known as katmon, is an endemic plant in the Philippines with bioactive compounds associated with several therapeutic benefits. The present study represents the first scientific inquiry into the antihyperuricemic potential of compounds isolated from D. philippinensis. This study aimed to assess the interaction of URAT-1 with …

Synthesis Of 3-Methyl-3-Buten-1-Ol By Supercritical Co2 In Coordination With Hzsm-5 Catalyzed Formaldehyde-Isobutene Prins Reaction, Hang Yuan, Gui-Ping Cao, Hui Lv

Turkish Journal of Chemistry

The reaction solvent and catalyst play an essential role in the Prins reaction for the synthesis of 3-methyl-3-buten-1-ol (MBO) from formaldehyde and isobutene. The reactivity of the solid base catalyzed Prins condensation reaction by formaldehyde and isobutene in supercritical CO2 was investigated using CsH2PO4 modified HZSM-5. We finds that the alkaline sites of the alkali-loaded catalyst can extract the α-H on isobutene to generate olefin carbon negative ions, while the supercritical CO2 with weak Lewis acidity can activate formaldehyde to carbon positive ions, which can combine more easily with the carbon negative isobutene to react, thus improving the reactivity of …

Liquefaction Optimization Of Grape Pulp Using Response Surface Methodology For Biopolyol Production And Bio-Based Polyurethane Foam Synthesis, Furkan Çolakoğlu, Emre Akdoğan, Murat Erdem

Turkish Journal of Chemistry

Both environmental and economic disadvantages of using petroleum-based products have been forcing researchers to work on environmentally friendly, sustainable, and economical alternatives. The purpose of this study is to optimize the solvothermal liquefaction process of grape pomace using response surface methodology coupled with a central composite design. After investigating the physicochemical properties of the liquified products (biopolyol) in detail, a bio-based rigid polyurethane foam (RPUF) was synthesized and characterized. The hydroxyl and acid numbers and viscosity values of all the biopolyols were analyzed. According to variance analysis results (%95 confidence range), both the reaction temperature and catalyst loading were determined …

Magnetic Solid-Phase Extraction Technique Based On Fe3o4@Coppy-Pth Nanocomposite For Extraction Of Cobalt, Chromium, And Nickel Prior To Determination By Micro-Sample Injection System-Flame Atomic Absorption Spectrometry In Alcoholic And Nonalcoholic Beverages, Meli̇ke Küçüksakalli, Qamar Salamat, Buket Ti̇reli̇, Şükrü Gökhan Elçi̇

Turkish Journal of Chemistry

A novel Fe3O4@coPPy-PTH nanocomposite-based sorbent was prepared via in-situ oxidative polymerization using Fe3O4 nanoparticles with spherical and flower-like morphologies of thiophene and pyrrole as the feedstocks. The synthesized nanocomposite utilized sensitive extraction and determination of the metal ions Co(II), Cr(III), and Ni(II) without a chelating agent, followed by a micro-sample injection system-flame atomic absorption spectrometer (MIS-FAAS). The composition and morphology of Fe3O4@coPPy-PTH nanocomposite were characterized by advanced spectroscopic and imaging techniques like SEM and FT-IR. SEM observations showed the size of Fe3O4 nanoparticles changed from 30 nm to 120 nm in diameter after the copolymer (PPy-PTH) coating. The Fe3O4@coPPy-PTH nanocomposite …

Synthesis And Characterization Of New Hexahydroquinoline Derivatives, Evaluation Of Their Cytotoxicity, Intracellular Ros Production And Inhibitory Effects On Inflammatory Mediators, Ezgi̇ Pehli̇vanlar, Deni̇z Arca Çakir, Sonia Sanajou, Hülya Tezel Yalçin, Terken Baydar, Pinar Erkekoğlu, Hani̇fe Avci, Rahi̇me Şi̇mşek

Turkish Journal of Chemistry

Inflammation is a response to injury and infection in the organism. It can be categorized as acute and chronic inflammation. Chronic inflammation is the underlying cause of many diseases such as Alzheimer's, diabetes, rheumatoid arthritis, atherosclerosis and cardiovascular diseases. Recent studies have proven the anti-inflammatory properties of 1,4-dihydropyridines (1,4-DHPs) and its derivatives, which have many biological properties including calcium channel blockers. The structures of the synthesized compounds were elucidated by IR, 1H-NMR, 13C-NMR and HRMS methods. The cytotoxic properties of the compounds were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in 3T3 cell line. Among the 15 compounds, the three compounds …

Exploring The Efficiency Of Nitrogenated Carbon Quantum Dots/Tio2 S-Scheme Heterojunction In Photodegradation Of Ciprofloxacin In Aqueous Environments, Yilmaz Ateş, Zafer Eroğlu, Özkan Açişli, Önder Meti̇n, Semra Karaca

Turkish Journal of Chemistry

The usability of polyvinyl chloride-based quaternary triethanol ammonium chloride anionite (PVC-TEAC) as a potential extractant for tungstate was investigated to recover tungstate from Gabal Qash Amir, Egypt, assaying 70.91% WO3. Structure elucidation for PVC-TEAC anionite was successfully carried out using several techniques. Experimental measurements, such as pH, agitation time, initial tungsten concentration, anionite dose, co-ions, temperature, and eluting agents, have been optimized. It was found that PVC-TEAC anionite has a maximum capacity of 63 mg per gram. From the distribution isotherm modeling, Langmuir’s model fits the experimental results better than Freundlich’s, with a theoretical value of 61.728 mg g–1. According …

Identification Of Blood At Simulated Crime Scenes Using Silver Nanoparticles With Sers, Uğur Köroğlu, Necdet Sağlam, Uğur Tamer, Ramazan Akcan, İsmai̇l Hakki Boyaci, Eylül Evran

Turkish Journal of Chemistry

Analysis of substances and samples obtained from the crime scene are very important in solving forensic cases. In order to determine the variables involved in a crime and to expedite the investigation process, especially the rapid analysis of body fluids in a small quantity and within an environment containing diverse components is necessary. For this reason, it is of great importance to analyse biological fluids with rapid, non-chemical contamination, non-destructive, low-cost and accurate techniques. In recent years, with advancements in laser technology, spectroscopic methods have been introduced as an analytical technique in forensic medicine and chemical studies. This study focuses …