Chemistry Commons^™

Computational Design Of Potent Sirna For Braf Oncogene Silencing For Enhancing Cancer Therapy, Muhammad Hermawan Widyananda, Ricadonna Raissa

Karbala International Journal of Modern Science

The discovery of oncogenic BRAF mutations has prompted the development of inhibitors, yet resistance remains widespread. A more effective strategy involves targeting BRAF mRNA with siRNA to overcome resistance to BRAF inhibitors. This study aims to design potent siRNA for BRAF oncogene silencing using a computational approach. The full coding sequence of BRAF was retrieved from the NCBI database and potential siRNAs were predicted using the Ui-Tei, Reynolds, and Amarzguioui rules. Identified siRNAs were further analyzed using various prediction systems and parameters, including their interaction with the hAgo2 protein. The results identified that seven siRNAs (siRNA 23, siRNA 24, siRNA …

Computational Lipophilicity Calculations Of Fluorinated Morphine Derivatives For Improved Pain Management, Mirabella Romano, Allison Vu, Emily Chen

Student Scholar Symposium Abstracts and Posters

The opioid epidemic impacts 60 million people worldwide every year. Morphine, a commonly prescribed opioid, binds to the μ opioid receptor (MOR) in the body via protonation of the tertiary amino group of morphine and the MOR. An unfortunate side effect of this binding process is its non-selectivity in both peripheral and central tissues. While activation within inflamed peripheral tissues results in pain relief, activation within central tissues results in the unwanted and addictive side effects of opioids. Because there is a discrepancy in pH between healthy (central) and inflamed (peripheral) tissue, selective binding within the inflamed tissues results in …

Nifuroxazide And 4-Hydroxybenzhydrazone Derivatives As New Antiparasitic (Trypanosoma Cruzi And Leishmania Mexicana) And Anti-Mycobacterium Tuberculosis Agents, Timoteo Delgado-Maldonado, Diana V. Navarrete-Carriola, Lenci K. Vazquez-Jimenez, Alma D. Paz-Gonzalez, Baojie Wan, Scott Franzblau, Othman Mueen Mohammed, Lorena Rodríguez-Páez, Charmina Aguirre-Alvarado, Debasish Bandyopadhyay

School of Integrative Biological & Chemical Sciences Faculty Publications

Background/Objectives: Nifuroxazide (Nfz) is a drug that has been used as a scaffold for designing antimicrobial and antiparasitic agents. This study aimed to synthesize and evaluate in vitro of Nfz and twenty-five 4-hydroxybenzhydrazone derivatives as potential anti-Trypanosoma cruzi, anti-Leishmania mexicana, and anti-Mycobacterium tuberculosis agents.

Methods: The compounds were synthesized by condensing 4-hydroxybenzhydrazide with appropriate aldehydes in acidic conditions and structurally confirmed by spectroscopic techniques. All compounds were evaluated in vitro against T. cruzi strains (NINOA and A1), L. mexicana (M379 and FCQEPS strains), and M. tuberculosis (H37Rv strain), followed by enzymatic assays against T. cruzi …

Vanadyl Phthalocyanine As A Low-Temperature/Low-Pressure Catalyst For The Conversion Of Fructose To Methyl Levulinate, Juan Luna, Mataz Alcoutlabi, Elizabeth M. Fletes, Helia Magali Morales, Jason Parsons

School of Integrative Biological & Chemical Sciences Faculty Publications

In this study, a vanadyl phthalocyanine was synthesized and characterized using XRD, FTIR, and XPS, confirming the successful metalation of the phthalocyanine ring. XRD analysis showed the vanadyl phthalocyanine crystallized in the P-1 crystal lattice, with unit cell parameters a = 12.058 Å, b = 12.598 Å, and c = 8.719 Å, and the lattice angels were 96.203°, 94.941°, and 68.204°. FTIR spectroscopy supported the metalation by the disappearance of the N-H stretch of the non-metalated phthalocyanine. The vanadyl phthalocyanine was tested as a heterogenous catalyst for the conversion of fructose into methyl levulinate in H2SO4–methanol and HCl–methanol systems. The …

Treatment Wastewater Of Oil Refinery By Fe2o3 Nps Produce By The Novel Alishewanella Jeotgali Strain Haq8., Hawraa Qays Al-Assdy, Wijdan Hussein Al-Tamimi, Asia Fadhile Almansoory

Karbala International Journal of Modern Science

Metal oxide nanoparticles like iron oxide (Fe₂O₃) exhibit strong reactivity and photolytic features in wastewater treatment and serve as an effective adsorbent for water purification due to its substantial surface area and affinity for different functionalized groups. Iron oxide nanoparticles) IONPs) are currently applied to treat oil-contaminated water. Fe₂O₃NPs were produced using an extracellular approach utilizing the Alishewanella jeotgali strain HAQ8. IONPs were characterized using UV-vis, FT-IR, XRD, AFM, SEM-EDX, and Zeta potential. λ max for the synthesized nanoparticles observed at (358) nm. The bands at 485 cm⁻¹ in the FT-IR spectrum confirmed the formation of …

Ability Of Strained C Atoms To Act As An Electron Donor, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

There is a great deal of strain within the propellane and pyramidane hydrocarbon molecules. Quantum chemical calculations evaluate how this strain affects the ability of the bridgehead C atom to act as an electron donor in hydrogen, halogen, chalcogen, pnicogen, and tetrel bonds, despite the absence of a formal C lone pair or CC multiple bond. The strain induces the formation of a substantial region of negative electrostatic potential on this C atom which can attract the σ-hole of an electrophile. Each such molecule also contains an occupied molecular orbital that can be described as either a C lone pair …

Expanding The Toolbox For Supramolecular Chemistry: Probing Host–Guest Interactions And Binding With In Situ Ftir Spectroscopy, Shiva Moaven, Douglas A. Vander Griend, Darren W. Johnson, Michael D. Pluth

University Faculty Publications and Creative Works

Association constant (Ka) measurements provide fundamental information on host–guest interactions in supramolecular chemistry and other areas of science. Here we report the use of in situ FTIR spectroscopy to measure the Ka values across three classes of host–guest complexes that involve hydrogen bonding and halogen bonding. This approach can be performed with minimal sample preparation, does not require deuterated solvents, can measure association based on changes in host or guest vibrations, and benefits from a much shorter timescale than NMR spectroscopy. Due to its fast timescale, FTIR spectroscopy also provides details on host/guest conformational changes, such as the presence of …

First-Principles Studies Of Electrical Polarization Effects In Ferroelectrics, Antiferroelectrics And Defects, Louis Alaerts

Dartmouth College Ph.D Dissertations

Over the last few decades, density functional theory (DFT) has emerged as a formidable tool in the field of computational material science. Not only has it become a complementary method approach to experiments by rationalizing the many complex properties of materials but its formidable predictive power can also be used to identify the most promising candidates for specific applications. Point defects in semiconductors have become an important platform for the development of quantum networks due to their ability to act as spin-photon interfaces. Spectral diffusion, the broadening of the optical emission line, can significantly impact the performance of these defect-based …

Typical Electron-Withdrawing Groups Are Ortho, Meta-Directors Rather Than Meta-Directors In Electrophilic Aromatic Substitution, Paul R. Rablen

Chemistry & Biochemistry Faculty Works

Electron-withdrawing groups are traditionally considered meta-directing in aromatic substitution reactions. However, when the pre-existing substituent is a π-acceptor, both experiment and calculation indicate that substantial amounts of ortho as well as meta substitution occur, with very little para reactivity. A simple perturbative MO argument rationalizes this finding. It is therefore suggested that these substituents are best understood as ortho, meta-directors, with a preference for meta, just as electron-donating groups are considered ortho, para-directors, with a preference for para.

Development Of A Mechanochemical Synthesis For A Palladacycle: Exploring Solvent Characteristics And Reaction Kinetics, Kyle Lintzenich

Honors College Theses

Palladacycles are a class of palladium complexes that show utility in catalyzing carbon-carbon cross coupling reactions. Mechanochemistry provides a greener alternative to synthesizing these palladacycles via repeated impacts that transfer mechanical energy into the reaction mixture, promoting formation of the desired complex. Specifically, liquid assisted grinding (LAG) has proven to be a viable tradeoff to neat mechanosynthesis of adding a small amount of liquid to decrease synthesis times or improve conversion. Some liquids actively participate in the reaction in a process termed as non-innocent LAG. This work focuses on the development of a mechanosynthetic method using non-innocent LAG for a …

Toxicity And Biodegradability Of Novel Boronium Vs Conventional Ammonium Based Anti Microbial Compounds In Wastewater Treatment Systems, Noor Shalan

Poster Presentations

Quaternary ammonium compounds (QACs) are highly effective as disinfectants, herbicides, and pesticides; thus, overuse causes elevated levels of residual toxicity in domestic and industrial wastewater. QACs can be toxic to essential bacteria breaking down pollutants in wastewater treatment plants (WWTPs) and can remain untreated in effluent, harming the environment, and contributing to antibiotic resistance, posing risks to human health. Novel boronium-based antimicrobial compounds have demonstrated efficacy in eliminating bacteria, fungi, and viruses. If the boronium compounds exhibit lower residual toxicity, they could offer a promising alternative to QACs. Because these compounds are still in development, their potential toxicity to the …

Linear Dicyclopentadiene Copolymers: Synthesis And Thermal Analysis, Connor Lewis

Poster Presentations

To retain the existing advantages of L-pDCPD and to enhance its material properties, an incorporation of functionalized comonomers is being investigated. It is hypothesized that such functionalization will allow for higher theoretical molecular weights, increased oxidative resistance, and more durable thermal properties following air exposure. The use of heteroatoms in exemplary oxa-norbornene-based compounds is thought to strengthen intermolecular interactions and thus improve the structural stability of L-pDCPD. To better understand the polymerization initiated by GC3 and to identify potential ROCM processes, IR-active nitrile and hydroxyl groups were specifically incorporated. For this study, the comonomers were synthesized from exo-3,6-epoxy- 1,2,3,6 tetrahydrophthalic …

Molecular Insights: Advances In Single Molecule And Single Particle Detection For Analysis Of Chemical, Physical, And Biological Phenomena, James Ethan Batey

Chemistry & Biochemistry Undergraduate Honors Theses

This thesis is focused on recent advancements made in the field of chemical imaging, optical microscopy, and recent developments that have improved spatial, temporal, or spectral resolution or have made certain techniques more accessible and cost effective for their wider adoption. This thesis is organized based on the systems of interest we studied with each new technique. Although, it is important to note that many of the methods here can be used with a multitude of systems even if not explicitly mentioned. The first chapter of this thesis will discuss the current state of chemical imaging, common terminology, and important …

Bioavailability Of Lead In Terre Haute Soils, Terre Haute, Indiana, Zach Kemp

All-Inclusive List of Electronic Theses and Dissertations

Contamination of soils from heavy metal pollution has been a global concern for decades. Heavy metals are released into the soil from natural and anthropogenic releases. The largest producers of heavy metal pollution include mining, industrial production, and the combustion of fossil fuels. Vigo County formed in 1818, and Terre Haute was established in 1832. After the discovery of coal in Clay County in 1867, Terre Haute became the third largest coal producer and fifth largest iron manufacturer in the state during that time. Lead, in particular, is a heavy metal of concern because of the harmful effects to humans …

Using Gaussian Process Regression To Learn Thermodynamic Equations Of State With Uncertainty Quantification, Austen T. Lee

Chemical Engineering Undergraduate Honors Theses

This study investigates the use of derivative-informed Gaussian Process (GP) models to estimate thermodynamic behavior across temperature and density by building a Helmholtz-based equation of state. Argon, a stable monatomic gas, was chosen as a case study within the vapor region. The GP model was trained using values of experimentally measurable properties found by taking first and second derivatives of the original potential function. Results show that while the GP model offered uncertainty quantification and informed thermodynamic behavior, it predicted values that deviated from the ground truth depending on the property. The model exhibited high confidence in regions with substantial …

Protein Structural Changes Of Envelope Glycoprotein In Human Immunodeficiency Virus Type 1, Abigail S. Bridges

Chemistry & Biochemistry Undergraduate Honors Theses

The envelope glycoprotein (Env), present on the viral surface of human immunodeficiency virus type 1 (HIV-1) facilitates host cell infection, making it a critical target for immune responses and vaccine development. Env is able to transition through three prevalent prefusion conformational states, state-1 (pre-triggered), state-2 (closed), and state-3 (open). By transitioning through these conformation states, Env can successfully evade immune responses and initiate viral entry into the host cell. This study uses molecular dynamics (MD) simulations to analyze the conformational dynamics of the mature, cleaved Env glycoprotein in the state-2 conformation (PDB ID: 4ZMJ). Simulations were conducted with five replicates, …

A Pure Rotational Spectroscopic Study Of Two Nearly-Equivalent Structures Of Hexafluoroacetone Imine, (Cf3)C=Nh, Daniel A. Obenchain, Beppo Hartwig, Daniel J. Frohman, Garry S. Grubbs, B. E. Long, Wallace C. Pringle, Stewart E. Novick, S. A. Cooke

Chemistry Faculty Research & Creative Works

Rotational spectra for hexafluoroacetone imine, the singly substituted 13C isotopologues, and the 15N isotopologue, have been recorded using both cavity and chirped pulse Fourier transform microwave spectrometers. The spectra observed present as being doubled with separations between each pair of transitions being on the order of a few tens of kilohertz which is consistent with a large amplitude motion producing two torsional substates. The observed splitting is most likely due to the combined motions of the CF₃ groups, for which the calculated barrier is small. However, no transitions between states could be observed and, similarly, no Coriolis coupling parameters …

Development Of Novel Pharmaceutical For Optimization Of Opioid Overdose Treatment, Larae Kram

Celebrating Scholarship and Creativity Day (2018-)

Although opioids are highly effective drugs for pain management, their overuse and addictive nature has caused an opioid epidemic, resulting in many cases of opioid addiction and overdose. There are two current opioid overdose drugs that are FDA approved: naloxone and nalmefene. These drugs have a higher affinity to the active binding pocket on the opioid receptor than opioids do and displace the opioids, preventing any further binding of the opioid and halting the opioid’s effects. However, naloxone is not active long enough to outlast the duration of the opioid and nalmefene causes severe withdrawal symptoms. The development of more …

Synthesis And Characterization Of 3,5 Trifluoromethyl Tpm With A Metal Carbonyl Complex, Emily P. Berkman

Undergraduate Honors Thesis Collection

Tris(pyrazolyl)methane (Tpm) ligands have a central carbon with 3 pyrazole rings attached. These were discovered in 1970 and have since been synthesized with many substituents on the rings. Based on the parent structure, my goal was to synthesize a fluorinated Tpm derivative. By adapting existing procedures, I have synthesized a Tpm derivative with trifluorinated methyl groups in the 3 and 5 positions of the pyrazole ring. The fluorinated ligand is expected to be electron withdrawing and exhibit interesting chemistry when bound to a metal center. Future directions of the project will be discussed.

Disulfide-Cleavable Linkers In Antibody-Drug Conjugates For Targeted Cancer Therapy, Emily Hwang

Undergraduate Honors Thesis Collection

This project aims to discover a way to improve the safety of and reduce adverse side effects of disulfide-linked antibody-drug conjugates. Disulfide-cleavable linkers for antibody-drug conjugates function by exploiting the differential concentrations of dominant thiol species in the blood plasma and in the cytosol of malignant cells. This project aimed to identify a relationship between the stability of disulfide cleavable linkers in the blood plasma and disulfide linker structure, to prevent premature release of the cytotoxic drug. Three disulfide linker analogs with varying carbon chain lengths were synthesized through reaction with 2,2’-dipyridyl disulfide. Each analog was conjugated to a fluorescent …

Cultural Health Benefits And Challenges Of Food Preparation And Consumption: A Comparative Study Of The United States, Italy, And Norway, Natalie G. Link

Undergraduate Honors Thesis Collection

This study aims to investigate the cultural health benefits and challenges associated with food preparation and consumption in the United States, Italy, and Norway, with a particular focus on citizens in lower socioeconomic levels. By examining the dietary habits, social structures, and health outcomes in these three countries, this research aims to uncover broader insights into the health status and well-being of their respective populations. The study will employ secondary data analysis approach examining existing research on cultural practices and social support systems. The findings of this research will contribute to a deeper understanding of the complex interplay between food …

Semiconductors In Space: Data Analysis Of Microgravity's Impact On Crystal Formation, Keegan Jo Jackson

Undergraduate Honors Thesis Collection

Comprehensive data analysis on crystal growth in microgravity is a requisite to inform understanding of prior work. Our research constructed and analyzed a database containing data gathered from research focusing on semiconductors grown in microgravity. Data curation spanned multiple decades, countries, and semiconductor materials. All relevant reported information was recorded in the database, notably data regarding the metrics used to determine the impact space had on crystal growth: size, structure, uniformity, and performance. After data cleaning and data processing, the database was organized and readied for analysis. Data analysis was performed using RStudio and SciKit-learn. RStudio was employed for data …

Linking The Past And The Future: Understanding How Pollutants Cause Corrosion During An Oddy Test, Kylie Blair Blake

Undergraduate Honors Thesis Collection

Artifacts and artwork continue to tell a story long after a time or culture has disappeared. Preventive art conservation science involves careful and responsible management of the objects entrusted in the care of the museum staff to ensure environmental and display conditions do not cause damage so future generations can observe and learn about past cultures. An accelerated metal corrosion test, the Oddy test, has been used to help determine the suitability of display and storage materials. The Oddy test is subjective, so newer methods are being developed involving the use of gas chromatography and mass spectrometry to identify specific …

A New Transition Metal Borate, Co6(B24O39(Oh)6(H2O) 6·2.21h2O, Synthesized Via A Mild Hydrothermal Synthesis, Alevtina Maksimova, Patrick Belt, Nilah Whitfield, Mark D. Smith, Gopabandhu Panigrahi, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

A new transition metal borate hydrate, Co₆B₂₄O₃₉(OH)₆(H₂O)₆·2.21H₂O, was synthesized via a mild hydrothermal method using boric acid as the melt. The compound crystallizes in the trigonal space group P 3‾ with lattice parameters a = b = 13.17840(10) Å, c = 12.3287(2) Å, and a unit cell volume of 1854.27(4) ų (Z = 2). This borate hydrate crystallizes in a new structure type comprised of layers containing [BO3] trigonal planar units and [BO4] tetrahedra that are linked by CoO6 and Co(OH)2(H2O)4 octahedra via corner-sharing. The …

Atomic Level Characterization For The Transport Cycle Conformational Pathways Of Multidrug Resistance Protein 1 (Mrp1), Samuel Wamwere Mwatha

Graduate Theses and Dissertations

The multidrug resistance-associated protein 1 (MRP1/ABCC1) is an ATP-binding cassette (ABC) transporter that mediates the cellular efflux of endogenous and xenobiotic substrates, including therapeutic drugs. Its overexpression is a major contributor to multidrug resistance in cancer, which tends to result in negative clinical results. Even with considerable progress made in structural biology, the intricate details of how membrane lipid composition affects the conformational changes and functional switches of MRP1 still lack explanation.

This thesis employs long-timescale, all-atom molecular dynamics (MD) simulations to study the influence of various lipids on MRP1 lipid bilayer environments. Both inward-facing and outward-facing conformations of MRP1 …

Electrodeposition Of Gallium Nitride_Unraveling The Role Of Precursors, Deposition Conditions, And Substrate Effects For Semiconductor Applications, Mauricio Azier Leyva Aranzabal

Open Access Theses & Dissertations

Gallium nitride (GaN) is a wide-bandgap semiconductor noted for its remarkable optoelectronic and structural characteristics, rendering it a potential material for high-power, high-frequency, and optoelectronic device applications. This dissertation investigates the electrochemical synthesis of GaN thin films by potentiostatic and galvanostatic electrodeposition techniques using aqueous solutions of gallium nitrate (Ga(NO3)3), ammonium nitrate (NH4NO3), and auxiliary agents like potassium nitrate and urea. The main aim is to examine the essential elements affecting nitrogen incorporation and film shape while assessing electrochemical performance on various conductive substrates.A thorough investigation was performed to evaluate the impacts of electrodeposition duration, electrolyte pH, precursor molar concentrations, …

Binary Solid/Liquid Equilibrium Of Mixtures Of Thermally Robust Salts And Molecular Compounds For Use As Heat Transfer Fluids, Jared Ridge Mathews

Honors Theses

Fossil fuels, contributors to climate change that may bear catastrophic consequences, power the entire world. The human species is almost entirely dependent on fossil fuels for energy, but other sources of renewable and environmentally friendly energy must be developed. Concentrated solar power (CSP) is a promising source of renewable energy with hampered potential—better heat transfer fluids (HTFs) are needed for it to be economically feasible. Currently, the HTFs in industrial use are predominantly either synthetic oils or nitrate-based molten salts. Synthetic oils are only stable up to 400 °C, and molten salts often have high melting temperatures, making them prone …

Development And Characterization Of Aso-Based Ribonuclease Targeting Chimera For The Degradation Of Cug Rna Repeat Expansion In Myotonic Dystrophy Type, Audrey Coons

Chemistry

Myotonic Dystrophy Type 1 is a multisystemic genetic disorder that primarily affects the muscles in the body leading to such pathologies as myotonia, muscle atrophy, insulin resistance and even neurological deficits. This disorder is caused by a series of CUG repeats in the 3’ untranslated region of the DMPK gene; symptoms appear after around 34 repeats. These repeats form foci when MBNL1 protein that deals with alternative splicing of many events in the body, forms aggregations around these repeats. These foci render the MBNL 1 proteins useless. There is no FDA approved therapeutic, but many RNA targeting therapeutics have been …

Synthesis Of Single Chain Polymer Nanoparticle Networks By Reinitiating Raft Polymerization, Dallas Donovan

Honors Theses

Hydrogel materials, which are polymer networks comprised mostly of water, hold significant promise for biomedical applications due to their compatibility with biological systems. Conventional hydrogel materials are often brittle and weak, but most applications in biomedical systems require materials to be strong and tough. The topology of a polymer network dictates its mechanical properties. An important strategy for designing tougher hydrogels is the release of stored length, such as from the unfolding of polyprotein cross-linkers. Inspired by the success of the strategy, we report progress towards a fully synthetic design using single chain nanoparticles (SCNPs) into a hydrogel. SCNPs, which …

Linear Polydicyclopentadiene Copolymers: Synthesis And Thermal Properties, Connor Lewis

Honors Theses

No abstract provided.