Chemistry Commons^™

Developing A Course-Based Undergraduate Research Experience For Chem 122, Melanie J. Harvey Phd

Sabbatical Projects

Sabbatical presentation from a 2022 Sabbatical

Identification Of Alkynyl Nicotinamide Hsn748 As A Ret Solvent-Front Mutant Inhibitor With Intracranial Efficacy, Ujjwol Khatri, Neetu Dayal, Kofi B Owusu, Mandeep Kaur Hunjan, Shriya Pandey, Haley Anne Harper, Carli Mcmahan, Bennett D Elzey, Tao Shen, Xueqing Hu, Kurt W Evans, Ahmed El-Sheikh, Seong Jun Jo, Frederick W Holtsberg, M Javad Aman, Funda Meric-Bernstam, Sukyung Woo, Herman O Sintim, Jie Wu

Faculty, Staff and Student Publications

RET solvent-front G810C/R/S mutations confer resistance to the currently approved RET protein tyrosine kinase inhibitors (TKIs) selpercatinib and pralsetinib. Moreover, RET fusion-positive lung adenocarcinoma frequently metastasizes to the brain. To address these challenges, it is imperative to develop a RET TKI that is effective against solvent-front mutations and exhibits intracranial activity. We synthesized alkynyl nicotinamide-based RET TKIs and tested their efficacy in cell cultures in inhibiting selpercatinib/pralsetinib-resistant RET solvent-front mutants G810C/R/S found in cancer patients, and in BaF3/KIF5B-RET(G810C) cell-derived subcutaneous and intracranial tumors in vivo. We also evaluated alkynyl nicotinamide RET TKIs in KIF5B-RET-induced lung tumors in immune competent …

Computational Investigation Of The Structural And Electronic Effects Of Phenyl, Alkyl, And Halogen Fully Substituted Acenes, Emily A A Jarvis, Viraj Jain, Georgia Grace Tully, Peter W. Jarvis

Chemistry and Biochemistry Faculty Works

Acenes are a class of polycyclic aromatic hydrocarbons that may hold promise as organic semiconductors (OSCs) in solar cells and electronic devices. Their instability and poor solubility present challenges that may be improved by replacing the hydrogens with phenyl, halogen or alkyl substituents to sterically induce a helical twist to these otherwise planar molecules. This twisted structure also impacts the optical properties of these molecules. We employ time-dependent density functional theory (TD DFT) to investigate acenes spanning from naphthalene to heptacene. We focus on the structural and electronic effects of fully substituting these molecular backbones to create seven distinct substituent …

Growth Of Cylindrical Micelles And Their Use To Prepare Porous Materials With Tailored Dimensions And Alignment, Mengxue Zhang, Xiaomeng Li, Chuanbing Tang, Morgan Stefik

Faculty Publications

Materials with cylindrical pores are optimal for electrochemical devices and filtration due to their straight paths with minimal tortuosity when aligned. Polymer templates have led to many individual cylindrical architectures however the independent tailoring of pore and wall dimensions has remained elusive. Here short cylindrical micelle templates (PEO-b-PS) with glassy cores enabled the fabrication of sample series with constant cylindrical pore diameter (∼63 nm) and tailored wall thickness (TiO₂, ∼45–100 nm). This ShortCyl series (aspect ratio 4.25) had modest alignment that was attributed to the low free-energy cost for misalignment. Though the plasticized micelles (DCM present) …

Magnetospectroscopic Studies Of A Series Of Fe(Ii) Scorpionate Complexes: Assessing The Relationship Between Halide Identity And Zero-Field Splitting, Daniel J. Santa Lucia, Laxmi Devkota, Sergey Lindeman, Andrew Ozarowski, J. Krzystek, Mykhaylo Ozerov, Samuel M. Greer, Daniel C. Cummins, Klaus H. Theopold, Mihail Atanasov, Joshua Telser, Adam T. Fiedler

Chemistry Faculty Research and Publications

Ferrous ions in four-coordinate environments are common in protein structures, synthetic catalysts, and molecular magnets. The 3d⁶ configuration of high-spin Fe(II) imparts an S = 2 ground state, whose analysis using conventional spectroscopic methods is often hindered by substantial zero-field splitting (ZFS). Herein, we provide detailed electronic-structure descriptions for [Fe^IIX(Tp^tBu,Me)] (1-X; X = F, Cl, Br, I), where (Tp^tBu,Me)− is hydrotris(3-tert-butyl-5-methyl-pyrazol-1-yl)borate. The three pyrazolyl N-donors of the “scorpionate” ligand facially coordinate to Fe(II), giving idealized C_3v symmetry with the halide occupying the axial position. Although originally reported …

Epitaxial Electrodeposition Of Cu-Btc Metal-Organic Framework Thin Films Onto The (100), (110), And (111) Surfaces Of Single-Crystal Gold And Cuprous Oxide Buffer Layers, Xiaoting Zhang, John Z. Tubbesing, Jay A. Switzer

Chemistry Faculty Research & Creative Works

Metal-organic frameworks (MOFs) have well-defined pore structures. Epitaxial MOFs can produce films with uniform pore sizes and open porosity. However, the growth of epitaxial MOF thin films has remained a challenge. Herein, we demonstrate a cathodic electrodeposition method for the epitaxial growth of a well-known MOF material, copper (II)-benzene-1,3,5-tricarboxylate (Cu-BTC), from solution precursors. The epitaxial electrodeposition of Cu-BTC was achieved in a Cu (NO₃)₂-H₃BTC-H₂O₂ bath using H₂O₂ reduction to deprotonate the H₃BTC molecule. The Cu-BTC films can be grown to micrometer thicknesses with Faradaic efficiencies up …

Wear Of High Entropy Alloys: Understanding Effects Of Cryogenic Temperatures And Surface Nitriding On Wear Behavior, Aubrey Yu Tang

Dartmouth College Ph.D Dissertations

Cryogenic tribological applications have become increasingly important with the development and innovation of advanced equipment in aerospace, polar regions, superconductivity, and more. Traditional lubrication methods are not viable under these harsh environments, so metallic materials must be able to maintain excellent mechanical properties and withstand the constant impact and wear alone. High entropy alloys (HEAs) have emerged as potential candidates for these applications because of their wide variety of excellent room temperature properties and apparent improvement of mechanical properties of some HEAs at extremely low temperatures. Despite their promising nature, very limited work has been done on understanding the wear …

64th Annual Rocky Mountain Conference On Magnetic Resonance

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 64th annual meeting of the Rocky Mountain Conference on Magnetic Resonance. Held in the Snowbird Resort and Conference Center, Snowbird, Utah, August 3-7, 2025.

Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ongoing evolution of SARS-CoV-2 variants has underscored the need to understand not only the structural basis of antibody recognition but also the dynamic and allosteric mechanisms that could underlie complexity of broad and escape-resistant neutralization. In this study, we employed a multi-scale approach integrating structural analysis, hierarchical molecular simulations, mutational scanning and network-based allosteric modeling to dissect how Class 4 antibodies (represented by S2X35, 25F9, and SA55) and Class 5 antibodies (represented by S2H97, WRAIR-2063 and WRAIR-2134) can modulate conformational behavior, binding energetics, allosteric interactions and immune escape patterns of the SARS-CoV-2 spike protein. Using hierarchical simulations of the …

Harnessing Emergent Multiple Scattering Resonances In A Photonic Glass Structure For Photoelectrochemical Energy Conversion, Ashlyn G. Descarpentrie, Robert H. Coridan

Chemistry & Biochemistry Faculty Publications and Presentations

Light trapping nanostructures are often necessary to improve carrier collection yields in semiconductor photoelectrodes with intrinsically poor electron transport. Photonic crystal templates can generate tailorable light trapping via periodic and precise nanostructure, though this is not a scalable strategy for photoelectrochemical (PEC) applications. It is therefore critical to identify alternative mechanisms for light trapping that tolerate disorder. Light trapping in disordered media is generated by the diffusive transport caused by multiple scattering. In some cases, multiple scattering can generate resonances that resemble those observed in photonic crystals. While resonant multiple scattering is a disorder tolerant light trapping mechanism, it is …

Developing Microelectrode Arrays As Multiplex Point-Of-Care Diagnostics, Yu-Chia Chang

Arts & Sciences Graduate Student Theses and Dissertations

Antibiotic resistance poses a significant global health challenge, particularly in urinary tract infections (UTIs), where 92% of cases exhibit resistance to at least one antibiotic, causing over 260,000 deaths annually. The emergence of antibiotic-resistant bacteria and growing awareness of the adverse effects of unnecessary antibiotic use highlight the urgent need for better UTI diagnostics. Current state-of-the-art methods are either expensive and time-consuming, or they lack specific details about the nature of the antibiotic and only determine inflammation. This hinders timely and effective treatment decisions regarding whether an antibiotic is actually necessary. Given this backdrop, there is a demand for a …

An Enzyme-Coupled Isotope Dilution Mass Spectrometry Assay For Non-Adjacent Dna Photoproducts As Intrinsic Probes For G-Quadruplexes In Vitro, Savannah Sharee Scruggs

Arts & Sciences Graduate Student Theses and Dissertations

G-quadruplexes are noncanonical secondary structures that form in guanine-rich nucleic acid sequences and are thought to be involved in the control of gene expression.1 Unfortunately, it has been difficult to prove that these structures exist in vivo because of their dynamic nature. Rather than try to develop G-quadruplex specific binders as others have done,2 our idea is to photochemically trap certain types of G-quadruplexes by irreversible photoproduct formation3–5 and then detect the stable G-quadruplex-specific photoproducts by Isotopic Dilution Mass Spectrometry (IDMS).6 This IDMS method could then be used to unambiguously confirm the presence of specific types of G-quadruplexes in vivo …

Antifungal Peptides From Casein Milk Of Etawa Crossbreed (Capra Hircus) As Biopreservation Agent For Bread And Molecular Docking Studies, Dian Riana Ningsih, Winarto Haryadi, Rachma Wikandari, Tri Joko Raharjo

Karbala International Journal of Modern Science

Bread without peptide fraction treatment started to grow mold on the fourth day with a total of 24x10⁷ fungi colonies/ml. Meanwhile, the addition of peptide fractions GMC5, GMC6, GMC7, and GMC8 effectively preserved bread for up to 4 days, indicated by no mold growth. The best treatment was the GMC6 peptide fraction on day 8 which grew the least amount of fungus at 7x10⁷ spores/ml. Peptide interaction with the CaATPase receptor Aspergillus sp. was carried out using HADDOCK 2.4. The 3D CaATPase structure prediction resulted in a model with good structural quality. This was supported by residues in …

Assembly Of Non-Close-Packed Poly(N-Isopropylacrylamide) Microgels On Metal Halide Perovskite Films, Amal Alruwaili, Osama M. Alkhudhari, Ran Wang, Zhenyu Jia, Jennifer M. Saunders, Eugenio Picheo, Daniel T.W. Toolan, L. Andrew Lyon, Brian R. Saunders

Engineering Faculty Articles and Research

Hypothesis

Experiments

Extreme Value Theory View Of High Emitter Diesel Vehicles In The Us From 1991 To 2021, M. Matti Maricq, Gary A. Bishop

Fuel Efficiency Automobile Test Publications

Extreme value theory (EVT) is a statistical method to characterize the tails of distributions, such as high emitter vehicle emissions. The present work addresses the United States (US) diesel fleet. EVT confirms that high emitters contribute disproportionately to adverse air quality. It further reveals that high emitter emissions have responded differently to progressively tighter emissions standards compared to fleet averages. Carbon monoxide (CO) and hydrocarbons (HC) high emitter emissions fell in concert with the fleet average after widespread implementation of the diesel oxidation catalyst to meet US Environmental Protection Agency (EPA) Tier 1 emissions standards, but remained unchanged after introduction …

Linking Ruthenium(Ii) Polypyridyl Complexes Into Metal-Organic Frameworks Using Iron(Ii) And Zinc(Ii), Taofeek Mayowa Ogungbade

Masters Theses & Specialist Projects

Renewable energy has attracted significant interest in recent years as society seeks to minimize its dependence on fossil fuels. Among the various strategies proposed to achieve this goal, one promising approach is the conversion of carbon dioxide into organic fuels using photocatalysts. Unlike traditional semiconductor photocatalysts, metal-organic frameworks (MOFs) offer advantages such as absorption of visible light, tunable structures, and uniform pore sizes, which enhance their efficiency in the photocatalytic reduction of carbon dioxide.

In this thesis, we report the synthesis, structure, and properties of two novel heteronuclear MOFs that incorporate ruthenium(II) complexes and 3d-block transition metals using 2,2’-bipyridine-5,5’-dicarboxylic acid …

Understanding Structure-Property Relationships Within Polyolefin-Derived Vitrimer Systems, Mikaela Sadri

Dissertations

Polyolefins are extremely ubiquitous materials due to their satisfactory material properties, ease of synthesis, and low cost. Unfortunately, their extensive use has led to a global plastic waste mismanagement problem. As such, notable efforts have recently focused on converting these commodity polymers into vitrimers, or dynamic networks, to extend their use-life and tailor their properties. However, the fundamental polymer physics of these emerging materials, remain largely underexplored, hindering their widespread implementation. To address this challenge and enable a more sustainable future, the overarching goal of my dissertation research is to understand the fundamental structure-property relationships within complex polyolefin-derived vitrimer systems. …

Mechanochemical Investigation Of The Solid-State Reduction Of Metal Oxide Species, Trevor Webster

Masters Theses & Specialist Projects

Redox reactions are commonly performed in aqueous solutions. Mechanochemistry offers an alternative route to conduct these reactions in the absence of a solvent. The current research project investigates the feasibility of performing solid-state redox reactions using mechanochemistry as a means to initiate. Utilizing a Wig-L-Bug, sodium metavanadate and vanadium(V) oxide are milled with various inorganic and organic reducing agents. Zn, Mg, Na₂SO₃, ascorbic acid, and benzoic acid were selected due to the agents’ high reduction potential and ability to reduce vanadium(V) species in acidic or basic solutions. The use of X-ray powder diffraction (XRD) and scanning …

Deposition Of Nickel/Iron Oxide Co-Catalysts Onto Titanium Dioxide Towards Water Photolysis, Md Towhidul Islam Tareqe

Masters Theses & Specialist Projects

Photocatalytic water splitting is one potential approach for sustainable hydrogen production, offering an environmentally friendly alternative to fossil fuels. This process typically employs metal–semiconductor hybrid systems, where the semiconductor absorbs sunlight to generate charge carriers, and the metal cocatalyst facilitates charge separation and surface redox reactions. Titanium dioxide (TiO₂) is a widely studied semiconductor due to its stability and abundance, but its limited absorption of the solar spectrum requires the incorporation of efficient cocatalysts. Platinum is regarded as the benchmark cocatalyst due to strong proton binding energy that easily facilitates the reduction of water to produce hydrogen gas. …

The Development Of High Throughput Assays For Identification And Evaluation Of Small Molecule Modulators Of The Pri-Microrna-18a—Hnrnp A1 Interaction, Emile N. Van Meter

Dissertations

Therapeutics targeting RNA is a rapidly growing field. While only 1.5% of the human genome encodes genes for protein, over 70% o=f the human genome contains the genes for noncoding RNAs that regulate protein expression and function. Expanding the paradigm of small molecule drug discovery from traditional protein targets to include RNA would broaden the therapeutic landscape and provide new methods to modulate previously undruggable targets. miRNAs (miRs) have been found to be aberrantly expressed in many disease states, including neurodegenerative diseases and cancers making them promising therapeutic targets. The production of functional, mature miRs requires multiple proteins in a …

Comparative Expression Of Cgmp-Dependent Protein Kinase G (Pkg) From Plasmodium And Toxoplasma, Tsopmo Asaah

Theses, Dissertations and Culminating Projects

Malaria and Toxoplasmosis are life threatening diseases to humans. The search for a cure and control of these diseases is still one of the major challenges of scientists worldwide. In this research we focused on two Malaria species; Plasmodium bergei² (Pb) and Plasmodium falciparum¹ (Pf) and also on Toxoplasma gondii. Part of the life cycle of these organisms is regulated by the enzyme cyclic GMP-dependent protein kinase G (PKG)⁴. This is our drug target in this research. We believe that inhibiting this enzyme will be a great step in fighting these diseases. In this research, we devised a comparative study …

Investigating The Influence Of Experimental Parameters On The Formation Of Gold Nanoparticles: A Green Synthesis And Design Of Experiments Approach, Isaac Opeyemi Subuloye

Master's Theses

This thesis examines the green synthesis of gold nanoparticles using catechin, a naturally occurring plant-derived compound, as both a reducing and capping agent. The synthesis process was guided by a structured Design of Experiments (DOE) methodology to ensure systematic investigation and optimization. A two-phase experimental approach was adopted. First, a full factorial screening design was used to evaluate the effects of catechin concentration, NaOH concentration, and pre-reaction time. This was followed by an optimization phase using a face-centered composite design to identify conditions that produce nanoparticles with ideal characteristics. The nanoparticles were analyzed using UV-visible spectroscopy and dynamic light scattering …

Reductive And Nucleophilic Cleavage Of Peroxides And Synthesis Of Tocotrienols As Radioprotective Targets, Amber Marie Schuster

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

I. SET CLEAVAGE OF PEROXIDES: INFLUENCE OF REDUCTANT AND PEROXIDE ON THE RATE AND MODE OF ALKOXY RADICAL FORMATION

The reductive cleavage of organic peroxides to generate alkoxy radicals is frequently accomplished via single-electron transfer (SET) from a reductant. Previous reports employ either symmetrical peroxides or peroxides with predictable cleavage behavior, such as peresters. We were interested in how the structure of the peroxide and the nature of the reducing system combine to impact the rate of reaction and the selectivity for alkoxy radical formation during cleavage of unsymmetric peroxides. In this dissertation, one will find the reactions of a …

Aptamer Selection And Development Of Electrochemical Aptamer-Based Sensors For Neuropeptide Y, Evelyn Adela Carreto Guevara

Department of Chemistry: Dissertations, Theses, and Student Research

In this thesis, we report the results of four aptamers obtained from an aptamer selection process called the systematic evolution of ligands by exponential enrichment (SELEX) with affinity to Neuropeptide Y (NPY). NPY is a highly abundant peptide transmitter with widespread distribution throughout the body which affects various physiological functions. These functions include energy homeostasis, appetite regulation, stress response, and anxiety regulation. Dynamic monitoring of NPY levels is crucial for better understanding behaviors in individuals with neurological disorders associated with NPY. Aptamers are synthetic oligonucleotides obtained through SELEX which have a binding affinity to a target of interest when in …

Enhancing Gaas Solar Cell Efficiency Through Nanostructured Features: A Comprehensive Review Of Recent Advances, Challenges And Future Outlook, Mohammad Nur-E-Alam, Boon Kar Yap, Tiong Sieh Kiong, Mohammad Khairul Basher, Tarek Abedin, Mohammad Aminul Islam, Mohd Adib Ibrahim, Mayeen Uddin Khandaker, Narottam Das

Research outputs 2022 to 2026

This article aims to provide a synopsis of recent advances in the use of nanostructured features to augment the conversion efficiency of gallium arsenide (GaAs) solar cells. GaAs are a very well-known and highly advantageous material for solar cells because they possess an extraordinary bandgap (i.e., approximately 1.4 eV), wide spectral absorption coefficient, and favorable carrier mobility. Numerous studies have explored the use of nanostructures, such as antireflection (AR) nanofilms/nanocoatings, nanoparticles (NPs), and nanogratings (NG), to improve the conversion efficiency of GaAs-based solar cells. These structures are generally designed to enhance light transmission capacity and absorption while reducing light reflection …

Mechanistic And Evolutionary Insights Into A Group Of Nicotine And Hydroxynicotine Degrading Flavoenzymes, Zhiyao Zhang

Dissertations

Flavoprotein amine oxidases (FAOs) are key enzymes in various kinds of metabolic pathways, mediating redox reactions via flavin cofactors. While most FAOs function as oxidases that readily reduce oxygen to hydrogen peroxide, a few outliers of the FAO family act as dehydrogenases that suppress the reaction with oxygen. The molecular basis for this divergence in function remains poorly understood.

The work presented in this study investigates the fundamental mechanisms of how flavincontaining enzymes activate or suppress their reaction with different electron acceptors to achieve high turnover rates. The overall body of work is divided into three different sections that (1) …

Comparative Nitrene-Transfer Chemistry To Olefins Mediated By First-Row Transition Metal Catalysts Supported By A Pyridinophane Macrocycle With N4 Ligation, Himanshu Bhatia, Lillian P. Adams, Ingrid Cordsiemon, Suraj Kumar Sahoo, Amitava Choudhury, Thomas R. Cundari, Pericles Stavropoulos

Chemistry Faculty Research & Creative Works

A 12-membered pyridinophane scaffold containing two pyridine and two tertiary amine residues is examined as a prototype ligand (^tBuN4) for supporting nitrene transfer to olefins. The known [(^tBuN4)M^II(MeCN)2]²⁺ (M = Mn, Fe, Co, and Ni) and [(^tBuN4)Cu^I(MeCN)]⁺ cations are synthesized with the hexafluorophosphate counteranion. The aziridination of para-substituted styrenes with PhI=NTs (Ts = tosyl) in various solvents proved to be high yielding for the Cu(I) and Cu(II) reagents, in contrast to the modest efficacy of all other metals. For α-substituted styrenes, aziridination is accompanied by products of aziridine …

Visceral, Neural, And Immunotoxicity Of Per- And Polyfluoroalkyl Substances: A Mini Review, Pietro Martano, Samira Mahdi, Tong Zhou, Yasmin Barazandegan, Rebecca Iha, Hannah Do, Joel Burken, Paul Ki-Souk Nam, Qingbo Yang, Ruipu Mu

Chemistry Faculty Research & Creative Works

Per- and polyfluoroalkyl substances (PFASs) have gained significant attention due to their widespread distribution in the environment and potential adverse health effects. While ingestion, especially through contaminated drinking water, is considered the primary route of human exposure, recent research suggests that other pathways, such as inhalation and dermal absorption, also play a significant role. This review provides a concise overview of the toxicological impacts of both legacy and emerging PFASs, such as GenX and perfluoro butane sulfonic acid (PFBS), with a particular focus on their effects on the liver, kidneys, and immune and nervous systems, based on findings from recent …

Computational Investigation Of Energetic Materials: Influence Of Electronic And Steric Properties On Sensitivity And Decomposition Mechanisms, Elizabeth Ruth Zengel

Chemistry & Biochemistry Theses & Dissertations

Developing novel high energy density materials (HEDMs) requires knowledge of the causes and mechanisms of detonation. These chemical events are almost instantaneous and involve the release of a large amount of energy, which limits the experimental studies that can be performed on them. Computational methods including density functional theory (DFT) and molecular dynamics (MD) simulations have been used to investigate trigger bonds, those which break to initiate detonation. These bonds are commonly found within explosophores, substituents that increase the explosive potential of a molecule.

The Wiberg bond index (WBI) is an estimation of orbital overlap and bond strength between two …

Mixture Effects On Metal Accumulation In The Asian Clam, Corbicula Fluminea, Mark A. Huff

Electronic Theses and Dissertations

Field collected Corbicula fluminea were exposed to trace level copper, lead, and zinc with the aim of examining the preferential accumulation between the soft tissue and shell. Metal levels were based on those in a permitted industrial effluent. At 1X effluent and 2X effluent exposure levels, copper was found to preferentially accumulate in the clam soft tissue, lead was found to preferentially accumulate in the clam shell, and zinc was found to excrete back into the diluent after preferentially accumulating in the clam soft tissue. When exposed as a mixture at 1X effluent levels, copper and lead were found to …