Physical Sciences and Mathematics Commons^™

A Conceptual Understanding Of Concepts In Organic Chemistry, Timerra Chisham

Theses/Capstones/Creative Projects

As students continue to make the transfer into organic chemistry from general chemistry, they will have to adjust to the new type of thinking required so that they will not fall behind in understanding material and will have success in the course. For this research project, I explored which concepts taught in organic chemistry are the most difficult for students to grasp. I had two main goals for this project. The first one is the central idea that I focused on, which was to see which concepts that have been taught in Organic Chemistry 1 the students are most confident …

The Effects Of Prior Calculus Classes On Success In Organic Chemistry, Tori Williamson

Theses/Capstones/Creative Projects

Within University of Nebraska – Omaha (UNO) chemistry-based degree programs, organic chemistry along with at least two semesters of calculus are required courses. There is, however, no requirement for the order in which these courses should be taken. This is mainly due to the notion that for chemistry courses, organic chemistry is detached from the typical quantitative concepts studied in other chemistry-based courses. This is untrue, however, as many organic chemistry concepts rely on three-dimensional spatial visualizations and manipulations. Spatial awareness skills are strengthened within higher-level calculus classes. A survey was administered to organic chemistry students enrolled in 2022-2023. The …

The Impact Of Glacial Proximity On The Elemental Composition Of Leachate Derived From Sediment Weathering, Karoline Ford

Theses/Capstones/Creative Projects

This study assesses chemical weathering trends as they relate to glacial retreat. The chemical environment of surfaces exposed to the atmosphere differs significantly from beneath a glacier. As a glacier melts, changes to the biogeochemical processes generate environmental gradients. This study analyzed chemical weathering signals at different distances from a glacial front by comparing the elemental composition of leachate derived from sediments in southeastern Greenland. Samples from proglacial, nonglacial, and moraine locations were weathered in a laboratory setting, and ion chromatography was used to determine the elemental composition of the products. Divergent trends in leachate composition were observed as distance …

The Impact Of Service-Learning On General Chemistry Ii Students At The University Of Nebraska At Omaha, Kayla Rud

Theses/Capstones/Creative Projects

Service-learning has been shown to enhance academic and leadership skills while promoting community engagement and exposing students to different career opportunities (Esson et al., 2005). While the benefits of service-learning courses are clear, few STEM courses include service-learning components (Esson et al., 2005). Here, students in a totally online 2nd semester UNO chemistry course completed a service-learning project where they remotely led a live, inquiry-based STEM activity for Girl Scouts. To quantify the impact of service-learning on professional development, future career plans, and future volunteerism, a series of pre and post surveys were administered. Paired-sample t-tests revealed a statistically significant …

Determination Of Atrazine In Glacier Creek Using Gas Chromatography-Mass Spectrometry, Spencer Witte

UNO Student Research and Creative Activity Fair

Atrazine is a commonly used herbicide in agriculture that has been shown to cause adverse health-effects on biological organisms. Glacier Creek Preserve (GCP), a prairie preserve near Omaha, NE, contains restored prairie and agricultural land uses within a single watershed. Surface water samples were collected at various locations of GCP from May to July to quantify atrazine concentrations. Sample preparation included filtering with a 0.45 micron filter and solid-phase extraction (SPE) with a reversed-phase cartridge. The analyte was eluted off the cartridge with ethyl acetate and analyzed by gas chromatography-mass spectrometry (GC/MS). Quantitation was performed with an internal standard calibration …

High-Frequency Data Reveal Differential Dissolved And Suspended Solids Behavior From A Mixed Restored Prairie And Agricultural Catchment, Andrew Miller, Ashlee L. Dere, Tracy Coleman

Chemistry Faculty Publications

Quantifying temporal variability and fluxes within hydrologic catchments is critical to understanding the underlying chemical and physical processes leading to material transport. Measuring variability and fluxes requires sampling at time scales similar to the time scale of process occurrence. This demand has led to the development of automated sampling systems designed to sample at high frequencies, on the order of minutes. While widely deployed in a variety of systems, we installed two high-frequency sampling devices in a single drainage comprised of restored prairie and agricultural land uses in temperate Eastern Nebraska. The sampling systems determined flow rate, conductivity, and turbidity …

Characterization Of Dimerization Domains On The Mannose-6-Phosphate/Insulin-Like Growth Factor 2 Receptor, Tyler Degener

UNO Student Research and Creative Activity Fair

The mannose-6-phosphate/insulin-like growth factor 2 (M6P/IGF2) receptor is a transmembrane protein with the ability to sequester growth factors from the extracellular matrix. This behavior links the receptor to tumor suppression. On a structural level, the extracellular portion of the protein is segmented into 15 homologous repeats, which can be divided further into 5 triplet domains, labelled 1-3, 4-6, 7-9, 10-12, and 13-15. Each triplet receptor displays its own unique ligand binding affinity, including the ability to form dimers with triplets on a second M6P/IGF2 receptor. In fact, previous studies indicate that this protein functions optimally when dimerized. Thus, the purpose …

Design, Construction, And Characterization Of A Low-Cost Spectrometer With Interchangeable Parts, Jack Godek

UNO Student Research and Creative Activity Fair

A low-cost spectrometer was designed for the purpose of teaching spectroscopy. The spectrometer can be built by the student and contains interchangeable pieces such as slit width, grating, and lenses. This will allow the student to understand how changing these variables effects resolution. The spectrometer was constructed from PVC pipe, a plastic electrical box, and a USB webcam. The actual resolution of the spectrometer is close to the theoretical value, depending on which lens and grating is used. In addition, an extra piece can be added that allows absorption spectra to be collected. Having the student piece together the spectrometer …

Aromatic Hydrazide Compounds That Inhibit The Growth Of Mycobacterium Tuberculosis, Ronald Bartzatt, Preeti Sule, Thushara Galbadage, Jeffrey D. Cirillo

Chemistry Faculty Publications

Aims: To demonstrate the efficacy of aromatic hydrazide compounds to inhibit growth of Mycobacterium tuberculosis.

Study Design: To synthesize tuberculostats and test their antibacterial activity in-vitro.

Place and Duration of Study: University of Nebraska, Durham Science Center, 6001 Dodge Street, Omaha NE 68182, and Texas A&M Health Science Center, Department of Microbial Pathogenesis and Immunology, 8447 State Hwy 47, Medical Research and Education Building, Room #3012, Bryan, TX 7780. From March 2019 to October 2019.

Methodology: Hydrazide functional groups were formed by covalently bonding hydrazine onto a carbonyl carbon that is a substituent of a single aromatic …

Characterization Of The Dimerization Domains On The Mannose-6-Phosphate/Insulin-Like Growth Factor Ii Receptor, Tyler Degener

Theses/Capstones/Creative Projects

The mannose-6-phosphate/insulin-like growth factor II (M6P/IGF2) receptor is a transmembrane protein known to sequester growth factors from the extracellular matrix. This behavior suggests a mechanism of tumor suppression. Structurally, the receptor’s extracellular region is segmented into 15 homologous repeats, which are divided further into 5 triplet domains, labelled 1-3, 4-6, 7-9, 10-12, and 13-15. What is notable about the triplets is their propensity to form dimers with triplets on a second M6P/IGF2 receptor. In fact, previous studies indicate that this protein functions optimally when dimerized. Thus, the purpose of this experiment is to characterize these domain interactions. Using a urea …

Molecular Modeling Studies On The Binding Mode Of The Pd-1/Pd-L1 Complex Inhibitors, Suliman Almahmoud, Haizhen A. Zhong

Chemistry Faculty Publications

The programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) is an immune checkpoint (ICP) overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. To determine important residues for ligand binding, we applied molecular docking studies to PD-1/PD-L1 complex inhibitors against the PD-L1 protein. Our data revealed that the residues Tyr56, Asp122, and Lys124 play critical roles in ligand binding to the PD-L1 protein and they could be used to design ligands that are active against the PD-1/PD-L1 complex. The formation of H-bonds with Arg125 of the PD-L1 protein …

Assay Of Vitamin B6 (Pyridoxine Hydrochloride) Utilizing Isocratic Reversed Phase High Performance Liquid Chromatography, Ronald Bartzatt, Purnima Gajmer, Mai Han Cassandra Nguyen, Alexndra My-Hanh Tran

Chemistry Faculty Publications

Aims: To demonstrate an analysis for vitamin B6 from commercial aqueous nutritional drinks and solid tablets, utilizing isocratic conditions with high performance liquid chromatography (HPLC) and UV detection at 290 nm. Study Design: Vitamin B6 in the form of pyridoxine hydrochloride is assayed by HPLC from various samples. Place and Duration of Study: Department of Chemistry, Durham Science Center, University of Nebraska, Omaha Nebraska from May to August 2016. Methodology: Utilizing a reversed-phase C-18 column with eluent solvent (19% ethanol, 77% water, 4% acetic acid), the samples were prepared in sample solvent (19% ethanol, 81% distilled water). Detection of vitamin …

Conformational Studies Of Glucose Transporter 1 (Glut1) As An Anticancer Drug Target, Suliman Almahmoud, Xiaofang Wang, Jonathan L. Vennerstrom, Haizhen A. Zhong

Chemistry Faculty Publications

Glucose transporter 1 (GLUT1) is a facilitative glucose transporter overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. GLUT1 works through conformational switching from an outward-open (OOP) to an inward-open (IOP) conformation passing through an occluded conformation. It is critical to determine which conformation is preferred by bound ligands because the success of structure-based drug design depends on the appropriate starting conformation of the target protein. To find out the most favorable GLUT 1 conformation for ligand binding, we ran systemic molecular docking studies for different conformations of GLUT1 using known …

Examining Electrochemical Properties Of O-Quinone And Sulfur Adducts Using Bisphenol A-3,4-Quinone Platform, Barbara Mullen

Theses/Capstones/Creative Projects

o-Quinones are toxic electrophiles that can disrupt cellular macromolecules. Whether endogenous or xenobiotic, o-quinones are reactive compounds that are difficult to isolate. This work uses the o-quinone of bisphenol(BPA), bisphenol A-3,4-quinone(BPAQ), which can be efficiently synthesized and isolated, to study the electrochemical properties of o-quinones and their sulfur adducts in order to understand their metabolic fate. Cyclic voltammetry and equilibrium analysis were used to determine the relative oxidation potential of the BPA catechol and adducts, formed by reacting glutathione(GSH) and N-acetylcysteine(NAC) with BPAQ. BPAQ-sulfur adducts with 5-position substitution displayed lower oxidation potentials when compared to the …

Lake Sediment Analysis At Heron Haven Nature Center, Erik Lato

UNO Student Research and Creative Activity Fair

Understanding the chemical composition of a wetland sanctuary lakebed can help us understand how recent developments may have changed the chemical composition. Due to recent dredging by the U.S. Army Corps of Engineers and previous research on water composition at Heron Haven, the goal of this project was to determine the chemical composition as a function of sediment depth. The concentration of seven different metals and nutrients were analyzed in terms of depth. The aluminum, iron, and phosphate concentrations had no real discernible concentration change as a function of depth. There is some hint of a steady increase of manganese …

Investigating Daily Variation In Lotic Prairie Ecosystems, Dominick Caniglia

UNO Student Research and Creative Activity Fair

The goal of this project is to investigate the hydrochemistry of the prairie stream system at Glacier Creek Preserve, namely to determine the chemical behavior as it varies over time. Past sampling revealed annual/seasonal trends, which prompted this study investigating possible changes over the course of a day. To accomplish this, water samples were taken hourly for a twelve hour period in September and November 2018, and were analyzed at the Durham Science Center. All samples were obtained at the furthest downstream site available. The main focus was to study alkalinity and dissolved mineral content. Preliminary data suggests that alkalinity …

Synthesis Of A Sulfur Variant For Treatment Of Trypanosomiasis, Carlos Vera-Esquivel

UNO Student Research and Creative Activity Fair

Previous work in our lab has found diphenyl ether benzylamines showed a successful response with a micromolar concentration of our lead compound to treat the deadly Trypanosamiosis rhodesience. Furthermore, mammalian cell lines saw promising resistance towards damages. The goal of this study was to synthesize a diphenyl thio benzylamine variant. This variant was more active toward T. b. rhodesience but showed more toxicity to both rat 10 (IC₅₀ mM) and human cell lines (HFF, HC-₀₄, U-₂ OS, and HEK₂₉₃). The selectivity index (ratio of toxicity to activity in the same concentration units (SI)) …

Detection And Assay Of Isoniazid Utilizing Isocratic High-Performance Liquid Chromatography, Cassandra Nguyen

Theses/Capstones/Creative Projects

To demonstrate an analysis for isoniazid from aqueous mixtures and solid tablets, utilizing isocratic conditions, with high performance liquid chromatography (HPLC) and UV detection. Isoniazid in solid and liquid samples is assayed utilizing HPLC. Isoniazid is a tuberculostat, that is assayed by high performance liquid chromatography that utilizes a reversed-phase C-18 column. The eluent solvent is 5.3% ethanol, 93.7% water, and 1% acetic acid. Aqueous samples are prepared in distilled water as the solvent. The ultraviolet-visible detection of isoniazid is accomplished at 265 nm, which is the wavelength having the highest sensitivity for isoniazid. Having a column pump pressure at …

Supercell Crystal Structure Of Na2ga2(Bo3)2, Grace Brown

UNO Student Research and Creative Activity Fair

Na₂Ga₂(BO₃)₂O is an oxyborate with a reported crystal structure in the trigonal space group P1c. The literature states that the three-dimensional structure is created from infinite stacking of parallel [NaGa₂(BO₃)₂] ∞ sheets separated by sodium layers. Our single-crystal X-ray diffraction data requires some modification to this structure. We believe that Na₂Ga₂(BO₃)₂O actually possesses a supercell crystal structure with lower symmetry. The borate anions within the [NaGa₂(BO₃)₂ ] sheets are not parallel to each …

Structural Identification And Kinetic Analysis Of The In Vitro Products Formed By Reaction Of Bisphenol A‑3,4-Quinone With N‑Acetylcysteine And Glutathione, Douglas E. Stack, John A. Conrad, Bejan Mahmud

Chemistry Faculty Publications

Bisphenol A (BPA) has received considerable attention as an endocrine disrupting chemical and a possible substrate for genotoxic metabolites. BPA metabolism leads to formation of electrophilic o-quinones cable of binding to DNA and other endogenous nucleophiles. We have structurally identified the products resulting from the reaction of bisphenol A-3,4-quinone (BPAQ) with N-acetylcysteine (NAC) and glutathione (GSH). The major and minor isomers are both the result of 1,6-conjugate addition and are produced almost instantly in high yield. Reactions using 1.3 equiv of GSH showed the presence of a bis-glutathionyl adduct which was not observed using higher GSH concentration relative to BPAQ. …

Prediction Of Novel Anti-Ebola Virus Compounds Utilizing Artificial Neural Network (Ann), Ronald Bartzatt

Chemistry Faculty Publications

Artificial Neural Network (ANN) analysis is shown to predict the molecular properties of new anti-EBOLA compounds following training/learning by use of 60 previously known and studied drugs. Following training/learning by applying properties of 60 known drugs the TIBERIUS ANN system can efficiently predict the molecular properties of comparable new drugs. Molecular weight (MW) is an important and dominant property of perspective drugs considered for clinical trials. TIBERIUS ANN was able to predict comparable values of MW for drugs following training cycles. One-way ANOVA, F and T tests indicate that actual and predicted MW have the same means (P=.99). Passing-Bablok regression …

Neurological Impact Of Zinc Excess And Deficiency In Vivo, Ronald Bartzatt

Chemistry Faculty Publications

Zinc is an essential mineral that can cause pathological effects whether in excess or deficiency. Zinc is a component for over 250 enzymes and is required for cell growth, cell division, and cell function. Zinc is found in muscle and bones, with the prostrate, liver, skin, and kidney having detectable levels of zinc. However, zinc present in excess or deficiency can cause significant pathology in patients that include deleterious effects neurologically. Zinc in excess in vivo can cause focal neuronal pathology, while zinc deficiency can bring about mental lethargy, neuropsychiatric disorders, and reduced nerve conduction. Zinc is assimilated within the …

Pyrimethamine Based Anti-Protozoan Agents From Isostere And Heuristic Structure-Similarity Search, Ronald Bartzatt

Chemistry Faculty Publications

Aims: To generate new medicaments for control and treatment of the parasitic protozoan Toxoplasma gondii.

Study Design: Structure similarity search and isostere search was conducted over a broad range of structure categories. Correlation and highest similarity scores were implemented to select the best drug candidates.

Place and Duration of Study: University of Nebraska, Department of Chemistry, Durham Science Center, 6001 Dodge Street, Omaha Nebraska 68182, from June 2016 to February 2017.

Methodology: Utilizing pyrimethamine as the parent compound, a broad range of similar structures and isosteres were found by applying search methods. The compounds having the highest correlation and …

Design, Synthesis And Biological Evaluation Of Novel Hedgehog Inhibitors For Treating Pancreatic Cancer, Vinod Kumar, Amit Kumar Chaudhary, Yuxiang Dong, Haizhen Zhong, Goutam Mondal, Feng Lin, Virender Kumar, Ram I. Mahato

Chemistry Faculty Publications

Hedgehog (Hh) pathway is involved in epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC) maintenance resulting in tumor progression. GDC-0449, an inhibitor of Hh pathway component smoothened (Smo) has shown promise in the treatment of various cancers including pancreatic cancer. However, the emergence of resistance during GDC-0449 treatment with numerous side effects limits its use. Therefore, here we report the design, synthesis and evaluation of novel GDC-0449 analogs using N-[3-(2-pyridinyl) phenyl] benzamide scaffold. Cell-based screening followed by molecular simulation revealed 2-chloro-N1-[4-chloro-3-(2-pyridinyl)phenyl]-N4,N4-bis(2-pyridinylmethyl)-1,4- benzenedicarboxamide (MDB5) as most potent analog, binding with an extra interactions in seventransmembrane (7-TM) domain of Smo due to …

Comparative Analysis Of Antihistamines And Nonsteroidal Anti-Inflammatory Drugs (Nsaids): Properties, Structure And Prediction Of New Potential Drugs, Ronald Bartzatt

Chemistry Faculty Publications

Aims: To determine the molecular properties of common antihistamines and non-steroidal antiinflammatory agents (NSAIDs). To identify interrelationships among these two groups of drugs utilizing pattern recognition methods and statistical analysis.

Study Design: After determination of molecular properties, values thereof are examined using pattern recognition methods and other numerical analysis for underlying relationships and similarities.

Place and Duration of Study: Durham Science Center, University of Nebraska, Omaha, Nebraska from September 2016 to January 2017.

Methodology: Thirty compounds were identified as antihistamines and 27 compounds identified as NSAIDs. Properties such as Log P, molecular weight, polar surface area, etc. are determined. Molecular …

Synthesis Of Small Molecule Anti-Trypanosomal Drugs, Samuel Anderson

UNO Student Research and Creative Activity Fair

Demand for novel chemotherapeutic agents that treat Human African Trypanosomaiasis (HAT) persists. A series of compounds sharing a 3,4’diphephyl ether skeleton were prepared for a structure activity relationship (SAR) study evaluating antitrypansomal drug candidates. Trypanocidal assays performed in vitro by the Swiss Tropical and Public Health Institute identified a lead with an IC50 of 1.35 μg/mL analogous to a compound previously made in our laboratory. A slight improvement in activity (10%) was observed when changing the molecular substitution pattern from 4,4’ to 3,3’; however, the result is equivocal. Furthermore, in vitro test results demonstrated the weakness of amides as side …

Could O-Aminoquinones Of Estrogen Metabolites Serve As Platforms For Redox Cycling?, Rachel Miller

UNO Student Research and Creative Activity Fair

The metabolism of estrogen can lead to the formation of two isomeric o-quinones, estrogen-2,3-quinone (E-2,3-Q) and estrogen-3,4-Q (E-3,4-Q). The more reactive E-3,4-Q is genotoxic and can damage DNA by forming apurinic sites; whereas, E-2,3-Q does not form apurinic sites. Estrogen quinones may also be involved in redox cycling to produce reactive oxygen species (ROS), which is another genotoxic pathway. What is not yet clear, is why E-3,4-Q would undergo redox cycling while the non-carcinogenic E-2,3-Q would not. Nitrogen nucleophiles react with the E-3,4-Q at the 1-position. With DNA bases as the nitrogen (sp2) nucleophile, the adducts formed are catechols. We …

Characterization Of The Mannose-6-Phosphate/Insulin-Like Growth Factor Ii Receptor Using 1-3mh, Zechariah Craig

UNO Student Research and Creative Activity Fair

The mannose-6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R), a recombinant triplet protein receptor for studies involving receptor dimerization, plays a pivotal role in mediating cellular growth. This receptor is comprised of fifteen similar units that fold into five triplet subunits. The goal of this experiment is to investigate how to make the 1-3MH protein more stable at the DNA level and generate a larger yield from DNA extractions for more effective transfections. This was accomplished by minorly changing the protocols for the DNA purification. Instead of using a standard column DNA purification kit, a crude DNA purification was done instead. This …

Docking Studies Of Isoform-Selectivity Of Phosphatidylinositol 3-Kinase (Pi3k) Inhibitors, Kaitlin Goettsch

UNO Student Research and Creative Activity Fair

Phosphatidylinositol 3-kinases (PI3Ks) and their related pathways are reputed targets for drug-based anticancer therapies. Mutations in PI3K genes, expression, and pathways are frequent among multiple cancer types. Four isoforms of PI3Ks exist: α, β, γ, & δ and studies have identified several ligands for each isoform which are capable of serving as inhibitory therapeutic compounds. However, the biochemical efficacy of these molecules varies and the isoform selectivity is not well understood. In this study, we applied in silico docking methods and free energy calculation methods to estimate the binding of reported PI3K ligands against 5 PI3K structures: PI3Kα (PBD ID: …

Crystal Structure Of Li3ga(Bo3)2, Robert W. Smith, Darien Holman, Eric M. Villa

Chemistry Faculty Publications

The crystal structure of trilithium gallium bis(orthoborate), Li3Ga(BO3)2, is isotypic with Li3Al(BO3)2 in a triclinic cell in space-group type P1. The three Li and the unique Ga atom are coordinated by four O atoms each in tetrahedra, and the two B atoms are coordinated by three O atoms in orthoborate triangles. Chains with composition [Ga2(BO3)4] 6 extend along the a axis. The Li atoms interleave these chains in tetrahedral interstices. A comparison is made between the structure model of the title compound and that of a previously reported model for a compound with the same composition [Abdullaev & Mamedov (1972). …