Chemistry Commons^™

Addressing Knowledge And Data Gaps That Limit Pesticide Risk Assessment For Managed Solitary Bees Used For Alfalfa Pollination, Kimberly J. Hageman

Funded Research Records

No abstract provided.

Pesticide Dissipation In Agroecosystems – Exploring Pesticide Fate And Transport Mechanisms To Protect Alternative Pollinators, Calvin Luu

All Graduate Theses and Dissertations, Fall 2023 to Present

Honey bees are the most well-known pollinators, but there exists thousands of other bee species that contribute to pollination; one such group of bees are the solitary bees. True to their namesake, solitary bees do not live in hives like honey bees. Some solitary bees, like alfalfa leafcutting bees (ALCB) and blue orchard bees, can pollinate crops more efficiently than honey bees. However, since they live solitary lives, pesticide exposure is much more harmful to their overall population. If one honey bee dies from pesticide exposure, the hive can still survive, and the queen bee will continue producing offspring. If …

Method Validation Of The Cdc Bottle Bioassay And A Historical Record Of Polycyclic Aromatic Hydrocarbons In Glacier National Park, Evah F. Peard

All Graduate Theses and Dissertations, Fall 2023 to Present

Certain contaminants can persist in the environment for long periods of time, build up within living tissues, travel far from their origin, and harm both ecosystems and organisms. This thesis focuses on two types of contaminants: insecticides and polycyclic aromatic hydrocarbons (PAHs). Insecticides are manufactured to control pests while PAHs are found in oil and gas products and can be produced by industry, vehicle engines, and wildfires. Understanding how harmful these contaminants are and where they end up in the environment is critical for protecting environmental health.

First, I evaluated a widely used test developed by the Centers for Disease …

Utilizing Pine Needles To Compare Spatial Profiles Of Polycyclic Aromatic Hydrocarbons (Pahs) In Two Urban Areas, Autumn Jensen

Undergraduate Honors Capstone Projects

Polycyclic aromatic hydrocarbons (PAHs) are an important class of semivolatile air pollutants known for their adverse health impacts. This research used conifer needles as passive air samplers to create spatial maps of two Utah cities (Rose Park and Spanish Fork) to compare overall PAH exposure and identify any differences in their congener profiles or PAH “fingerprints”. Conifer needles were chosen due to their prevalence as a passive air sampler in previous research and their ubiquity in urban and suburban environments. Second year needles were collected and the concentrations are considered to be an annually averaged view of the PAH concentrations …

Climate Change-Related Effects On Carbon Emissions And Net Ammonification Across Lowland To Upland Soils From A High-Latitude Coastal Ecosystem, Jenna M. Ross, Karen H. Beard, Katharine C. Kelsey, Matteo Petit Bon, A. Joshua Leffler

Wildland Resources Faculty Publications

Warming, sea-level rise, and changing herbivory patterns are affecting ecosystem processes in northern coastal soils, including carbon and nitrogen cycling, although their combined effects are poorly understood. We studied the impact of these changes in a full-factorial microcosm experiment using four distinct soil types from the Yukon-Kuskokwim Delta of western Alaska. Soil was collected from three coastal wetlands, which differ in flooding frequency and use by migratory geese, and one rarely-flooded upland tundra used by geese in late summer. Microcosms containing these soils were incubated for 16 weeks at 10°C or 18°C, with or without three short-term floods, and with …

Plants Have A Chemical Defense To Protect Themselves From Herbivory, Isis Cordova

Research on Capitol Hill

All plants produce compounds for survival. My work focuses on how plants remember past attacks and whether that memory leads to stronger/faster responses.

Early Detection Of Harmful Algal Blooms (Habs) Using Qpcr And Predictive Modeling, Emily Samuels

Research on Capitol Hill

Harmful algal blooms (HABs) threaten drinking water, recreation, and public health in Utah Lake and waterbodies due to cyanotoxin production. Current monitoring methods detect toxins only after blooms are already established.

Interface Catalysts Of In Situ-Grown Tio2/Mxenes For High-Faraday-Efficiency Co2 Reduction, Shaun Debow, Zichen Shen, Arjun Sathyan Kulathuvayal, Fuzhan Song, Tong Zhang, Haley Fisher, Jesse B. Brown, Yuqin Qian, Zhi-Chao Huang-Fu, Hui Wang, Zachary Zander, Mark S. Mirotznik, Robert L. Opila, Yanqing Su, Yi Rao

Chemistry and Biochemistry Student Research

Climate change and the global energy crisis have led to an increasing need for greenhouse gas remediation and clean energy sources. The electrochemical CO₂ reduction reaction (CO₂RR) is a promising solution for both issues as it harvests waste CO₂ and chemically reduces it to more useful forms. However, the high overpotential required for the reaction makes it electrochemically unfavorable. Here, we fabricate a novel electrode composed of TiO₂ nanoparticles grown in situ on MXene charge acceptor 2D sheets with excellent CO₂RR characteristics. A straightforward solvothermal method was used to grow the nanoparticles on …

Structural Evolution Of Nitrogenase Over 3 Billion Years, Bruno Cuevas Zuviría, Franka Detemple, Kaustubh Amritkar, Amanda K. Garcia, Lance Seefeldt, Betül Kaçar

Chemistry and Biochemistry Faculty Publications

Previously, we identified the only dinitrogen reduction mechanism known to date as an ancient feature conserved from nitrogenase ancestors, which we directly tested by resurrecting and integrating synthetic ancestral nitrogenases into the genome of Azotobacter vinelandii (Garcia et al., 2023), a genetically tractable, nitrogen-fixing model bacterium. Here, we extend this paleomolecular approach to investigate the structural evolution of nitrogenase over billions of years of evolution by combining phylogenetics, ancestral sequence reconstruction, protein crystallography, and deep-learning based predictions. This study reveals that nitrogenase, while maintaining a conserved multimeric core, evolved novel modular features aligned with major environmental transitions, suggesting that subtle …

The Next Frontier In The Study Of Noncovalent Bonding: Transition Metals, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

As work continues unabated in the study of noncovalent bonding, particularly σ-hole bonds, new challenges have emerged as the participation of transition metals in interactions of this sort is fast becoming appreciated. While there are certain similarities with the halogen, chalcogen, etc, bonds, in which the main group elements participate, there are certain unique properties of these metal atoms that must be analyzed before a complete understanding can be attained. As one example, these atoms tend to act simultaneously as both electron donors and acceptors, a synergistic action that amplifies the overall bond strength. Ideas are expressed in this paper …

Enhancing Stability And Emissions In Metal Halide Perovskite Nanocrystals Through Mn2+ Doping, Thi Thu Trinh Phan, Thi Thuy Kieu Nguyen, Trung Kien Mac, Minh Tuan Trinh

Chemistry and Biochemistry Student Research

Metal halide perovskite (MHP) nanocrystals (NCs) offer great potential for high-efficiency optoelectronic devices; however, they suffer from structural softness and chemical instability. Doping MHP NCs can overcome this issue. In this work, we synthesize Mn-doped methylammonium lead bromide (MAPbBr₃) NCs using the ligand-assisted reprecipitation method and investigate their structural and optical stability. X-ray diffraction confirms Mn²⁺ substitution at Pb²⁺ sites and lattice contraction. Photoluminescence (PL) measurements show a blue shift, significant PL quantum yield enhancement, reaching 72% at 17% Mn²⁺ doping, and a 34% increase compared to undoped samples, attributed to effective defect passivation and …

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 …

To Bee Or Not To Bee: Investigating Pesticide Behavior Inside And Outside Of Semi-Field Cages, Mallory Bingham

Undergraduate Honors Capstone Projects

Bees play an important role in ecosystems and food production through pollination. One such bee, the alfalfa leaf cutting bee (ALCB) is a very efficient pollinator and is essential in alfalfa seed production. However, bees face increasing harm, most notably due to the deleterious effect of pesticides used in agriculture, and much research is dedicated to investigating the extent of effects that pesticides have on different bee populations. One common tool used to study the effects of pesticide exposure on bees is semi-field cages. These cages have some key advantages, such as restricting bee foraging to plots sprayed with pesticides …

Determining The Structure And Function Of Type Iv-A Anti-Crisprs, Olivine Redman

All Graduate Theses and Dissertations, Fall 2023 to Present

Bacteria face a constant existential threat in the form of infection by viruses along with other forms of mobile genetic elements, such as bacteriophage and transposable elements. To survive, bacteria and other prokaryotes have evolved various immune systems to evade these would-be invaders. One such immune system is the CRISPR-Cas system, an adaptive immune system able to record the genetic signature of invading viruses in order to recognize and destroy them should they be encountered again in the future. In this thesis I present data that sheds light on the mechanism of one particular subtype of CRISPR-Cas systems: the type …

To Bee Or Not To Bee: Investigating Pesticide Behavior Inside And Outside Semi-Field Cages, Mallory Bingham

Student Research Symposium

Background

Pesticides are vital in preventing crop damage from pests but are cited as a key factor in decreasing bee populations.¹ The alfalfa leaf cutting bee is essential in alfalfa seed production in the Western US.² Current research seeks to examine the effects of pesticides on these solitary bees to maintain healthy populations while controlling pests.³

One research tool commonly used to examine pesticide effects on bees is field-cages. Field cages are thought to simulate agroecosystem conditions while restricting bees to plots that have been sprayed with pesticides.^1,4

However, environmental conditions can be different inside and …

Expressing And Purifying Homologs Of Crispr Systems, Gabe Parrish

Student Research Symposium

CRISPR (Clustered Regularly Interspaced Palindromic Repeat)-Cas (CRISPR- associated) is a protein-nucleic acid adaptive immune system in Bacterial and Archaeal organisms that defends against invading foreign genetic material.

Solving The Structure Of An Ancestral Protein Tyrosine Phosphatase, Natalie Turcsanski, Edna Armah

Student Research Symposium

Protein tyrosine phosphatases (PTPs) regulate cell signaling by removing phosphate groups from tyrosine residues. Malfunction of these enzymes can lead to diseases such as diabetes and cancer. A conserved feature among PTPs is the catalytic acid loop, essential for phosphate removal. Computational analysis of PTP structures revealed that ancestral PTPs have considerable variation in conformations of this loop, sparking interest in their further study. The Asgard group, identified as ancestral to eukaryotic PTPs, was successfully expressed and purified under optimized conditions. Current efforts focus on optimizing crystallization to obtain larger crystals for structural analysis. This project will investigate the allosteric …

Determining The Function Of Type Iv-B Crispr-Cas Systems, Eric Jenkins, Brendon Guinn

Student Research Symposium

CRISPR-Cas systems are a diverse group of prokaryotic adaptive immune systems that defend against Mobile Genetic Elements (MGEs) such as bacteriophages and plasmids. CRISPR-associated (Cas) proteins bind to guide RNAs (crRNAs) transcribed from a DNA repeat array (CRISPR array) containing spacers complementary to MGEs. Upon infection by a MGE, the Cas protein-crRNA complex binds to the target sequence in the invaders genome and cleaves the nucleic acid.

An Alternative To Biliverdin, Mesobiliverdin Ixα And Mesobiliverdin-Enriched Microalgae: A Review On The Production And Applications Of Mesobiliverdin-Related Products, Naveena Poudyal, Jon Y. Takemoto, Yuan-Yu Lin, Cheng-Wei T. Chang

Chemistry and Biochemistry Student Research

Despite attracting interest for decades due to its anti-inflammatory and antioxidant capabilities, the use of biliverdin IXα (BV) in medicine and agriculture is hampered by uncertain purity and limited availability. A significant amount of effort has been devoted to the production and application of BV, but with limited success. Mesobiliverdin IXα (MBV), a natural BV analog derived from microalgae, offers a path to overcome the limitations of BV. MBV production is scalable, and it can be obtained at high purity. MBV and BV share important structural features (e.g., bridging propionate groups) and both are substrates of biliverdin reductase A (BVRA), …

Redefining The Limits Of Functional Continuity In The Early Evolution Of P-Loop Ntpases, Andrey O. Demkiv, Saacnicteh Toledo-Patiño, Encarnación Medina-Carmona, Andrej Berg, Gaspar P. Pinto, Antonietta Parracino, Jose M. Sanchez-Ruiz, Alvan C. Hengge, Paola Laurino, Liam M. Longo, Shina Caroline Lynn Kamerlin

Chemistry and Biochemistry Faculty Publications

At the heart of many nucleoside triphosphatases is a conserved phosphate-binding sequence motif. A current model of early enzyme evolution proposes that this six to eight residue motif could have sparked the emergence of the very first nucleoside triphosphatases—a striking example of evolutionary continuity from simple beginnings, if true. To test this provocative model, seven disembodied Walker A-derived peptides were extensively computationally characterized. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected. Simulations suggest that phosphate binding is nonspecific, with a preference for GTP over orthophosphate. Control …

Development Of Interface-Specific Two-Dimensional Vibrational-Electronic (I2d-Ve) Spectroscopy For Vibronic Couplings At Interfaces, Yuqin Qian, Zhi-Chao Huang-Fu, Jesse B. Brown, Yi Rao

Chemistry and Biochemistry Faculty Publications

Bulk 2D electronic–vibrational (2D-EV) and 2D vibrational–electronic spectroscopies (2D-VE) were previously developed to correlate the electronic and vibrational degrees of freedom simultaneously, which allow for the study of couplings between electronic and vibrational transitions in photo-chemical systems. Such bulk-dominated methods have been used to extensively study molecular systems, providing unique information such as coherence sensitivity, molecular configurations, enhanced resolution, and correlated states and their dynamics. However, the analogy of interfacial 2D spectroscopy has fallen behind. Our recent work presented interface-specific 2D-EV spectroscopy (i2D-EV). In this work, we develop interface-specific two-dimensional vibrational–electronic spectroscopy (i2D-VE). The fourth-order spectroscopy is based on a …

Insights From Diverse Environments: Investigating The Fate And Transport Of Semivolatile Organic Contaminants In Alpine, Arctic, And Arid Regions, Jeffrey Perala-Dewey

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation investigates the fate and transport of pollutants through four field-based studies in a diverse array of environments. These pollutants travel through the atmosphere and end up in places far from their original sources. In this work I explore how chemical properties of the pollutants and the environmental processes that are present change the way the pollutants travel through the environment. In the first study, pollutants from car engines were quantified in the vegetation along transects in three alpine valleys. Using these measurements, I investigated how the chemical properties of the pollutants impacted their interplay with wind systems in …

A Preliminary Fuzzy Inference System For Predicting Atmospheric Ozone In An Intermountain Basin, John R. Lawson, Seth N. Lyman

Mathematics and Statistics Faculty Publications

High concentrations of ozone in the Uinta Basin, Utah, can occur after sufficient snowfall and a strong atmospheric anticyclone creates a persistent cold pool that traps emissions from oil and gas operations, where sustained photolysis of the precursors builds ozone to unhealthy concentrations. The basin's winter-ozone system is well understood by domain experts and supported by archives of atmospheric observations. Rules of the system can be formulated in natural language ("sufficient snowfall and high pressure leads to high ozone"), lending itself to analysis with a fuzzy-logic inference system. This method encodes human expertise as machine intelligence in a more prescribed …

Assimilating Satellite-Derived Snow Cover And Albedo Data To Improve 3-D Weather And Photochemical Models, Colleen Jones, Huy Tran, Trang Tran, Seth Lyman

Chemistry and Biochemistry Faculty Publications

During wintertime temperature inversion episodes, ozone in the Uinta Basin sometimes exceeds the standard of 70 ppb set by the US Environmental Protection Agency. Since ozone formation depends on sunlight, and less sunlight is available during winter, wintertime ozone can only form if snow cover and albedo are high. Researchers have encountered difficulties replicating high albedo values in 3-D weather and photochemical transport model simulations for winter episodes. In this study, a process to assimilate MODIS satellite data into WRF and CAMx models was developed, streamlined, and tested to demonstrate the impacts of data assimilation on the models’ performance. Improvements …

Metal Assisted O2-Dependent Carbon-Carbon Bond Cleavage Of Β-Diketones And Flavonols, Stephen N. Anderson

All Graduate Theses and Dissertations, Fall 2023 to Present

Almost everything we interact with on a daily basis has been synthesized by chemists ranging from plastics, food preservatives, and medications. The diversity of synthetic molecules are achieved by the formation of new bonds between existing molecules and/or through the cleaving of bonds found in a molecule. There are uncountable amount of conditions reported to facilitate chemical reactions which all depend on the nature of molecules being used and the environment it is used in.

In recent years, more attention has been paid to identify chemical reactions that can use more environmentally favorable conditions and reduce the use of limited …

Functional Electrolytes Designing And Studying For Lithium Metal And Non-Aqueous Zinc Metal Batteries, Liping Zhang

All Graduate Theses and Dissertations, Fall 2023 to Present

Our current energy policy relies heavily on burning fossil fuels, raising serious concerns due to CO₂-related global warming. Consequently, significant progress is being made in pursuing renewable and green energy sources, such as solar, wind, and geothermal energy. These renewable energies require rechargeable batteries as energy storage systems to compensate for their intermittent nature.

Over the decades, lithium-ion batteries (LIBs) have become the dominant power sources for portable electronic devices. Current LIBs rely on graphite anodes with a limited theoretical capacity (372 mAh g^-1), which restricts their advanced applications. Li metal (Li⁰) anodes, with …

Comparison Of Various Theoretical Measures Of Aromaticity Within Monosubstituted Benzene, Caleb K. Swain, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The effects of monosubstitution on the aromaticity of benzene are assessed using a number of different quantitative schemes. The ability of the mobile π-electrons to respond to an external magnetic field is evaluated using several variants of the NICS scheme which calculate the shielding of points along the axis perpendicular to the molecule. Another class of measures is related to the drive toward the uniformity of C-C bond lengths and strengths. Several energetic quantities are devised to approximate an aromatic stabilization energy and the tendency of the molecule to maintain planarity. There is a lack of consistency in that the …

Search For Osme Bonds With Π Systems As Electron Donors, Xin Wang, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO₄ (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C₂H₂ , C₂H₄ , C₆H₆ , C₄H₅N, C₄H₄O, and C₄H₄S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, …

Mechanical Properties Of Natural Osmia Lignaria Silk And Recombinant Expression Of The Silk Proteins, Jackson Morley

Undergraduate Honors Capstone Projects

The use of petroleum-based plastic and the subsequent waste has led researchers to explore alternatives in the form of biopolymers. Spider silk and hagfish intermediate filaments show the potential to be advantageously utilized in textile and biomedical industries. Bee silk is a sparsely studied biopolymer that has shown potential to be added to these other impressive biopolymers. Osmia lignaria, is a solitary bee native to the western United States. Silk from these bees can be isolated while the larvae are spinning their silk. The silk from these bees has been mechanically tested for strength, stress, strain, and elasticity. Cocoon …

Computational Study About Noncovalent Bonding Systems Involving Halogen, Chalcogen And Pnicogen Bonds, Jia Lu

All Graduate Theses and Dissertations, Fall 2023 to Present

First terms used in this thesis are introduced and defined as follows. In the periodic table, the elements in the 17^th column are named halogen including fluorine (F), chlorine (Cl), bromine (Br) and iodine (I). The elements in the 16^th column are named chalcogen including oxygen (O), sulfur (S), selenium (Se) and tellurium (Te). The elements in the 15^th column are named pnicogen including nitrogen (N), phosphorus (P), arsenic (As) and antimony (Sb).

After hydrogen bonds (B-H⋅⋅⋅B) are well studied and understood by scientists and researchers, halogen bonds (R-X⋅⋅⋅B) have drawn attention due to the similarities in …