Physical Sciences and Mathematics Commons^™

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, …

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 …

Designing And Studying Redox-Active Molecules For Energy Storage And Desalination, Wenda Wu

All Graduate Theses and Dissertations, Fall 2023 to Present

Since the fast growth of the global population, energy scarcity has become a new threat to modern society. Those commonly seen resources like fossil, coal, and natural gas are nonrenewable energies, which cannot be replenished by human-scale time. In contrast, wind, solar, and hydropower are the three main renewable green energies under development with great efforts around the world. However, the intermittent character of these powers raises a new question: how to store them properly on large scales? By 2021, more than 90% of the electricity storage was taken by Lithium-ion batteries (LIBs). The usage of lithium brings concerns about …

Relation Between Halogen Bond Strength And Ir And Nmr Spectroscopic Markers, Akhtam Amonov, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C–X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded …

C···O And Si···O Tetrel Bonds: Substituent Effects And Transfer Of The Sif3 Group, Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF₃-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO₂, CN, F, CH₃, OH, OCH₃, NH₂, and Li) is examined by quantum chemical means. The Si···O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C···O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite …

Assessing The Possibility And Properties Of Types I And Ii Chalcogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Type I and II halogen bonds are well-recognized motifs that commonly occur within crystals. Quantum calculations are applied to examine whether such geometries might occur in their closely related chalcogen bond cousins. Homodimers are constructed of the R1R2C=Y and R1R2Y monomers, wherein Y represents a chalcogen atom, S, Se, or Te; R1 and R2 refer to either H or F. A Type II (T2) geometry wherein the lone pair of one Y is closely aligned with a σ-hole of its partner represents a stable arrangement for all except YH2, although not all such structures are true minima. The symmetric T1 …

The Concept Of Multicenter Bonds In Chemistry And Materials Science, Nikolay V. Tkachenko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chemical bonds are components of a universal and compact language of chemistry that was empirically developed before the modern concepts of quantum physics. This language explains how molecules and solids keep together. In particular, Lewis’s shared electron-pair bonding model may be considered the most successful and generally accepted theory of chemical bonding due to its simplicity and predictive power. However, there is an entire world of chemical species where the classical Lewis bonding language fails to describe the bonding pattern adequately. Those cases include but are not limited to compounds with a significant electron delocalization (where electron density spread on …

Investigations Of Prokaryotic Defense Systems, Hannah Domgaard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bacteria are constantly threatened with infection by mobile genetic elements (MGE) such as bacteriophage and plasmids. Bacteriophage and plasmids require the bacteria's cellular infrastructure to replicate their genomes. Rampant replication can lead to cell death which is one reason why bacteria have developed a diverse array of immune systems to prevent or limit infection. This thesis studies three types of bacterial immune systems, type IV-A CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeat –CRISPR associated), type V-A2 CRISPR-Cas systems, and Wadjet systems.

The type IV-A system lies adjacent to a dinG-like helicase gene. Research has shown that this system can target …

Development Of In Situ Second-Order Nonlinear Optical Scatterings For Molecular Behaviors At Aerosol Surfaces, Yuqin Qian

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Aerosol particles are one of the most important components of the atmosphere. During the growth of aerosol particles, they directly or indirectly affect air quality, human health, and environmental chemistry. Therefore, understanding the chemical and physical properties of such particles is an important scientific, engineering, and medical issue. The growth of aerosol particles in the atmosphere is closely related to the chemical structure at its surface, as well as the heterogeneous reactions which take place at and below the particle’s surface. However, there is a lack of suitable surface-specific analytical techniques which directly measure the chemical structure of aerosol particle …

Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Similarly to people, bacteria are under the treat of infection by viruses. To circumvent these threats, bacteria evolve complex immune systems. Our understanding of some of these immune systems has led to many advancements in the field of Biotechnology including tools that made expressing proteins for study in a lab easier, tools that revolutionized the feasibility of gene editing, and tools that could change the way we think about viral diagnostics and cancer therapeutics. A certain type of immune system that bacteria use to fight virus is called a CRISPR system. Presented here is work to understand the function of …

Structural And Functional Studies Of Mtr4 And The Tramp Rna Surveillance Complex, Sean Johnson

Funded Research Records

No abstract provided.

Collaborative Research: Developing Advanced Magnesium Electrolytes Toward Low Cost, High Energy Density Mg Batteries, Tianbiao Liu

Funded Research Records

No abstract provided.

Pesticide-Leaf Interactions And Their Implications For Pesticide Fate Modeling, Ashlie Kinross

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work described here provides measured data to improve the understanding of the interaction between a pesticide and leaf surface after application. Two methods were developed, one using a newly introduced instrument, for the extraction of pesticides from leaves. This is required to measure the concentration of pesticide in the leaves. Using one of the developed extraction methods, measurements were made to determine how a pesticide equilibrates between a leaf and the air above it. These measurements were incorporated into a pesticide fate model that predicts how a pesticide moves through the environment after application to an agricultural field. The …

Collaborative Research: Surface-Specific Aerosol Chemistry: Direct Observations, Kinetics, And Environmental Impact, Yi Rao

Funded Research Records

No abstract provided.

Stability, Electronic Structure, And Nonlinear Optical Properties In Clusters And Materials: A Synergistic Experimental-Computational Analysis, Maksim Kulichenko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The main objective of Chemistry as a science is an understanding of how and why certain atoms are bonded together and what effects these bonds cause. Modern computational chemistry offers a wide range of tools that greatly assist the exploration of vast chemical space replacing expensive trial-and-error experimental approaches. Computational chemistry may serve to characterize newly synthesized compounds and provide atomic scale insights inaccessible to experimentalists’ vision. Moreover, predictive power of computational chemistry may be used as a guidance for future experiments and for the rational design of new compounds with desired properties.

This dissertation demonstrates the capabilities of joint …

Designing And Decoding Chemical Bonds: A Computational Pipeline Backed Up By Magnetic Criteria And Experiment, Nikita Fedik

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

You may find plenty of definitions of chemistry but all of them, explicitly or not, are centered around chemical bonds. When we say “chemical properties”, “reactivity”, “stability”, “structure” etc., we have in mind chemical bonds and their reorganization which almost completely defines the behavior of the matter. Why some materials are ultrahard and can cut through steel while others are so soft that you can form them with your bare hands? You probably have already guessed that it occurs because their chemical bonding is very different. Although the elemental composition could be the same! In this Dissertation, we report results …

Investigating Position 312 In Prmt1 For Future Fluorescent Labeling Studies, Sarah Nielson

Student Research Symposium

Protein arginine methyltransferase 1 (PRMT1) is an enzyme that post-translationally methylates other proteins in the cell. These methylation events play critical roles in maintaining cellular health. Labeling PRMT1 site-specifically will enable further research in PRMT1 oligomeric state in vivo and can be applied in future fluorescent studies. The intention of this research was to identify a position to label PRMT1 that does not affect oligomerization or activity. Position 312 was chosen as the site for specific tagging as it will have less interference in oligomerization, minimizes free rotation of fluorescent tags, and is surface-exposed. To confirm that position 312 was …

Synthesis Of A Novel Carbon Monoxide-Releasing Gallium Flavonol Complex, Joel Ashton

Student Research Symposium

Carbon monoxide (CO) has unique therapeutic properties including anti-cancer effects. Flavonols such as 3-hydroxyflavone can release CO upon exposure to visible light. Gallium(III) also has anti-cancer properties and can replace Fe(III) in biological processes. This research was focused on synthesizing a complex of gallium(III) and 3-hydroxyflavone which can hopefully combine the anti-cancer properties of both gallium and CO. Initial attempts to synthesize the complex mimicked those of transition metal flavonol complexes using a base to deprotonate the flavonol and stirring with gallium salt. The most successful synthesis developed involved dissolving 3-hydroxyflavone and gallium nitrate in ethanol and DMSO, adjusting the …

Can Superoxide-Responsive Co Delivery Molecules Be Developed?, Taylor Dittmar

Student Research Symposium

Although known for its toxicity, carbon monoxide (CO) has now been identified as producing beneficial health effects when present at low concentrations. CO is generated in the human body during the breakdown of heme. It is known for its anti-cancer, cardioprotective, and anti-inflammatory effects. To enhance these therapeutic effects, CO delivery molecules have been developed. Fluorescent flavonol-based CO delivery molecules are gaining broad interest due to their triggerable, trackable, and targetable properties. Flavonols can also be used as dual functioning molecules, with additional capabilities such as the detection of reactive oxygen species (ROS) being possible to incorporate in addition to …

The Connections Between Musculoskeletal Injury And Global Reaction, Keaton Reel

Student Research Symposium

The peripheral effects of severe musculoskeletal injury are a well-studied phenomenon, but less well studied are the neural deficits. Past research has demonstrated that such severe injuries, specifically torn and reconstructed anterior cruciate ligament (ACL), may increase cognitive burden due to lack of afferent feedback from damaged nerves. This has previously shown to lead to delayed voluntary reactions in the lower extremities, but global neural changes are currently unknown. The goal of the conducted research was to determine whether neuromuscular deficits due to ACL injury and reconstruction in one limb influences motor behavior on a global level. Simple reaction time, …

Air Pollutant Emissions From Natural Gas-Fueled Pumpjack Engines In The Uinta Basin, Seth Lyman

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We measured a comprehensive suite of pollutants emitted from 58 natural gas-fueled pumpjack engines in Utah’s Uinta Basin between January and May 2021, with repeat measurements of five engines in January 2022. We documented the emissions composition of several makes and models of commonly used engines, including Ajax E42, E565, DP60, and DP80 engines; Arrow L795, C101, and C106 engines; and GM Vortec.

Elemental And Oxidized Mercury In The Atmosphere At Horsepool, Utah, January-July 2019, Seth Lyman

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This is a dataset of elemental and oxidized mercury in the ambient atmosphere at latitude 40.143° N and longitude 109.469° W. This is the location of the Horsepool monitoring station in the Uinta Basin, Utah. We collected these measurements using a dual-channel atmospheric mercury speciation instrument, which is described by Lyman, S. N., Gratz, L. E., Dunham-Cheatham, S. M., Gustin, M. S., & Luippold, A. (2020). Improvements to the accuracy of atmospheric oxidized mercury measurements. Environmental Science & Technology, 54(21), 13379-13388.

Phosphomimetic Tyrosine Mutations In Spa47 Inhibit Type Three Secretion Atpase Activity And Shigella Virulence Phenotype, Koleton D. Hardy, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Shigella is a highly infectious human pathogen responsible for 269 million infections and 200,000 deaths per year. Shigella virulence is absolutely reliant on the injection of effector proteins into the host cell cytoplasm via its type three secretion system (T3SS). The protein Spa47 is a T3SS ATPase whose activity is essential for the proper function of the Shigella T3SS needle-like apparatus through which effectors are secreted. A phosphoproteomics study recently found several Shigella T3SS proteins, including Spa47, to be tyrosine phosphorylated, suggesting a means of regulating Spa47 enzymatic activity, T3SS function, and overall Shigella virulence. The work presented here employs …

Rapid Quantitative Analysis Of Toxic Norditerpenoid Alkaloids In Larkspur (Delphinium Spp.) By Flow Injection - Electrospray Ionization – Mass Spectrometry, Dale R. Gardner, Stephen T. Lee, Daniel Cook

Poisonous Plant Research (PPR)

A rapid flow injection - electrospray ionization – mass spectrometry (FI-ESI-MS) method for the quantitative and qualitative analysis of norditerpenoid alkaloids in larkspur plants was developed. The FI-ESI-MS method was calibrated for alkaloid concentrations with larkspur plant samples against an existing Fourier transform infrared spectroscopy FTIR method. There was a strong correlation (r = 0.9926, r = 0.9891) between the FTIR and FI-ESI-MS methods. The relative standard deviation (RSD) for all measurements were ≤ 6.2 % except for the sample with the lowest concentration which was 19%. The sample throughput of the FI-ESI-MS method is much higher than the FTIR …

Nickel Catalyzed Electrochemical C-C Cross-Coupling Reactions, T. Leo Liu

Funded Research Records

No abstract provided.

Foliar Photodegradation In Pesticide Environmental Modeling, Sean M. Lyons

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work described here was conducted to better understand how pesticides will behave following their application to crops or soil. This understanding will allow for better use of pesticides which will protect the environment and non-target organisms while remaining effective against pests. The Pesticide Dissipation form Agricultural Land (PeDAL) model was developed to simulate pesticide behavior following application and laboratory experiments focused on the photodegradation of select pesticides on alfalfa leaves were conducted to support this model.

Data From: Hydrated Sulfate Clusters So4(2-)(H2o)N(N=1-40): Charge Distribution Through Solvation Shells And Stabilization, Alexander I. Boldyrev, Maksim Kulichenko

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In the current work, we report our computational study of hydrated sulfate clusters SO4(2–)(H2O)n (n = 1–40) in order to understand the nature of stabilization of this important anion by water molecules. We showed that the most significant charge transfer from dianion SO4(2–) to H2O takes place at a number of H2O molecules n ≤ 7. The SO4(2–) directly donates its charge only to the first solvation shell and surprisingly, a small amount of electron density of 0.15|e| is enough to be transferred in order to stabilize the dianion.

Data From: Expansion Of Aromaticity Magnetic Criteria On Multi-Layer Structures. Magnetic Response And Spherical Aromaticity Of Matryoshka-Like [Sn@Cu12@Sn20]12- Cluster, Alexander I. Boldyrev, Maksim Kulichenko

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Structural characterization of the discrete [Sn@Cu12@Sn20]12− cluster exposed a fascinating architecture composed of three concentric structural layers in which an endohedral Sn atom is enclosed in a Cu12 icosahedron, which in turn is embedded in an Sn20 dodecahedron. Herein, the possibility of sustaining aromatic behavior for this prototypical multilayered species was evaluated, in order to extend this concept to more complex clusters on the basis of magnetic response and bonding analysis by the AdNDP approach. This revealed characteristic features of spherical aromatics, given by the ability to sustain the shielding cone property, similar to archetypal aromatics.

Data From: Σ-Aromaticity In The Mos2 Monolayer, Alexander I. Boldyrev, Maksim Kulichenko

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As is shown using the SSAdNDP approach, Mo and S form 2-centered bonds and there is a lone pair on each S. Most importantly, the remaining electrons are distributed over Mo atoms and form conjugated aromatic σ-bonds inside every hexagonal ring, which makes molybdenum the main carrier of σ-aromaticity.

Data From: Periodic F-Defects On The Mgo Surface As Potential Single-Defect Catalysts With Non-Linear Optical Properties, Alexander I. Boldyrev, Maksim Kulichenko

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In this paper we suggest a new type of a single-atom (or single-defect) catalyst – MgO with periodic defects on the (0 0 1) surface – which possesses noticeable non-linear optical properties. Periodicity of these defects leads to the significant extensive increase in the activity of a catalyst by growth of the concentration of active sites. In this work we showed the presence of diffuse electride-like multi-center bonds inside every periodic F-center. We also discovered that MgO with periodic defects on the surface gains non-linear optical properties due to electride-like polarizable bonds inside every defect. And most importantly, such defective …