Chemistry 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, …

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 …

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 …

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 …

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 …

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 …

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 …

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.

Air Quality Measurements In Ephraim, Ut, Alex Allred

Utah Space Grant Consortium

Standard Air Quality indicators: NO, NOx, SO2, CO, O3 and PM2.5 were measured in Ephraim, Sanpete county, Utah from Dec 16, 2020 -Mar 6, 2021. The Air quailty monitoring station was installed in December 2020 and is currently operating. Ephraim is located in a high mountain valley at 5541 feet elevation. Events of interest were evaluated using back trajectories and wind rose analysis.

Evaluating Gallium As A Catalyst For Silicon Nanodot Synthesis, Rylan Woods

Utah Space Grant Consortium

Silicon nanostructures, such as silicon nanowires and silicon nanodots, exhibit notably different thermoelectric, electric, and optical properties from bulk silicon. These nanostructures are ideal for utilization in a variety of electronic and optical devices ranging from batteries to solar panels. While various synthesis methods and catalysts exist for making silicon nanowires, gallium exhibits unique nanowire shapes compared to other catalyst metals such as gold or silver. This experiment uses gallium as a catalyst to form silicon nanostructures onoriented silicon substrate at temperatures of 0, 850, and 900ºC. Analyzing dosed samples via SEM resulted in several samples showing possible evidence of …

Renewable Energy Conversion: Organic Redox Flow Batteries And Electrocatalytic Carbon Dioxide Reduction, Camden R. Debruler

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Steadily increasing global energy demands have pushed the industry to investigate renewable energy sources like solar and wind to help alleviate the strain on fossil fuel based non-renewable energy sources while also reducing carbon emissions. However, the energy producing power of these renewable technologies is limited by factors such as weather and the day-night cycle. Additional energy storage technologies are needed which are capable of storing excess energy during periods of high productivity, and delivering it when production rates fluctuate.

Batteries represent one possible energy storage device to meet this need. Specifically, redox flow batteries (RFBs) offer advantages in terms …

Developing Advanced Electrodes And Electrolytes For Energy Storage Beyond Li Ion Batteries, Kevin V. Nielson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Electric vehicles, smart phones, and portable computers are all powered by lithium-ion batteries. This is because Li-ion batteries can store more energy in less space than other battery technologies. Also, they are rechargeable and last for a long time. The most recent 2019 Nobel prize in chemistry was awarded to John Goodenough, M. Stanley Whittingham and Akira Yoshino “for the development of lithium-ion batteries”. Through their work, they have made possible cars that do not burn fossil fuels and phones that are wireless and portable. Not only can Li-ion power your phone, it is an incredibly efficient way to store …

Anion–Anion Interactions In Aerogen-Bonded Complexes. Influence Of Solvent Environment, Anna Grabarz, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio calculations are applied to the question as to whether a AeX₅− anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F−, Cl−, or CN−. The latter approaches the central Ae atom from above the molecular plane, along its C₅ axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are …

Noncovalent Bonds Through Sigma And Pi-Hole Located On The Same Molecule. Guiding Principles And Comparisons, Wiktor Ziekiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems …

Collaborative Research: Development Of A Better Understanding Of Ambient Rm Chemistry, Reactions Forming, And Methods For Measurement, Seth Lyman

Funded Research Records

No abstract provided.

Career: Time-Resolved Studies Of Charge Transfer And Chemical Reactivity At Photoelectrode-Electrolyte Interfaces, Yi Rao

Funded Research Records

No abstract provided.

Eager Sentinels: The Pcr-Free Biosensor For A Fast, Simple, And Sensitive Detection Of Rna, Artavazd Badalyan

Funded Research Records

No abstract provided.

Comparison Of Bifurcated Halogen With Hydrogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way …