Chemistry Commons^™

Pure Breeding At Its Finest, Justin Hunter

Fall Student Research Symposium 2020

This is a poster of my research on the affects pure breeding has on dogs and their health. There is a focus as well on the focus on neoteny and its affects on dogs.

Synthesizing Octahedral Polyomavirus Capsids For Cryogenic Electron Microscopy, Miles Robertson

Fall Student Research Symposium 2020

Polyomavirus capsids are polymorphic under different chemical conditions. These capsids have been synthesized artificially using purified VP1, the primary building block of the capsid. Five VP1 proteins come together and form a highly stable structure called a pentamer, and these pentamers can form capsids (Figure 1). Depending on chemical conditions, the capsids can form three distinct sizes: T=7, octahedral and icosahedral (Figure 2). Only one form is found in infectious virions, and its structure has been well studied. However, no high-resolution structure of the octahedral capsid currently exists. The goal of this research is to solve the structure of the …

Dogs In The Home Improve The Quality Of Life Of The People Living Inside, Tanner Stevenson

Fall Student Research Symposium 2020

This poster explores how dogs improve the quality of life of the people they interact with. Regardless of underlying issues that the human faces, every dog helps to improve the situation of that human. From service animals helping to improve the quality of life of their owners in other ways than what meets the eye, to dogs improving the chance of allergy immunity for children, dogs impact the lives of humans for good. This project explores the way that studies have proven the worth of the dog in the home.

Enabling Mars Farms Through Microbial Remediation Of Wastewater, Tyler Wallentine

Fall Student Research Symposium 2020

This research evaluates the capacity of photoheterotrophic purple non-sulfur bacteria to utilize wastewater organics to grow and produce nitrogen-rich biomass. Inhibitory components of wastewater are determined. A scaled up production system is designed and utilized to culture bacteria in wastewater. The application of this technology in the production of agriculturally viable amounts of nitrogen-rich biomass is evaluated in the context of a Mars mission and enabling agriculture in a barren environment.

Triggerable, Targetable, And Trackable Flavonol-Based Carbon Monoxide-Releasing Molecules, Livia S. Lazarus

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Long known as a toxic gas, carbon monoxide (CO) has been recently redefined as a health beneficial molecule produced endogenously in humans. The biological activity of CO has been extensively examined in inflammatory conditions, vasoprotection, anti-apoptotic and anticancer studies, although the mechanisms of action are still not well defined. Because CO is a gaseous molecule, a straightforward administration would be inhalation. However, this delivery method is limited to use in hospital settings under professional supervision. For improved control over the amount and location of CO delivery, metal-free and light-triggered carbon monoxide-releasing molecules are of particular current interest. Our lab is …

“Bottled” Spiro-Doubly Aromatic Trinuclear [Pd2ru]+ Complexes, Maksim Kulichenko, Nikita Fedik, Anna Monfredini, Alvaro Muñoz-Castro, Davide Balestri, Alexander I. Boldyrev, Giovanni Maestri

Chemistry and Biochemistry Faculty Publications

Following an ongoing interest in the study of transition metal complexes with exotic bonding networks, we report herein the synthesis of a family of heterobimetallic triangular clusters involving Ru and Pd atoms. These are the first examples of trinuclear complexes combining these nuclei. Structural and bonding analyses revealed both analogies and unexpected differences for these [Pd₂Ru]⁺ complexes compared to their parent [Pd₃]⁺ peers. Noticeably, participation of the Ru atom in the π-aromaticity of the coordinated benzene ring makes the synthesized compound the second reported example of ‘bottled’ double aromaticity. This can also be referred …

A Sandwich-Type Cluster Containing Ge@Pd3 Planar Fragment Flanked By Aromatic Nonagermanide Caps, Hong-Lei Xu, Nikolay V. Tkachenko, Zi-Chuan Wang, Wei-Xing Chen, Lei Qiao, Alvaro Muñoz-Castro, Alexander I. Boldyrev, Zhong-Ming Sun

Chemistry and Biochemistry Faculty Publications

Sandwich-type clusters with the planar fragment containing a heterometallic sheet have remained elusive. In this work, we introduce the [K(2,2,2-crypt)]₄{(Ge₉)₂[η⁶-Ge(PdPPh₃)₃]} complex that contains a heterometallic sandwich fragment. The title compound is structurally characterized by means of single-crystal X-ray diffraction, which reveals the presence of an unusual heteroatomic metal planar fragment Ge@Pd₃. The planar fragment contains a rare formal zerovalent germanium core and a peculiar bonding mode of sp²-Ge@(PdPPh₃)₃ trigonal planar structure, whereas the nonagermanide fragments act as capping ligands. The …

Versatility Of The Cyano Group In Intermolecular Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH₃ base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature …

Determining The Structure And Function Of Newly Discovered Immune Systems, Ryan N. Jackson

Funded Research Records

No abstract provided.

Effect Of Carbon Hybridization In C—F Bond As An Electron Donor In Triel Bonds, Qingqing Yang, Zongqing Chi, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The ability of the F atom of HC≡CF, H₂C=CHF and H₃CCH₂F to serve as an electron donor to the triel (Tr) atom of TrR₃ in the context of a triel bond is assessed by ab initio calculations. The triel bond formed by C_sp3—F is strongest, as high as 30 kcal/mol, followed by C_sp2—F, and then by C_sp—F whose triel bonds can be as small as 1 kcal/mol. The noncovalent bond strength diminishes in the order Tr = Al > Ga > B, consistent with the intensity of the π-hole …

Comparison Of Accelerated Solvent Extraction (Ase) And Energized Dispersive Guided Extraction (Edge) For The Analysis Of Pesticides In Leaves, Ashlie D. Kinross, Kimberly J. Hageman, William J. Doucette, Alexandria L. Foster

Chemistry and Biochemistry Faculty Publications

Various techniques have been evaluated for the extraction and cleanup of pesticides from environmental samples. In this work, a Selective Pressurized Liquid Extraction (SPLE) method for pesticides was developed using a Thermo Fisher Scientific Accelerated Solvent Extraction (ASE) system. This instrument was compared to the newly introduced (2017) extraction instrument, the Energized Dispersive Guided Extraction (EDGE) system, which combines Pressurized Liquid Extraction (PLE) and dispersive Solid Phase Extraction (dSPE). We first optimized the SPLE method using the ASE instrument for pesticide extraction from alfalfa leaves using layers of Florisil and graphitized carbon black (GCB) downstream of the leaf homogenate in …

Collaborative Research: Mechanism And Target Recognition Of Protein Arginine Methyltransferases (Prmts), Joan Hevel

Funded Research Records

No abstract provided.

Strong Temporal Variability In Methane Fluxes From Natural Gas Well Pad Soils, Seth N. Lyman, Huy N. Q. Tran, Marc L. Mansfield, Ric Bowers, Ann Smith

Bingham Research Center

We measured methane and carbon dioxide fluxes at natural gas well pad soils and undisturbed soils in the Rocky Mountain and Gulf Coast regions of the United States, including producing and gas storage wells. We collected both short-term (15 min) and multi-day (between 3 and 8), continuous measurements at 47 well pads and two undisturbed locations. Methane fluxes varied by more than an order of magnitude over periods as short as 30 min (e.g., 19–593 mg m⁻² h⁻¹ in one instance), and diurnal and seasonal variability was also significant (e.g., spring-to-fall change from 509 to 14174 mg m …

Influence Of Adjuvants On Pesticide Soil-Air Partition Coefficients: Laboratory Measurements And Predicted Effects On Volatilization, Supta Das, Kimberly J. Hageman

Chemistry and Biochemistry Faculty Publications

A solid-phase fugacity meter was used to measure the soil–air partition coefficients of three semivolatile pesticides (chlorpyrifos, pyrimethanil, and trifluralin) in the absence of additional adjuvants (K_{soil–air,AI}), as part of commercial formulations (K_{soil–air,formulation}), and as formulation mixtures with an additional spray adjuvant added (K_{soil–air,formulation+spray adjuvant}). Chlorpyrifos K_{soil–air,formulation} values were also measured over 15–30 °C, allowing for the change in internal energy of the phase transfer reaction (Δ_soil–airU) to be calculated and compared to the Δ_soil–airU for K_{soil–air,AI} from the literature. Measured K_soil–air values …

N3-Ligated Nickel(Ii) Diketonate Complexes: Synthesis, Characterization And Evaluation Of O2 Reactivity, Josiah G. D. Elsberg, Austin Peterson, Amy L. Fuller, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Interest in O₂-dependent aliphatic carbon–carbon (C–C) bond cleavage reactions of first row divalent metal diketonate complexes stems from the desire to further understand the reaction pathways of enzymes such as DKE1 and to extract information to develop applications in organic synthesis. A recent report of O₂-dependent aliphatic C–C bond cleavage at ambient temperature in Ni(II) diketonate complexes supported by a tridentate nitrogen donor ligand [(MBBP)Ni(PhC(O)CHC(O)Ph)]Cl (7-Cl; MBBP = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine) in the presence of NEt₃ spurred our interest in further examining the chemistry of such complexes. A series of new TERPY-ligated Ni(II) diketonate complexes of the …

Materials Design For High-Performance Organic Redox Flow Batteries And Electrocatalytic Carbon Dioxide And Nitrogen Reduction, Bo Hu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nowadays, the utilization of renewable energy resources such as solar and wind energy has been realized to be a sustainable and environmentally benign strategy to alleviate the world’s severe dependency on traditional fossil fuels, and thus enables the environmental recovery and sustainable development of the economy. The massive commercialization of solar and wind energy raises the demands for advanced energy storage technologies, among which the redox flow battery has been recognized as a promising solution due to it is low cost, safe, environmentally benign, and easy to be scaled up. All vanadium redox flow battery stands for the most important …

Co Sense And Release Flavonols: Progress Toward The Development Of An Analyte Replacement Photocorm For Use In Living Cells, Marina Popova, Tatiana Soboleva, Abby D. Benninghoff, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Carbon monoxide (CO) is a signaling molecule in humans. Prior research suggests that therapeutic levels of CO can have beneficial effects in treating a variety of physiological and pathological conditions. To facilitate understanding of the role of CO in biology, molecules that enable fluorescence detection of CO in living systems have emerged as an important class of chemical tools. A key unmet challenge in this field is the development of fluorescent analyte replacement probes that replenish the CO that is consumed during detection. Herein, we report the first examples of CO sense and release molecules that involve combining a common …

Modeling The Alkaline Hydrolysis Of Diaryl Sulfate Diesters: A Mechanistic Study, Klaudia Szeler, Nicholas H. Williams, Alvan C. Hengge, Shina C. Kamerlin

Chemistry and Biochemistry Faculty Publications

Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good …

Boron-Made N2: Realization Of A B≡B Triple Bond In The B2al3− Cluster, Nikita Fedik, Chaonan Mu, Ivan A. Popov, Wei Wang, Jie Wang, Haopeng Wang, Kit H. Bowen, Alexander I. Boldyrev, Xinxing Zhang

Chemistry and Biochemistry Faculty Publications

Until now, all B≡B triple bonds have been achieved by adopting two ligands in the L→B≡B←L manner. Herein, we report an alternative route of designing the B≡B bonds based on the assumption that by acquiring two extra electrons, an element with the atomic number Z can have properties similar to those of the element with the atomic number Z+2. Specifically, we show that due to the electron donation from Al to B, the negatively charged B≡B kernel in the B2Al3− cluster mimics a triple N≡N bond. Comprehensive computational searches reveal that the global minimum structure of B2Al3− exhibits a …

Competition Between Intra And Intermolecular Triel Bonds. Complexes Between Naphthalene Derivatives And Neutral Or Anionic Lewis Bases, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A TrF₂ group (Tr = B, Al, Ga, In, Tl) is placed on one of the α positions of naphthalene, and its ability to engage in a triel bond (TrB) with a weak (NCH) and strong (NC⁻) nucleophile is assessed by ab initio calculations. As a competitor, an NH₂ group is placed on the neighboring C^α, from which point it forms an intramolecular TrB with the TrF₂ group. The latter internal TrB reduces the intensity of the π-hole on the Tr atom, decreasing its ability to engage in a second external TrB. The …

Can Aromaticity Be A Kinetic Trap? Example Of Mechanically Interlocked Aromatic [2-5]Catenanes Built From Cyclo[18]Carbon, Nikita Fedik, Maksim Kulichenko, Dmitriy Steglenko, Alexander I. Boldyrev

Chemistry and Biochemistry Faculty Publications

The unusual stability of cyclo[18]carbon arising from its aromaticity might be used to provide the kinetic trapping needed in the design of interlocked systems. The kinetic barrier separating the interlocked rings and the chemically bonded complex is about 30 kcal mol−1. In addition, the rings can slide freely, which is a promising property for the design of molecular gears and motors.

Dominant Negative Effects By Inactive Spa47 Mutants Inhibit T3ss Function And Shigella Virulence, Jamie L. Burgess, Heather B. Case, R. Alan Burgess, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Type three secretion systems (T3SS) are complex nano-machines that evolved to inject bacterial effector proteins directly into the cytoplasm of eukaryotic cells. Many high-priority human pathogens rely on one or more T3SSs to cause disease and evade host immune responses, underscoring the need to better understand the mechanisms through which T3SSs function and their role(s) in supporting pathogen virulence. We recently identified the Shigella protein Spa47 as an oligomerization-activated T3SS ATPase that fuels the T3SS and supports overall Shigella virulence. Here, we provide both in vitro and in vivo characterization of Spa47 oligomerization and activation in the presence and absence …

Coordination Of Anions By Noncovalently Bonded Σ-Hole Ligands, Steve Scheiner, Mariusz Michalczyk, Wiktor Zierkiewicz

Chemistry and Biochemistry Faculty Publications

Research on σ-hole interactions that include halogen, chalcogen, pnicogen, and tetrel bonding has been accelerating in recent years. These cousins of the H-bond have many similar properties, including geometric preferences and energetics. Most of the work to date has focused on neutral complexes, with less known about these bonds to anions. This review summarizes the current state of knowledge about the complexes of anions with ligands that engage in these sorts of noncovalent bonds. Of particular interest are comparisons with H-bonds, and how the geometry of the fully coordinated complex varies as the number of surrounding ligands increases. A specific …

Cost-Effective Synthesis, Bioactivity And Cellular Uptake Study Of Aminoglycosides With Antimicrobial And Connexin Hemichannel Inhibitory Activity, Yagya P. Subedi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Amphiphilic kanamycin is one of the promising class of compounds for the treatment of fungal infections in plants and animal. Factor that lead to the restricting of compounds for commercialization includes, the higher cost of production and poor stability of the compound. However, the new lead, identified from the synthesis and biological testing, can be synthesized on a large scale with a cost comparable to commercial antifungals. The newly reported lead is stable at the acidic and basic conditions. Additionally, this compound has an excellent activity towards Candida auris, a multidrug-resistant superbug.

Heart disease is the leading cause of death …

An Updated Review Of Atmospheric Mercury, Seth N. Lyman, Irene Cheng, Lynne E. Gratz, Peter Weiss-Penzias, Leiming Zhang

Chemistry and Biochemistry Faculty Publications

The atmosphere is a key component of the biogeochemical cycle of mercury, acting as a reservoir, transport mechanism, and facilitator of chemical reactions. The chemical and physical behavior of atmospheric mercury determines how, when, and where emitted mercury pollution impacts ecosystems. In this review, we provide current information about what is known and what remains uncertain regarding mercury in the atmosphere. We discuss new ambient, laboratory, and theoretical information about the chemistry of mercury in various atmospheric media. We review what is known about mercury in and on solid- and liquid-phase aerosols. We present recent findings related to wet and …

The Hydrogen Bond: A Hundred Years And Counting, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Since its original inception, a great deal has been learned about the nature, properties, and applications of the H-bond. This review summarizes some of the unexpected paths that inquiry into this phenomenon has taken researchers. The transfer of the bridging proton from one molecule to another can occur not only in the ground electronic state, but in various excited states as well. Study of the latter process has developed insights into the relationships between the nature of the state, the strength of the H-bond, and the height of the transfer barrier. The enormous broadening of the range of atoms that …

Aerial And Ground-Based Optical Gas Imaging Survey Of Uinta Basin Oil And Gas Wells, Seth N. Lyman, Trang Tran, Marc L. Mansfield, Arvind P. Ravikumar

Bingham Research Center

We deployed a helicopter with an infrared optical gas imaging camera to detect hydrocarbon emissions from 3,428 oil and gas facilities (including 3,225 producing oil and gas well pads) in Utah’s Uinta Basin during winter and spring 2018. We also surveyed 419 of the same well pads from the ground. Winter conditions led to poor contrast between emission plumes and the ground, leading to a detection limit for the aerial survey that was between two and six times worse than a previous summertime survey. Because the ground survey was able to use the camera’s high-sensitivity mode, the rate of detected …

Structures And Energetics Of Clusters Surrounding Diatomic Anions Stabilized By Hydrogen, Halogen, And Other Noncovalent Bonds, Steve Scheiner, Mariusz Michalczyk, Rafal Wysokiński, Wiktor Zierkiewicz

Chemistry and Biochemistry Faculty Publications

Diatomic anions CN-, NO-, and OH- are surrounded by 2, 3, and 4 ligand molecules drawn from the HF, HCl, XF, YF2, ZF3, TF4, and TrF3 set wherein X= Cl,Br, Y=S,Se, Z=P,As, T=Si,Ge, and Tr=Al,Ga. In the case of two ligands, both interact with the N of NO- and the O of OH-, but one approaches either end of CN-. Unlike the H and halogen bonding units, as the number of ligands increases there is a tendency for chalcogen, pnicogen, tetrel, and triel-bonding ligands to form a cage around the central anion, with strong inter-ligand noncovalent bonds. There are a …

An Efficient Viologen-Based Electron Donor To Nitrogenase, Artavazd Badalyan, Zhi-Yong Yang, Bo Hu, Jian Luo, Maowei Hu, T. Leo Liu, Lance C. Seefeldt

Chemistry and Biochemistry Faculty Publications

Nitrogenase catalyzes the reduction of N₂ to NH₃, supporting all biological nitrogen fixation. Electron donors to this enzyme are ferredoxin or flavodoxin (in vivo) and sodium dithionite (in vitro). Features of these electron donors put a limit on spectrophotometric studies and electrocatalytic applications of nitrogenase. Although it is common to use methyl viologen as an electron donor for many low-potential oxidoreductases, decreased nitrogenase activity is observed with an increasing concentration of methyl viologen, limiting its utility under many circumstances. In this work, we suggest that this concentration-dependent decrease in activity can be explained …

The Total Syntheses Of Jbir-94 And Two Synthetic Analogs And Their Cytotoxicities Against A549 (Ccl-185) Human Small Lung Cancer Cells, Cathy L. Mangum, Mica B. Munford, Alyssa Sam, Sandra K. Young, Jeremy T. Beales, Yagya Prasad Subedi, Chad D. Mangum, Tanner J. Allen, Miranda S. Liddell, Andrew I. Merrell, Diana I. Saavedra, Becky L. Williams, Nicole Evans, Joseph L. Beales, Mike A. Christiansen

Chemistry and Biochemistry Faculty Publications

We here disclose the total syntheses of the natural polyphenol JBIR-94 and two nonnatural analogs, whose structures are of interest for their bioactivity potential as radical scavengers. Although we initially attempted this by dually acylating both of putrecine’s amine nitrogens in a single pot, our endeavors with this method (which has been successfully reported by other groups) proved ineffectual. We accordingly opted for the lengthier approach of acylating each amine individually, which gratuitously prevailed and also aligns with separate literature precedent. Moreover, we here share our analysis of these target compounds’ cytotoxicities and IC₅₀ values against A549 (CCL-185) human …