Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

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 …

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 …

Fate Of The Organophosphate Insecticide, Chlorpyrifos, In Leaves, Soil, And Air Following Application, Supta Das, Kimberly J. Hageman, Madeleine Taylor, Sue Michelsen-Heath, Ian Stewart

Chemistry and Biochemistry Faculty Publications

A field study was conducted to further our understanding about the fate and transport of the organophosphate insecticide, chlorpyrifos, and its degradation product, chlorpyrifos oxon. Leaf, soil and air sampling was conducted for 21 days after chlorpyrifos application to a field of purple tansy (Phacelia tanacetifolia). Air samples were collected using a high-volume air sampler (HVAS) and seven battery-operated medium-volume active air samplers placed around the field and on a 500-m transect extending away from the field. Chlorpyrifos was detected every day of the sampling period in all matrices, with concentrations decreasing rapidly after application. Chlorpyrifos oxon was …

Aromatic Character Of [Au13]5+ And [Mau12]4+/6+ (M = Pd, Pt) Cores In Ligand Protected Gold Nanoclusters – Interplay Between Spherical And Planar Σ-Aromatics, Nikita Fedik, Alexander I. Boldyrev, Alvaro Muñoz-Castro

Chemistry and Biochemistry Faculty Publications

The most characteristic feature of planar π-aromatics is the ability to sustain a long-range shielding cone under a magnetic field oriented in a specific direction. In this article, we showed that similar magnetic responses can be found in σ-aromatic and spherical aromatic systems. For [Au₁₃]⁵⁺, long-range characteristics of the induced magnetic field in the bare icosahedral core are revealed, which are also found in the ligand protected [Au₂₅(SH)₁₈]− model, proving its spherical aromatic properties, also supported by the AdNDP analysis. Such properties are given by the 8-ve of the structural core satisfying …

Data From: Cavitation Clusters In Lipid Systems – The Generation Of A Bifurcated Streamer And The Dual Collapse Of A Bubble Cluster, Silvana Martini, Peter Birkin, Tadd T. Truscott

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Over the past decade several studies have reported the use of high intensity ultrasound (HIU) to induce the crystallization of lipids. The effect that HIU has on lipid crystallization is usually attributed to the generation of cavities but acoustic cavitation has never been fully explored in lipids. The dynamics of a particular cavitation cluster next to a piston like emitter in an oil, was investigated in this study. The lipid systems, which are important in food processing, are studied with high-speed camera imaging, laser scattering and pressure measurements. A sequence of stable clusters were noted. In addition, a bifurcated streamer …

Definition Of The Chalcogen Bond (Iupac Recommendations 2019), Christer B. Aakeroy, David L. Bryce, Gautam R. Desiraju, Antonio Frontera, Anthony C. Legon, Francesco Nicotra, Kari Rissanen, Steve Scheiner, Giancarlo Terraneo, Pierangelo Metrangolo, Giuseppe Resnati

Chemistry and Biochemistry Faculty Publications

This recommendation proposes a definition for the term “chalcogen bond”; it is recommended the term is used to designate the specific subset of inter- and intramolecular interactions formed by chalcogen atoms wherein the Group 16 element is the electrophilic site.

Theoretical Studies Of Ir And Nmr Spectral Changes Induced By Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, And Tetrel Bonds In A Model Protein Environment, Mariusz Michalczyk, Wiktor Zierkiewicz, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Various types of σ-hole bond complexes were formed with FX, HFY, H₂FZ, and H₃FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A–F bond, which lies opposite the base and is responsible for …

Chalcogen Bonding Of Two Ligands To Hypervalent Yf4 (Y=S, Se, Te, Po), Wiktor Zierkiewicz, Rafal Wysokiński, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The ability of two NH3 ligands to engage in simultaneous chalcogen bonds to a hypervalent YF4 molecule, with Y=S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis structure places the two ligands adjacent to one another ina pseudo-octahedral geometry, held there by a pair of σ-hole chalcogen bonds. The bases can also lie nearly opposite one another, in a distorted octahedron containing one π-hole and one strained σ-hole bond. The cis geometry is favored for Y=S, while Te,and Po tend toward the trans structure; they are nearly equally …

Computational Insights Into Mg-Cl Complex Electrolytes For Rechargeable Magnesium Batteries, Jared B. Moss, Liping Zhang, Kevin V. Nielson, Yujing Bi, Chao Wu, Steve Scheiner, Tianbiao Leo Liu

Chemistry and Biochemistry Faculty Publications

DFT calculations were conducted to provide insightful and unprecedented thermodynamic insights on tetrahydrofuran (THF) solvation, isomerization, chlorination, and complexation of possible Mg-Cl coordination species for the popular Mg-Cl electrolytes. Computational results using the M06-2x functional with the 6-31+G(d) basis set indicate trigonal bipyramidal e, e-cis-tbp-MgCl2(THF)3 dichloride species and octahedral [MgCl(THF)5]+ monochloride species are the dominant mononuclear species. These two can combine to form the active dinuclear species, [(μ-Cl)3Mg2(THF)6]+ with a free energy -6.30 kcal/mol, which is calculated to be the dominant Mg-Cl species in solution. Two mono-cation species, [(μ-Cl)3Mg2(THF)6]+ and [MgCl(THF)5]+ have comparable LUMO energies, thus both of them can …

Anisotropic Singlet Fission In Single Crystalline Hexacene, Dezheng Sun, Gang-Hua Deng, Bolei Xu, Enshi Xu, Xia Li, Yajing Wu, Yuqin Qian, Yu Zhong, Colin Nuckolls, Avetik R. Harutyunyan, Hai-Lung Dai, Gugang Chen, Hanning Chen, Yi Rao

Chemistry and Biochemistry Faculty Publications

Singlet fission is known to improve solar energy utilization by circumventing the Shockley-Queisser limit. The two essential steps of singlet fission are the formation of a correlated triplet pair and its subsequent quantum decoherence. However, the mechanisms of the triplet pair formation and decoherence still remain elusive. Here we examined both essential steps in single crystalline hexacene and discovered remarkable anisotropy of the overall singlet fission rate along different crystal axes. Since the triplet pair formation emerges on the same timescale along both crystal axes, the quantum decoherence is likely responsible for the directional anisotropy. The distinct quantum decoherence rates …

Spectroscopic Description Of The E1 State Of Mo Nitrogenase Based On Mo And Fe X‑Ray Absorption And MöSsbauer Studies, Casey Van Stappen, Roman Davydov, Zhi-Yong Yang, Ruixi Fan, Yisong Guo, Eckhard Bill, Lance C. Seefeldt, Brian M. Hoffman, Serena Debeer

Chemistry and Biochemistry Faculty Publications

Mo nitrogenase (N2ase) utilizes a two-component protein system, the catalytic MoFe and its electron-transfer partner FeP, to reduce atmospheric dinitrogen (N₂) to ammonia (NH₃). The FeMo cofactor contained in the MoFe protein serves as the catalytic center for this reaction and has long inspired model chemistry oriented toward activating N₂. This field of chemistry has relied heavily on the detailed characterization of how Mo N2ase accomplishes this feat. Understanding the reaction mechanism of Mo N2ase itself has presented one of the most challenging problems in bioinorganic chemistry because of the ephemeral nature of its …

Status And Prospects Of Organic Redox Flow Batteries Toward Sustainable Energy Storage, Jian Luo, Bo Hu, Maowei Hu, Yu Zhao, T. Leo Liu

Chemistry and Biochemistry Faculty Publications

Redox flow batteries (RFBs) are regarded a promising technology for large-scale electricity energy storage to realize efficient utilization of intermittent renewable energy. Redox -active materials are the most important components in the RFB system because their physicochemical and electrochemical properties directly determine their battery performance and energy storage cost. Designable, tunable, and potentially low-cost redox-active organic compounds are promising alternatives to traditional redox-active inorganic compounds for RFB applications. Herein, the representative designs of redox-active molecules, recent development of organic RFBs (ORFBs), and advantages/disadvantages of different ORFB are reviewed. Especially the relationship between redox-active molecules’ physicochemical properties and their battery performance …

Vibronic Fingerprint Of Singlet Fission In Hexacene, Gang-Hua Deng, Qianshun Wei, Jian Han, Yuqin Qian, Jun Luo, Avetik R. Harutyunyan, Gugang Chen, Hongtao Bian, Hanning Chen, Yi Rao

Chemistry and Biochemistry Faculty Publications

Singlet fission has the great potential to overcome the Shockley–Queisser thermodynamic limit and thus promotes solar power conversion efficiency. However, the current limited understandings of detailed singlet fission mechanisms hinder a further improved design of versatile singlet fission materials. In the present study, we combined ultrafast transient infrared spectroscopy with ab initio calculations to elucidate the roles played by the vibrational normal modes in the process of singlet fission for hexacene. Our transient infrared experiments revealed three groups of vibrational modes that are prominent in vibronic coupling upon photoexcitation. Through our computational study, those normal modes with notable Franck-Condon shifts …

Effects Of Halogen, Chalcogen, Pnicogen, And Tetrel Bonds On Ir And Nmr Spectra, Jia Lu, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes were formed pairing FX, FHY, FH₂Z, and FH₃T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH₃ in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A–F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This …

Violation Of Electrostatic Rules: Shifting Balance Between Pnicogen Bond And Lone Pair−Π Interaction Tuned By Substituents, Zongqing Chi, Tong Yan, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes were formed pairing ZCl3 (Z=P, As, Sb) with C2R4 (R= H, F, CN). The first interaction present is a pnicogen bond between the Z atom and the C=C π-bond. This bond weakens as the H atoms of ethylene are replaced by electron-withdrawing F and CN and the potential above the alkene switches from negative to positive. In the latter two cases, another set of noncovalent bonds is formed between the Cl lone pairs of ZCl3 and the π*(C=C) antibonding orbital, as well as with the F or CN substituents. The growing strength of these interactions, coupled with a large …

New Ideas From An Old Concept: The Hydrogen Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ongoing studies of the hydrogen bond (HB), in which a hydrogen (H) atom acts as a bridge between a pair of chemical groups, continues to offer new ideas about this interaction that have applications to biochemical processes. The ability of a proton to transfer within a HB can be controlled by conformational changes that cause small alterations to the HB geometry. The CH group, widely prevalent in biological systems, participates in HBs and contributes to the structure and stability of commonly occurring protein secondary structures such as the β-sheet. The concept of the HB has been extended to systems where …

Computational And Experimental Studies On Energy Storage Materials And Electrocatalysts, Jared B. Moss

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

With the growing global population comes the ever-increasing consumption of energy in powering cities, electric vehicles, and portable devices such as cell-phones. While the power grid is used to distribute energy to consumers, the energy sources needed to power the grid itself are unsustainable and inefficient. The primary energy sources powering the grid, being fossil fuels, natural gas, and nuclear, are unsustainable as the economically-accessible reserves are continually depleted in exchange for detrimental emissions and air-pollutants. Cleaner, renewable sources, such as solar, wind, and hydroelectric, are intermittent and unreliable during the peak hours of energy usage, that is dawn and …

Synthesis And Biological Studies Of Amphiphilic Compounds Derived From Saccharides And Aminoglycosides, Madher N. Alfindee

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Adjacent cells communicate through gap junctions (GJs). These GJs are formed by head to head docking of two hemichannels (HCs) from two adjacent cells. HCs are connexin hexamer proteins. Connexin mutation is the most frequent cause of childhood hearing loss. This hearing impairment affects 2 in every 2000 children. Inhibition of the HCs might be the key factor to treat such disorders. A library of amphiphilic kanamycins was synthesized to be tested as HC inhibitors. These compounds showed excellent inhibition activity in comparison with the parent compound (kanamycin A) with less toxicity.

A library of monosaccharide esters with varying carbon …

Electronic Transmutation: An Aid For The Rational Design Of New Chemical Materials Using The Knowledge Of Bonding And Structure Of Neighboring Elements, Katie A. Lundell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Everything in the universe is made up of elements from the periodic table. Each element has its own role that it plays in the formation of things it makes up. For instance, pencil lead is graphite. A series of honeycomb-like structures made up of carbon stacked on top of one another. Carbon’s neighbor to the left, boron doesn’t like to form such stacked honeycomb-like structures. But, what if there was a way to make boron act like carbon so it did like to form such structures? That question is the basis of the electronic transmutation concept presented in this dissertation. …

Highly Active Nanostructured Cos2/Cos Heterojunction Electrocatalysts For Aqueous Polysulfide/Iodide Redox Flow Batteries, Dui Ma, Bo Hu, Wenda Wu, Xi Liu, Jiantao Zai, Chen Shu, Tsegaye Tadesse Tsega, Liwei Chen, Xuefeng Qian, T. Leo Liu

Chemistry and Biochemistry Faculty Publications

Aqueous polysulfide/iodide redox flow batteries are attractive for scalable energy storage due to their high energy density and low cost. However, their energy efficiency and power density are usually limited by poor electrochemical kinetics of the redox reactions of polysulfide/iodide ions on graphite electrodes, which has become the main obstacle for their practical applications. Here, CoS₂/CoS heterojunction nanoparticles with uneven charge distribution, which are synthesized in situ on graphite felt by a one-step solvothermal process, can significantly boost electrocatalytic activities of I⁻/I₃⁻ and S²⁻/S_x²⁻redox reactions by improving absorptivity of …

Current-Use Pesticides In New Zealand Streams: Comparing Results From Grab Samples And Three Types Of Passive Samplers, Kimberly J. Hageman, Christopher H.F. Aebig, Kim Hoang Luong, Sarit L. Kaserzon, Charles S. Wong, Tim Reeks, Michelle Greenwood, Samuel Macaulay, Christoph D. Matthaei

Chemistry and Biochemistry Faculty Publications

New Zealand uses more than a ton of pesticides each year; many of these are mobile, relatively persistent, and can make their way into waterways. While considerable effort goes into monitoring nutrients in agricultural streams and programs exist to monitor pesticides in groundwater, very little is known about pesticide detection frequencies, concentrations, or their potential impacts in New Zealand streams. We used the ‘Polar Organic Chemical Integrative Sampler’ (POCIS) approach and grab water sampling to survey pesticide concentrations in 36 agricultural streams in Waikato, Canterbury, Otago and Southland during a period of stable stream flows in Austral summer 2017/18. We …

Optical Gas Imaging Survey Of Oil And Gas Wells In The Uinta Basin, Utah, Seth Lyman, Trang Tran, Marc L. Mansfield

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This is a dataset of oil and gas well pads which were surveyed for hydrocarbon emissions with an optical gas imaging camera deployed from the ground at pad edges. The data are described thoroughly in a peer-reviewed paper: Lyman S., Tran, T., Mansfield, M. Ravikumar, A., 2019. Aerial and Ground-Based Optical Gas Imaging Survey of Uinta Basin Oil and Gas Wells.

These are example videos collected during a hydrocarbon emissions survey of oil and gas well pads in Utah.

ExampleGroundVideo.mp4 is a video created with an optical gas imaging camera of an emission plume from well pad equipment. The video …

Comparison Of Halogen With Proton Transfer. Symmetric And Asymmetric Systems, Jia Lu, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The transfer of the halogen atom X within (A⸳⸳X⸳⸳A)+ systems was calculated for A = NH3, OH2, and CH3, and where X=Cl, Br, and I. These potentials are similar to those computed for equivalent proton transfers. Each contains a single symmetric well for short R(A⸳⸳A) distances. As R is stretched a second minimum appears, separated from the first by a transfer barrier E† which climbs quickly as R is elongated. The central X prefers association with the N in asymmetric systems (H3NX⸳⸳OH2)+, but a second (H3N⸳⸳XOH2)+ minimum, albeit less stable than the first, can appear if R(N⸳⸳O) is stretched.

The Ability Of A Tetrel Bond To Transition A Neutral Amino Acid Into A Zwitterion, Mingchang Hou, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The interaction between glycine and F2CO/F2SiO occurs through the formation of a π-tetrel bond between the C/Si atom and a carboxyl O atom. The interaction energy is some 20 kJ/mol for the C···O tetrel bond, but exceeds 300 kJ/mol for Si···O. As part of the latter complexation process, the proton engaged in the intramolecular OH··N H-bond is transferred across to the N, forming a zwitterion. This Si···O tetrel bond is more effective at inducing this proton transfer than is placement of the glycine in an aqueous medium, complexation with an anionic BH4-, or adding an electron to the glycine.