Chemistry Commons^™

Ability Of Ir And Nmr Spectral Data To Distinguish Between A Tetrel Bond And A Hydrogen Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The placement of a nucleophile X along the R-CH3 axis of a methyl group can be described as either a trifurcated H-bond or as a tetrel bond between C and X. Quantum calculation of the vibrational and NMR spectral features of a number of systems are used to provide a framework by which to distinguish between the presence of a tetrel or H-bond. Both cationic and neutral methyl-containing Lewis acids (SMe3+, NMe4+, SMe2) are paired with both neutral and anionic Lewis bases (NH3, OH2, OCHNH2, OCH3-, OH-, HCOO-). As the base is moved away from the R-CH3 axis of the …

Regium Bonds Between Mn Clusters (M=Cu,Ag,Au And N=2-6) And Nucleophiles Nh3 And Hcn, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The most stable geometries of the coinagemetal (or regium) atom (Cu, Ag, Au) clusters Mn for n up to 6 are all planar, and adopt the lowest possible spin multiplicity. Clusters with even numbers of M atoms are thus singlets, while those with odd n are open-shell doublets. Examination of the molecular electrostatic potential (MEP) of each cluster provides strong indications of the most likely site of attack by an approaching nucleophile, generally one of two positions. A nucleophile (NH3 or HCN) most favorably approaches one particular M atom of each cluster, rather than a bond midpoint or face. In …

Piezoresponse, Mechanical, And Electrical Characteristics Of Synthetic Spider Silk Nanofibers, Nader Shehata, Ishac Kandas, Ibrahim Hassounah, Patrik Sobolčiak, Igor Krupa, Miroslav Mrlik, Anton Popelka, Jesse Steadman, Randolph V. Lewis

Biology Faculty Publications

This work presents electrospun nanofibers from synthetic spider silk protein, and their application as both a mechanical vibration and humidity sensor. Spider silk solution was synthesized from minor ampullate silk protein (MaSp) and then electrospun into nanofibers with a mean diameter of less than 100 nm. Then, mechanical vibrations were detected through piezoelectric characteristics analysis using a piezo force microscope and a dynamic mechanical analyzer with a voltage probe. The piezoelectric coefficient (d₃₃) was determined to be 3.62 pC/N. During humidity sensing, both mechanical and electric resistance properties of spider silk nanofibers were evaluated at varying high-level …

Investigations Into Factors Affecting The Wpd-Loop In The Protein Tyrosine Phosphatases Yoph And Ptp1b, Gwendolyn Moise

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research in this dissertation documents connections between the primary amino acid sequence of proteins, the dynamics of proteins, and their catalytic function. This research project studied two proteins called protein-tyrosine phosphatases (PTPs): the human enzyme PTP1B, and the bacterial enzyme YopH. PTP1B is a human enzyme that down regulates the insulin receptor on the outer cellular membrane, and causes the insulin receptor to be less responsive to insulin. A deeper knowledge of how PTP1B is different from other human PTPs might be useful in designing drugs to increase insulin sensitivity in diabetics. Yersinia Pestis is the bacteria that caused …

Comparative Strengths Of Tetrel, Pnicogen, Chalcogen, And Halogen Bonds And Contributing Factors, Wenbo Dong, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio calculations are employed to assess the relative strengths of various noncovalent bonds. Tetrel, pnicogen, chalcogen, and halogen atoms are represented by third-row atoms Ge, As, Se, and Br, respectively. Each atom was placed in a series of molecular bonding situations, beginning with all H atoms, then progressing to methyl substitutions, and F substituents placed in various locations around the central atom. Each Lewis acid was allowed to engage in a complex with NH3 as a common nucleophile, and the strength and other aspects of the dimer were assessed. In the context of fully hydrogenated acids, the strengths of …

Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH4, TH3F, and TH2F2 (T = Si, Ge, Sn) and the latter by TH2=CH2, THF=CH2, and TF2=CH2, all paired with NH3 as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of …

Tetrel Bonding As A Vehicle For Strong And Selective Anion Binding, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Tetrel atoms T (T = Si, Ge, Sn, and Pb) can engage in very strong noncovalent interactions with nucleophiles, which are commonly referred to as tetrel bonds. The ability of such bonds to bind various anions is assessed with a goal of designing an optimal receptor. The Sn atom seems to form the strongest bonds within the tetrel family. It is most effective in the context of a -SnF3 group and a further enhancement is observed when a positive charge is placed on the receptor. Connection of the -SnF3 group to either an imidazolium or triazolium provides a strong halide …

Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield

Chemistry and Biochemistry Faculty Publications

Solid or sludgy hydrocarbon waste is a byproduct of oil and gas exploration and production. One commonly-used method of disposing of this waste is landfarming. Landfarming involves spreading hydrocarbon waste on soils, tilling it into the soil, and allowing it to biodegrade. We used a dynamic flux chamber to measure fluxes of methane, a suite of 54 non-methane hydrocarbons, and light alcohols from an active and a remediated landfarm in eastern Utah, U.S.A. Fluxes from the remediated landfarm were not different from a PTFE sheet or from undisturbed soils in the region. Fluxes of methane, total non-methane hydrocarbons, and alcohols …

Water-Mediated Carbon–Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition In The Reactivation Domain Of Cobalamin-Dependent Methionine Synthase, Robert J. Fick, Mary C. Clay, Lucas Vander Lee, Steve Scheiner, Hashim M. Al-Hashimi, Raymond C. Trievel

Chemistry and Biochemistry Faculty Publications

The C-terminal domain of cobalamin-dependent methionine synthase (MetH) has an essential role in catalyzing the reactivation of the enzyme following the oxidation of its cobalamin cofactor. This reactivation occurs through reductive methylation of the cobalamin using S-adenosylmethionine (AdoMet) as the methyl donor. Herein, we examine the molecular recognition of AdoMet by the MetH reactivation domain utilizing structural, biochemical, and computational approaches. Crystal structures of the Escherichia coli MetH reactivation domain in complex with AdoMet, the methyl transfer product S-adenosylhomocysteine (AdoHcy), and the AdoMet analogue inhibitor sinefungin illustrate that the ligands exhibit an analogous conformation within the solvent-exposed substrate binding cleft …

Hydrodeoxygenation Of Pinyon-Juniper Catalytic Pyrolysis Oil Using Red Mud-Supported Nickel Catalysts, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

Red mud (RM) is an alkaline waste generated in the Bayer process of alumina production. In the present study red mud supported nickel catalysts (Ni/RM) were prepared at different concentrations of nickel (10, 20, 30, 40, 50, and 65 wt.%) and used to hydrodeoxygenate (HDO) pinyon-juniper (PJ) catalytic pyrolysis oil. Increasing the nickel content improved the activity of Ni/RM catalysts for HDO reactions. Maximum organic liquid yield (68.6%) was obtained when 40%Ni/RM was used. The upgraded oil had oxygen content of 1.35 wt.% and higher heating value of 45.77 MJ/kg compared to 24.88 wt.% and 28.41 MJ/kg, respectively, for the …

Sequential And Differential Interaction Of Assembly Factors During Nitrogenase Mofe Protein Maturation, Emilio Jimenez-Vicente, Zhi-Yong Yang, W. Keith Ray, Carlos Echavarri-Erasun, Valerie L. Cash, Luis M. Rubio, Lance C. Seefeldt, Dennis R. Dean

Chemistry and Biochemistry Faculty Publications

Nitrogenases reduce atmospheric nitrogen, yielding the basic inorganic molecule ammonia. The nitrogenase MoFe protein contains two cofactors, a [7Fe-9S-Mo-C-homocitrate] active-site species, designated FeMo-cofactor, and a [8Fe-7S] electron-transfer mediator called P-cluster. Both cofactors are essential for molybdenum-dependent nitrogenase catalysis in the nitrogen-fixing bacterium Azotobacter vinelandii. We show here that three proteins, NafH, NifW, and NifZ, copurify with MoFe protein produced by an A. vinelandii strain deficient in both FeMo-cofactor formation and P-cluster maturation. In contrast, two different proteins, NifY and NafY, copurified with MoFe protein deficient only in FeMo-cofactor formation. We refer to proteins associated with immature MoFe protein in …

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …

Structural Characterization Of The P1+ Intermediate State Of The P-Cluster Of Nitrogenase, Stephen M. Keable, Oleg A. Zadvornyy, Lewis E. Johnson, Bojana Ginovska, Andrew J. Rasmussen, Karamatullah Danyal, Brian J. Eilers, Gregory A. Prussia, Axl X. Levan, Simone Raugei, Lance C. Seefeldt, John W. Peters

Chemistry and Biochemistry Faculty Publications

Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N₂) to ammonia (NH₃) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum–iron protein (MoFe protein) that contains the iron–molybdenum cofactor (FeMo-co) sites where N₂ is reduced to NH₃. The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the …

Elucidating Molecular Interactions Of Shigella Type Three Secretion System Components Critical For Pathogenesis, R. Alan Burgess

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Shigella are pathogenic bacteria which commonly infect human hosts through the fecal-oral route. As the causative agent of shigellosis, a disease characterized by severe diarrhea, nausea, and vomiting, Shigella are responsible for an estimated 90 million infections and 100,000 deaths each year. With the emergence of antibiotic resistant strains of Shigella, the need for alternative treatments methods has become critical to fighting outbreaks of shigellosis and drug resistant strains. One such method is to target the infection system of the bacteria, called the type three secretion system (T3SS). The T3SS includes a complex needle and syringe-like apparatus that is …

Effect Of Magnesium Bond On The Competition Between Hydrogen Bond And Halogen Bond And The Induction Of Proton And Halogen Transfer, Hui-Li Xu, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

HOX (X=Cl, Br, I, and At) can engage in either a H‐bond (HB) or halogen bond (XB) with a base‐like HCN, NH3, and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY2 forms a Mg‐bond with the O atom of HOX, which grows stronger in the order X=Cl

Magnetic Properties Of Acenes And Their O-Quinone Derivatives: Computer Simulation, A. A. Starikova, A. G. Starikov, R. M. Minyaev, Alexander I. Boldyrev, V. I. Minkin

Chemistry and Biochemistry Faculty Publications

Quantum chemical study (DFT UB3LYP/6-311++G(d,p)) of the structure and properties of acenes functionalized with two o-benzoquinone groups and their complexes with sodium cations has been performed. An increase in the number of fused rings has been shown to result in the stabilization of biradicaloid state of acenes and the switching of the character of exchange interactions between redox-active moieties from antiferromagnetic to ferromagnetic. The obtained results allow one to consider o-quinone acene derivatives as a basis for designing magnetoactive compounds.

Emissions Of Organic Compounds From Produced Water Ponds I: Characteristics And Speciation, Seth N. Lyman, Marc L. Mansfield, Huy N. Q. Tran, Jordan D. Evans, Colleen Jones, Trevor O'Neil, Ric Bowers, Ann Smith, Cara Keslar

Chemistry and Biochemistry Faculty Presentations

We measured fluxes of methane, a suite of non-methane hydrocarbons (C2–C11), light alcohols, and carbon dioxide from oil and gas produced water storage and disposal ponds in Utah (Uinta Basin) and Wyoming (Upper Green River Basin) United States during 2013–2016. In this paper, we discuss the characteristics of produced water composition and air-water fluxes, with a focus on flux chamber measurements. In companion papers, we will (1) report on inverse modeling methods used to estimate emissions from produced water ponds, including comparisons with flux chamber measurements, and (2) discuss the development of mass transfer coefficients to estimate emissions and place …

Mxin Differentially Regulates Monomeric And Oligomeric Species Of The Shigella Type Three Secretion System Atpase Spa47, Heather B. Case, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at the base of the Shigella needle-like type three secretion apparatus (T3SA), supporting protein secretion through the apparatus and providing a likely means for native virulence regulation by Shigella and a much needed target for non-antibiotic therapeutics to treat Shigella infections. Here, we show that MxiN is a differential regulator of Spa47 and that its regulatory impact is determined by the oligomeric state of the Spa47 ATPase, with …

Halogen, Chalcogen, And Pnicogen Bonding Involving Hypervalent Atoms, Steve Scheiner, Jia Lu

Chemistry and Biochemistry Faculty Publications

The additional substituents arising from hypervalency present a number of complicating issues for the formation of noncovalent bonds. The XF5 molecule (X=Cl, Br, I) was allowed to form a halogen bond with NH3 as base. Hypervalent chalcogen bonding is examined by way of YF4 and YF6 (Y=S, Se, Te), and ZF5 (Z=P, As, Sb) is used to model pnicogen bonding. Pnicogen bonds are particularly strong, with interaction energies approaching 50 kcal/mol, and also involve wholesale rearrangement from trigonal bipyramidal in the monomer to square pyramidal in the complex, subject to a large deformation energy. YF4 chalcogen bonding is also strong, …

Electron Injection From A Carboxylic Anchoring Dye To Tio2 Nanoparticles In Aprotic Solvents, Hui Fang, Yuhao Wu, Danielle L. Kuhn, Brendan G. Delacy, Yi Rao, Hai-Lung Dai

Chemistry and Biochemistry Faculty Publications

Injection of photoexcited electrons in the para-Ethyl Red dye to TiO₂ nanoparticles (Anatase, 40 nm diameter) is characterized by transient absorption on ultrafast time scales. This study focuses on understanding the effect of aprotic solvents on the injection rate. Transient absorption at 1900 cm⁻¹ is probed following a 400 nm pulse which excites the electronic transition of p-ER adsorbed on TiO₂ through its carboxylic group. Measurements conducted in three different solvents show that electron injection lifetimes are in the 250–300 fs range but display a trend in correlation with solvent polarity: the electron injection lifetime is the …

Electrolyzer Design For Flexible Decoupled Water Splitting And Organic Upgrading With Electron Reservoirs, Wei Li, Nan Jiang, Bo Hu, Xuan Liu, Fuzhan Song, Guanqun Han, Taylor J. Jordan, Tanner B. Hanson, T. Leo Liu, Yujie Sun

Chemistry and Biochemistry Faculty Publications

The Bigger Picture

Electrocatalytic water splitting is a green approach to producing clean H₂ fuel, especially when it is driven by renewable energy sources. Conventional water electrolysis always produces H₂ and O₂ simultaneously under corrosive acidic or alkaline conditions with large voltage inputs, posing safety concerns of H₂/O₂ mixing. Therefore, it is desirable to develop a new electrolyzer design for decoupled water splitting in an eco-friendly neutral solution with small voltage inputs to enable separated H₂ and O₂ evolution. Herein, we report (ferrocenylmethyl)trimethylammonium chloride and Na₄[Fe(CN)₆] as proton-independent …

Electron Transfer To Nitrogenase In Different Genomic And Metabolic Backgrounds, Saroj Poudel, Daniel R. Colman, Kathryn R. Fixen, Rhesa N. Ledbetter, Yanning Zheng, Natasha Pence, Lance C. Seefeldt, John W. Peters, Caroline S. Harwood, Eric S. Boyd

Chemistry and Biochemistry Faculty Publications

Nitrogenase catalyzes the reduction of dinitrogen (N₂) using low-potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP-dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O₂)-sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds, including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd-/Fld-reducing enzymes in 359 genomes of putative N₂ fixers (diazotrophs). Six distinct lineages …

Implications Of Monomer Deformation For Tetrel And Pnicogen Bonds, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A series of TF₄ and ZF₅ molecules (T = Si, Ge, Sn and Z = P, As, Sb) were allowed to engage in tetrel and pnicogen bonds, respectively, with NH₃, pyrazine, and HCN. The interaction energies are quite large, approaching 50 kcal mol^-1 in some cases. The formation of each complex is accompanied by substantial geometrical deformation of the Lewis acid to accommodate the approaching base. The energy associated with this monomer rearrangement is the largest for the smaller central atoms Si and P, where it exceeds 20 kcal mol^-1. The total reaction …

Steric Crowding In Tetrel Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The tetravalent character of tetrel atoms leaves only limited room for an incoming nucleophile to approach and engage in a noncovalent bond with a tetrel atom. Any such approach can only occur at the expense of internal geometric distortions. The balance between attractive forces and repulsive steric crowding was studied for a series of Lewis acids of the type FTR₃ (T = Si, Ge, Sn, Pb) which were allowed to interact with various bases. The strength and other properties of the tetrel bond are examined as the R groups are made progressively larger, varying from H and CH_{3 …}

Pi Tetrel Bonds, And Their Influence On Hydrogen Bonds And Proton Transfers, Yuanxin Wei, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The positive region that lies above the plane of F2TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H‐bond. The T atom of F2TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F2TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F2SiO engages in a much stronger interaction than does F2CO, reaching nearly 200 kJ mol−1. The π‐tetrel bond strengthens/weakens the MDA H‐bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an …

Aerogen Bonds Formed Between Aeof2 (Ae = Kr, Xe) And Diaziness: Comparisons Between Σ-Hole And Π-Hole Complexes, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The interaction between KrOF2 or XeOF2 and the 1,2, 1,3, and 1,4 diazines is characterized chiefly by a Kr/Xe···N aerogen bond, as deduced from ab initio calculations. The most stable dimers take advantage of the σ-hole on the aerogen atom, wherein the two molecules lie in the same plane. The interaction is quite strong, as much as 18 kcal mol-1. A second class of dimer geometry utilizes the π-hole above the aerogen atom in an approximate perpendicular arrangement of the two monomers; these structures are not as strongly bound: 6-8 kcal mol-1. Both sorts of dimers contain auxiliary CH···F H-bonds …

Computational Assessment Of An Elusive Aromatic N3p3 Molecule, Alyona A. Starikova, Natalia M. Boldyreva, Ruslan M. Minyaev, Alexander I. Boldyrev, Vladimir I. Minkin

Chemistry and Biochemistry Faculty Publications

We computationally proved that the planar aromatic hexagonal isomer N₃P₃ with the alteration of N and P is the second most stable structure for the N₃P₃ stoichiometry. We found that the aromatic isomer has high barriers for transition into the global minimum structure or into the three isolated NP molecules, making this structure kinetically stable. We showed that the sandwich N₃P₃CrN₃P₃ molecule corresponds to a minimum on the potential energy surface; thus, the aromatic N₃P₃ molecule has a potential to be a new ligand …

Transplanting A Bacterial Immune System: Determining The Function Of A Novel Crispr System, Riannon Smith, Melena Garrett

Research on Capitol Hill

CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) loci and cas (CRISPR-associated) genes provide adaptive immunity (see panel below) in bacteria and have recently been repurposed for genome editing.

Systems are structurally and functionally diverse.

• 2 classes, 6 types, 33 subtypes
• Very few have been studied experimentally
• None of the Type IV systems have been characterized

Emissions Of Organic Compounds From Produced Water Ponds, Seth Lyman

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We measured fluxes of methane, a suite of non-methane hydrocarbons (C2-C11), light alcohols, and carbon dioxide from oil and gas produced water storage and disposal ponds in Utah (Uinta Basin) and Wyoming (Upper Green River Basin) United States during 2013-2016. In this paper, we discuss the characteristics of produced water composition and air-water fluxes, with a focus on flux chamber measurements. In companion papers, we will (1) report on inverse modeling methods used to estimate emissions from produced water ponds, including comparisons with flux chamber measurements, and (2) discuss the development of mass transfer coefficients to estimate emissions and place …

Mechanistic Studies Of The Iron And Molybdenum Nitrogenases, Derek Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a basic building block in many biological molecules the element nitrogen (N) is essential for life. Dinitrogen (N2) is abundant in Earth’s atmosphere, but this form is biologically unavailable. To be biologically available N2 must undergo an energy demanding reduction reaction to the fixed form, ammonia (NH3). The industrial Haber-Bosch process, which accounts for approximately 50% of the worlds fixed nitrogen, uses energy from fossil fuels to achieve high pressures and temperatures to facilitate the reaction. The energy used by Haber-Bosch accounts for approximately 2% of the world’s annual supply. The remainder of fixed nitrogen is produced biologically by …