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Articles 1 - 30 of 112

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

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 Aug 2019

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

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 ...


On The Ability Of Pnicogen Atoms To Engage In Both Σ And Π-Hole Complexes. Heterodimers Of Zf2C6H5 (Z = P, As, Sb, Bi) And Nh3, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner May 2019

On The Ability Of Pnicogen Atoms To Engage In Both Σ And Π-Hole Complexes. Heterodimers Of Zf2C6H5 (Z = P, As, Sb, Bi) And Nh3, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH3 base lies opposite one F atom. In addition to this σ-hole complex, the ZF2C6H5 molecule can distort in such a way that the NH3 approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4–13 ...


Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Nikolay V. Tkachenko, Alexander I. Boldyrev Apr 2019

Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Nikolay V. Tkachenko, Alexander I. Boldyrev

Chemistry and Biochemistry Faculty Publications

Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge9]4−, [Ge9{P(NH2)2}3], Cu[Ge9{P(NH2)2}3] and Cu(NHC)[Ge9{P(NH2)2}3]) and obtained a simple and chemically intuitive bonding pattern which can explain the variety of active sites ...


Interactions Of (My) 6 (M = Zn, Cd; Y = O, S, Se) Quantum Dots With N-Bases, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner Apr 2019

Interactions Of (My) 6 (M = Zn, Cd; Y = O, S, Se) Quantum Dots With N-Bases, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

(MY)6 clusters, with M = Zn and Cd and Y = O, S, Se, form double-layer drum-like structures containing M–Y covalent bonds. The positive regions near the M atoms attract the N atom of both NH3 and NMe3 so as to form a noncovalent M···N bond. This bond is quite strong, with interaction energies exceeding 35 kcal/mol. The bond strength diminishes with reduced electronegativity of the Y atom (O > S > Se) and is stronger for M = Zn than for Cd. Trimethylation of the base enhances the bond strength. The interaction is dominated by the electrostatic component ...


The Nifz Accessory Protein Has An Equivalent Function In Maturation Of Both Nitrogenase Mofe Protein P-Clusters, Emilio Jimenez-Vicente, Zhi-Yong Yang, Julia S. Martin Del Campo, Valarie L. Cash, Lance C. Seefeldt, Dennis R. Dean Apr 2019

The Nifz Accessory Protein Has An Equivalent Function In Maturation Of Both Nitrogenase Mofe Protein P-Clusters, Emilio Jimenez-Vicente, Zhi-Yong Yang, Julia S. Martin Del Campo, Valarie L. Cash, Lance C. Seefeldt, Dennis R. Dean

Chemistry and Biochemistry Faculty Publications

The Mo-dependent nitrogenase comprises two interacting components called the Fe protein and the MoFe protein. The MoFe protein is an α2β2 heterotetramer that harbors two types of complex metalloclusters, both of which are necessary for N2reduction. One type is a 7Fe-9S-Mo-C-homocitrate species designated FeMo-cofactor, which provides the N2-binding catalytic site, and the other is an 8Fe-7S species designated the P-cluster, involved in mediating intercomponent electron transfer to FeMo-cofactor. The MoFe protein's catalytic partner, Fe protein, is also required for both FeMo-cofactor formation and the conversion of an immature form of P-clusters to ...


Optical Stability Of 1,1′-Binaphthyl Derivatives, Nikolay V. Tkachenko, Steve Scheiner Mar 2019

Optical Stability Of 1,1′-Binaphthyl Derivatives, Nikolay V. Tkachenko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The racemization process of various 1,1′-binaphthyl derivatives is studied by quantum calculations. The preferred racemization pathway passes through a transition state belonging to the Ci symmetry group. The energy barrier for this process is independent of solvation, the electron-withdrawing/releasing power of substituents, or their ability to engage in H-bonds within the molecule. The primary factor is instead the substituent size. The barrier is thus reduced when the −OH groups of 1,1′-bi-2-naphthol are replaced by H. There is a drop in the barrier also when the substituents are moved from the 2,2′ positions to ...


Molecular Relatedness Of Two Distinct Type Iv Crispr-Associated (Cas) Proteins, Matt Armbrust Mar 2019

Molecular Relatedness Of Two Distinct Type Iv Crispr-Associated (Cas) Proteins, Matt Armbrust

Research on Capitol Hill

CRISPR-Cas systems are prokaryotic adaptive immune systems. Bacteria use CRISPR systems as a defense against foreign nucleic acid invasion such as phage infection.


Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner Jan 2019

Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When an N-base approaches the tetrel atom of TF4(T = Si, Ge, Sn) the latter moleculedeforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situateitself at either an axial or equatorial position, leading to two different equilibrium geometries.The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol,which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform thetetrahedral monomer into the equatorial structure is much higher than the equivalent deformationenergy in the axial dimer. When these two opposite trends are ...


Differential Binding Of Tetrel-Bonding Bipodal Receptors To Monatomic And Polyatomic Anions, Steve Scheiner Jan 2019

Differential Binding Of Tetrel-Bonding Bipodal Receptors To Monatomic And Polyatomic Anions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl was thus compared to that of HCOO, HSO4, and H2PO4 with a wide variety of bidentate receptors. A pair of SnFH2 groups, as strong ...


Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf Dec 2018

Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf

Fall Student Research Symposium 2018

Aerosol particles are thought to impact climate properties. The ability to probe aerosols to understand their chemical properties has been difficult due to a lack of appropriate analytical techniques. Here we present interface-specific SHS techniques to allow for in situ analysis of aerosol particles. Transportation of aerosols from their collection site to the laboratory disturbs their chemical and physical properties thus making it difficult to take accurate measurements of aerosol particles. We show that using a CCD detector is a more effective option for producing more sensitive results and can greatly reduce sampling time and could possibly detect measurements from ...


A Simple Metabolic Switch May Activate Apomixis In Arabidopsis Thaliana, David Alan Sherwood Dec 2018

A Simple Metabolic Switch May Activate Apomixis In Arabidopsis Thaliana, David Alan Sherwood

All Graduate Theses and Dissertations

Apomixis, asexual or clonal seed production in plants, can decrease the cost of producing hybrid seed and enable currently open pollinated crops to be converted to more vigorous and higher yielding hybrids that can reproduce themselves through their own seed. Sexual reproduction may be triggered by a programmed stress signaling event that occurs in both the meiocyte, just prior to meiosis, and later in the egg just prior to embryo sac maturation. The prevention of stress signaling and the activation of a pro-growth signal prior to meiosis triggered apomeiosis, the first half of apomixis. The same approach was used prior ...


Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner Nov 2018

Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in SN2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the SN2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered ...


Role Of Nucleotide Identity In Effective Crispr Target Escape Mutations, Tim Künne, Yifan Zhu, Fausia Da Silva, Nico Konstantinides, Rebecca E. Mckenzie, Ryan N. Jackson, Stan J.J. Brouns Aug 2018

Role Of Nucleotide Identity In Effective Crispr Target Escape Mutations, Tim Künne, Yifan Zhu, Fausia Da Silva, Nico Konstantinides, Rebecca E. Mckenzie, Ryan N. Jackson, Stan J.J. Brouns

Chemistry and Biochemistry Faculty Publications

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets ...


Electron Flow And Management In Living Systems: Advancing Understanding Of Electron Transfer To Nitrogenase, Rhesa N. Ledbetter Aug 2018

Electron Flow And Management In Living Systems: Advancing Understanding Of Electron Transfer To Nitrogenase, Rhesa N. Ledbetter

All Graduate Theses and Dissertations

Nitrogen is a critical nutrient for growth and reproduction in living organisms. Although the Earth’s atmosphere is composed of ~80% nitrogen gas (N2), it is inaccessible to most living organisms in that form. Biological nitrogen fixation, however, can be performed by microbes that harbor the enzyme nitrogenase. This enzyme converts N2 into bioavailable ammonia (NH3) and accounts for at least half of the “fixed”nitrogen on the planet. The other major contributor to ammonia production is the industrial Haber-Bosch process. While the Haber-Bosch process has made significant advances in sustaining the global food supply through the generation of fertilizer ...


Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner Jun 2018

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 ...


Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield May 2018

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 ...


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 May 2018

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 ...


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 Apr 2018

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.


Mxin Differentially Regulates Monomeric And Oligomeric Species Of The Shigella Type Three Secretion System Atpase Spa47, Heather B. Case, Nicholas E. Dickenson Mar 2018

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 ...


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 Feb 2018

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 Feb 2018

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 energy of binding, which ...


Pi Tetrel Bonds, And Their Influence On Hydrogen Bonds And Proton Transfers, Yuanxin Wei, Qingzhong Li, Steve Scheiner Feb 2018

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 ...


Special Issue: Intramolecular Hydrogen Bonding 2017, Steve Scheiner Sep 2017

Special Issue: Intramolecular Hydrogen Bonding 2017, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Even after more than a century of study [1–6], scrutiny, and detailed examination, the H-bond continues [7–12] to evoke a level of fascination that surpasses many other phenomena. Perhaps it is the ability of the simple H atom, with but a single electron, to act as a glue that maintains contact between much more complicated species. Or it might be its geometry, which prefers to hold the bridging proton on a direct line between the two heavy atoms. Not to be ignored are the spectral features of the H-bond: the large red shift of the stretching frequency of ...


Unraveling The Interactions Of The Physiological Reductant Flavodoxin With The Different Conformations Of The Fe Protein In The Nitrogenase Cycle, Natasha Pence, Monika Tokmina-Lukaszewska, Zhi-Yong Yang, Rhesa N. Ledbetter, Lance C. Seefeldt, Brian Bothner, John W. Peters Aug 2017

Unraveling The Interactions Of The Physiological Reductant Flavodoxin With The Different Conformations Of The Fe Protein In The Nitrogenase Cycle, Natasha Pence, Monika Tokmina-Lukaszewska, Zhi-Yong Yang, Rhesa N. Ledbetter, Lance C. Seefeldt, Brian Bothner, John W. Peters

Chemistry and Biochemistry Faculty Publications

Nitrogenase reduces dinitrogen (N2) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of Pi, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of Pi. Because the Fe ...


A Bipyridine-Ligated Zinc(Ii) Complex With Bridging Flavonolate Ligation: Synthesis, Characterization, And Visible-Light-Induced Co Release Reactivity, Shayne Sorenson, Marina Popova, Atta M. Arif, Lisa M. Berreau Aug 2017

A Bipyridine-Ligated Zinc(Ii) Complex With Bridging Flavonolate Ligation: Synthesis, Characterization, And Visible-Light-Induced Co Release Reactivity, Shayne Sorenson, Marina Popova, Atta M. Arif, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Metal-flavonolate compounds are of significant current interest as synthetic models for quercetinase enzymes and as bioactive compounds of importance to human health. Zinc-3-hydroxyflavonolate compounds, including those of quercetin, kampferol, and morin, generally exhibit bidentate coordination to a single ZnII center. The bipyridine-ligated zinc-flavonolate compound reported herein, namely bis(μ-4-oxo-2-phenyl-4H-chromen-3-olato)-κ3O3:O3,O4;κ3O3,O4:O3-bis[(2,2′-bipyridine-κ2N,N′)zinc(II)] bis(perchlorate), {[Zn2(C15H9O3)2(C10H8N2)2](ClO4)2}n, (1), provides an unusual example of bridging 3-hydroxyflavonolate ligation in a dinuclear metal complex. The symmetry-related ZnII centers of (1) exhibit a distorted octahedral geometry, with weak coordination of ...


First-Row Transition Metal Sulfides And Phosphides As Competent Electrocatalysts For Water Splitting, Nan Jiang May 2017

First-Row Transition Metal Sulfides And Phosphides As Competent Electrocatalysts For Water Splitting, Nan Jiang

All Graduate Theses and Dissertations

Conversion of renewable energy resources (such as solar and wind) through water splitting to hydrogen and oxygen has attracted increasing attention. The sole product of hydrogen combustion is water, rendering a carbon-neutral energy cycle. Water splitting consists of two redox half reactions: hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Both of these two transformations involve multi- electron/proton movement and thus are kinetically sluggish. In order to accelerate the reaction rates for practical application, efficient catalysts are needed. State-of-the-art catalysts for water splitting are usually composed of noble metals, such as platinum, ruthenium, and iridium, whose scarcity and ...


Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan May 2017

Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan

All Graduate Theses and Dissertations

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B ...


Mechanism Of Substrate Reduction By Nitrogenase, Nimesh Khadka May 2017

Mechanism Of Substrate Reduction By Nitrogenase, Nimesh Khadka

All Graduate Theses and Dissertations

Nitrogen (N) is a chemical constituent for almost all biological molecules including proteins, DNA, RNA, lipids and is therefore vital for life. The ultimate source of nitrogen is the atmospheric dinitrogen (N2) but that only becomes bioavailable through a process of nitrogen fixation, the process that converts N2 to ammonia (NH3). The industrial Haber-Bosch process and biological nitrogen fixation account for the majority of nitrogen fixed every year. However, due to its high temperature, pressure and fossil fuel requirements, Haber-Bosch is an expensive process. Every year, approximately 3% of the global energy demand is used to manufacture ...


Identifying Multiple Predictors Of Physical Rehabilitation Outcomes, Jacklyn M. Sullivan, Elizabeth B. Fauth, Sydney Y. Schaeffer Jan 2017

Identifying Multiple Predictors Of Physical Rehabilitation Outcomes, Jacklyn M. Sullivan, Elizabeth B. Fauth, Sydney Y. Schaeffer

Research on Capitol Hill

Previous studies have suggested that disability in activities of daily living (ADLs) is an outcome of cognitive impairment, physical limitations, psychosocial factors, and environmental constraints. We hypothesis that cognitive abilities and psychosocial factors measured at admission can be used to predict a patients physical therapy progression in a transitional care facility. Environmental conditions were held constant for all patients and physical limitations were not used as a predictor of therapy progression, as the test for therapy progression is based on physical ability. In a sample of adults (n=93) aged 38-98 receiving physical rehabilitation treatment, we collected Minimum Data Set ...


Monitoring The Charge Distribution During Proton And Sodium Ion Conduction Along Chains Of Water Molecules And Protein Residues, Steve Scheiner Aug 2016

Monitoring The Charge Distribution During Proton And Sodium Ion Conduction Along Chains Of Water Molecules And Protein Residues, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to determine the level of delocalization of the charge of a cation as it translates along a chain of water molecules or glycine residues. Charge dispersal is monitored via the molecular electrostatic potential and the dipole moment of the entire system. The positive charge is largely localized on the water molecule on which the proton is situated, but becomes more intense and extended as the proton moves along the chain. The positive charge is more delocalized in protonated polyglycine, where it extends over at least an entire residue. Displacement of the proton along the chain intensifies ...