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Articles 1 - 30 of 78
Full-Text Articles in Physical Sciences and Mathematics
Relation Between Halogen Bond Strength And Ir And Nmr Spectroscopic Markers, Akhtam Amonov, Steve Scheiner
Relation Between Halogen Bond Strength And Ir And Nmr Spectroscopic Markers, Akhtam Amonov, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C–X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded …
C···O And Si···O Tetrel Bonds: Substituent Effects And Transfer Of The Sif3 Group, Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner
C···O And Si···O Tetrel Bonds: Substituent Effects And Transfer Of The Sif3 Group, Zhihao Niu, Qiaozhuo Wu, Qingzhong Li, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The tetrel bond (TB) between 1,2-benzisothiazol-3-one-2-TF3-1,1-dioxide (T = C, Si) and the O atom of pyridine-1-oxide (PO) and its derivatives (PO-X, X = H, NO2, CN, F, CH3, OH, OCH3, NH2, and Li) is examined by quantum chemical means. The Si···O TB is quite strong, with interaction energies approaching a maximum of nearly 70 kcal/mol, while the C···O TB is an order of magnitude weaker, with interaction energies between 2.0 and 2.6 kcal/mol. An electron-withdrawing substituent on the Lewis base weakens this TB, while an electron-donating group has the opposite …
Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser
Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser
All Graduate Theses and Dissertations, Spring 1920 to Summer 2023
Similarly to people, bacteria are under the treat of infection by viruses. To circumvent these threats, bacteria evolve complex immune systems. Our understanding of some of these immune systems has led to many advancements in the field of Biotechnology including tools that made expressing proteins for study in a lab easier, tools that revolutionized the feasibility of gene editing, and tools that could change the way we think about viral diagnostics and cancer therapeutics. A certain type of immune system that bacteria use to fight virus is called a CRISPR system. Presented here is work to understand the function of …
Structural And Functional Studies Of Mtr4 And The Tramp Rna Surveillance Complex, Sean Johnson
Structural And Functional Studies Of Mtr4 And The Tramp Rna Surveillance Complex, Sean Johnson
Funded Research Records
No abstract provided.
Collaborative Research: Developing Advanced Magnesium Electrolytes Toward Low Cost, High Energy Density Mg Batteries, Tianbiao Liu
Collaborative Research: Developing Advanced Magnesium Electrolytes Toward Low Cost, High Energy Density Mg Batteries, Tianbiao Liu
Funded Research Records
No abstract provided.
Collaborative Research: Surface-Specific Aerosol Chemistry: Direct Observations, Kinetics, And Environmental Impact, Yi Rao
Funded Research Records
No abstract provided.
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
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 …
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
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
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 (Ksoil–air,AI), as part of commercial formulations (Ksoil–air,formulation), and as formulation mixtures with an additional spray adjuvant added (Ksoil–air,formulation+spray adjuvant). Chlorpyrifos Ksoil–air,formulation values were also measured over 15–30 °C, allowing for the change in internal energy of the phase transfer reaction (Δsoil–airU) to be calculated and compared to the Δsoil–airU for Ksoil–air,AI from the literature. Measured Ksoil–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
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 …
Modeling The Alkaline Hydrolysis Of Diaryl Sulfate Diesters: A Mechanistic Study, Klaudia Szeler, Nicholas H. Williams, Alvan C. Hengge, Shina C. Kamerlin
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 …
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
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 …
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
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 …
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
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
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 …
Consumption Of Black Raspberries Altered The Composition Of The Fecal Microbiome In Mice Fed A Western Type Diet (Or04-01-19), Abby D. Benninghoff, Sumira Phatak, Korry Hintze
Consumption Of Black Raspberries Altered The Composition Of The Fecal Microbiome In Mice Fed A Western Type Diet (Or04-01-19), Abby D. Benninghoff, Sumira Phatak, Korry Hintze
Chemistry and Biochemistry Faculty Publications
Dietary strategies to reduce colonic inflammation and promote gut homeostasis may markedly reduce the risk of colitis-associated colorectal cancer. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption a Western type diet in mice. In this study, our goal was to assess the impact of consumption of the TWD with and without black raspberry supplementation on the composition of the fecal microbiome over the course of disease development.
Dietary Intervention With Black Raspberries To Reduce Colitis Symptoms In Mice Fed Either Standard Ain93g Diet Or The Total Western Diet (P05-021-19), Daphne Michelle Rodriguez Jimenez, Michaela Brubaker, Elizabeth Park, Canyon Neal, Korry Hintze, Abby D. Benninghoff
Dietary Intervention With Black Raspberries To Reduce Colitis Symptoms In Mice Fed Either Standard Ain93g Diet Or The Total Western Diet (P05-021-19), Daphne Michelle Rodriguez Jimenez, Michaela Brubaker, Elizabeth Park, Canyon Neal, Korry Hintze, Abby D. Benninghoff
Chemistry and Biochemistry Faculty Publications
Approximately 1.4 million people suffer from inflammatory bowel disease, which is a major risk factor for developing colitis associated colorectal cancer (CAC). Dietary interventions with the goal to reduce colon inflammation and encourage gut microbiome homeostasis may be a strategy to reduce the risk of CAC. The antioxidants and anti-inflammatory compounds present in black raspberries (BRB) have demonstrated protective effects in the colon epithelium and may alter the composition of the gut microbiome. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption of a Western type diet in mice. The …
Interactions Of (My) 6 (M = Zn, Cd; Y = O, S, Se) Quantum Dots With N-Bases, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner
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 …
Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation, Yi Rao, Yuqin Qian, Gang-Hua Deng, Ashlie Kinross, Nicholas J. Turro, Kenneth B. Eisenthal
Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation, Yi Rao, Yuqin Qian, Gang-Hua Deng, Ashlie Kinross, Nicholas J. Turro, Kenneth B. Eisenthal
Chemistry and Biochemistry Faculty Publications
This paper presents the first study of the rotations of rigid molecules in 3 dimensions at the air/water interface, using the femtosecond time resolved sum frequency generation (SFG) technique. For the purpose of this research, the aromatic dye molecule C153 was chosen as an example of a molecule having two functional groups that are SFG active, one being the hydrophilic −−C==O group and the other the hydrophobic −−CF3 group. From polarized SFG measurements, the orientations of the two chromophores with respect to the surface normal were obtained. On combining these results with the known relative orientation of the two …
Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase, Bert Van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder
Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase, Bert Van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder
Chemistry and Biochemistry Faculty Publications
Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyses sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PASWT has a much less negative Brønsted coefficient (ßleaving group obs-Enz=-0.33) than the uncatalyzed reaction (ßleaving group obs=-1.81). This situation is diminished when cationic active site groups are exchanged for alanine. …
Catalytic Mechanism For The Conversion Of Salicylate Into Catechol By The Flavin-Dependent Monooxygenase Salicylate Hydroxylase, Débora M. A. Costa, Stefanya V. Gómez, Simara S. De Araújo, Mozart S. Pereira, Rosemeire B. Alves, Denize C. Favaro, Alvan C. Hengge, Ronaldo A. P. Nagem, Tiago A. S. Brandão
Catalytic Mechanism For The Conversion Of Salicylate Into Catechol By The Flavin-Dependent Monooxygenase Salicylate Hydroxylase, Débora M. A. Costa, Stefanya V. Gómez, Simara S. De Araújo, Mozart S. Pereira, Rosemeire B. Alves, Denize C. Favaro, Alvan C. Hengge, Ronaldo A. P. Nagem, Tiago A. S. Brandão
Chemistry and Biochemistry Faculty Publications
Salicylate hydroxylase (NahG) is a flavin-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of salicylate into catechol in the naphthalene degradation pathway in Pseudomonas putida G7. We explored the mechanism of action of this enzyme in detail using a combination of structural and biophysical methods. NahG shares many structural and mechanistic features with other versatile flavin-dependent monooxygenases, with potential biocatalytic applications. The crystal structure at 2.0 Å resolution for the apo form of NahG adds a new snapshot preceding the FAD binding in flavin-dependent monooxygenases. The kcat/Km for the salicylate reaction catalyzed by the holo form is …
Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner
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 combined, it is the axial …
Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao
Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao
Chemistry and Biochemistry Faculty Publications
Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultra fast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB3O6 crystal-based optical parametric amplifier, which generates a …
Carbene Triel Bonds Between Trr3 (Tr=B, Al) And N-Heterocyclic Carbenes, Zongqing Chi, Wenbo Dong, Qingzhong Li, Xin Yang, Steve Scheiner, Shufeng Liu
Carbene Triel Bonds Between Trr3 (Tr=B, Al) And N-Heterocyclic Carbenes, Zongqing Chi, Wenbo Dong, Qingzhong Li, Xin Yang, Steve Scheiner, Shufeng Liu
Chemistry and Biochemistry Faculty Publications
The carbene triel bond is predicted and characterized by theoretical calculations. The C lone pair of N‐heterocyclic carbenes (NHCs) is allowed to interact with the central triel atom of TrR3 (Tr = B and Al; R = H, F, Cl, and Br). The ensuing bond is very strong, with an interaction energy of nearly 90 kcal/mol. Replacement of the C lone pair by that of either N or Si weakens the binding. The bond is strengthened by electron‐withdrawing substituents on the triel atom, and the reverse occurs with substitution on the NHC. However, these effects do not strictly follow …
Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf
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 …
Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner
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 …
Dependence Of Nmr Chemical Shifts Upon Ch Bond Lengths Of A Methyl Group Involved In A Tetrel Bond, Steve Scheiner
Dependence Of Nmr Chemical Shifts Upon Ch Bond Lengths Of A Methyl Group Involved In A Tetrel Bond, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Four different Lewis acids that might participate in a tetrel bond with a nucleophile (SEt2Me+, NMe4+, SMe2, NMe3) are examined. The NMR chemical shifts of the methyl C and H atoms are calculated as the CH bond lengths are systematically stretched and contracted, in the absence of a base. The C shielding diminishes by roughly 2 ppm for a stretch of 0.01 Å, while that of H drops by only 0.3 ppm. The deshieldings caused purely by the bond length changes are far too small to account for the …
Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner
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 …
Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield
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 …
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
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 …