Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Biochemistry, Biophysics, and Structural Biology (204)
- Life Sciences (204)
- Biochemistry (194)
- Physics (14)
- Analytical Chemistry (7)
-
- Education (3)
- Computational Chemistry (2)
- Organic Chemistry (2)
- Biophysics (1)
- Curriculum and Instruction (1)
- Educational Methods (1)
- Environmental Sciences (1)
- Higher Education (1)
- Materials Chemistry (1)
- Oil, Gas, and Energy (1)
- Physical Chemistry (1)
- Science and Mathematics Education (1)
- University Extension (1)
- Institution
- Keyword
-
- NBO (27)
- AIM (23)
- Molecular electrostatic potential (16)
- MEP (13)
- Biomass burning (12)
-
- MP2 (11)
- NH3 (9)
- Pnicogen bond (9)
- Hydrogen (8)
- Tetrel bond (8)
- Charge transfer (7)
- Dispersion (7)
- Energy decomposition (7)
- Nitrogenase (7)
- Study (7)
- Π-hole (7)
- Σ-hole (7)
- Ab (6)
- Chalcogen bond (6)
- Comparison (6)
- Initio (6)
- Properties (6)
- Proton (6)
- Ammonia (5)
- Bonded (5)
- Complexes (5)
- Electronic (5)
- H2O (5)
- HCl (5)
- HF (5)
Articles 61 - 90 of 384
Full-Text Articles in Chemistry
Comparison Of Halogen With Proton Transfer. Symmetric And Asymmetric Systems, Jia Lu, Steve Scheiner
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
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.
Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter And Sulfur Dioxide From Vehicles And Brick Kilns And Their Impacts On Air Quality In The Kathmandu Valley, Nepal, Min Zhong, Eri Saikawa, Alexander Avramov, Chen Chen, Boya Sun, Wenlu Ye, William C. Keene, Robert J. Yokelson, Thilina Jayarathne, Elizabeth A. Stone, Maheswar Rupakheti, Arnico K. Panday
Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter And Sulfur Dioxide From Vehicles And Brick Kilns And Their Impacts On Air Quality In The Kathmandu Valley, Nepal, Min Zhong, Eri Saikawa, Alexander Avramov, Chen Chen, Boya Sun, Wenlu Ye, William C. Keene, Robert J. Yokelson, Thilina Jayarathne, Elizabeth A. Stone, Maheswar Rupakheti, Arnico K. Panday
Chemistry and Biochemistry Faculty Publications
Air pollution is one of the most pressing environmental issues in the Kathmandu Valley, where the capital city of Nepal is located. We estimated emissions from two of the major source types in the valley (vehicles and brick kilns) and analyzed the corresponding impacts on regional air quality. First, we estimated the on-road vehicle emissions in the valley using the International Vehicle Emissions (IVE) model with local emissions factors and the latest available data for vehicle registration. We also identified the locations of the brick kilns in the Kathmandu Valley and developed an emissions inventory for these kilns using emissions …
Comparison Between Hydrogen And Halogen Bonds In Complexes Of 6-Ox-Fulvene With Pnicogen And Chalcogen Electron Donors, Mingchang Hou, Qing-Zhong Li, Steve Scheiner
Comparison Between Hydrogen And Halogen Bonds In Complexes Of 6-Ox-Fulvene With Pnicogen And Chalcogen Electron Donors, Mingchang Hou, Qing-Zhong Li, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
Quantum chemical calculations are applied to complexes of 6‐OX‐fulvene (X=H, Cl, Br, I) with ZH3/H2Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H‐bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order O
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 …
Interfacial Amino Acids Support Spa47 Oligomerization And Shigella Type Three Secretion System Activation, Hannah J. Demler, Heather B. Case, Yalemi Morales, Abram R. Bernard, Sean J. Johnson, Nicholas E. Dickenson
Interfacial Amino Acids Support Spa47 Oligomerization And Shigella Type Three Secretion System Activation, Hannah J. Demler, Heather B. Case, Yalemi Morales, Abram R. Bernard, Sean J. Johnson, Nicholas E. Dickenson
Chemistry and Biochemistry Faculty Publications
Like many Gram-negative pathogens, Shigella rely on a type three secretion system (T3SS) for injection of effector proteins directly into eukaryotic host cells to initiate and sustain infection. Protein secretion through the needle-like type three secretion apparatus (T3SA) requires ATP hydrolysis by the T3SS ATPase Spa47, making it a likely target for in vivo regulation of T3SS activity and an attractive target for small molecule therapeutics against shigellosis. Here, we developed a model of an activated Spa47 homo-hexamer, identifying two distinct regions at each protomer interface that we hypothesized to provide intermolecular interactions supportingSpa47 oligomerization and enzymatic activation. Mutational analysis …
Forty Years Of Progress In The Study Of The Hydrogen Bond, Steve Scheiner
Forty Years Of Progress In The Study Of The Hydrogen Bond, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
The author looks back at developments over the last few decades concerning the H–bond. The list of atoms involved as proton donor and acceptor has broadened dramatically, including most electronegative atoms and even metals. The factors that control the transfer of the proton across the H–bond have been elucidated and show the importance of even minor changes in its geometry. Small stretches can shut down the transfer entirely, and certain bends can force a proton to transfer against a pK gradient. Along with the recognition that a CH..O interaction can represent a true H–bond, and one with strength comparable to …
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
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 kcal/mol. On …
Structures Of Clusters Surrounding Ions Stabilized By Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner, Mariusz Michalczyk, Wiktor Zierkiewicz
Structures Of Clusters Surrounding Ions Stabilized By Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner, Mariusz Michalczyk, Wiktor Zierkiewicz
Chemistry and Biochemistry Faculty Publications
Four H-binding HCl and HF molecules position themselves at the vertices of a tetrahedron when surrounding a central Cl-. Halogen bonding BrF and ClF form a slightly distorted tetrahedron, a tendency that is amplified for ClCN which forms a trigonal pyramid. Chalcogen bonding SF2, SeF2, SeFMe, and SeCSe occupy one hemisphere of the central ion, leaving the other hemisphere empty. This pattern is repeated for pnicogen bonding PF3, SeF3 and AsCF. The clustering of solvent molecules on one side of the Cl- is attributed to weak attractive interactions between them, including chalcogen, pnicogen, halogen, and hydrogen bonds. Binding energies of …
Influence Of Monomer Deformation On The Competition Between Two Types Of Σ-Holes In Tetrel Bonds, Rafal Wysokiński, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner
Influence Of Monomer Deformation On The Competition Between Two Types Of Σ-Holes In Tetrel Bonds, Rafal Wysokiński, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
One of several tetrel (T) atoms was covalently attached to three F atoms and a substituted phenyl ring. A NH3 base can form a tetrel bond with TF3C6H2R3(T = Si, Ge, Sn, Pb; R = H, F, CH3) in a position opposite either an F atom or the ring. The σ-hole opposite the highly electron-withdrawing F (T-F) is more intense than that opposite the ring (T-C). However, when the Lewis base deforms from a tetrahedral to a trigonal bipyramidal shape so as to accommodate the base, it is the T-C σ-hole that is more intense. Accordingly, it is the T-C …
Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Nikolay V. Tkachenko, Alexander I. Boldyrev
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 …
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 …
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
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 the …
Hydrated Sulfate Clusters So42–(H2o)N (N = 1–40): Charge Distribution Through Solvation Shells And Stabilization, Maksim Kulichenko, Nikita Fedik, Konstantin V. Bozhenko, Alexander I. Boldyrev
Hydrated Sulfate Clusters So42–(H2o)N (N = 1–40): Charge Distribution Through Solvation Shells And Stabilization, Maksim Kulichenko, Nikita Fedik, Konstantin V. Bozhenko, Alexander I. Boldyrev
Chemistry and Biochemistry Faculty Publications
Investigations of inorganic anion SO42– interactions with water are crucial for understanding the chemistry of its aqueous solutions. It is known that the isolated SO42– dianion is unstable, and three H2O molecules are required for its stabilization. In the current work, we report our computational study of hydrated sulfate clusters SO42–(H2O)n (n = 1–40) in order to understand the nature of stabilization of this important anion by water molecules. We showed that the most significant charge transfer from dianion SO42– to H2O takes …
On The Capability Of Metal-Halogen Groups To Participate In Halogen Bonds, Steve Scheiner
On The Capability Of Metal-Halogen Groups To Participate In Halogen Bonds, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
A number of halogen (X) atoms were covalently attached to a metal (M) and the ability of the X atom to act as electron acceptor in a halogen bond to nucleophile NCH was assessed. Both Cl and Br were considered as halogen atom, with NH3 and CO as other ligands attached to the metal. Metals tested were Ti, Mn, and Zn in various combinations of oxidation state, coordination, and overall charge. In the majority of cases, the strong electron-releasing power of the metal imbues the halogen atom with a high negative partial charge and minimizes the development of a σ-hole. …
3-Hydroxyflavones And 3-Hydroxy-4-Oxoquinolines As Carbon Monoxide-Releasing Molecules, Tatiana Soboleva, Lisa M. Berreau
3-Hydroxyflavones And 3-Hydroxy-4-Oxoquinolines As Carbon Monoxide-Releasing Molecules, Tatiana Soboleva, Lisa M. Berreau
Chemistry and Biochemistry Faculty Publications
Carbon monoxide-releasing molecules (CORMs) that enable the delivery of controlled amounts of CO are of strong current interest for applications in biological systems. In this review, we examine the various conditions under which CO is released from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines to advance the understanding of how these molecules, or derivatives thereof, may be developed as CORMs. Enzymatic pathways from quercetin dioxygenases and 3-hydroxy-4-oxoquinoline dioxygenases leading to CO release are examined, along with model systems for these enzymes. Base-catalyzed and non-redox-metal promoted CO release, as well as UV and visible light-driven CO release from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines, are summarized. The visible …
Optical Stability Of 1,1′-Binaphthyl Derivatives, Nikolay V. Tkachenko, Steve Scheiner
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 6,6′, where they will not come …
Production Of Secondary Organic Aerosol During Aging Of Biomass Burning Smoke From Fresh Fuels And Its Relationship To Voc Precursors, A. T. Ahern, E. S. Robinson, D. S. Tkacik, R. Saleh, L. E. Hatch, K. C. Barsanti, C. E. Stockwell, R. J. Yokelson, A. A. Presto, A. L. Robinson, R. C. Sullivan, N. M. Donahue
Production Of Secondary Organic Aerosol During Aging Of Biomass Burning Smoke From Fresh Fuels And Its Relationship To Voc Precursors, A. T. Ahern, E. S. Robinson, D. S. Tkacik, R. Saleh, L. E. Hatch, K. C. Barsanti, C. E. Stockwell, R. J. Yokelson, A. A. Presto, A. L. Robinson, R. C. Sullivan, N. M. Donahue
Chemistry and Biochemistry Faculty Publications
After smoke from burning biomass is emitted into the atmosphere, chemical and physical processes change the composition and amount of organic aerosol present in the aged, diluted plume. During the fourth Fire Lab at Missoula Experiment, we performed smog-chamber experiments to investigate formation of secondary organic aerosol (SOA) and multiphase oxidation of primary organic aerosol (POA). We simulated atmospheric aging of diluted smoke from a variety of biomass fuels while measuring particle composition using high-resolution aerosol mass spectrometry. We quantified SOA formation using a tracer ion for low-volatility POA as a reference standard (akin to a naturally occurring internal standard). …
In Situ Measurements Of Trace Gases, Pm, And Aerosol Optical Properties During The 2017 Nw Us Wildfire Smoke Event, Vanessa Selimovic, Robert J. Yokelson, Gavin R. Mcmeeking, Sarah Coefield
In Situ Measurements Of Trace Gases, Pm, And Aerosol Optical Properties During The 2017 Nw Us Wildfire Smoke Event, Vanessa Selimovic, Robert J. Yokelson, Gavin R. Mcmeeking, Sarah Coefield
Chemistry and Biochemistry Faculty Publications
In mid-August through mid-September of 2017 a major wildfire smoke and haze episode strongly impacted most of the NW US and SW Canada. During this period our ground-based site in Missoula, Montana, experienced heavy smoke impacts for ∼ 500h (up to 471μ-3 hourly average PM2.5). We measured wildfire trace gases, PM2.5 (particulate matter ≤2.5μm in diameter), and black carbon and submicron aerosol scattering and absorption at 870 and 401nm. This may be the most extensive real-time data for these wildfire smoke properties to date. Our range of trace gas ratios for δNH3 δCO and δC2H4 δCO confirmed that the smoke …
Hexacoordinated Tetrel-Bonded Complexes Between Tf4 (T = Si, Ge, Sn, Pb) And Nch. Competition Between Σ- And Π-Holes, Mariusz Michalczyk, Wiktor Zierkiewicz, Rafal Wysokiński, Steve Scheiner
Hexacoordinated Tetrel-Bonded Complexes Between Tf4 (T = Si, Ge, Sn, Pb) And Nch. Competition Between Σ- And Π-Holes, Mariusz Michalczyk, Wiktor Zierkiewicz, Rafal Wysokiński, Steve Scheiner
Chemistry and Biochemistry Faculty Publications
In order to accommodate the approach of two NCH bases, a tetrahedral TF4 molecule (T=Si,Ge,Sn,Pb) distorts into an octahedral structure in which the two bases can be situated either cis or trans to one another. The square planar geometry of TF4, associated with the trans arrangement of the bases, is higher in energy than its see-saw structure which corresponds to the cis trimer. On the other hand, the square geometry offers an unobstructed path of the bases to the π-holes above and below the tetrel atom so enjoys a higher interaction energy than is the case for the σ-holes approached …
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. …
Structural And Functional Characterization Of Sulfonium Carbon-Oxygen Hydrogen Bonding In The Deoxyamino Sugar Methyltransferase Tyim1, Robert J. Fick, Scott Horowitz, Brandon G. Mcdole, Mary C. Clay, Ryan A. Mehl, Hashim M. Al-Hashimi, Steve Scheiner, Raymond C. Trievel
Structural And Functional Characterization Of Sulfonium Carbon-Oxygen Hydrogen Bonding In The Deoxyamino Sugar Methyltransferase Tyim1, Robert J. Fick, Scott Horowitz, Brandon G. Mcdole, Mary C. Clay, Ryan A. Mehl, Hashim M. Al-Hashimi, Steve Scheiner, Raymond C. Trievel
Chemistry and Biochemistry Faculty Publications
The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH•••O) hydrogen bonds between the substrate’s sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine …
Comparison Of Σ-Hole And Π-Hole Tetrel Bonds In Complexes Of Borazine With Th3f And F2to/H2to (T=C,Si,Ge), Jingru Zhang, Qingze Hu, Qing-Zhong Li, Steve Scheiner, Shufeng Liu
Comparison Of Σ-Hole And Π-Hole Tetrel Bonds In Complexes Of Borazine With Th3f And F2to/H2to (T=C,Si,Ge), Jingru Zhang, Qingze Hu, Qing-Zhong Li, Steve Scheiner, Shufeng Liu
Chemistry and Biochemistry Faculty Publications
The complexes between borazine and TH3F/F2TO/H2TO (T=C, Si, Ge) are investigated with high-level quantum chemical calculations. Borazine has three sites of negative electrostatic potential: the N atom, the ring center, and the H atom of the B-H bond, while TH3F and F2TO/H2TO provide the σ-hole and π-hole, respectively, for the tetrel bond. The N atom of borazine is the favored site for both the σ and π-hole tetrel bonds. Less stable dimers include a σ-tetrel bond to the borazine ring center and to the BH proton. The π-hole tetrel-bonded complexes are more strongly bound than aretheirσ-hole counterparts. Due to the …
Switchable Aromaticity In An Isostructural Mn Phthalocyanine Series Isolated In Five Separate Redox States, Camden Hunt, Madeline Peterson, Cassidy Anderson, Tieyan Chang, Guang Wu, Steve Scheiner, Gabriel Ménard
Switchable Aromaticity In An Isostructural Mn Phthalocyanine Series Isolated In Five Separate Redox States, Camden Hunt, Madeline Peterson, Cassidy Anderson, Tieyan Chang, Guang Wu, Steve Scheiner, Gabriel Ménard
Chemistry and Biochemistry Faculty Publications
The synthesis and characterization of a new phthalocyanine(Pc) Mn-nitride complex, (OEtPc)MnN (2; OEtPc= 1,4,8,11,15,18,22,25-octaethoxy-Pc), as well as its stable, readily accessible oxidized (2+ and 22+) and reduced (2-, 22-) congeners is reported. This unique isostructural series displays switchable aromatic character spanning the aromatic (2), non-aromatic (22+), and antiaromatic (22-) triad, in addition to the open-shell radical states (2+, 2-). All complexes were structurally characterized and displayed significant structural distortions at the redox extrema (22+, 22-) consistent with proposed [16 or 18]annulene π ring circuit models. Spectroscopic and computational studies further support these models. This isolated, fully characterized, isostructural series spanning …
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 …
Speciated And Total Emission Factors Of Particulate Organics From Burning Western Us Wildland Fuels And Their Dependence On Combustion Efficiency, Coty N. Jen, Lindsay E. Hatch, Vanessa Selimovic, Robert J. Yokelson, Robert Weber, Arantza E. Fernandez, Nathan M. Kreisberg, Kelley C. Barsanti, Allen H. Goldstein
Speciated And Total Emission Factors Of Particulate Organics From Burning Western Us Wildland Fuels And Their Dependence On Combustion Efficiency, Coty N. Jen, Lindsay E. Hatch, Vanessa Selimovic, Robert J. Yokelson, Robert Weber, Arantza E. Fernandez, Nathan M. Kreisberg, Kelley C. Barsanti, Allen H. Goldstein
Chemistry and Biochemistry Faculty Publications
Western US wildlands experience frequent and large-scale wildfires which are predicted to increase in the future. As a result, wildfire smoke emissions are expected to play an increasing role in atmospheric chemistry while negatively impacting regional air quality and human health. Understanding the impacts of smoke on the environment is informed by identifying and quantifying the chemical compounds that are emitted during wildfires and by providing empirical relationships that describe how the amount and composition of the emissions change based upon different fire conditions and fuels. This study examined particulate organic compounds emitted from burning common western US wildland fuels …
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 …