Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Life Sciences (11)
- Other Chemistry (11)
- Environmental Chemistry (8)
- Medicine and Health Sciences (7)
- Chemicals and Drugs (6)
-
- Oceanography and Atmospheric Sciences and Meteorology (6)
- Biochemistry, Biophysics, and Structural Biology (5)
- Amino Acids, Peptides, and Proteins (4)
- Biochemistry (4)
- Botany (4)
- Other Oceanography and Atmospheric Sciences and Meteorology (4)
- Other Plant Sciences (4)
- Plant Sciences (4)
- Earth Sciences (3)
- Fresh Water Studies (3)
- Hydrology (3)
- Pharmacy and Pharmaceutical Sciences (3)
- Plant Biology (3)
- Atmospheric Sciences (2)
- Biology (2)
- Computer Sciences (2)
- Ecology and Evolutionary Biology (2)
- Environmental Monitoring (2)
- Environmental Sciences (2)
- Genetics (2)
- Genetics and Genomics (2)
- Medicinal-Pharmaceutical Chemistry (2)
- Keyword
-
- CDOM (2)
- Conformational analysis (2)
- Peatland (2)
- (N-methyl)-isosparteinium (1)
- (N-methyl)-sparteinium (1)
-
- 13C (1)
- 1H (1)
- 2016 (1)
- 2016 Nobel Prize (1)
- 2016 Nobel Prize in Chemistry (1)
- Ab initio calculations (1)
- Acetone (1)
- Acetylcholine receptors (1)
- Adsorption (1)
- Air‐sea exchange (1)
- Allosteric regulation (1)
- Anaerobic carbon mineralization (1)
- Anaerobic methanogenesis (1)
- Apigenin (1)
- Autism spectrum disorder (1)
- BTBR mice (1)
- Biaryls (1)
- C cycle (1)
- C-H bond activation (1)
- Carbonyl compounds (organic) (1)
- Catalysis (1)
- Catalysts (1)
- Centrality (1)
- Charge-transfer transitions (1)
- Chemistry (1)
- Publication Year
- Publication
-
- Biology, Chemistry, and Environmental Sciences Faculty Articles and Research (22)
- Student Scholar Symposium Abstracts and Posters (3)
- Mathematics, Physics, and Computer Science Faculty Articles and Research (2)
- Pharmacy Faculty Articles and Research (2)
- Computational and Data Sciences (MS) Theses (1)
- Publication Type
Articles 1 - 30 of 30
Full-Text Articles in Organic Chemistry
Apigenin Alleviates Autistic-Like Stereotyped Repetitive Behaviors And Mitigates Brain Oxidative Stress In Mice, Petrilla Jayaprakash, Dmytro Isaev, Keun-Hang Susan Yang, Rami Beiram, Murat Oz, Bassem Sadek
Apigenin Alleviates Autistic-Like Stereotyped Repetitive Behaviors And Mitigates Brain Oxidative Stress In Mice, Petrilla Jayaprakash, Dmytro Isaev, Keun-Hang Susan Yang, Rami Beiram, Murat Oz, Bassem Sadek
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Studying the involvement of nicotinic acetylcholine receptors (nAChRs), specifically α7-nAChRs, in neuropsychiatric brain disorders such as autism spectrum disorder (ASD) has gained a growing interest. The flavonoid apigenin (APG) has been confirmed in its pharmacological action as a positive allosteric modulator of α7-nAChRs. However, there is no research describing the pharmacological potential of APG in ASD. The aim of this study was to evaluate the effects of the subchronic systemic treatment of APG (10–30 mg/kg) on ASD-like repetitive and compulsive-like behaviors and oxidative stress status in the hippocampus and cerebellum in BTBR mice, utilizing the reference drug aripiprazole (ARP, 1 …
The Emergence Of Zerovalent Carbon Compounds From Structural Curiosities To Organocatalysts, Allegra L. Liberman-Martin
The Emergence Of Zerovalent Carbon Compounds From Structural Curiosities To Organocatalysts, Allegra L. Liberman-Martin
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Low-valent main group compounds have reactivity patterns and properties reminiscent of transition metals. While divalent carbon compounds such as carbenes are widely studied ligands and organocatalysts, zerovalent carbon species have received considerably less attention. This perspective highlights the properties and reactivity of zerovalent carbon compounds, focusing on their first applications as organocatalysts for small molecule reduction and polymerization reactions.
A Model For The Rapid Assessment Of Solution Structures For 24-Atom Macrocycles: The Impact Of Β-Branched Amino Acids On Conformation, Alexander J. Menke, Camryn J. Gloor, Liam E. Claton, Magy A. Mekhail, Hongjun Pan, Mikaela D. Stewart, Kayla N. Green, Joseph H. Reibenspies, Giovanni M. Pavan, Riccardo Capelli, Eric E. Simanek
A Model For The Rapid Assessment Of Solution Structures For 24-Atom Macrocycles: The Impact Of Β-Branched Amino Acids On Conformation, Alexander J. Menke, Camryn J. Gloor, Liam E. Claton, Magy A. Mekhail, Hongjun Pan, Mikaela D. Stewart, Kayla N. Green, Joseph H. Reibenspies, Giovanni M. Pavan, Riccardo Capelli, Eric E. Simanek
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Experiment and computation are used to develop a model to rapidly predict solution structures of macrocycles sharing the same Murcko framework. These 24-atom triazine macrocycles result from the quantitative dimerization of identical monomers presenting a hydrazine group and an acetal tethered to an amino acid linker. Monomers comprising glycine and the β-branched amino acids threonine, valine, and isoleucine yield macrocycles G-G, T-T, V-V, and I-I, respectively. Elements common to all members of the framework include the efficiency of macrocyclization (quantitative), the solution- and solid-state structures (folded), the site of protonation (opposite the auxiliary dimethylamine group), the …
Chromophoric Dissolved Organic Matter And Dissolved Organic Carbon In Lakes Across An Elevational Gradient From The Mountains To The Sea, Kyle Juetten, Angela L. Strecker, Aaron Harrison, Zachary Landram, Warren J. De Bruyn, Catherine D. Clark
Chromophoric Dissolved Organic Matter And Dissolved Organic Carbon In Lakes Across An Elevational Gradient From The Mountains To The Sea, Kyle Juetten, Angela L. Strecker, Aaron Harrison, Zachary Landram, Warren J. De Bruyn, Catherine D. Clark
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Dissolved organic matter (DOM) in lakes across elevation gradients is a complex function of topography, climate, vegetation coverage, land use, and lake properties. To examine sources and processing of DOM from sea level to mountain lakes (3–1,574 m), we measured dissolved organic carbon (DOC) concentrations and chromophoric dissolved organic matter (CDOM) optical properties, lake characteristics, and water quality parameters in 62 freshwater lakes in the Pacific Northwest, USA. Higher elevation lakes had lower DOC concentrations and absorbance. These lakes had higher forest cover and minimal wetlands in their watershed, in addition to low nutrients, water temperatures, and chlorophyll a in …
Technical Note: On Uncertainties In Plant Water Isotopic Composition Following Extraction By Cryogenic Vacuum Distillation, Haoyu Diao, Philipp Schuler, Gregory R. Goldsmith, Rolf T. W. Siegwolf, Matthias Saurer, Marco M. Lehmann
Technical Note: On Uncertainties In Plant Water Isotopic Composition Following Extraction By Cryogenic Vacuum Distillation, Haoyu Diao, Philipp Schuler, Gregory R. Goldsmith, Rolf T. W. Siegwolf, Matthias Saurer, Marco M. Lehmann
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Recent studies have challenged the interpretation of plant water isotopes obtained through cryogenic vacuum distillation (CVD) based on observations of a large 2H fractionation. These studies have hypothesized the existence of an H-atom exchange between water and organic tissue during CVD extraction with the magnitude of H exchange related to relative water content of the sample; however, clear evidence is lacking. Here, we systematically tested the uncertainties in the isotopic composition of CVD-extracted water by conducting a series of incubation and rehydration experiments using isotopically depleted water, water at natural isotope abundance, woody materials with exchangeable H, and organic materials …
Ketone Hydrosilylation Studies Using A Carbodiphosphorane Catalyst, Liam Sullivan, Allegra Liberman-Martin
Ketone Hydrosilylation Studies Using A Carbodiphosphorane Catalyst, Liam Sullivan, Allegra Liberman-Martin
Student Scholar Symposium Abstracts and Posters
The objective of this research is to discover an effective, safe, and low-cost catalyst for ketone hydrosilylation reactions, which involve the addition of a silicon–hydrogen bond across a C=O double bond. Improving catalyst efficiency could benefit the organic synthesis industry, as carbonyl hydrosilylation is used industrially in the synthesis of alcohol products. Use of the carbodiphosphorane catalyst as a replacement for toxic heavy-metal-containing catalysts could reduce waste and emissions harmful to the environment, while also providing an alternative means for accomplishing ketone reduction. Using a cyclic carbodiphosphorane catalyst, we have compared catalytic activity toward acetophenone hydrosilylation for a range of …
Understanding The Transition From General To Organic Chemistry, Hannah Chan
Understanding The Transition From General To Organic Chemistry, Hannah Chan
Student Scholar Symposium Abstracts and Posters
Organic chemistry is commonly known to have high failure rates and regarded as one of the most difficult courses offered in undergrad. This study assessed whether a modified general chemistry curriculum allowing for more time focused on foundational organic chemistry concepts in general chemistry can improve students’ grade outcome and/or self efficacy when transitioning from general to organic chemistry courses. Two separate variables were tested: grade outcome and self efficacy. Using an independent sample t-test, a comparison of the two groups (modified versus traditional general chemistry) was performed. Grades were assessed by giving students four questions (out of 4 points …
Methanol Decomposition On Ni(111) And O/Ni(111), Henrik Öström, Bingjie Zhang, Tiffany Vallejo, Bryn Merrill, Jeremy Huang, Jerry Larue
Methanol Decomposition On Ni(111) And O/Ni(111), Henrik Öström, Bingjie Zhang, Tiffany Vallejo, Bryn Merrill, Jeremy Huang, Jerry Larue
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Methanol decomposition on Ni(111) surfaces has been studied in the presence and absence of oxygen using temperature-programmed desorption and temperature-dependent sum frequency generation spectroscopy. Under both conditions the C–H and O–H bonds break, forming carbon monoxide and atomic hydrogen on the surface. No C–O bond scission was observed, limiting the number of reaction pathways. The O–H bonds break first (>150 K), forming surface methoxy, followed by C–H bond breakage (>250 K). All atomic hydrogen desorbs from the surface as H2 through H+H recombinative desorption. H2 desorbs at a higher temperature in the presence of oxygen (>300 K) …
Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham
Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not …
Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem
Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem
Computational and Data Sciences (MS) Theses
Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …
Mechanistic Insights Into Iron-Catalyzed C–H Bond Activation And C–C Coupling, Samantha M. Brewer, Timothy M. Schwartz, Magy A. Mekhail, Lara S. Turan, Timothy J. Prior, Timothy J. Hubin, Benjamin G. Janesko, Kayla N. Green
Mechanistic Insights Into Iron-Catalyzed C–H Bond Activation And C–C Coupling, Samantha M. Brewer, Timothy M. Schwartz, Magy A. Mekhail, Lara S. Turan, Timothy J. Prior, Timothy J. Hubin, Benjamin G. Janesko, Kayla N. Green
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Iron-catalyzed C–C coupling reactions of pyrrole provide a unique alternative to the traditional Pd-catalyzed counterpart. However, many details regarding the actual mechanism remain unknown. A series of macrocyclic iron(III) complexes were used to evaluate specifics related to the role of O2, radicals, and μ-oxodiiron-complex participation in the catalytic cycle. It was determined that the mononuclear tetra-azamacrocyclic complex is a true catalyst and not a stoichiometric reagent, while more than one equivalent of a sacrificial oxidant is needed. Furthermore, the reaction does not proceed through an organic radical pathway. μ-Oxodiiron complexes are not involved in the main catalytic pathway, …
Global Atmospheric Budget Of Acetone: Air-Sea Exchange And The Contribution To Hydroxyl Radicals, Siyuan Wang, Eric C. Apel, Rebecca H. Schwantes, Kelvin H. Bates, Daniel J. Jacob, Emily V. Fischer, Rebecca S. Hornbrook, Alan J. Hills, Louisa K. Emmons, Laura L. Pan, Shawn Honomichl, Simone Tilmes, Jean‐François Lamarque, Mingxi Yang, Christa A. Marandino, E. S. Saltzman, Warren J. De Bruyn, Sohiko Kameyama, Hiroshi Tanimoto, Yuko Omori, Samuel R. Hall, Kirk Ullmann, Thomas B. Ryerson, Chelsea R. Thompson, Jeff Peischl, Bruce C. Daube, Róisín Commane, Kathryn Mckain, Colm Sweeney, Alexander B. Thames, David O. Miller, William H. Brune, Glenn S. Diskin, Joshua P. Digangi, Steven C. Wofsy
Global Atmospheric Budget Of Acetone: Air-Sea Exchange And The Contribution To Hydroxyl Radicals, Siyuan Wang, Eric C. Apel, Rebecca H. Schwantes, Kelvin H. Bates, Daniel J. Jacob, Emily V. Fischer, Rebecca S. Hornbrook, Alan J. Hills, Louisa K. Emmons, Laura L. Pan, Shawn Honomichl, Simone Tilmes, Jean‐François Lamarque, Mingxi Yang, Christa A. Marandino, E. S. Saltzman, Warren J. De Bruyn, Sohiko Kameyama, Hiroshi Tanimoto, Yuko Omori, Samuel R. Hall, Kirk Ullmann, Thomas B. Ryerson, Chelsea R. Thompson, Jeff Peischl, Bruce C. Daube, Róisín Commane, Kathryn Mckain, Colm Sweeney, Alexander B. Thames, David O. Miller, William H. Brune, Glenn S. Diskin, Joshua P. Digangi, Steven C. Wofsy
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Acetone is one of the most abundant oxygenated volatile organic compounds (VOCs) in the atmosphere. The oceans impose a strong control on atmospheric acetone, yet the oceanic fluxes of acetone remain poorly constrained. In this work, the global budget of acetone is evaluated using two global models: CAM‐chem and GEOS‐Chem. CAM‐chem uses an online air‐sea exchange framework to calculate the bidirectional oceanic acetone fluxes, which is coupled to a data‐oriented machine‐learning approach. The machine‐learning algorithm is trained using a global suite of seawater acetone measurements. GEOS‐Chem uses a fixed surface seawater concentration of acetone to calculate the oceanic fluxes. Both …
Synthesis Of 12-Membered Tetra-Aza Macrocyclic Pyridinophanes Bearing Electron-Withdrawing Groups, Akop Yepremyan, Magy A. Mekhail, Brian P. Niebuhr, Kristof Pota, Nishanth Sadagopan, Timothy M. Schwartz, Kayla N. Green
Synthesis Of 12-Membered Tetra-Aza Macrocyclic Pyridinophanes Bearing Electron-Withdrawing Groups, Akop Yepremyan, Magy A. Mekhail, Brian P. Niebuhr, Kristof Pota, Nishanth Sadagopan, Timothy M. Schwartz, Kayla N. Green
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The number of substituted pyridine pyridinophanes found in the literature is limited due to challenges associated with 12-membered macrocycle and modified pyridine synthesis. Most notably, the electrophilic character at the 4-position of pyridine in pyridinophanes presents a unique challenge for introducing electrophilic chemical groups. Likewise, of the few reported, most substituted pyridine pyridinophanes in the literature are limited to electron-donating functionalities. Herein, new synthetic strategies for four new macrocycles bearing the electron-withdrawing groups CN, Cl, NO2, and CF3 are introduced. Potentiometric titrations were used to determine the protonation constants of the new pyridinophanes. Further, the influence of …
Molecular Machines: Synthesis, Modeling, And Applications, Syd Kotar
Molecular Machines: Synthesis, Modeling, And Applications, Syd Kotar
Student Scholar Symposium Abstracts and Posters
While some of the smallest, most useful machines known to science are the biological molecules that keep living organisms alive, there is a growing advancement of the creation of artificial molecules that have the same function and are more efficient. Molecular machines were invented in 1983 when scientists in France created a machine formed of two interlinked molecular rings. In 2016, the Nobel prize in chemistry was awarded to Feringa, Stoddart, and Sauvage who finally documented molecular machines and put them into energy‐filled states in which their movements could be controlled. From this, molecular machines became known as a group …
Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith
Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Rain recharges soil water storages and either percolates downward into aquifers and streams or is returned to the atmosphere through evapotranspiration. Although it is commonly assumed that summer rainfall recharges plant-available water during the growing season, the seasonal origins of water used by plants have not been systematically explored. We characterize the seasonal origins of waters in soils and trees by comparing their midsummer isotopic signatures (δ2H) to seasonal isotopic cycles in precipitation, using a new seasonal origin index. Across 182 Swiss forest sites, xylem water isotopic signatures show that summer rain was not the predominant water source …
Vibrational Analysis Of A Rate-Slowing Conformational Kinetic Isotope Effect, O. Maduka Ogba, Zichen Liu, Daniel J. O'Leary
Vibrational Analysis Of A Rate-Slowing Conformational Kinetic Isotope Effect, O. Maduka Ogba, Zichen Liu, Daniel J. O'Leary
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
An enthalpy-entropy approach to analyzing a rate-slowing conformational kinetic isotope effect (CKIE) in a deuterated doubly-bridged biaryl system is described. The computed isotope effect (kH/kD = 1.075, 368 K) agrees well with the measured value (kH/kD = 1.06, 368 K). The rateslowing (normal isotope effect) nature of the computed CKIE is shown to originate from a vibrational entropy contribution defined by the twenty lowest frequency normal modes in the ground state and transition state structures. This normal entropy contribution is offset by an inverse vibrational enthalpy contribution, which also arises from the twenty lowest frequency normal modes. Zero point vibrational …
Atom-Specific Activation In Co Oxidation, Simon Schreck, Elias Diesen, Jerry Larue, Hirohito Ogasawara, Kess Marks, Dennis Nordlund, Matthew Weston, Martin Beye, Filippo Cavalca, Fivos Perakis, Jonas Sellberg, André Eilert, Kyung Hwan Kim, Giacomo Coslovich, Ryan Coffee, Jacek Krzywinski, Alex Reid, Stefan Moeller, Alberto Lutman, Henrik Öström, Lars G. M. Pettersson, Anders Nilsson
Atom-Specific Activation In Co Oxidation, Simon Schreck, Elias Diesen, Jerry Larue, Hirohito Ogasawara, Kess Marks, Dennis Nordlund, Matthew Weston, Martin Beye, Filippo Cavalca, Fivos Perakis, Jonas Sellberg, André Eilert, Kyung Hwan Kim, Giacomo Coslovich, Ryan Coffee, Jacek Krzywinski, Alex Reid, Stefan Moeller, Alberto Lutman, Henrik Öström, Lars G. M. Pettersson, Anders Nilsson
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
We report on atom-specific activation of CO oxidation on Ru(0001) via resonant X-ray excitation. We show that resonant 1s core-level excitation of atomically adsorbed oxygen in the co-adsorbed phase of CO and oxygen directly drives CO oxidation. We separate this direct resonant channel from indirectly driven oxidation via X-ray induced substrate heating. Based on density functional theory calculations, we identify the valence-excited state created by the Auger decay as the driving electronic state for direct CO oxidation. We utilized the fresh-slice multi-pulse mode at the Linac Coherent Light Source that provided time-overlapped and 30 fs delayed pairs of soft …
1h And 13c Nmr Assignments For (N-Methyl)-(−)-(Α)-Isosparteinium Iodide And (N-Methyl)-(−)-Sparteinium Iodide, Kavoos Kolahdouzan, O. Maduka Ogba, Daniel J. O'Leary
1h And 13c Nmr Assignments For (N-Methyl)-(−)-(Α)-Isosparteinium Iodide And (N-Methyl)-(−)-Sparteinium Iodide, Kavoos Kolahdouzan, O. Maduka Ogba, Daniel J. O'Leary
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
(‒)-Sparteine (1) and (–)-(α)-isosparteine (2) are members of the lupine alkaloid family.[1-2] Sparteine has found extensive use in asymmetric organic transformations, including lithiations[3] and Pd-catalyzed oxidations.[4-7] (α)-Isosparteine, which can be made from sparteine, has been utilized as a chiral ligand for a limited number of stereoselective reactions.[8-9] The two compounds differ in that 1 displays an exo-endo arrangement of the bridgehead hydrogens at C-11 and C-6, respectively, while 2 retains an exo-exo arrangement of these atoms (Figure 1). This study is focused on assigning 1H chemical shifts and coupling constants and 13C chemical shifts for N-methyl …
No Evidence For Trace Metal Limitation On Anaerobic Carbon Mineralization In Three Peatland Soils, Jason K. Keller, Jillian Wade
No Evidence For Trace Metal Limitation On Anaerobic Carbon Mineralization In Three Peatland Soils, Jason K. Keller, Jillian Wade
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Peatlands store roughly one-third of the terrestrial soil carbon and release the potent greenhouse gas methane (CH4) to the atmosphere, making these wetlands among the most important ecosystems in the global carbon cycle. Despite their importance, the controls of anaerobic decomposition of organic matter to carbon dioxide (CO2) and CH4 within peatlands are not well understood. It is known, however, that the enzymes responsible for CH4 production require cobalt, iron and nickel, and there is a growing appreciation for the potential role of trace metal limitation in anaerobic decomposition. To explore the possibility of …
Ensemble-Based Modeling And Rigidity Decomposition Of Allosteric Interaction Networks And Communication Pathways In Cyclin-Dependent Kinases: Differentiating Kinase Clients Of The Hsp90-Cdc37 Chaperone, Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker
Ensemble-Based Modeling And Rigidity Decomposition Of Allosteric Interaction Networks And Communication Pathways In Cyclin-Dependent Kinases: Differentiating Kinase Clients Of The Hsp90-Cdc37 Chaperone, Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK …
Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury
Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury
Mathematics, Physics, and Computer Science Faculty Articles and Research
Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at …
Hydrogenation Of Organic Matter As A Terminal Electron Sink Sustains High Co2:Ch4 Production Ratios During Anaerobic Decomposition, Rachel M. Wilson, Malak M. Tfaily, Virginia I. Rich, Jason K. Keller, Scott D. Bridgham, Cassandra Medvedeff Zalman, Laura Meredith, Paul J. Hanson, Mark Hines, Laurel Pfeifer-Meister, Scott R. Saleska, Patrick Crill, William T. Cooper, Jeff P. Chanton, Joel E. Kostka
Hydrogenation Of Organic Matter As A Terminal Electron Sink Sustains High Co2:Ch4 Production Ratios During Anaerobic Decomposition, Rachel M. Wilson, Malak M. Tfaily, Virginia I. Rich, Jason K. Keller, Scott D. Bridgham, Cassandra Medvedeff Zalman, Laura Meredith, Paul J. Hanson, Mark Hines, Laurel Pfeifer-Meister, Scott R. Saleska, Patrick Crill, William T. Cooper, Jeff P. Chanton, Joel E. Kostka
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Once inorganic electron acceptors are depleted, organic matter in anoxic environments decomposes by hydrolysis, fermentation, and methanogenesis, requiring syntrophic interactions between microorganisms to achieve energetic favorability. In this classic anaerobic food chain, methanogenesis represents the terminal electron accepting (TEA) process, ultimately producing equimolar CO2 and CH4 for each molecule of organic matter degraded. However, CO2:CH4 production in Sphagnum-derived, mineral-poor, cellulosic peat often substantially exceeds this 1:1 ratio, even in the absence of measureable inorganic TEAs. Since the oxidation state of C in both cellulose-derived organic matter and acetate is 0, and CO2 has …
Palladium-Catalyzed Intramolecular Cross-Dehydrogenative Coupling: Synthesis Of Fused Imidazo[1,2‑A]Pyrimidines And Pyrazolo[1,5‑A]Pyrimidines, Siva K. Reddy Kotla, Jaya Kishore Vandavasi, Jeh-Jeh Wang, Keykavous Parang, Rakesh Tiwari
Palladium-Catalyzed Intramolecular Cross-Dehydrogenative Coupling: Synthesis Of Fused Imidazo[1,2‑A]Pyrimidines And Pyrazolo[1,5‑A]Pyrimidines, Siva K. Reddy Kotla, Jaya Kishore Vandavasi, Jeh-Jeh Wang, Keykavous Parang, Rakesh Tiwari
Pharmacy Faculty Articles and Research
A palladium-catalyzed intramolecular dehydrogenative coupling reaction was developed for the synthesis of fused imidazo[1,2-a]pyrimidines and pyrazolo[1,5-a]- pyrimidines. The developed protocol provides a practical approach for the synthesis of biologically important substituted pyrimidines from easily available substrates, with a broad substrate scope under mild reaction conditions.
Mida Boronates Are Hydrolysed Fast And Slow By Two Different Mechanisms, Jorge A. Gonzalez, O. Maduka Ogba, Gregory F. Morehouse, Nicholas Rosson, Kendall N. Houk, Andrew G. Leach, Paul H.-Y. Cheong, Martin D. Burke, Guy C. Lloyd-Jones
Mida Boronates Are Hydrolysed Fast And Slow By Two Different Mechanisms, Jorge A. Gonzalez, O. Maduka Ogba, Gregory F. Morehouse, Nicholas Rosson, Kendall N. Houk, Andrew G. Leach, Paul H.-Y. Cheong, Martin D. Burke, Guy C. Lloyd-Jones
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
MIDA boronates (N-methylimidodiacetic boronic acid esters) serve as an increasingly general platform for building-block-based small molecule construction, largely due to the dramatic and general rate differences with which they are hydrolysed under various basic conditions. Yet the mechanistic underpinnings of these rate differences have remained unclear, hindering efforts to address current limitations of this chemistry. Here we show that there are two distinct mechanisms for this hydrolysis: one is base-mediated and the other neutral. The former can proceed more than three orders of magnitude faster, and involves rate-limiting attack at a MIDA carbonyl carbon by hydroxide. The alternative ‘neutral’ hydrolysis …
Theoretical Investigation Of Interaction Between The Set Of Ligands And Α7 Nicotinic Acetylcholine Receptor, O. E. Glukhova, Tatiana Prytkova, D. S. Shmygin
Theoretical Investigation Of Interaction Between The Set Of Ligands And Α7 Nicotinic Acetylcholine Receptor, O. E. Glukhova, Tatiana Prytkova, D. S. Shmygin
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between …
Temporal Variation In Optical Properties Of Chromophoric Dissolved Organic Matter (Cdom) In Southern California Coastal Waters With Nearshore Kelp And Seagrass, Catherine D. Clark, Warren J. De Bruyn, Paige Aiona
Temporal Variation In Optical Properties Of Chromophoric Dissolved Organic Matter (Cdom) In Southern California Coastal Waters With Nearshore Kelp And Seagrass, Catherine D. Clark, Warren J. De Bruyn, Paige Aiona
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Optical properties of chromophoric dissolved organic matter (CDOM) were measured in surf zone waters in diurnal field studies at a Southern California beach with nearshore kelp and seagrass beds and intertidal plant wrack. Absorption coefficients (aCDOM(300 nm)) ranged from 0.35 m21 to 3.7 m21 with short-term variability<1 h, increases at ebb and flood tides and higher values (6 m21) during an offshore storm event. Spectral slopes (S) ranged from 0.0028 nm21 to 0.017 nm21, with higher values after the storm; S was generally inversely correlated with aCDOM(300 nm). 3-D excitation–emission matrix spectra (EEMs) for samples with lower S values had humic-type peaks associated with terrestrial material (A, C), marine microbial material (M) and protein peaks, characteristic of freshly produced organic material. Samples with high S values had no or reduced protein peaks, consistent with aged material. Fluorescent indexes (f450/f500 >2.5, BIX>1.1) were consistent with microbial aquatic sources. Leachates of senescent kelp and seagrass had protein and humic-type EEM peaks. After solar simulator irradiation (4 h), protein peaks rapidly photochemically degraded, humic-type peak C increased in intensity and peak M disappeared. Optical characteristics of kelp leachates were most similar to field samples, …
Optical Characterization And Distribution Of Chromophoric Dissolved Organic Matter (Cdom) In Soil Porewater From A Salt Marsh Ecosystem, Catherine D. Clark, Paige Aiona, Jason K. Keller, Warren J. De Bruyn
Optical Characterization And Distribution Of Chromophoric Dissolved Organic Matter (Cdom) In Soil Porewater From A Salt Marsh Ecosystem, Catherine D. Clark, Paige Aiona, Jason K. Keller, Warren J. De Bruyn
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
To characterize chromophoric dissolved organic matter (CDOM) in marsh porewaters and its contribution as a carbon source, optical properties (absorbance, fluorescence indices, 3-dimensional excitation-emission matrices [EEMs]) of soil porewater and surface water were measured in a southern Californian salt marsh. Absorption coefficients and fluorescence intensities were higher in porewater than in overlying surface waters, consistent with higher CDOM concentration at depth. Humic-type peaks A and C were observed in EEMs in all samples, and peak M was observed in surface waters and shallow porewater to -5 cm depth. Fluorescence:absorbance (flu:abs) ratios and spectral slopes (S) decreased across the surface interface, …
Advances In Functionalized Ionic Liquids As Reagents And Scavengers In Organic Synthesis, Manoj Kumar Muthyala, Kavya Velisetti, Keykavous Parang, Anil Kumar
Advances In Functionalized Ionic Liquids As Reagents And Scavengers In Organic Synthesis, Manoj Kumar Muthyala, Kavya Velisetti, Keykavous Parang, Anil Kumar
Pharmacy Faculty Articles and Research
Functionalized ionic liquids (FILs) synthesized with specific desired chemical properties have shown promising results in various areas of organic synthesis. In supported organic synthesis, FILs have become known as a new alternative to commonly used PEG and fluorous soluble supports. This review summarizes the progress of recent development in the synthesis of functionalized ionic liquids with emphasis on their applications as reagents and scavengers in organic synthesis.
Coupling Coherence Distinguishes Structure Sensitivity In Protein Electron Transfer, Tatiana Prytkova, Igor V. Kurnikov, David Beratan
Coupling Coherence Distinguishes Structure Sensitivity In Protein Electron Transfer, Tatiana Prytkova, Igor V. Kurnikov, David Beratan
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.
Flavin Charge Transfer Transitions Assist Dna Photolyase Electron Transfer, Spiros S. Skourtis, Tatiana Prytkova, David Beratan
Flavin Charge Transfer Transitions Assist Dna Photolyase Electron Transfer, Spiros S. Skourtis, Tatiana Prytkova, David Beratan
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
This contribution describes molecular dynamics, semi-empirical and ab-initio studies of the primary photo-induced electron transfer reaction in DNA photolyase. DNA photolyases are FADH−-containing proteins that repair UV-damaged DNA by photo-induced electron transfer. A DNA photolyase recognizes and binds to cyclobutatne pyrimidine dimer lesions of DNA. The protein repairs a bound lesion by transferring an electron to the lesion from FADH−, upon photo-excitation of FADH− with 350–450 nm light. We compute the lowest singlet excited states of FADH− in DNA photolyase using INDO/S configuration interaction, time-dependent density-functional, and time-dependent Hartree-Fock methods. The calculations identify the lowest singlet excited state of FADH− …