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Articles 31 - 60 of 110
Full-Text Articles in Other Chemistry
Crystal Structure Of 2-(2,6-Diisopropylphenyl)-N,Ndiethyl- 3,3-Dimethyl-2-Azaspiro[4.5]Decan-1- Amine: A Diethylamine Adduct Of A Cyclic(Alkyl)- (Amino)Carbene (Caac), Roxanne A. Naumann, Joseph W. Ziller, Allegra Liberman-Martin
Crystal Structure Of 2-(2,6-Diisopropylphenyl)-N,Ndiethyl- 3,3-Dimethyl-2-Azaspiro[4.5]Decan-1- Amine: A Diethylamine Adduct Of A Cyclic(Alkyl)- (Amino)Carbene (Caac), Roxanne A. Naumann, Joseph W. Ziller, Allegra Liberman-Martin
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The structure of the title compound, C27H46N2, at 93 K has monoclinic (P21/n) symmetry. The title compound was prepared by treatment of 2-(2,6-diisopropylphenyl)-3,3-dimethyl-2-azaspiro[4.5]dec-1-en-2-ium hydrogen dichloride with two equivalents of lithium diethylamide. Characterization of the title compound by single-crystal X-ray diffraction and 1H and 13C NMR spectroscopy is presented. Formation of the diethylamine adduct of the cyclic(alkyl)(amino)carbene (CAAC) was unexpected, as deprotonation using lithium diisopropylamide results in free CAAC formation.
Ultrafast Adsorbate Excitation Probed With Subpicosecond-Resolution X-Ray Absorption Spectroscopy, Elias Diesen, Hsin-Yi Wang, Simon Schreck, Matthew Weston, Hirohito Ogasawara, Jerry Larue, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Luca Giannessi, Martin Beye, Filippo Cavalca, Boyang Liu, Jörgen Gladh, Sergey Koroidov, Piter S. Miedema, Roberto Costantini, Tony F. Heinz, Frank Abild-Pedersen, Johannes Voss, Alan C. Luntz, Anders Nilsson
Ultrafast Adsorbate Excitation Probed With Subpicosecond-Resolution X-Ray Absorption Spectroscopy, Elias Diesen, Hsin-Yi Wang, Simon Schreck, Matthew Weston, Hirohito Ogasawara, Jerry Larue, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Luca Giannessi, Martin Beye, Filippo Cavalca, Boyang Liu, Jörgen Gladh, Sergey Koroidov, Piter S. Miedema, Roberto Costantini, Tony F. Heinz, Frank Abild-Pedersen, Johannes Voss, Alan C. Luntz, Anders Nilsson
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
We use a pump-probe scheme to measure the time evolution of the C K-edge x-ray absorption spectrum from CO/Ru(0001) after excitation by an ultrashort high-intensity optical laser pulse. Because of the short duration of the x-ray probe pulse and precise control of the pulse delay, the excitation-induced dynamics during the first picosecond after the pump can be resolved with unprecedented time resolution. By comparing with density functional theory spectrum calculations, we find high excitation of the internal stretch and frustrated rotation modes occurring within 200 fs of laser excitation, as well as thermalization of the system in the picosecond …
A Bacterial Inflammation Sensor Regulates C-Di-Gmp Signaling, Adhesion, And Biofilm Formation, Arden Perkins, Dan A. Tudorica, Raphael D. Teixeira, Tilman Schirmer, Lindsay Zumwalt, O. Maduka Ogba, C. Keith Cassidy, Phillip J. Stansfeld, Karen Guillemin
A Bacterial Inflammation Sensor Regulates C-Di-Gmp Signaling, Adhesion, And Biofilm Formation, Arden Perkins, Dan A. Tudorica, Raphael D. Teixeira, Tilman Schirmer, Lindsay Zumwalt, O. Maduka Ogba, C. Keith Cassidy, Phillip J. Stansfeld, Karen Guillemin
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Bacteria that colonize animals must overcome, or coexist, with the reactive oxygen species products of inflammation, a front-line defense of innate immunity. Among these is the neutrophilic oxidant bleach, hypochlorous acid (HOCl), a potent antimicrobial that plays a primary role in killing bacteria through nonspecific oxidation of proteins, lipids, and DNA. Here, we report that in response to increasing HOCl levels, Escherichia coli regulates biofilm production via activation of the diguanylate cyclase DgcZ. We identify the mechanism of DgcZ sensing of HOCl to be direct oxidation of its regulatory chemoreceptor zinc-binding (CZB) domain. Dissection of CZB signal transduction reveals that …
Cown Sustains Nitrogenase Turnover In The Presence Of The Inhibitor Carbon Monoxide, Michael S. Medina, Kevin O. Bretzing, Richard A. Aviles, Kiersten M. Chong, Alejandro Espinoza, Chloe Nicole G. Garcia, Benjamin B. Katz, Ruchita N. Kharwa, Andrea Hernandez, Justin L. Lee, Terrence M. Lee, Christine Lo Verde, Max W. Strul, Emily Y. Wong, Cedric P. Owens
Cown Sustains Nitrogenase Turnover In The Presence Of The Inhibitor Carbon Monoxide, Michael S. Medina, Kevin O. Bretzing, Richard A. Aviles, Kiersten M. Chong, Alejandro Espinoza, Chloe Nicole G. Garcia, Benjamin B. Katz, Ruchita N. Kharwa, Andrea Hernandez, Justin L. Lee, Terrence M. Lee, Christine Lo Verde, Max W. Strul, Emily Y. Wong, Cedric P. Owens
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N2) to ammonia (NH3). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, …
The Mechanism Of Β-N-Methylamino-L-Alanine Inhibition Of Trna Aminoacylation And Its Impact On Misincorporation, Nien-Ching Han, Tammy J. Bullwinkle, Kaeli F. Loeb, Kym F. Faull, Kyle Mohler, Jesse Rinehart, Michael Ibba
The Mechanism Of Β-N-Methylamino-L-Alanine Inhibition Of Trna Aminoacylation And Its Impact On Misincorporation, Nien-Ching Han, Tammy J. Bullwinkle, Kaeli F. Loeb, Kym F. Faull, Kyle Mohler, Jesse Rinehart, Michael Ibba
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
β-N-methylamino-l-alanine (BMAA) is a nonproteinogenic amino acid that has been associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD). BMAA has been found in human protein extracts; however, the mechanism by which it enters the proteome is still unclear. It has been suggested that BMAA is misincorporated at serine codons during protein synthesis, but direct evidence of its cotranslational incorporation is currently lacking. Here, using LC-MS–purified BMAA and several biochemical assays, we sought to determine whether any aminoacyl-tRNA synthetase (aaRS) utilizes BMAA as a substrate for aminoacylation. Despite BMAA's previously predicted misincorporation at serine …
Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker
Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of …
Mechanism And Chemoselectivity For Hocl-Mediated Oxidation Of Zinc-Bound Thiolates, Lindsay Zumwalt, Arden Perkins, O. Maduka Ogba
Mechanism And Chemoselectivity For Hocl-Mediated Oxidation Of Zinc-Bound Thiolates, Lindsay Zumwalt, Arden Perkins, O. Maduka Ogba
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Quantum mechanical calculations reveal the preferred mechanism and origins of chemoselectivity for HOCl‐mediated oxidation of zinc‐bound thiolates implicated in bacterial redox sensing. Distortion/interaction models show that minimizing geometric distortion at the zinc complex during the rate‐limiting nucleophilic substitution step controls the mechanistic preference for OH over Cl transfer with HOCl and the chemoselectivity for HOCl over H2O2.
Mechanism And Chemoselectivity For Hocl-Mediated Oxidation Of Zinc-Bound Thiolates, Lindsay Zumwalt, Arden Perkins, O. Maduka Ogba
Mechanism And Chemoselectivity For Hocl-Mediated Oxidation Of Zinc-Bound Thiolates, Lindsay Zumwalt, Arden Perkins, O. Maduka Ogba
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Quantum mechanical calculations reveal the preferred mechanism and origins of chemoselectivity for HOCl‐mediated oxidation of zinc‐bound thiolates implicated in bacterial redox sensing. Distortion/interaction models show that minimizing geometric distortion at the zinc complex during the rate‐limiting nucleophilic substitution step controls the mechanistic preference for OH over Cl transfer with HOCl and the chemoselectivity for HOCl over H2O2.
Design And Synthesis Of Core–Shell Microgels With One‐Step Clickable Crosslinked Cores And Ultralow Crosslinked Shells, Molla R. Islam, Chelsea Nguy, Sanika Pandit, L. Andrew Lyon
Design And Synthesis Of Core–Shell Microgels With One‐Step Clickable Crosslinked Cores And Ultralow Crosslinked Shells, Molla R. Islam, Chelsea Nguy, Sanika Pandit, L. Andrew Lyon
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The present study is conducted to explore the engineering of core–shell microgels such that the core can be rapidly labeled with a variety of fluorophores, while the shell retains the softness needed in specific biomedical applications. Azide containing crosslinked core particles based on a crosslinked poly(N‐isopropylacrylamide) particle, using a one‐pot, multistep polymerization is synthesized. A core–shell microgel is then synthesized by growing a crosslinker‐free poly(N‐isopropylacrylamide)‐co‐acrylic acid (ULC10AAc) shell through a two‐step seed and feed polymerization. A simple “click” reaction between the azide present on the core and dibenzocyclooctyne containing fluorophores to make dyed core–shell …
Capsaicin Is A Negative Allosteric Modulator Of The 5-Ht3 Receptor, Eslam El Nebrisi, Tatiana Prytkova, Dietrich Ernst Lorke, Luke Howarth, Asma Hassan Alzaabi, Keun-Hang Susan Yang, Frank Christopher Howarth, Murat Oz
Capsaicin Is A Negative Allosteric Modulator Of The 5-Ht3 Receptor, Eslam El Nebrisi, Tatiana Prytkova, Dietrich Ernst Lorke, Luke Howarth, Asma Hassan Alzaabi, Keun-Hang Susan Yang, Frank Christopher Howarth, Murat Oz
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
In this study, effects of capsaicin, an active ingredient of the capsicum plant, were investigated on human 5-hydroxytryptamine type 3 (5-HT3) receptors. Capsaicin reversibly inhibited serotonin (5-HT)-induced currents recorded by two-electrode voltage clamp method in Xenopus oocytes. The inhibition was time- and concentration-dependent with an IC50 = 62 μM. The effect of capsaicin was not altered in the presence of capsazepine, and by intracellular BAPTA injections or trans-membrane potential changes. In radio-ligand binding studies, capsaicin did not change the specific binding of the 5-HT3 antagonist [3H]GR65630, indicating that it is a noncompetitive inhibitor of …
Highly Swelling Ph-Responsive Microgels For Dual Mode Near Infra-Red Fluorescence Reporting And Imaging, Mingning Zhu, Dongdong Lu, Qing Lian, Shanglin Wu, Wenkai Wang, L. Andrew Lyon, Weiguang Wan, Paulo Bártolo, Mark Dickinson, Brian R. Saunders
Highly Swelling Ph-Responsive Microgels For Dual Mode Near Infra-Red Fluorescence Reporting And Imaging, Mingning Zhu, Dongdong Lu, Qing Lian, Shanglin Wu, Wenkai Wang, L. Andrew Lyon, Weiguang Wan, Paulo Bártolo, Mark Dickinson, Brian R. Saunders
Engineering Faculty Articles and Research
Near infra-red (NIR) fluorescence is a desirable property for probe particles because such deeply penetrating light enables remote reporting of the local environment in complex surroundings and imaging. Here, two NIR non-radiative energy transfer (NRET) fluorophores (Cy5 and Cy5.5) are coupled to preformed pH-responsive poly(ethylacrylate-methacrylic acid-divinylbenzene) microgel particles (PEA-MAA-5/5.5 MGs) to obtain new NIR fluorescent probes that are cytocompatible and swell strongly. NIR ratiometric photoluminescence (PL) intensity analysis enables reporting of pH-triggered PEA-MAA-5/5.5 MG particle swelling ratios over a very wide range (from 1–90). The dispersions have greatly improved colloidal stability compared to a reference temperature-responsive NIR MG based on …
Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao
Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the “second secret of life.” The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of …
Leaf Traits Can Be Used To Predict Rates Of Litter Decomposition, Marc Rosenfield, Jennifer L. Funk, Jason K. Keller, Catrina Clausen, Kimberlee Cyphers
Leaf Traits Can Be Used To Predict Rates Of Litter Decomposition, Marc Rosenfield, Jennifer L. Funk, Jason K. Keller, Catrina Clausen, Kimberlee Cyphers
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Strong relationships exist between litter chemistry traits and rates of litter decomposition. However, leaf traits are more commonly found in online trait databases than litter traits and fewer studies have examined how well leaf traits predict litter decomposition rates. Furthermore, while bulk leaf nitrogen (N) content is known to regulate litter decomposition, few studies have explored the importance of N biochemistry fractions, such as protein and amino acid concentration. Here, we decomposed green leaves and naturally senesced leaf litter of nine species representing a wide range of leaf functional traits. We evaluated the ability of traits associated with leaf and …
Evaluation Of Tumor Necrosis Factor Alpha In Sleep-Deprived Menopausal- Induced Rats And The Impact On Bone Health, Nicole Ellsworth, Dwight Curry Iii, Cj Deleon, Frank Frisch
Evaluation Of Tumor Necrosis Factor Alpha In Sleep-Deprived Menopausal- Induced Rats And The Impact On Bone Health, Nicole Ellsworth, Dwight Curry Iii, Cj Deleon, Frank Frisch
Student Scholar Symposium Abstracts and Posters
Post-menopausal osteoporosis as a consequence of estrogen depletion is a growing concern for women in the United States. As more women take on executive positions and experience sleep deprivation, there is the potential for up regulation of pro-inflammatory cytokines, such as tumor necrosis factor alpha. It follows that the homeostatic imbalance of osteoclastic and osteoblastic activity leads to a greater risk of disease. Bisphosphonates generally, and Zolendronate specifically works by decreasing the number of osteoclasts. This current study investigated the impact of Zolendronate on the concentrations of tumor necrosis factor alpha-type (TNFɑ) in 32 ovariectomized Wistar rats. Throughout a five …
Time-Resolved Observation Of Transient Precursor State Of Co On Ru(0001) Using Carbon K-Edge Spectroscopy, Hsin-Yi Wang, Simon Schreck, Matthew Weston, Hirohito Ogasawara, Jerry Larue, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Luca Giannessi, Emanuele Pedersoli, Denys Naumenko, Ivaylo Nikolov, Lorenzo Raimondi, Carlo Spezzani, Martin Beye, Filippo Cavalca, Boyang Liu, Jörgen Gladh, Sergey Koroidov, Piter S. Miedema, Roberto Costantini, Lars G. M. Pettersson, Anders Nilsson
Time-Resolved Observation Of Transient Precursor State Of Co On Ru(0001) Using Carbon K-Edge Spectroscopy, Hsin-Yi Wang, Simon Schreck, Matthew Weston, Hirohito Ogasawara, Jerry Larue, Fivos Perakis, Martina Dell'angela, Flavio Capotondi, Luca Giannessi, Emanuele Pedersoli, Denys Naumenko, Ivaylo Nikolov, Lorenzo Raimondi, Carlo Spezzani, Martin Beye, Filippo Cavalca, Boyang Liu, Jörgen Gladh, Sergey Koroidov, Piter S. Miedema, Roberto Costantini, Lars G. M. Pettersson, Anders Nilsson
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The transient dynamics of carbon monoxide (CO) molecules on a Ru(0001) surface following femtosecond optical laser pump excitation has been studied by monitoring changes in the unoccupied electronic structure using an ultrafast X-ray free-electron laser (FEL) probe. The particular symmetry of perpendicularly chemisorbed CO on the surface is exploited to investigate how the molecular orientation changes with time by varying the polarization of the FEL pulses. The time evolution of spectral features corresponding to the desorption precursor state was well distinguished due to the narrow line-width of the C K-edge in the X-ray absorption (XA) spectrum, illustrating that CO molecules …
Using Green Emitting Ph-Responsive Nanogels To Report Environmental Changes Within Hydrogels: A Nanoprobe For Versatile Sensing, Mingning Zhu, Dongdong Lu, Shanglin Wu, Qing Lian, Wenkai Wang, L. Andrew Lyon, Weiguang Wang, Paulo Bártolo, Brian R. Saunders
Using Green Emitting Ph-Responsive Nanogels To Report Environmental Changes Within Hydrogels: A Nanoprobe For Versatile Sensing, Mingning Zhu, Dongdong Lu, Shanglin Wu, Qing Lian, Wenkai Wang, L. Andrew Lyon, Weiguang Wang, Paulo Bártolo, Brian R. Saunders
Engineering Faculty Articles and Research
Remotely reporting the local environment within hydrogels using inexpensive laboratory techniques has excellent potential to improve our understanding of the nanometer-scale changes that cause macroscopic swelling or deswelling. Whilst photoluminescence (PL) spectroscopy is a popular method for such studies this approach commonly requires bespoke and time-consuming synthesis to attach fluorophores which may leave toxic residues. A promising and more versatile alternative is to use a pre-formed nanogel probe that contains a donor/acceptor pair and then “dope” that into the gel during gel assembly. Here, we introduce green-emitting methacrylic acid-based nanogel probe particles and use them to report the local environment …
Nanogels And Microgels: From Model Colloids To Applications, Recent Developments, And Future Trends, Mattias Karg, Andrij Pich, Thomas Hellweg, Todd Hoare, L. Andrew Lyon, J. J. Crassous, Daisuke Suzuki, Rustam A. Gumerov, Stefanie Schneider, Igor I. Potemkin, Walter Richtering
Nanogels And Microgels: From Model Colloids To Applications, Recent Developments, And Future Trends, Mattias Karg, Andrij Pich, Thomas Hellweg, Todd Hoare, L. Andrew Lyon, J. J. Crassous, Daisuke Suzuki, Rustam A. Gumerov, Stefanie Schneider, Igor I. Potemkin, Walter Richtering
Engineering Faculty Articles and Research
Nanogels and microgels are soft, deformable, and penetrable objects with an internal gel-like structure that is swollen by the dispersing solvent. Their softness and the potential to respond to external stimuli like temperature, pressure, pH, ionic strength, and different analytes make them interesting as soft model systems in fundamental research as well as for a broad range of applications, in particular in the field of biological applications. Recent tremendous developments in their synthesis open access to systems with complex architectures and compositions allowing for tailoring microgels with specific properties. At the same time state-of-the-art theoretical and simulation approaches offer deeper …
Deswelling Induced Morphological Changes In Dual Ph And Temperature Responsive Ultra-Low Crosslinked Poly (N-Isopropyl Acrylamide)-Co-Acrylic Acid Microgels, Molla R. Islam, Maddie Tumbarello, L. Andrew Lyon
Deswelling Induced Morphological Changes In Dual Ph And Temperature Responsive Ultra-Low Crosslinked Poly (N-Isopropyl Acrylamide)-Co-Acrylic Acid Microgels, Molla R. Islam, Maddie Tumbarello, L. Andrew Lyon
Engineering Faculty Articles and Research
Poly(N-isopropylacrylamide) microgels prepared without exogenous cross-linker are extremely “soft” as a result of their very low cross-linking density, with network connectivity arising only from the self-crosslinking of pNIPAm chains. As a result of this extreme softness, our group and others have taken interest in using these materials in a variety of bioengineering applications, while also pursuing studies of their fundamental properties. Here, we report deswelling triggered structural changes in poly(N-isopropylacrylamide-co-acrylic acid) (ULC10AAc) microgels prepared by precipitation polymerization. Dynamic light scattering suggests that the deswelling of these particles not only depends on the collapse of …
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 …
Isolation Of Rna From A Mixture And Its Detection By Utilizing A Microgel-Based Optical Device, Molla R. Islam, Shakiba Azimi, Faranak Teimoory, Glen Loppnow, Michael J. Serpe
Isolation Of Rna From A Mixture And Its Detection By Utilizing A Microgel-Based Optical Device, Molla R. Islam, Shakiba Azimi, Faranak Teimoory, Glen Loppnow, Michael J. Serpe
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
In this investigation, we show that RNA can be separated from a solution containing DNA and RNA and the isolated RNA can be detected using poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons). The isolation of RNA was accomplished by using hairpin-functionalized magnetic beads (MMPDNA) and differential melting, based on the fact that the DNA–RNA hybrid duplex is stronger (i.e., high melting temperature) than the DNA–DNA duplex (i.e., low melting temperature). By performing concurrent etalon sensing and fluorescent studies, we found that the MMPDNA combined with differential melting was capable of selectively separating RNA from DNA. This selective separation and …
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 …
Microgel Core/Shell Architectures As Targeted Agents For Fibrinolysis, Purva Kodlekere, L. Andrew Lyon
Microgel Core/Shell Architectures As Targeted Agents For Fibrinolysis, Purva Kodlekere, L. Andrew Lyon
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
We demonstrate the utility of microgel core/shell structures conjugated to fibrin-specific peptides as fibrinolytic agents. Poly(N-isopropylmethacrylamide) (pNIPMAm) based microgels conjugated to the peptide GPRPFPAC (GPRP) were observed to bring about fibrin clot erosion, merely through exploitation of the dynamic nature of the clots. These results suggest the potential utility of peptide–microgel hybrids in clot disruption and clotting modulation.
Predicting Spatial Patterns In Precipitation Isotope (Δ2h And Δ18o) Seasonality Using Sinusoidal Isoscapes, Scott T. Allen, James W. Kirchner, Gregory R. Goldsmith
Predicting Spatial Patterns In Precipitation Isotope (Δ2h And Δ18o) Seasonality Using Sinusoidal Isoscapes, Scott T. Allen, James W. Kirchner, Gregory R. Goldsmith
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Understanding how precipitation isotopes vary spatially and temporally is important for tracer applications. We tested how well month‐to‐month variations in precipitation δ18O and δ2H were captured by sinusoidal cycles, and how well spatial variations in these seasonal cycles could be predicted, across Switzerland. Sine functions representing seasonal cycles in precipitation isotopes explained between 47% and 94% of the variance in monthly δ18O and δ2H values at each monitoring site. A significant sinusoidal cycle was also observed in line‐conditioned excess. We interpolated the amplitudes, phases, and offsets of these sine functions across the landscape, using multiple linear …
Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich
Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO® ChromaTOF® software and facilitates selection of analytes of interest based on peak area …
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 …
Phase Behavior Of Binary And Polydisperse Suspensions Of Compressible Microgels Controlled By Selective Particle Deswelling, A. Scotti, U. Gasser, E. S. Herman, Jun Han, A. Menzel, L. Andrew Lyon, A. Fernandez-Nieves
Phase Behavior Of Binary And Polydisperse Suspensions Of Compressible Microgels Controlled By Selective Particle Deswelling, A. Scotti, U. Gasser, E. S. Herman, Jun Han, A. Menzel, L. Andrew Lyon, A. Fernandez-Nieves
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
We investigate the phase behavior of suspensions of poly(N-isopropylacrylamide) (pNIPAM) microgels with either bimodal or polydisperse size distribution. We observe a shift of the fluid-crystal transition to higher concentrations depending on the polydispersity or the fraction of large particles in suspension. Crystallization is observed up to polydispersities as high as 18.5%, and up to a number fraction of large particles of 29% in bidisperse suspensions. The crystal structure is random hexagonal close-packed as in monodisperse pNIPAM microgel suspensions.We explain our experimental results by considering the effect of bound counterions. Above a critical particle concentration, these cause deswelling of the largest …
Nonlinear Oscillatory Dynamics Of The Hardening Of Calcium Phosphate Bone Cements, Vuk Uskoković, Julietta V. Rau
Nonlinear Oscillatory Dynamics Of The Hardening Of Calcium Phosphate Bone Cements, Vuk Uskoković, Julietta V. Rau
Pharmacy Faculty Articles and Research
Here we report on the nonlinear, oscillatory dynamics detected in the evolution of phase composition during the setting of different calcium phosphate cements, two of which evolved toward brushite and one toward hydroxyapatite as the final product. Whereas both brushite-forming cements contained iondoped b-tricalcium phosphate as the initial phase, the zinc-containing one yielded scholzite as an additional phase during setting and the oscillations between these two products were pronounced throughout the entire 80 h setting period, long after the hardening processes was over from the mechanical standpoint. Oscillations in the copper-containing system involved the amount of brushite as the main …