Chemistry Commons^™

Group 14 Metallocene Catalysts For Carbonyl Hydroboration And Cyanosilylation, Haley J. Robertson, Mallory N. Fujiwara, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of six Group 14 metallocene compounds (M = Ge, Sn, Pb) were studied as catalysts for carbonyl hydroboration and cyanosilylation reactions at room temperature. Both bis(pentamethylcyclopentadienyl) and tetramethyldisiloxa[3]metallocenophane compounds were compared. The tin and lead metallocenophanes exhibited the highest reactivity in hydroboration and cyanosilylation reactions. Hammett analysis of aldehyde hydroboration provided a ρ value of 0.73, suggesting a buildup of negative charge during the turnover-limiting step, consistent with the transition state for hydride transfer to the carbonyl center. NMR studies of Lewis acidity indicate that the Ge, Sn, and Pb tetramethyldisiloxa[3]metallocenophane compounds are weak Lewis acids.

Permafrost Carbon: Progress On Understanding Stocks And Fluxes Across Northern Terrestrial Ecosystems, Claire C. Treat, Anna-Maria Virkkala, Eleanor Burke, Lori Bruhwiler, Abhishek Chatterjee, Joshua B. Fisher, Josh Hashemi, Frans-Jan W. Parmentier, Brendan M. Rogers, Sebastian Westermann, Jennifer D. Watts, Elena Blanc-Betes, Matthias Fuchs, Stefan Kruse, Avni Malhotra, Kimberley Miner, Jens Strauss, Amanda Armstrong, Howard E. Epstein, Bradley Gay, Mathias Goeckede, Aram Kalhori, Dan Kou, Charles E. Miller, Susan M. Natali, Youmi Oh, Sarah Shakil, Oliver Sonnentag, Ruth K. Varner, Scott Zolkos, Edward A.G. Schuur, Gustaf Hugelius

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Significant progress in permafrost carbon science made over the past decades include the identification of vast permafrost carbon stocks, the development of new pan-Arctic permafrost maps, an increase in terrestrial measurement sites for CO₂ and methane fluxes, and important factors affecting carbon cycling, including vegetation changes, periods of soil freezing and thawing, wildfire, and other disturbance events. Process-based modeling studies now include key elements of permafrost carbon cycling and advances in statistical modeling and inverse modeling enhance understanding of permafrost region C budgets. By combining existing data syntheses and model outputs, the permafrost region is likely a wetland methane …

Mutational Analysis Of The Nitrogenase Carbon Monoxide Protective Protein Cown Reveals That A Conserved C‑Terminal Glutamic Acid Residue Is Necessary For Its Activity, Dustin L. Willard, Joshuah J. Arellano, Mitch Underdahl, Terrence M. Lee, Avinash S. Ramaswamy, Gabriella Fumes, Agatha Kliman, Emily Y. Wong, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN’s protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work …

Jwst: Deuterated Pahs, Pah-Nitriles, And Pah 4 Overtone And Combination Bands I: Program Description And First Look, C. Boersma, L. J. Allamandola, Vincent J. Esposito, A. Maragkoudakis, J. D. Bregman, P. Temi, T. J. Lee, R. C. Fortenberry, E. Peeters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A first look is taken at the NIRSpec 1–5 μm observations from James Webb Space Telescope program 1591 that targets seven objects along the low-mass stellar life cycle with polycyclic aromatic hydrocarbon (PAH) emission. Spectra extracted from a 1'.'5 radius circular aperture are explored, showing a wealth of features, including the 3 μm PAH complex, the PAH continuum, and atomic and molecular emission lines from H i, He, H₂, and other species. CO₂- and H₂O-ice absorption and CO emission is also seen. Focusing on the bright-PDR position in M17, the PAH CH stretch falls …

Inhibition Of Chromium(Iii) Oxidation Through Manganese(Iv) Oxide Passivation And Iron(Ii) Abiotic Reduction, Miranda L. Aiken, Macon J. Abernathy, Michael V. Schaefer, Ilkeun Lee, Samantha C. Ying

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Manganese (Mn) oxides are strong oxidants that are ubiquitous in soils and can oxidize redox-active metals, including chromium (Cr). In soil environments, trivalent chromium (Cr(III)) is a benign, immobile micronutrient, whereas the hexavalent Cr(VI) form is present as a highly mobile, toxic chromate oxyanion. Although many studies have characterized the capacity of Mn(III/IV) oxides to oxidize Cr(III) to toxic Cr(VI), the oxidative capacity of Mn oxides in the presence of potentially passivating soil constituents, specifically reduced soluble iron (Fe(II)aq), remains unresolved. We hypothesized that chemical processes at redox interfaces, such as diffusion-limited environments within soil aggregates, can lead to decreased …

Volcanic Diffuse Volatile Emissions Tracked By Plant Responses Detectable From Space, Robert R. Bogue, Peter M. J. Douglas, Joshua B. Fisher, John Stix

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Volcanic volatile emissions provide information about volcanic unrest but are difficult to detect with satellites. Volcanic degassing affects plants by elevating local CO2 and H2O concentrations, which may increase photosynthesis. Satellites can detect plant health, or a reaction to photosynthesis, through a Normalized Difference Vegetation Index (NDVI). This can act as a potential proxy for detecting changes in volcanic volatile emissions from space. We tested this method by analyzing 185 Landsat 5 and 8 images of the Tern Lake thermal area (TLTA) in northeast Yellowstone caldera from 1984 to 2022. We compared the NDVI values of the thermal area with …

Carbodiimide And Isocyanate Hydroboration By A Cyclic Carbodiphosphorane Catalyst, Ben A. Janda, Julie A. Tran, Daniel K. Chang, Gabriela C. Nerhood, O. Maduka Ogba, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report hydroboration of carbodiimide and isocyanate substrates catalyzed by a cyclic carbodiphosphorane catalyst. The cyclic carbodiphosphorane outperformed the other Lewis basic carbon species tested, including other zerovalent carbon compounds, phosphorus ylides, an N-heterocyclic carbene, and an N-heterocyclic olefin. Hydroborations of seven carbodiimides and nine isocyanates were performed at room temperature to form N-boryl formamidine and N-boryl formamide products. Intermolecular competition experiments demonstrated the selective hydroboration of alkyl isocyanates over carbodiimide and ketone substrates. DFT calculations support a proposed mechanism involving activation of pinacolborane by the carbodiphosphorane catalyst, followed by hydride transfer and B−N bond formation.

Anharmonic Ir Absorption Spectra Of The Prototypical Interstellar Pahs Phenanthrene, Pyrene, And Pentacene In Their Neutral And Cation States, Vincent J. Esposito, Louis J. Allamandola, Christiaan Boersma, Jesse D. Bregman, Ryan C. Fortenberry, Alexandros Maragkoudakis, Pasquale Temi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Combination band and overtone transitions of polycyclic aromatic hydrocarbon (PAH) cations in the 2000–2900 cm^-1 (5-3.5 µm) region are implicated as carriers of the ‘quasi-continuum’ observed in the near-infrared (IR) emission spectra of many astronomical objects. In neutral PAHs, the strongest absorption features are concentrated in the 700–900 cm^-1 (14–11 µm) range, which are associated with CH out-of-plane bending motions. Upon ionization, this shifts to the 1000–1600 cm^-1 (10–6 µm) range, where bands are associated with C=C stretches and CH in-plane bends. Anharmonicity is required to accurately characterize the IR absorption spectrum of PAHs, indicated herein by …

Hydrogen Peroxide Disproportionation Activity Is Sensitive To Pyridine Substitutions On Manganese Catalysts Derived From 12-Membered Tetra-Aza Macrocyclic Ligands, David M. Freire, Hannah M. Johnston, Katherine J. Smith, Kristof Pota, Magy A. Mekhail, Sugam Kharel, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The abundance of manganese in nature and versatility to access different oxidation states have made manganese complexes attractive as catalysts for oxidation reactions in both biology and industry. Macrocyclic ligands offer the advantage of substantially controlling the reactivity of the manganese center through electronic tuning and steric constraint. Inspired by the manganese catalase enzyme, a biological catalyst for the disproportionation of H₂O₂ into water and O₂, the work herein employs 12-membered tetra-aza macrocyclic ligands to study how the inclusion of and substitution to the pyridine ring on the macrocyclic ligand scaffold impacts the reactivity of …

The Structure Of A Lactobacillus Helveticus Chlorogenic Acid Esterase And The Dynamics Of Its Insertion Domain Provide Insights Into Substrate Binding, Kellie K. Omori, Charles T. Drucker, Tracie L. S. Okumura, Nathaniel B. Carl, Brianna T. Dinn, Destiny Ly, Kylie N. Sacapano, Allie Tajii, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Chlorogenic acid esterases (ChlEs) are a useful class of enzymes that hydrolyze chlorogenic acid (CGA) into caffeic and quinic acid. ChlEs can break down CGA in foods to improve their sensory properties and release caffeic acid in the digestive system to improve the absorption of bioactive compounds. This work presents the structure, molecular dynamics, and biochemical characterization of a ChlE from Lactobacillus helveticus (Lh). Molecular dynamics simulations suggest that substrate access to the active site of LhChlE is modulated by two hairpin loops above the active site. Docking simulations and mutational analysis suggest that two residues within …

Anharmonicity And Deuteration In The Ir Absorption And Emission Spectra Of Phenylacetylene, Vincent J. Esposito, Pierro Ferrari, Wybren Jan Buma, Christiaan Boersma, Cameron J. Mackie, Alessandra Candian, Ryan C. Fortenberry, Alexander G. G. M. Tielens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Anharmonic cascade emission simulations, herein evinced by full reproduction and deep insights into recent emission spectroscopy experiments of phenylacetylene, are integral to the future successful analysis of JWST observational spectra. Experimental infrared absorption experiments conducted in this study reveal a complex spectrum dominated by quantum effects that are uncovered by anharmonic computational analysis. From this work, it becomes clear that phenylacetylene exhibits strong resonance coupling between fundamental and two-quanta combination modes as well as giving indication for coupling with higher-order, three-quanta combination bands. This study benchmarks the development of advanced computational methods that will be extended to larger systems of …

Additive Effects Of Cyclic Peptide [R4w4] When Added Alongside Azithromycin And Rifampicin Against Mycobacterium Avium Infection, Melissa Kelley, Kayvan Sasaninia, Arbi Abnousian, Ali Badaoui, James Owens, Abrianna Beever, Nala Kachour, Rakesh Kumar Tiwari, Vishwanath Venketaraman

Pharmacy Faculty Articles and Research

Mycobacterium avium (M. avium), a type of nontuberculous mycobacteria (NTM), poses a risk for pulmonary infections and disseminated infections in immunocompromised individuals. Conventional treatment consists of a 12-month regimen of the first-line antibiotics rifampicin and azithromycin. However, the treatment duration and low antibiotic tolerability present challenges in the treatment of M. avium infection. Furthermore, the emergence of multidrug-resistant mycobacterium strains prompts a need for novel treatments against M. avium infection. This study aims to test the efficacy of a novel antimicrobial peptide, cyclic [R4W4], alongside the first-line antibiotics azithromycin and rifampicin in reducing M. avium survival. Colony-forming unit (CFU) …

Ruthenium Olefin Metathesis Catalysts Featuring Chelating Benzylidene-Triazole Ligands, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this issue of Chem Catalysis, Shi and co-workers describe the synthesis and olefin metathesis activity of ruthenium complexes with chelating benzylidene-triazole ligands. Catalyst decomposition is slow at up to 80°C, which enables challenging catalytic reactions, including cross-metathesis of trans-alkenes and macrocycle synthesis by dynamic covalent chemistry.

Probing Conformational Landscapes Of Binding And Allostery In The Sars-Cov-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations And Perturbation-Based Profiling Approaches: Hidden Role Of Omicron Mutations As Modulators Of Allosteric Signaling And Epistatic Relationships, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 spike protein complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which can be contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using the dynamics-based mutational scanning of spike residues, we identified structural stability and binding affinity hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational …

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.

Symbiotic Ucyn-A Strains Co-Occurred With El Niño, Relaxed Upwelling, And Varied Eukaryotes Over 10 Years Off Southern California, Colette Fletcher-Hoppe, Yi-Chun Yeh, Yubin Raut, J. L. Weissman, Jed A. Fuhrman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation, the conversion of N₂ gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon …

Updating The Dual C And O Isotope—Gas-Exchange Model: A Concept To Understand Plant Responses To The Environment And Its Implications For Tree Rings, Rolf T. W. Siegwolf, Marco M. Lehmann, Gregory R. Goldsmith, Olga V. Churakova (Sidorova), Cathleen Mirande-Ney, Galina Timoveeva, Rosmarie B. Weigt, Matthias Saurer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The combined study of carbon (C) and oxygen (O) isotopes in plant organic matter has emerged as a powerful tool for understanding plant functional responses to environmental change. The approach relies on established relationships between leaf gas exchange and isotopic fractionation to derive a series of model scenarios that can be used to infer changes in photosynthetic assimilation and stomatal conductance driven by changes in environmental parameters (CO₂, water availability, air humidity, temperature, nutrients). We review the mechanistic basis for a conceptual model, in light of recently published research, and discuss where isotopic observations do not match our …

Vibrational, Rotational And Electronic Spectroscopy For Possible Interstellar Detection Of Alnh2 And Halnh, Tarek Trabelsi, Vincent J. Esposito, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We obtained accurate vibrational frequencies, rotational constants, and vertical transition energy for AlNH₂(X¹A₁) and HAlNH(X¹A′) isomers using ab initio calculations at various levels of theory. These two isomers are potential candidates for astronomical observation. AlNH₂ and HAlNH are thermodynamically stable, with Al-NH₂ and HAl-NH bond dissociation energies predicted to be 4.39 and 3.60 eV, respectively. The two isomers are characterized by sizable dipole moments of 1.211 and 3.64 D, respectively. The anharmonic frequencies and spectroscopic constants reported for the two isomers should facilitate their experimental differentiation. In addition, we evaluated …

Development And Validation Of A Uplc-Ms/Ms Method To Investigate The Plasma Pharmacokinetics Of A KCa2.2/KCa2.3 Positive Allosteric Modulator In Mice, Mohammad Asikur Rahman, Devaraj Venkatapura Chandrashekar, Young-Woo Nam, Basir Syed, David Salehi, Hamidreza Montazeri Aliabadi, Miao Zhang, Reza Mehvar

Pharmacy Faculty Articles and Research

Rationale

There is currently no treatment for spinocerebellar ataxias (SCAs), which are a group of genetic disorders that often cause a lack of coordination, difficulty walking, slurred speech, tremors, and eventually death. Activation of K_Ca2.2/K_Ca2.3 channels reportedly exerts beneficial effects in SCAs. Here, we report the development and validation of an analytical method for quantitating a recently-developed positive allosteric modulator of K_Ca2.2/K_Ca2.3 channels (compound 2q) in mouse plasma.

Methods

Mouse plasma samples (10 μL) containing various concentrations of 2q were subjected to protein precipitation in the presence of a structurally similar internal …

Balancing Functional Tradeoffs Between Protein Stability And Ace2 Binding In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic And Energetic Changes, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and …

Small Community Water Systems Have The Highest Prevalence Of Mn In Drinking Water In California, Usa, Miranda Aiken, Samantha C. Ying

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Manganese (Mn) is currently regulated as a secondary contaminant in California, USA; however, recent revisions of the World Health Organization drinking water guidelines have increased regulatory attention of Mn in drinking water due to increasing reports of neurotoxic effects in infants and children. In this study, Mn concentrations reported to California’s Safe Drinking Water Information System were used to estimate the potentially exposed population within California based on system size. We estimate that between 2011 and 2021, over 525,000 users in areas with reported Mn data are potentially exposed to Mn concentrations exceeding the WHO health-based guideline (80 μg L …

Structure-Guided Mutagenesis Reveals The Catalytic Residue That Controls The Regiospecificity Of C6-Indole Prenyltransferases, Ahmed R. Aoun, Nagaraju Mupparapu, Diem N. Nguyen, Tae Ho Kim, Christopher M. Nguyen, Zhengfeiyue Pan, Sherif I. Elshahawi

Pharmacy Faculty Articles and Research

Indole is a significant structural moiety and functionalization of the C−H bond in indole-containing molecules expands their chemical space, and modifies their properties and/or activities. Indole prenyltransferases (IPTs) catalyze the direct regiospecific installation of prenyl moieties on indole-derived compounds. IPTs have shown relaxed substrate flexibility enabling them to be used as tools for indole functionalization. However, the mechanism by which certain IPTs target a specific carbon position is not fully understood. Herein, we use structure-guided site-directed mutagenesis, in vitro enzymatic reactions, kinetics and structural-elucidation of analogs to verify the key catalytic residues that control the regiospecificity of all characterized regiospecific …

Studying Competing Reaction Pathways In Methanol Decomposition On Platinum Catalysts Under Ultra-High Vacuum (Uhv) Conditions Using Tpd And Sfg Spectroscopy, Quy Loi, Kevin Alvorado Jimenez, Sarah Lelea, Lauren Villegas, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Catalysts are important in manufacturing processes, as they make them more efficient and useful. To develop better catalysts, we need to know how they work by studying how methanol breaks down on platinum. TPD and TD-SFG spectroscopy are used to study by providing the vibrational spectra of methanol on the platinum surface as temperature changes.

Computational Design And Molecular Modeling Of Morphine Derivatives For Preferential Binding In Inflamed Tissue, Makena Augenstein, Nayiri Alexander, Matthew Gartner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The opioid epidemic has impacted over 10 million Americans in 2019. Opioids, like morphine, bind non-selectively in both peripheral tissue, leading to effective pain relief, and central tissue, resulting in dangerous side effects and addiction. The inflamed conditions of injured tissues have a lower pH (pH = 6–6.5) environment than healthy tissue (pH = 7.4). We aim to design a morphine derivative that binds selectively within inflamed tissue using molecular extension and dissection techniques. Morphine binds to the μ-opioid receptor (MOR) when the biochemically active amine group is protonated. Fluorination of a β-carbon from the tertiary amine group led to …

Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable …

Increased Efficiency Of A Functional Sod Mimic Achieved With Pyridine Modification On A Pyclen-Based Copper(Ii) Complex, Magy A. Mekhail, Katherine J. Smith, David M. Freire, Kristof Pota, Nam Nguyen, Marianne E. Burnett, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of Cu(II) complexes with the formula [Cu^RPyN₃]²⁺ varying in substitution on the pyridine ring were investigated as superoxide dismutase (SOD) mimics to identify the most efficient reaction rates produced by a synthetic, water-soluble copper-based SOD mimic reported to date. The resulting Cu(II) complexes were characterized by X-ray diffraction analysis, UV–visible spectroscopy, cyclic voltammetry, and metal-binding (log β) affinities. Unique to this approach, the modifications to the pyridine ring of the PyN₃ parent system tune the redox potential while exhibiting high binding stabilities without changing the coordination environment of the metal complex within …

Virtual And In Vitro Screening Of Natural Products Identifies Indole And Benzene Derivatives As Inhibitors Of Sars-Cov-2 Main Protease (MPro), Dony Ang, Riley Kendall, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with …

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 …

Dinitrogen Emissions Dominate Nitrogen Gas Emissions From Soils With Low Oxygen Availability In A Moist Tropical Forest, Maya Almaraz, Peter M. Groffman, Whendee L. Silver, Steven J. Hall, Yang Lin, Christine S. O'Connell, Stephen Porder

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Lowland tropical forest soils are relatively N rich and are the largest global source of N₂O (a powerful greenhouse gas) to the atmosphere. Despite the importance of tropical N cycling, there have been few direct measurements of N₂ (an inert gas that can serve as an alternate fate for N₂O) in tropical soils, limiting our ability to characterize N budgets, manage soils to reduce N₂O production, or predict the future role that N limitation to primary productivity will play in buffering against climate change. We collected soils from across macro- and micro-topographic gradients …

Arginine Methylation Of The Pgc-1Α C‑Terminus Is Temperature- Dependent, Meryl Mendoz, Mariel Mendoza, Tiffany Lubrino, Sidney Briski, Immaculeta Osuji, Janielle Cuala, Brendan Ly, Ivan Ocegueda, Harvey Peralta, Benjamin A. Garcia, Cecilia Zurita-Lopez

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We set out to determine whether the C-terminus (amino acids 481–798) of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α, UniProt Q9UBK2), a regulatory metabolic protein involved in mitochondrial biogenesis, and respiration, is an arginine methyltransferase substrate. Arginine methylation by protein arginine methyltransferases (PRMTs) alters protein function and thus contributes to various cellular processes. In addition to confirming methylation of the C-terminus by PRMT1 as described in the literature, we have identified methylation by another member of the PRMT family, PRMT7. We performed in vitro methylation reactions using recombinant mammalian PRMT7 and PRMT1 at 37, 30, 21, 18, and 4 °C. …