Structures and Energetics of Proteins and their Active Sites

Heterogeneous catalysts, used in industry for the production of fuels and chemicals, are microporous solids characterized by a high internal surface area. The catalyticly active sites may occur at the surface of the bulk solid or of small crystallites deposited on a porous support. An example of the former case would be a zeolite, and of the latter, a supported metal catalyst. Since the activity and selectivity of a catalyst are known to be a function of surface composition and structure, it is highly desirable to characterize catalyst surfaces with atomic scale resolution. Where the active phase is dispersed on a support, it is also important to know the dispersion of the deposited phase, as well as its structural and compositional uniformity, the latter characteristics being particularly important in the case of multicomponent catalysts. Knowledge of the pore size and shape is also important, since these can influence the transport of reactants and products through a catalyst and the dynamics of catalyst deactivation.

Scanning luminescence x-ray microscopy: Progress toward selective staining using microspheres

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100168104 ◽

1994 ◽

Vol 52 ◽

pp. 74-75

Author(s):

C. Jacobsen ◽

J. Fu ◽

S. Mayer ◽

Y. Wang ◽

S. Williams

Keyword(s):

Visible Light ◽

Active Sites ◽

Light Emission ◽

Chinese Hamster ◽

Polystyrene Spheres ◽

Good Resistance ◽

X Ray ◽

Selective Staining ◽

Visible Light Emission ◽

Specific Labelling

In scanning luminescence x-ray microscopy (SLXM), a high resolution x-ray probe is used to excite visible light emission (see Figs. 1 and 2). The technique has been developed with a goal of localizing dye-tagged biochemically active sites and structures at 50 nm resolution in thick, hydrated biological specimens. Following our initial efforts, Moronne et al. have begun to develop probes based on biotinylated terbium; we report here our progress towards using microspheres for tagging.Our initial experiments with microspheres were based on commercially-available carboxyl latex spheres which emitted ~ 5 visible light photons per x-ray absorbed, and which showed good resistance to bleaching under x-ray irradiation. Other work (such as that by Guo et al.) has shown that such spheres can be used for a variety of specific labelling applications. Our first efforts have been aimed at labelling ƒ actin in Chinese hamster ovarian (CHO) cells. By using a detergent/fixative protocol to load spheres into cells with permeabilized membranes and preserved morphology, we have succeeded in using commercial dye-loaded, spreptavidin-coated 0.03μm polystyrene spheres linked to biotin phalloidon to label f actin (see Fig. 3).

The design and catalytic performance of molybdenum active sites on an MCM-41 framework for the aerobic oxidation of 5-hydroxymethylfurfural to 2,5-diformylfuran

Catalysis Science & Technology ◽

10.1039/c8cy02291g ◽

2019 ◽

Vol 9 (3) ◽

pp. 811-821 ◽

Cited By ~ 7

Author(s):

Zhao-Meng Wang ◽

Li-Juan Liu ◽

Bo Xiang ◽

Yue Wang ◽

Ya-Jing Lyu ◽

...

Keyword(s):

Catalytic Activity ◽

Active Sites ◽

Aerobic Oxidation ◽

Catalytic Performance ◽

Mcm 41

The catalytic activity decreases as –(SiO)3Mo(OH)(O) > –(SiO)2Mo(O)2 > –(O)4–MoO.

A novel ligand with –NH2 and –COOH-decorated Co/Fe-based oxide for an efficient overall water splitting: dual modulation roles of active sites and local electronic structure

Catalysis Science & Technology ◽

10.1039/d0cy01109f ◽

2020 ◽

Vol 10 (18) ◽

pp. 6266-6273

Author(s):

Yalan Zhang ◽

Zebin Yu ◽

Ronghua Jiang ◽

Jung Huang ◽

Yanping Hou ◽

...

Keyword(s):

Electronic Structure ◽

Water Splitting ◽

Energy Demand ◽

Active Sites ◽

Electrode Materials ◽

Global Energy ◽

Overall Water Splitting ◽

Local Electronic Structure ◽

Electrochemical Water Splitting

Excellent electrochemical water splitting with remarkable durability can provide a solution to satisfy the increasing global energy demand in which the electrode materials play an important role.

Active sites in butan-2-ol conversion over magnésium and zinc phosphates

Journal de Chimie Physique ◽

10.1051/jcp/1997942007 ◽

1997 ◽

Vol 94 ◽

pp. 2007-2015 ◽

Cited By ~ 1

Author(s):

M Kacimi ◽

M Ziyad

Keyword(s):

Active Sites ◽

Zinc Phosphates

“Active Sites” on Platelet Membranes

Thrombosis and Haemostasis ◽

10.1055/s-0038-1651374 ◽

1975 ◽

Vol 34 (03) ◽

pp. 859-860

Author(s):

M. G Davey

Keyword(s):

Active Sites ◽

Platelet Membranes

A Pyridinic Fe-N4 Macrocycle Effectively Models the Active Sites in Fe/N-Doped Carbon Electrocatalysts

10.26434/chemrxiv.10008545.v2 ◽

2020 ◽

Author(s):

Travis Marshall-Roth ◽

Nicole J. Libretto ◽

Alexandra T. Wrobel ◽

Kevin Anderton ◽

Nathan D. Ricke ◽

...

Keyword(s):

Oxygen Reduction ◽

Active Sites ◽

Catalytic Properties ◽

Reduction Reaction ◽

Iron Phthalocyanine ◽

Electrochemical Studies ◽

Onset Potential ◽

Nitrogen Doped Carbon ◽

Iron Active Sites

Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum in fuel cells, but their active site structures are poorly understood. A leading postulate is that iron active sites in this class of materials exist in an Fe-N4 pyridinic ligation environment. Yet, molecular Fe-based catalysts for the oxygen reduction reaction (ORR) generally feature pyrrolic coordination and pyridinic Fe-N4 catalysts are, to the best of our knowledge, non-existent. We report the synthesis and characterization of a molecular pyridinic hexaazacyclophane macrocycle, (phen2N2)Fe, and compare its spectroscopic, electrochemical, and catalytic properties for oxygen reduction to a prototypical Fe-N-C material, as well as iron phthalocyanine, (Pc)Fe, and iron octaethylporphyrin, (OEP)Fe, prototypical pyrrolic iron macrocycles. N 1s XPS signatures for coordinated N atoms in (phen2N2)Fe are positively shifted relative to (Pc)Fe and (OEP)Fe, and overlay with those of Fe-N-C. Likewise, spectroscopic XAS signatures of (phen2N2)Fe are distinct from those of both (Pc)Fe and (OEP)Fe, and are remarkably similar to those of Fe-N-C with compressed Fe–N bond lengths of 1.97 Å in (phen2N2)Fe that are close to the average 1.94 Å length in Fe-N-C. Electrochemical studies establish that both (Pc)Fe and (phen2N2)Fe have relatively high Fe(III/II) potentials at ~0.6 V, ~300 mV positive of (OEP)Fe. The ORR onset potential is found to directly correlate with the Fe(III/II) potential leading to a ~300 mV positive shift in the onset of ORR for (Pc)Fe and (phen2N2)Fe relative to (OEP)Fe. Consequently, the ORR onset for (phen2N2)Fe and (Pc)Fe is within 150 mV of Fe-N-C. Unlike (OEP)Fe and (Pc)Fe, (phen2N2)Fe displays excellent selectivity for 4-electron ORR with <4% maximum H2O2 production, comparable to Fe-N-C materials. The aggregate spectroscopic and electrochemical data establish (phen2N2)Fe as a pyridinic iron macrocycle that effectively models Fe-N-C active sites, thereby providing a rich molecular platform for understanding this important class of catalytic materials.

On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment

10.26434/chemrxiv.11558430.v1 ◽

2020 ◽

Author(s):

Robert Stepic ◽

Lara Jurković ◽

Ksenia Klementyeva ◽

Marko Ukrainczyk ◽

Matija Gredičak ◽

...

Keyword(s):

Active Sites ◽

Realistic Model ◽

Binding Energies ◽

Inhibition Mechanism ◽

Aqueous Environment ◽

Binding Modes ◽

Carboxylate Groups ◽

Dissolved Ions ◽

Living Organisms ◽

Dynamics Simulations

In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth.

Catalytic Resonance Theory: Parallel Reaction Pathway Control

10.26434/chemrxiv.10271090 ◽

2019 ◽

Author(s):

M. Alexander Ardagh ◽

Manish Shetty ◽

Anatoliy Kuznetsov ◽

Qi Zhang ◽

Phillip Christopher ◽

...

Keyword(s):

Chemical Reactions ◽

Active Site ◽

Active Sites ◽

Reaction Pathway ◽

Control Strategies ◽

Oscillation Amplitude ◽

Catalytic Performance ◽

Parallel Reaction ◽

Resonance Theory ◽

Static Conditions

Catalytic enhancement of chemical reactions via heterogeneous materials occurs through stabilization of transition states at designed active sites, but dramatically greater rate acceleration on that same active site is achieved when the surface intermediates oscillate in binding energy. The applied oscillation amplitude and frequency can accelerate reactions orders of magnitude above the catalytic rates of static systems, provided the active site dynamics are tuned to the natural frequencies of the surface chemistry. In this work, differences in the characteristics of parallel reactions are exploited via selective application of active site dynamics (0 < ΔU < 1.0 eV amplitude, 10-6 < f < 104 Hz frequency) to control the extent of competing reactions occurring on the shared catalytic surface. Simulation of multiple parallel reaction systems with broad range of variation in chemical parameters revealed that parallel chemistries are highly tunable in selectivity between either pure product, even when specific products are not selectively produced under static conditions. Two mechanisms leading to dynamic selectivity control were identified: (i) surface thermodynamic control of one product species under strong binding conditions, or (ii) catalytic resonance of the kinetics of one reaction over the other. These dynamic parallel pathway control strategies applied to a host of chemical conditions indicate significant potential for improving the catalytic performance of many important industrial chemical reactions beyond their existing static performance.

Dose COVID-19 Uncovered a New Feature of Metronidazole Drug?

10.26434/chemrxiv.12526277.v2 ◽

2020 ◽

Author(s):

Mohammad Seyedhamzeh ◽

Bahareh Farasati Far ◽

Mehdi Shafiee Ardestani ◽

Shahrzad Javanshir ◽

Fatemeh Aliabadi ◽

...

Keyword(s):

Molecular Docking ◽

Drug Discovery ◽

Virtual Screening ◽

Active Sites ◽

Initial Plasma ◽

New Feature ◽

Metronidazole Benzoate ◽

Global Health Problem ◽

A Current ◽

Pro Inflammatory Cytokines

Studies of coronavirus disease 2019 (COVID-19) as a current global health problem shown the initial plasma levels of most pro-inflammatory cytokines increased during the infection, which leads to patient countless complications. Previous studies also demonstrated that the metronidazole (MTZ) administration reduced related cytokines and improved treatment in patients. However, the effect of this drug on cytokines has not been determined. In the present study, the interaction of MTZ with cytokines was investigated using molecular docking as one of the principal methods in drug discovery and design. According to the obtained results, the IL12-metronidazole complex is more stable than other cytokines, and an increase in the surface and volume leads to prevent to bind to receptors. Moreover, ligand-based virtual screening of several libraries showed metronidazole phosphate, metronidazole benzoate, 1-[1-(2-Hydroxyethyl)-5- nitroimidazol-2-yl]-N-methylmethanimine oxide, acyclovir, and tetrahydrobiopterin (THB or BH4) like MTZ by changing the surface and volume prevents binding IL-12 to the receptor. Finally, the inhibition of the active sites of IL-12 occurred by modifying the position of the methyl and hydroxyl functional groups in MTZ.