Search results for "Oxyanion"

Silicic acid competes for dimethylarsinic acid (DMA) immobilization by the iron hydroxide plaque mineral goethite.

2015

Abstract A surface complexation modeling approach was used to extend the knowledge about processes that affect the availability of dimethylarsinic acid (DMA) in the soil rhizosphere in presence of a strong sorbent, e.g., Fe plaques on rice roots. Published spectroscopic and molecular modeling information suggest for the organoarsenical agent to form bidentate-binuclear inner-sphere surface complexes with Fe hydroxides similar to the inorganic As oxyanions. However, since also the ubiquitous silicic acid oxyanion form the same bidentate binuclear surface complexes, our hypothesis was that it may have an effect on the adsorption of DMA by Fe hydroxides in soil. Our experimental batch equilibr…

Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks f…

2015

Δ3,Δ2-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomalSaccharomyces cerevisiaeECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3′,5′-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bo…

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the R…

2021

We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as a warhead. These compounds are covalent inhibitors that inactivate the protease, forming a stable hemithioacetal complex. Inhibitor 11a is a potent inhibitor that has been already tested in vitro and in animals. Using a combination of classical and QM/MM simulations, we determined the binding mode of the inhibitor into the active site and the preferred rotameric state of the catalytic histidine. In the noncovalent complex, the aldehyde group is accommodated into the oxyanion hole formed by the NH main-chain groups of residues 143 …

A theoretical study of carbon-carbon bond formation by a Michael-type addition.

2012

A theoretical study of the Michael-type addition of 1,3-dicarbonyl compounds to α,β-unsaturated carbonyl compounds has been performed in the gas phase by means of the AM1 semiempirical method and by density functional theory (DFT) calculations within the B3LYP and M06-2X hybrid functionals. A molecular model has been selected to mimic the role of a base, which is traditionally used as a catalyst in Michael reactions, an acetate moiety to modulate its basicity, and point charges to imitate the stabilization of the negative charge developed in the substrate during the reaction when taking place in enzymatic environments. Results of the study of six different reactions obtained at the three di…

Influence of bacterial physiology on processing of selenite, biogenesis of nanomaterials and their thermodynamic stability

2019

We explored how Ochrobactrum sp. MPV1 can convert up to 2.5 mM selenite within 120 h, surviving the challenge posed by high oxyanion concentrations. The data show that thiol-based biotic chemical reaction(s) occur upon bacterial exposure to low selenite concentrations, whereas enzymatic systems account for oxyanion removal when 2 mM oxyanion is exceeded. The selenite bioprocessing produces selenium nanomaterials, whose size and morphology depend on the bacterial physiology. Selenium nanoparticles were always produced by MPV1 cells, featuring an average diameter ranging between 90 and 140 nm, which we conclude constitutes the thermodynamic stability range for these nanostructures. Alternativ…

Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17

2015

A recently designed enzyme, HG3.17, obtained by directed evolution, has shown a catalytic activity close to natural enzymes. Hybrid QM/MM molecular dynamics simulations for the Kemp elimination in this new enzyme have provided a deep insight into the origin of its catalytic efficiency. In this case, we have first demonstrated the presence of different conformations with significantly different reactivity. The larger reactivity is related with a better electrostatic preorganization of the environment that creates a more favorable electrostatic potential for the reaction to proceed. In HG3.17, efforts to improve the catalytic properties must be focused in possible mutations increasing the pre…

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Dynamics in the …

2020

<p>We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as warhead. These compounds are covalent inhibitors that inactivate the protease forming a stable hemithioacetal complex. Inhibitor 11a is a potent inhibitor that has been already tested in vitro and in animals. Using a combination of classical and QM/MM simulations we determined the binding mode of the inhibitor into the active site and the preferred rotameric state of the catalytic histidine. In the noncovalent complex the aldehyde group is accommodated into the oxyanion hole formed by the NH main chain groups of residues …

Oxyanion Holes and Their Mimics

2009

Bifunctional Acid-Base Catalysis

2011

Acid-base catalysis with bifunctional catalysts is a very prominent catalytic strategy in both small-molecule organocatalysts as well as enzyme catalysis. In both worlds, small-molecule catalysts and enzymatic catalysis, a variety of different general acids or hydrogen bond donors are used. In this chapter, important parallels between small molecule catalysts and enzymes are discussed, and a comparison is also made to the emerging field of frustrated Lewis pair catalysis.

LFER and the Effect of Temperature on Oxyanion Adsorption by Goethite

2019

A linear relationship between the Gibbs free energy, ΔGr,H+, of the aqueous complex deprotonation reaction, and the Gibbs free energy, ΔGr,ads, of bidentate surface complexation reaction of oxyanions was derived from modelling of temperature dependent batch equilibrium adsorption experiments. As exemplified in this study, this relationship may be exploited to predict temperature-dependent adsorption behavior of oxyanions not yet known such as pertechnetate.