Serine peptidase catalytic machinery: Cooperative one-step mechanism

1999 ◽  
Vol 73 (2) ◽  
pp. 161-174 ◽  
Author(s):  
G. Dive ◽  
D. Dehareng
Keyword(s):  
Serine Peptidase ◽  
One Step ◽  
Step Mechanism

scholarly journals Application of β-Phosphorylated Nitroethenes in [3+2] Cycloaddition Reactions Involving Benzonitrile N-Oxide in the Light of a DFT Computational Study

Organics ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 26-37
Author(s):  
Karolina Zawadzińska ◽  
Karolina Kula
Keyword(s):  
Density Functional ◽  
Reaction Path ◽  
Computational Study ◽  
Cyano Group ◽  
Cycloaddition Reactions ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Reaction Channels ◽  
One Step ◽  
Step Mechanism

The regiochemistry of [3+2] cycloaddition (32CA) processes between benzonitrile N-oxide 1 and β-phosphorylated analogues of nitroethenes 2a–c has been studied using the Density Functional Theory (DFT) at the M062X/6-31+G(d) theory level. The obtained results of reactivity indices show that benzonitrile N-oxide 1 can be classified both as a moderate electrophile and moderate nucleophile, while β-phosphorylated analogues of nitroethenes 2a–c can be classified as strong electrophiles and marginal nucleophiles. Moreover, the analysis of CDFT shows that for [3+2] cycloadditions with the participation of β-phosphorylatednitroethene 2a and β-phosphorylated α-cyanonitroethene 2b, the more favored reaction path forms 4-nitro-substituted Δ2-isoxazolines 3a–b, while for a reaction with β-phosphorylated β-cyanonitroethene 2c, the more favored path forms 5-nitro-substituted Δ2-isoxazoline 4c. This is due to the presence of a cyano group in the alkene. The CDFT study correlates well with the analysis of the kinetic description of the considered reaction channels. Moreover, DFT calculations have proven the clearly polar nature of all analyzed [3+2] cycloaddition reactions according to the polar one-step mechanism.

scholarly journals Unveiling the Unexpected Reactivity of Electrophilic Diazoalkanes in [3+2] Cycloaddition Reactions within Molecular Electron Density Theory

2020 ◽  
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
Nivedita Acharjee
Keyword(s):  
Electron Density ◽  
Complete Agreement ◽  
Slowing Down ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Electrophilic Character ◽  
Step Mechanism ◽  
Computational Level ◽  
Density Transfer

The [3+2] cycloaddition (32CA) reactions of strongly nucleophilic norbornadiene (NBD) with simplest diazoalkane (DAA) and three DAAs of increased electrophilicity have been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. These pmr-type 32CA reactions follow an asynchronous one-step mechanism with activation enthalpies ranging from 17.7 to 27.9 kcal·mol-1 in acetonitrile. The high exergonic character of these reactions makes them irreversible. The presence of electron-withdrawing (EW) substituents in the DAA increases the activation enthalpies, in complete agreement with the experimental slowing-down of the reactions, but contrary to the Conceptual DFT prediction. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather non-polar 32CA reactions. The present MEDT study allows establishing that the depopulation of the NNC core in this series of DAAs with the increase of the EW character of the substituents present at the carbon center is responsible for the experimentally found deceleration.

scholarly journals Understanding the Reactivity of Trimethylsilyldiazoalkanes Participating in [3+2] Cycloaddition Reactions towards Diethylfumarate with a Molecular Electron Density Theory Perspective

Organics ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 3-18
Author(s):  
Luis R. Domingo ◽  
Nivedita Acharjee ◽  
Haydar A. Mohammad-Salim
Keyword(s):  
Electron Density ◽  
Energy Cost ◽  
Trimethylsilyl Group ◽  
Gibbs Energies ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Step Mechanism

A Molecular Electron Density Theory (MEDT) study is presented here for [3+2] cycloaddition (32CA) reactions of three trimethylsilyldiazoalkanes with diethyl fumarate. The presence of silicon bonded to the carbon of these silyldiazoalkanes changes its structure and reactivity from a pseudomonoradical to that of a zwitterionic one. A one-step mechanism is predicted for these polar zw-type 32CA reactions with activation enthalpies in CCl4 between 8.0 and 19.7 kcal·mol−1 at the MPWB1K (PCM)/6-311G(d,p) level of theory. The negative reaction Gibbs energies between −3.1 and −13.2 kcal·mole−1 in CCl4 suggests exergonic character, making the reactions irreversible. Analysis of the sequential changes in the bonding pattern along the reaction paths characterizes these zw-type 32CA reactions. The increase in nucleophilic character of the trimethylsilyldiazoalkanes makes these 32CA reactions more polar. Consequently, the activation enthalpies are decreased and the TSs require less energy cost. Non-covalent interactions at the TSs account for the stereoselectivity found in these 32CA reactions involving the bulky trimethylsilyl group.

scholarly journals Thermal decomposition of ammonium hexachloroosmate

2016 ◽  
Vol 18 (48) ◽  
pp. 33134-33141 ◽  
Author(s):  
T. I. Asanova ◽  
I. Kantor ◽  
I. P. Asanov ◽  
S. V. Korenev ◽  
K. V. Yusenko
Keyword(s):  
Thermal Decomposition ◽  
Time Resolved ◽  
One Step ◽  
Step Mechanism

A one-step mechanism of the thermal decomposition of (NH4)2[OsCl6] suggested previously proves to be unworkable under a time-resolved ED XAFS and PXRD study.

Mechanism and regioselectivity of 1,3-dipolar cycloaddition reactions of bicyclic monoterpenes with aryl and heteroaryl nitrile oxides: a DFT study

2015 ◽  
Vol 93 (7) ◽  
pp. 749-753 ◽  
Author(s):  
Hossein Eshghi ◽  
Amir Khojastehnezhad ◽  
Farid Moeinpour ◽  
Mehdi Bakavoli
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Energy Surface ◽  
Dipolar Cycloaddition ◽  
Cycloaddition Reactions ◽  
Functional Theory ◽  
Nitrile Oxides ◽  
Reactivity Indices ◽  
One Step ◽  
Step Mechanism

The reactivity and regioselectivity of 1,3-dipolar cycloaddition reactions of aryl and heteroaryl nitrile oxides (1a–1c) with bicyclic monoterpenes (R)-(+)-a-pinene (2a) and (S)-(–)-b-pinene (2b) have been investigated by using density functional theory based on reactivity indices and activation energy calculations at the B3LYP/6-31G(d) level of theory in the gas phase. The potential energy surface analyses for both reactions are in agreement with the experimental observations. Moreover, our calculations on the geometries, bond orders, and global electron density transfers at the transition state structures shows that these 1,3- dipolar cycloaddition reactions occur via an asynchronous one-step mechanism.

scholarly journals On the Question of Zwitterionic Intermediates in the [3 + 2] Cycloaddition Reactions between C-arylnitrones and Perfluoro 2-Methylpent-2-ene

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7147
Author(s):  
Katarzyna Mitka ◽  
Katarzyna Fela ◽  
Aleksandra Olszewska ◽  
Radomir Jasiński
Keyword(s):  
Dft Calculations ◽  
Molecular Mechanism ◽  
Intermolecular Interactions ◽  
Cycloaddition Reaction ◽  
Reaction Centers ◽  
Cycloaddition Reactions ◽  
Reaction Paths ◽  
One Step ◽  
Step Mechanism

The molecular mechanism of the [3 + 2] cycloaddition reaction between C-arylnitrones and perfluoro 2-methylpent-2-ene was explored on the basis of DFT calculations. It was found that despite the polar nature of the intermolecular interactions, as well as the presence of fluorine atoms near the reaction centers, all reactions considered cycloaddition proceed via a one-step mechanism. All attempts for the localization of zwitterionic intermediates on the reaction paths were not successful. Similar results were obtained regardless of the level of theory applied.

scholarly journals Unveiling the Intramolecular Ionic Diels–Alder Reactions within Molecular Electron Density Theory

Chemistry ◽  
2021 ◽  
Vol 3 (3) ◽  
pp. 834-853
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
María José Aurell
Keyword(s):  
Electron Density ◽  
Electronic Structures ◽  
Activation Enthalpy ◽  
Topological Analysis ◽  
Chair Conformation ◽  
Diels Alder ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Step Mechanism

The intramolecular ionic Diels–Alder (IIDA) reactions of two dieniminiums were studied within the Molecular Electron Density Theory (MEDT) at the ωB97XD/6-311G(d,p) computational level. Topological analysis of the electron localization function (ELF) of dieniminiums showed that their electronic structures can been seen as the sum of those of butadiene and ethaniminium. The superelectrophilic character of dieniminiums accounts for the high intramolecular global electron density transfer taking place from the diene framework to the iminium one at the transition state structures (TSs) of these IIDA reactions, which are classified as the forward electro density flux. The activation enthalpy associated with the IIDA reaction of the experimental dieniminium, 8.7 kcal·mol−1, was closer to that of the ionic Diels–Alder (I-DA) reaction between butadiene and ethaniminium, 9.3 kcal·mol−1. However, the activation Gibbs free energy of the IIDA reaction was 12.7 kcal·mol−1 lower than that of the intermolecular I-DA reaction. The strong exergonic character of the IIDA reaction, higher than 20.5 kcal·mol−1, makes the reaction irreversible. These IIDA reactions present a total re/exo and si/endo diastereo selectivity, which is controlled by the most favorable chair conformation of the tetramethylene chain. ELF topological analysis of the single bond formation indicated that these IIDA reactions take place through a non-concerted two-stage one-step mechanism. Finally, ELF and atoms-in-molecules (AIM) topological analyses of the TS associated with the inter and intramolecular processes showed the great similarity between them.

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