scholarly journals Participation of Phosphorylated Analogues of Nitroethene in Diels–Alder Reactions with Anthracene: A Molecular Electron Density Theory Study and Mechanistic Aspect

Organics ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 36-48
Author(s):  
Agnieszka Kącka-Zych
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Diels Alder ◽  
Single Bond ◽  
Conceptual Density Functional Theory ◽  
Molecular Electron ◽  
Bet Analysis ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Step Mechanism

The structure and the contribution of the bis(2-chloroethyl) 2-nitro 1a and 2-bromo-2-nitroethenylphosphonates 1b with anthracene 2 in the Diels–Alder (DA) reactions have been studied within the Molecular Electron Density Theory (MEDT) at the B3LYP functional together with 6-31G(d), 6-31+G(d) and 6-31+G(d,p) basic sets. Analysis of the Conceptual Density Functional Theory (CDFT) reactivity indices indicates that 1a and 1b can be classified as a strong electrophile and marginal nucleophile, while 2 is classified as a strong electrophile and strong nucleophile. The studied DA reactions take place through a one-step mechanism. A Bonding Evolution Theory (BET) of the one path associated with the DA reaction of 1a with 2 indicates that it is associated with non-concerted two-stage one-step mechanism. BET analysis shows that the first C2-C3 single bond is formed in Phase VI, while the second C1-C6 single bond is formed in the Phase VIII. The formation of both single bonds occurs through the merging of two C2 and C3, C1 and C6 pseudoradical centers, respectively.

scholarly journals Unveiling the Different Reactivity of Bent and Linear Three-Atom-Components Participating in [3 + 2] Cycloaddition Reactions

Organics ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 274-286
Author(s):  
Mar Ríos-Gutiérrez ◽  
Luis R. Domingo ◽  
Fatemeh Ghodsi
Keyword(s):  
Density Functional Theory ◽  
Transition State ◽  
Electron Density ◽  
Density Functional ◽  
Geometrical Parameters ◽  
Single Bond ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

The reactivity of a series of pairs of bent and linear three-atom-component (B-TACs and L-TACs) participating in [3 + 2] cycloaddition (32CA) reactions towards ethylene and electrophilic dicyanoethylene (DCE) have been studied within the Molecular Electron Density Theory. While the pseudodiradical structure of B-TACs changes to that of pseudoradical or carbenoid L-TACs upon dehydrogenation, zwitterionic B-TACs remain unchanged. Conceptual Density Functional Theory (CDFT) indices characterize five of the nine TACs as strong nucleophiles participating in polar reactions towards electrophilic ethylenes. The activation energies of the 32CA reactions with electrophilic DCE range from 0.5 to 22.0 kcal·mol−1, being between 4.3 and 9.1 kcal·mol−1 lower than those with ethylene. In general, B-TACs are more reactive than their L-TAC counterparts. A change in the regioselectivity is found in these polar 32CA reactions; in general, while B-TACs are meta regioselective, L-TACs are ortho regioselective. The geometrical parameters of the transition state structures suggest that the formation of the single bond involving the most electrophilic carbon of DCE is more advanced. A change in the asynchronicity in the reactions involving B-TACs and L-TACs is also found.

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.

scholarly journals Understanding the Molecular Mechanism of the Rearrangement of Internal Nitronic Ester into Nitronorbornene in Light of the MEDT Study

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 462 ◽  
Author(s):  
Agnieszka Kącka-Zych
Keyword(s):  
Density Functional ◽  
Functional Theory ◽  
Molecular Electron ◽  
Bet Analysis ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Step Mechanism ◽  
Nitronic Ester ◽  
Computational Level

The characterization of the structure of nitronic esters and their rearrangement into nitronorbornene reactions has been analyzed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d) computational level. Quantum-chemical calculations indicate that this rearrangement takes place according to a one-step mechanism. The sequential bonding changes received from the Bonding Evolution Theory (BET) analysis of the rearrangement of internal nitronic ester to nitronorbornene allowed us to distinguish seven different phases. This fact clearly contradicts the formerly-proposed concerted pericyclic mechanism.

scholarly journals Understanding the Reactivity of C-Cyclopropyl-N-Methylnitrone Participating in [3+2] Cycloaddition Reactions Towards Styrene with a Molecular Electron Density Theory Perspective

2021 ◽  
Vol 65 (1) ◽  
Author(s):  
Haydar A. Mohammad-Salim
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Transition States ◽  
Free Energies ◽  
Conceptual Density Functional Theory ◽  
Covalent Bonds ◽  
Functional Theory ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory

Abstract. The [3+2] cycloaddition (32CA) reactions of C-cyclopropyl-N-methylnitrone 1 with styrene 2 have been studied within molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) level of theory. These zwitterionic type 32CA reactions occur through a one-step mechanism. The 32CA reactions undergo four stereo- and regioisomeric reaction paths to form four different products, 3, 4, 5 and 6.  Analysis of the conceptual density functional theory (CDFT) indices predict the global electronic flux from the strong nucleophilic nitrone 1 to the styrene 2. These 32CA reactions are endergonic with reactions Gibbs free energies between 2.83 and 7.39 kcal.mol-1 in the gas phase. The 32CA reaction leading to the formation of cycloadduct 3 presents the lowest activation enthalpy than the other paths due to a slightly increase in polar character evident from the global electron density transfer (GEDT) at the transition states and along the reaction path. The bonding evolution theory (BET) study suggests that these 32CA reactions occur through the coupling of pseudoradical centers and the formation of new C-C and C-O covalent bonds has not been started in the transition states.   Resumen.

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

2021 ◽  
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
María José Aurell
Keyword(s):  
Electron Density ◽  
Activation Enthalpy ◽  
Topological Analysis ◽  
Chair Conformation ◽  
Diels Alder ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Step Mechanism ◽  
Density Transfer

The intramolecular ionic Diel-Alder (IIDA) reactions of two dieniminiums have been studied within the Molecular Electron Density Theory (MEDT) at the B97XD/6-311G(d,p) computational level. ELF topological analysis of dieniminiums shows that its electronic structure 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 between the diene and iminium frameworks at the transition state structures (TSs) of these IIDA reactions. The activation enthalpy associated to the IIDA reaction of the experimental dieniminium, 8.7 kcal·mol-1, is 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 is 12.7 kcal·mol-1 lower than that of the intermolecular I-DA reaction. The strong exergonic character of the IIDA reaction, higher than 17 kcal·mol-1, makes the reaction irreversible. These IIDA reactions present a total re/exo and si/endo diastereoselectivity, which is controlled by the most favourable chair conformation of the tetramethylene chain. Electron localization function (ELF) topological analysis of the single bond formation indicates 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 to inter and intramolecular processes show the great similitude among them.

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 Unveiling the Different Chemical Reactivity of Diphenyl Nitrilimine and Phenyl Nitrile Oxide in [3+2] Cycloaddition Reactions with (R)-Carvone through the Molecular Electron Density Theory

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1085 ◽  
Author(s):  
Mar Ríos-Gutiérrez ◽  
Luis R. Domingo ◽  
M’hamed Esseffar ◽  
Ali Oubella ◽  
My Youssef Ait Itto
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Topological Analysis ◽  
Nitrile Oxide ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

The [3+2] cycloaddition (32CA) reactions of diphenyl nitrilimine and phenyl nitrile oxide with (R)-carvone have been studied within the Molecular Electron Density Theory (MEDT). Electron localisation function (ELF) analysis of these three-atom-components (TACs) permits its characterisation as carbenoid and zwitterionic TACs, thus having a different reactivity. The analysis of the conceptual Density Functional Theory (DFT) indices accounts for the very low polar character of these 32CA reactions, while analysis of the DFT energies accounts for the opposite chemoselectivity experimentally observed. Topological analysis of the ELF along the single bond formation makes it possible to characterise the mechanisms of these 32CA reactions as cb- and zw-type. The present MEDT study supports the proposed classification of 32CA reactions into pdr-, pmr-, cb- and zw-type, thus asserting MEDT as the theory able to explain chemical reactivity in Organic Chemistry.

scholarly journals Mpro-SARS-CoV-2 Inhibitors and Various Chemical Reactivity of 1-Bromo- and 1-Chloro-4-vinylbenzene in [3 + 2] Cycloaddition Reactions

Organics ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 1-16
Author(s):  
Mohammed El Idrissi ◽  
Mohamed El Ghozlani ◽  
Asli Eşme ◽  
Mar Ríos-Gutiérrez ◽  
Anas Ouled Aitouna ◽  
...  
Keyword(s):  
Electron Density ◽  
Chemical Reactivity ◽  
Cycloaddition Reactions ◽  
Two Stage ◽  
Docking Analysis ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Step Mechanism ◽  
Computational Level

The regioselectvity and the mechanism of the (32CA) cycloadditions reactions of 1-bromo-4-vinylbenzene 1 and 1-chloro-4-vinylbenzene 2 with benzonitrile oxide 3 were investigated under the molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) computational level. Evaluation of the ELF reveals that these zwitterionic type (zw-type) 32CA reactions take place in a two-stage one-step mechanism. This MEDT study shows that the meta isoxazolines are kinetically and thermodynamically favored over the ortho ones, these 32CA reactions being completely regioselective, in agreement with experimental outcomes. In addition, the efficiency of isoxazolines against SARS-CoV-2 have been also investigated. According to the docking analysis, the present study concludes that 5-(p-bromophenyl)-3-phenyl-2-isoxazoline (B-m) shows better interactions for the inhibition of SARS-CoV-2 in comparison to chloroquine.

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