scholarly journals Unveiling the regioselective synthesis of antiviral 5-isoxazol-5-yl-2'deoxyuridines with a molecular electron density theory perspective

2021 ◽  
pp. 106-106
Author(s):  
Nivedita Acharjee ◽  
Haydar Mohammad-Salim ◽  
Mrinmoy Chakraborty
Keyword(s):  
Gas Phase ◽  
Electron Density ◽  
Activation Enthalpy ◽  
Regioselective Synthesis ◽  
Polar Solvents ◽  
Aim Analysis ◽  
Covalent Bonds ◽  
Molecular Electron ◽  
Molecular Electron Density Theory ◽  
Density Transfer

The regioselective synthesis of a potent antiviral sugar nucleoside isoxazole analogue from the [3+2] cycloaddition (32CA) reaction of aceto-nitrile-N-oxide (ANO) and acetyl-protected 5-ethynyl-2?-deoxyuridine (EDU) has been studied at MPWB1K/6-311G(d,p) level within the molecular electron density theory (MEDT) perspective. ANO is classified as a zwitterionic species devoid of any pseudoradical or carbenoid center from the electron localization function (ELF) analysis. The ortho regioisomer is energetically preferred over the meta one by the activation enthalpy of 21.7-24.3 kJ mol-1, suggesting complete regioselectivity in agreement with the experiment. The activation enthalpy increases from 53.9 kJ mol-1 in gas phase to 71.5 kJ mol-1 in water suggesting more facile reaction in low polar solvents. The minimal global electron density transfer (GEDT) at the TSs suggests non-polar character and the formation of new covalent bonds has not been started at the located TSs showing non-covalent intermolecular interactions from Atoms-in-Molecules (AIM) study and in the Independent Gradient Model (IGM) isosurfaces. The AIM analysis shows more accumulation of electron density at the C-C interacting region relative to the C-O one, and earlier C-C bond formation is predicted from the bonding evolution theory (BET) study.

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

2021 ◽  
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
María J. Aurell
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Activation Energies ◽  
High Reactivity ◽  
Diels Alder ◽  
Electron Density Transfer ◽  
Molecular Electron ◽  
Iminium Cations ◽  
Molecular Electron Density Theory ◽  
Density Transfer

The ionic Diels-Alder (I-DA) reactions of a series of six iminium cations with cyclopentadiene have been studied within the Molecular Electron Density Theory (MEDT). The superelectrophilic character of iminium cations,  > 8.20 eV, accounts for the high reactivity of these species participating in I-DA reactions. The activation energies are found between 13 and 20 kcal·mol-1 lower in energy than those associated to the corresponding Diels-Alder (DA) reactions of neutral imines. These reactions are low endo selective as a consequence of the cationic character of the TSs, but highly regioselective. Solvents have poor effects on the relative energies, and an unappreciable effect in the geometries. In dichloromethane the activation energies increase slightly as a consequence of the better solvation of the iminium cations than the cationic TSs. ELF topological analysis of the bonding changes along the I-DA reactions shows that they are very similar to those in polar DA reactions. The present MEDT study makes it possible establishing that the global electron density transfer (GEDT) taking place at the TSs of I-DA reactions, and not steric (Pauli) repulsions such as have been recently proposed, are responsible for the features of these type of DA reactions.

On the nature of organic electron density transfer complexes within molecular electron density theory

2019 ◽  
Vol 17 (26) ◽  
pp. 6478-6488 ◽  
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez
Keyword(s):  
Physical Properties ◽  
Electron Density ◽  
Electron Density Transfer ◽  
Molecular Electron ◽  
Organic Electron ◽  
Molecular Electron Density Theory ◽  
Density Transfer

The global electron density transfer taking place from the nucleophile to the electrophile controls the formation and physical properties of electron density transfer complexes.

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

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3638
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
María José Aurell
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Activation Energies ◽  
High Reactivity ◽  
Diels Alder ◽  
Electron Density Transfer ◽  
Molecular Electron ◽  
Iminium Cations ◽  
Molecular Electron Density Theory ◽  
Density Transfer

The ionic Diels–Alder (I-DA) reactions of a series of six iminium cations with cyclopentadiene have been studied within the Molecular Electron Density Theory (MEDT). The superelectrophilic character of iminium cations, ω > 8.20 eV, accounts for the high reactivity of these species participating in I-DA reactions. The activation energies are found to be between 13 and 20 kcal·mol−1 lower in energy than those associated with the corresponding Diels–Alder (DA) reactions of neutral imines. These reactions are low endo selective as a consequence of the cationic character of the TSs, but highly regioselective. Solvents have poor effects on the relative energies, and an unappreciable effect on the geometries. In acetonitrile, the activation energies increase slightly as a consequence of the better solvation of the iminium cations than the cationic TSs. Electron localization function (ELF) topological analysis of the bonding changes along the I-DA reactions shows that they are very similar to those in polar DA reactions. The present MEDT study establishes that the global electron density transfer (GEDT) taking place at the TSs of I-DA reactions, and not steric (Pauli) repulsions such as have been recently proposed, are responsible for the features of these types of DA reactions.

A molecular electron density theory (MEDT) study of the role of halogens (X2 = F2, Cl2, Br2 and I2) on the aza-Michael-addition reactions

2020 ◽  
Vol 44 (44) ◽  
pp. 19002-19012
Author(s):  
Luis R. Domingo ◽  
Ahmad Seif ◽  
Elham Mazarei ◽  
Ehasn Zahedi ◽  
Temer S. Ahmadi
Keyword(s):  
Gas Phase ◽  
Electron Density ◽  
Michael Addition ◽  
Nucleophilic Attack ◽  
Addition Reactions ◽  
Energy Profile ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

The energy profile for gas phase F2-catalyzed nucleophilic attack of PYR R1 on the β-conjugated carbon of MA R2 marked.

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

Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 74-93
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 establishes 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 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.

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