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Dresler E, Wróblewska A, Jasiński R. Energetic Aspects and Molecular Mechanism of 3-Nitro-substituted 2-Isoxazolines Formation via Nitrile N-Oxide [3+2] Cycloaddition: An MEDT Computational Study. Molecules 2024; 29:3042. [PMID: 38998997 PMCID: PMC11243562 DOI: 10.3390/molecules29133042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Regioselectivity and the molecular mechanism of the [3+2] cycloaddition reaction between nitro-substituted formonitrile N-oxide 1 and electron-rich alkenes were explored on the basis of the wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was established that the thermodynamic factors allow for the formation of stable cycloadducts along all considered models. The analysis of the kinetic parameters of the main processes show that all [3+2] cycloadditions should be realized with full regioselectivity. In all cases, the formation of 5-substituted 3-nitro-2-isoxazolidines is clearly preferred. It is interesting that regiodirection is not determined by the local electrophile/nucleophile interactions but by steric effects. From a mechanistic point of view, all considered reactions should be treated as polar, one-step reactions. All attempts to locate the hypothetical zwitterionic intermediates along the cycloaddition paths were, however, not successful.
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Affiliation(s)
- Ewa Dresler
- Łukasiewicz Research Network-Institute of Heavy Organic Synthesis "Blachownia", Energetyków 9, 47-225 Kędzierzyn-Koźle, Poland
| | - Aneta Wróblewska
- Department of Organic Chemistry, University of Lodz, Tamka 12, 91-403 Łódź, Poland
| | - Radomir Jasiński
- Institute of Organic Chemistry and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland
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Richer M, Heidar-Zadeh F, Ríos-Gutiérrez M, Yang XD, Ayers PW. Spin-Polarized Conceptual Density Functional Theory from the Convex Hull. J Chem Theory Comput 2024; 20:4616-4628. [PMID: 38819213 DOI: 10.1021/acs.jctc.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We present a new, nonarbitrary, internally consistent, and unambiguous framework for spin-polarized conceptual density-functional theory (SP-DFT). We explicitly characterize the convex hull of energy, as a function of the number of electrons and their spin, as the only accessible ground states in spin-polarized density functional theory. Then, we construct continuous linear and quadratic models for the energy. The nondifferentiable linear model exactly captures the simplicial geometry of the complex hull about the point of interest and gives exact representations for the conceptual DFT reactivity indicators. The continuous quadratic energy model is the paraboloid of maximum curvature, which most tightly encloses the point of interest and neighboring vertices. The quadratic model is invariant to the choice of coordinate system (i.e., {N, S} vs {Nα, Nβ}) and reduces to a sensible formulation of spin-free conceptual DFT in the appropriate limit. Using the quadratic model, we generalize the Parr functions {P+(r), P-(r)} (and their derivatives with respect to number of electrons) to this new spin-polarized framework, integrating the Parr function concept into the context of (spin-polarized) conceptual DFT, and extending it to include higher-order effects.
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Affiliation(s)
- Michelle Richer
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Xiaotian Derrick Yang
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul W Ayers
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
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3
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Chalkha M, Nour H, Chebbac K, Nakkabi A, Bahsis L, Bakhouch M, Akhazzane M, Bourass M, Chtita S, Bin Jardan YA, Augustyniak M, Bourhia M, Aboul-Soud MA, El Yazidi M. Synthesis, Characterization, DFT Mechanistic Study, Antimicrobial Activity, Molecular Modeling, and ADMET Properties of Novel Pyrazole-isoxazoline Hybrids. ACS OMEGA 2022; 7:46731-46744. [PMID: 36570248 PMCID: PMC9773794 DOI: 10.1021/acsomega.2c05788] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
A series of new heterocycle hybrids incorporating pyrazole and isoxazoline rings was successfully synthesized, characterized, and evaluated for their antimicrobial responses. The synthesized compounds were obtained utilizing N-alkylation and 1,3-dipolar cycloaddition reactions, as well as their structures were established through spectroscopic methods and confirmed by mass spectrometry. To get more light on the regioselective synthesis of new hybrid compounds, mechanistic studies were performed using DFT calculations with B3LYP/6-31G(d,p) basis set. Additionally, the results of the preliminary screening indicate that some of the examined hybrids showed potent antimicrobial activity, compared to standard drugs. The results confirm that the antimicrobial activity is strongly dependent on the nature of the substituents linked pyrazole and isoxazoline rings. Furthermore, molecular docking studies were conducted to highlight the interaction modes between the investigated hybrid compounds and the Escherichia coli and Candida albicans receptors. Notably, the results demonstrate that the investigated compounds have strong protein binding affinities. The stability of the formed complexes by the binding between the hybrid compound 6c, and the target proteins was also confirmed using a 100 ns molecular dynamics simulation. Finally, the prediction of ADMET properties suggests that almost all hybrid compounds possess good pharmacokinetic profiles and no signs of observed toxicity, except for compounds 6e, 6f, and 6g.
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Affiliation(s)
- Mohammed Chalkha
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
| | - Hassan Nour
- Laboratory
of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, P.O. Box 7955, Casablanca, Morocco
| | - Khalid Chebbac
- Laboratory
of Biotechnology Conservation and Valorisation of Natural Resources,
Faculty of Sciences Dhar El Mahraz, Sidi
Mohammed Ben Abdallah University, P.O.
Box 1796, Fez 30000, Morocco
| | - Asmae Nakkabi
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
| | - Lahoucine Bahsis
- Laboratory
of Analytical and Molecular Chemistry, Polydisciplinary Faculty, Cadi Ayyad University, P.O. Box 4162, Safi 46000, Morocco
- Department
of Chemistry, Faculty of Sciences of El Jadida, Chouaïb Doukkali University,
P.O. Box 20, El Jadida 24000, Morocco
| | - Mohamed Bakhouch
- Laboratory
of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 24, El Jadida 24000, Morocco
| | - Mohamed Akhazzane
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
- Cité
de l’innovation, Université
Sidi Mohamed Ben Abdellah, Route Immouzer, P.O. Box 2626, 30000 Fez, Morocco
| | - Mohamed Bourass
- Université
de Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 351 Cours de la Libération, F-33405 Talence, Cédex France
| | - Samir Chtita
- Laboratory
of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, P.O. Box 7955, Casablanca, Morocco
| | - Yousef A. Bin Jardan
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, 11451 Riyadh, Saudi Arabia
| | - Maria Augustyniak
- Institute
of Biology, Biotechnology and Environmental Protection, Faculty of
Natural Sciences, University of Silesia
in Katowice, Bankowa 9, 40-007 Katowice, Poland
| | - Mohammed Bourhia
- Higher
Institute of Nursing Professions and Technical Health, Laayoune 70000, Morocco
| | - Mourad A.M. Aboul-Soud
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University,
P.O. Box 10219, Riyadh 11433, Saudi Arabia
| | - Mohamed El Yazidi
- Engineering
Laboratory of Organometallic, Molecular, Materials and Environment,
Faculty of Sciences Dhar EL Mahraz, Sidi
Mohamed Ben Abdellah University, P.O. Box 1796, 30000 Fez, Morocco
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Domingo LR, Ríos-Gutiérrez M, Chulan R, Mahmoud MHH, Ibrahim MM, El-Bahy SM, Rhyman L, Ramasami P. Unveiling the non-polar [3+2] cycloaddition reactions of cyclic nitrones with strained alkylidene cyclopropanes within a molecular electron density theory study. RSC Adv 2022; 12:25354-25363. [PMID: 36199340 PMCID: PMC9446111 DOI: 10.1039/d2ra03327e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
The role of cyclopropane substitution on the ethylene in zw-type [3+2] cycloaddition (32CA) reactions of cyclic nitrones has been studied within Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) computational level. Electron Localization Function (ELF) analysis of the ethylenes shows that the presence the cyclopropane only slightly increases the electron density in the C-C bonding region. Analysis of the Conceptual DFT reactivity indices indicates that the presence of the cyclopropane does not produce any remarkable change in the reactivity of these strained ethylenes. The marginal electrophilic character of ethylene makes the zw-type 32CA reactions of non-polar character. The presence of the cyclopropane in the ethylene decreases the activation enthalpy of the 32CA reactions by only 1.7 and 2.6 kcal mol-1, and also decreases the ortho regioselectivity. The loss of the strain present in the cyclopropane is responsible for the reduction of the activation enthalpy and the increase of the reaction enthalpy in these non-polar 32CA reactions. The presence of the cyclopropane does not cause any change, neither in the transition state structure (TS) geometries nor in their electronic structure. The very low global electron density transfer (GEDT) computed at the TSs confirms the non-polar character of these 32CA reactions. The ortho regioselectivity experimentally observed in these non-polar 32CA reactions is determined by the most favorable two-center interaction between the less electronegative C1 carbon of nitrone and the non-substituted methylene C5 carbon of the ethylenes.
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Affiliation(s)
- Luis R Domingo
- Department of Organic Chemistry, University of Valencia Dr Moliner 50 E-46100 Burjassot Valencia Spain
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia Dr Moliner 50 E-46100 Burjassot Valencia Spain
| | - Rishikesh Chulan
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius Réduit 80837 Mauritius
| | - M H H Mahmoud
- Department of Chemistry, College of Science, Taif University P.O. Box 11099 Taif 21944 Saudi Arabia
| | - Mohamed M Ibrahim
- Department of Chemistry, College of Science, Taif University P.O. Box 11099 Taif 21944 Saudi Arabia
| | - Salah M El-Bahy
- Department of Chemistry, Turabah University College, Taif University P.O. Box 11099 Taif 21944 Saudi Arabia
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius Réduit 80837 Mauritius
- Centre for Natural Product Research, Department of Chemical Sciences, University of Johannesburg Doornfontein Johannesburg 2028 South Africa
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius Réduit 80837 Mauritius
- Centre for Natural Product Research, Department of Chemical Sciences, University of Johannesburg Doornfontein Johannesburg 2028 South Africa
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On the Mechanism of the Synthesis of Nitrofunctionalised Δ2-Pyrazolines via [3+2] Cycloaddition Reactions between α-EWG-Activated Nitroethenes and Nitrylimine TAC Systems. ORGANICS 2022. [DOI: 10.3390/org3010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We investigated the reactivity of different substituted nitrylimine-type three atom components (TACs) in [3+2] cycloaddition (32CAs) reactions with electrophilically activated nitroethenes within molecular electron density theory (MEDT). In parallel research, the molecular mechanism of the considered transformation was examined through analysis of all possible reaction channels and full optimization of all critical structures. In particular, the existence of zwitterionic intermediates on reaction paths was verified. On the basis of the bonding evolution theory (BET), the mechanism of the 32CA reaction between C,N-diphenylnitrylimine and (E)-2-phenyl-1-cyano-1-nitroethene should be treated as a one-step two-stage mechanism.
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Theoretical Study of closo-Borate Anions [BnHn]2− (n = 5–12): Bonding, Atomic Charges, and Reactivity Analysis. Symmetry (Basel) 2021. [DOI: 10.3390/sym13030464] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This study has focused on the structure, bonding, and reactivity analysis of closo-borate anions [BnHn]2− (n = 5–12). Several descriptors of B–H interactions have been calculated. It has been found that the values of electron density and total energy at bond critical point are the most useful descriptors for investigation of B–H interactions. Using results from the descriptor analysis, one may conclude that orbital interactions in [BnHn]2− increase with increasing the boron cluster size. Several approaches to estimate atomic charges have been applied. Boron atoms in apical positions have more negative values of atomic charges as compared with atoms from equatorial positions. The mean values of boron and hydrogen atomic charges tend to be more positive with the increasing of boron cluster size. Global and local reactivity descriptors using conceptual density functional theory (DFT) theory have been calculated. Based on this theory, the closo-borate anions [BnHn]2− (n = 5–9) can be considered strong and moderate electrophiles, while the closo-borate anions [BnHn]2− (n = 10–12) can be considered marginal electrophiles. Fukui functions for electrophilic attack have been calculated. Fukui functions correlate well with atomic charges of the closo-borate anions. Boron atoms in apical positions have the most positive values of Fukui functions.
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Application of β-Phosphorylated Nitroethenes in [3+2] Cycloaddition Reactions Involving Benzonitrile N-Oxide in the Light of a DFT Computational Study. ORGANICS 2021. [DOI: 10.3390/org2010003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
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.
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Mpro-SARS-CoV-2 Inhibitors and Various Chemical Reactivity of 1-Bromo- and 1-Chloro-4-vinylbenzene in [3 + 2] Cycloaddition Reactions. ORGANICS 2021. [DOI: 10.3390/org2010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
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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