Abstract
Application of molecular electron density theory (MEDT) to investigate the [5+2] cycloaddition reaction between oxidopyrylium and ethervinylether, we discovered that oxidopyrylium is an electrophile and ethervinylether is a nucleophile by an examination of conceptual DFT indices. Analysis of energetical parameters shows clearly that this cycloaddition is both regio- and stereoselective, which is extremely consistent with the experience. Topological analysis of the electron localization function (ELF) has shown that this [5+2] cycloaddition is achieved by a two-step, single-step mechanism along the most favored route. Aside from that, docking outcomes show that the (1–20) oxabicyclo[3.2.1]octene derivatives have a significant anti-HIV potential.
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References
Schiavone D V, Kapkayeva DM, Murelli RP (2021) Investigations into a stoichiometrically equivalent intermolecular oxidopyrylium [5+2] cycloaddition reaction leveraging 3-hydroxy-4-pyrone-based oxidopyrylium dimers. J Org Chem 86(5). https://doi.org/10.1021/acs.joc.0c02655
Jasiński R (2021) On the question of stepwise [4+2] cycloaddition reactions and their stereochemical aspects. Symmetry (Basel) 13(10). https://doi.org/10.3390/sym13101911
Aitouna AO, Barhoumi A, Zeroual A (2023) A mechanism study and an investigation of the reason for the stereoselectivity in the [4+2] cycloaddition reaction between cyclopentadiene and gem-substituted ethylene electrophiles. Sci Radices 2(3):217–228. https://doi.org/10.58332/scirad2023v2i3a01
El Ghozlani M, Barhoumi A, Elkacmi R, Ouled Aitouna A, Zeroual A, El idrissi M (2020) Mechanistic study of hetero-Diels-Alder [4+2] cycloaddition reactions between 2-nitro-1H-pyrrole and isoprene. Chemistry Africa 3:901–909. https://doi.org/10.1007/s42250-020-00187-8
Zahnoune R, Asserne F, Ourhriss N, Ouled Aitouna A, Barhoumi A, Hakmaoui Y, Belghiti ME, Abouricha S, El ajlaoui R, Zeroual A (2022) Theoretical survey of Diels-Alder between acrylic acid and isoprene catalyzed by the titanium tetrachloride and titanium tertafluoride. J Mol Struct 1269:133630. https://doi.org/10.1016/j.molstruc.2022.133630
Aitouna AO, Belghiti ME, Eşme A, Anouar E, Aitouna AO, Zeroual A, Salah M, Chekroun A, El Abdallaoui HE, Benharref A, Mazoir N (2021) Chemical reactivities and molecular docking studies of parthenolide with the main protease of HEP-G2 and SARS-CoV-2. J Mol Struct 130705. https://doi.org/10.1016/j.molstruc.2021.130705
Ouled Aitouna Ab, Barhoumi A, El idrissi M, Ouled Aitouna A, Zeroual A, Mazoir N, Chakroun A, Benharref A (2021) Theoretical investigation of the mechanism, chemo- and stereospecifity in the epoxidation reaction of limonene with meta-chloroperoxybenzoic acid (m-CPBA). Mor J Chem 9(1):75–82. https://doi.org/10.48317/IMIST.PRSM/morjchem-v9i1.20462
Zeroual A, Ríos-Gutiérrez M, Amiri O, El idrissi M, Domingo LR (2019) An MEDT study of the mechanism, chemo- and stereoselectivity of the epoxidation reaction of R-carvone with peracetic acid. RSC Advances - Royal Society of Chemistry 9:28500–28509. https://doi.org/10.1039/c9ra05309c
Raji H, Aitouna AO, Barhoumi A, Chekroun A, Zeroual A, Syed A, Elgorban AM, Verma M, Benharref A, Varma RS (2023) Antiviral docking analysis, semisynthesis and mechanistic studies on the origin of stereo- and chemoselectivity in epoxidation reaction of α′-trans-himachalene. J Mol Liquid 385:122204. https://doi.org/10.1016/j.molliq.2023.122204
Breugst M, Reissig HU (2020) The Huisgen reaction: milestones of the 1,3-dipolar cycloaddition. Angew Chemie Int Ed 59(30). https://doi.org/10.1002/anie.202003115
Ouahdi Z, Ourhriss N, El idrissi M et al (2022) Exploration of the mechanism, chemospecificity, regiospecificity and stereoselectivity of the cycloaddition reaction between 9α-hydroxyparthenolide and nitrilimine: MEDT study. Theor Chem Acc 141:50. https://doi.org/10.1007/s00214-022-02913-6
El idrissi M, El ghozlani M, Eşme A, Ríos-Gutiérrez M, Ouled Aitouna A, Salah M, El Alaoui El Abdallaoui H, Zeroual A, Mazoir N, Domingo LR (2021) Mpro-SARS-CoV-2 inhibitors and various chemical reactivity of 1-bromo- and 1-chloro-4-vinylbenzene in [3+2] cycloaddition reactions. Organics 2:1–16. https://doi.org/10.3390/org2010001
Zeroual A, Ríos-Gutiérrez M, El Ghozlani M, El idrissi M, Ouled Aitouna A, Salah M, El Alaoui El Abdallaoui H, Domingo LR (2020) A molecular electron density theory investigation of the molecular mechanism, regioselectivity, stereoselectivity and chemoselectivity of cycloaddition reaction between acetonitrile N-oxide and 2,5-dimethyl-2H-[1,2,3]diazarsole. Theoret Chem Acc 139:37. https://doi.org/10.1007/s12039-019-1656-z
Siadati SA (2016) A theoretical study on stepwise- and concertedness of the mechanism of 1, 3-dipolar cycloaddition reaction between tetra amino ethylene and trifluoro methyl azide. Comb Chem High Throughput Screening 19(2):170–175
Siadati SA (2016) Beyond the alternatives that switch the mechanism of the 1, 3-dipolar cycloadditions from concerted to stepwise or vice versa: a literature review. Prog React Kinet Mech 41(4):331–344. https://doi.org/10.3184/146867816X14719552202168
Zeroual A, Ríos-Gutiérrez M, Salah M, Abdallaoui EAE, H, Domingo LR (2019) An investigation of the molecular mechanism, chemioselectivity and regioselectivity of cycloaddition reaction between acetonitrile N-oxide and 2,5-dimethyl-2H-[1,2,3]diazaphosphole: a MEDT study. J Chem Sci 131:75
Al-Rasheed HH, Al-Majid AM, Ali M et al (2022) [3+2] cycloadditions in asymmetric synthesis of spirooxindole hybrids linked to triazole and ferrocene units: X-ray crystal structure and MEDT study of the reaction mechanism. Symmetry (Basel) 14(10). https://doi.org/10.3390/sym14102071
Żmigrodzka M, Sadowski M, Kras J, Desler E, Demchuk OM, Kula K (2022) Polar [3+2] cycloaddition between N-methyl azomethine ylide and trans-3,3,3-trichloro-1-nitroprop-1-ene. Sci Radices 01(01). https://doi.org/10.58332/v22i1a02
El idrissi M, Eşme A, Hakmaoui Y, Ríos-Gutiérrez M, Ouled Aitouna A, Salah M (2021) A. Zeroual, L. R. Domingo, Divulging the various chemical reactivity of trifluoromethyl-4-vinyl-benzene as well as methyl-4-vinyl-benzene in [3+2] cycloaddition reactions. J Mol Graph Model 102:107760. https://doi.org/10.1016/j.jmgm.2020.107760
Mohammad-Salim Haydar A, Ahmed Basheer H, Abdallah HH, Zeroual A, Abdi Jamila L (2021) A molecular electron density theory study for [3+2] cycloaddition reactions of N-benzylcyclohexylnitrone with methyl-3-butenoate. New J Chem 45:262–267. https://doi.org/10.1039/D0NJ04049E
Domingo LR, Ríos-Gutiérrez M (2023) A useful classification of organic reactions based on the flux of the electron density. Sci Radices 2:1–24. https://doi.org/10.58332/scirad2023v2i1a01
Zawadzińska K, Gostyński B (2023) Nitrosubstituted analogs of isoxazolines and isoxazolidines: a surprising estimation of their biological activity via molecular docking. Sci Radices 2:25–46. https://doi.org/10.58332/scirad2023v2i1a02
Salah M, Zeroual A, Jorio S, El Hadki H, Kabbaj O, Marakchi K, Komiha N (2020) Theoretical study of the 1,3-DC reaction between fluorinated alkynes and azides: reactivity indices, transition structures, IGM and ELF analysis. J Mol Graph Model 94:107458. https://doi.org/10.1016/j.jmgm.2019.107458
Salah M, Belghiti ME, Aitouna AO, Zeroual A, Jorio S, El Alaoui AH, El Hadki H, Marakchi K, Komiha N (2021) MEDT study of the 1,3-DC reaction of diazomethane with psilostachyin and investigation about the interactions of some pyrazoline derivatives with protease (Mpro) of nCoV-2. J Mol Graph Model 102:107763. https://doi.org/10.1016/j.jmgm.2020.107763
Zeroual A, Ríos-Gutiérrez M, El idrissi M, El Alaoui El Abdallaoui H, Domingo Luis R (2019) An MEDT study of the mechanism and selectivities of the [3+2] cycloaddition reaction of tomentosin with benzonitrile oxide. Int J Quantum Chem 1–9. https://doi.org/10.1002/qua.25980
Xiao WL, Yang LM, Gong NB et al (2006) Rubriflordilactones A and B, two novel bisnortriterpenoids from Schisandra rubriflora and their biological activities. Org Lett 8(5). https://doi.org/10.1021/ol060062f
Kim E La, Li JL, Hong J et al (2016) An unusual 1(10 → 19)abeo steroid from a jellyfish-derived fungus. Tetrahedron Lett 57(25). https://doi.org/10.1016/j.tetlet.2016.05.050
Aoki S, Watanabe Y, Sanagawa M, Setiawan A, Kotoku N, Kobayashi M (2006) Cortistatins A, B, C, D anti-angiogenic steroidal alkaloids, from the marine sponge Corticium simplex. J Am Chem Soc 128(10). https://doi.org/10.1021/ja057404h
Nguyen TV, Hartmann JM, Enders D (2013) Recent synthetic strategies to access seven-membered carbocycles in natural product synthesis. Synthesis 45(7). https://doi.org/10.1055/s-0032-1318152
Battiste MA, Pelphrey PM, Wright DL (2006) The cycloaddition strategy for the synthesis of natural products containing carbocyclic seven-membered rings. Chem A Eur J 12(13). https://doi.org/10.1002/chem.200501083
Pellissier H (2018) Recent developments in the [5+2] cycloaddition. Adv Synth Catal 360(8). https://doi.org/10.1002/adsc.201701379
Gao K, Zhang YG, Wang Z, Ding H (2019) Recent development on the [5+2] cycloadditions and their application in natural product synthesis. Chem Commun 55(13). https://doi.org/10.1039/c8cc09077g
Yin Z, He Y, Chiu P (2018) Application of (4+3) cycloaddition strategies in the synthesis of natural products. Chem Soc Rev 47(23). https://doi.org/10.1039/c8cs00532j
Kącka-Zych A, Jasiński R (2022) Mechanistic aspects of the synthesis of seven-membered internal nitronates via stepwise [4+3] cycloaddition involving conjugated nitroalkenes: molecular electron density theory computational study. J Comput Chem 43(18). https://doi.org/10.1002/jcc.26885
Ylijoki KEO, Stryker JM (2013) Cycloaddition reactions in organic and natural product synthesis. Chem Rev 113(3). https://doi.org/10.1021/cr300087g
Toda Y, Shimizu M, Iwai T, Suga H (2018) Triethylamine enables catalytic generation of oxidopyrylium ylides for [5+2] cycloadditions with alkenes: an efficient entry to 8-oxabicyclo[3.2.1]octane frameworks. Adv Synth Catal 360(12). https://doi.org/10.1002/adsc.201800290
Sammes PG, Street LJ (1983) The preparation and some reactions of 3-oxidopyrylium. J Chem Soc Perkin Trans. https://doi.org/10.1039/p19830001261
Zhao C, Glazier DA, Yang D et al (2019) Intermolecular regio- and stereoselective hetero-[5+2] cycloaddition of oxidopyrylium ylides and cyclic imines. Angew Chemie Int Ed 58(3). https://doi.org/10.1002/anie.201811896
Bejcek LP, Garimallaprabhakaran AK, Suyabatmaz DM et al (2019) Maltol- and allomaltol-derived oxidopyrylium ylides: methyl substitution pattern kinetically influences [5 + 3] dimerization versus [5+2] cycloaddition reactions. J Org Chem 84(22). https://doi.org/10.1021/acs.joc.9b02137
Domingo LR, Zaragozá RJ (2000) Toward an understanding of the mechanisms of the intramolecular [5+2] cycloaddition reaction of γ-pyrones bearing tethered alkenes. A theoretical study. J Org Chem 65(18). https://doi.org/10.1021/jo000061f
Zahnoune R, Asserne F, Ourhriss N et al (2022) Theoretical survey of Diels-Alder between acrylic acid and isoprene catalyzed by the titanium tetrachloride and titanium tertafluoride. J Mol Struct 2022:1269. https://doi.org/10.1016/j.molstruc.2022.133630
Siadati SA, Rezazadeh S (2022) The extraordinary gravity of three atom 4π-components and 1,3-dienes to C20-nXn fullerenes; a new gate to the future of Nano technology. Sci Radices 01(01). https://doi.org/10.58332/v22i1a04
Asserne F, Ouahdi Z, Hakmaoui Y et al (2023) Molecular docking, regio, chemo and stereoselectivity study of the [3+2] cycloaddition reaction between pyridazi-3-one and nitrilimine. Chemistry Africa. https://doi.org/10.1007/s42250-023-00735-y
Barhoumi A, Ryachi K, Belghiti ME, Chafi M, Tounsi A, Syed A, El idrissi M, Wong LS, Zeroual A (2023) Chromatography scrutiny, molecular docking, clarifying the selectivities and the mechanism of [3+2] cycloloaddition reaction between linallol and chlorobenzene-nitrile-oxide. J Fluoresc. https://doi.org/10.1007/s10895-023-03411-z
Ouled Aitouna AB, Belghiti ME, Eşme A, Ouled Aitouna AN, Salah M, Chekroun A, El Alaoui El Abdallaoui H, Benharref A, Mazoir N, Zeroual A, Nejjari C (2021) Divulging the regioselectivity of epoxides in the ring-opening reaction, and potential himachalene derivatives predicted to target the antibacterial activities and SARS-CoV-2 spike protein with docking study. J Mol Struct 1244:130864. https://doi.org/10.5267/j.ccl.2023.3.008
Domingo LR (2016) Molecular electron density theory: a modern view of reactivity in organic chemistry. Molecules 21(10). https://doi.org/10.3390/molecules21101319
Seeman JI, Fukui K (2022) Frontier molecular orbital theory, and the Woodward-Hoffmann rules. Part II. A sleeping beauty in chemistry. Chem Rec 22(4). https://doi.org/10.1002/tcr.202100300
Becke AD (1990) Edgecombe KE. A simple measure of electron localization in atomic and molecular systems. J Chem Phys 92(9). https://doi.org/10.1063/1.458517
Matta CF (2017) On the connections between the quantum theory of atoms in molecules (QTAIM) and density functional theory (DFT): a letter from Richard F. W. Bader to Lou Massa. Struct Chem 28(5). https://doi.org/10.1007/s11224-017-0946-7
Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010) Revealing noncovalent interactions. J Am Chem Soc 132(18). https://doi.org/10.1021/ja100936w
Chai J Da, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem Chem Phys 10(44). https://doi.org/10.1039/b810189b
Hehre WJ (1976) Ab initio molecular orbital theory. Acc Chem Res 9(11). https://doi.org/10.1021/ar50107a003
Fukui K (1981) The path of chemical reactions - the IRC approach. Acc Chem Res 14(12). https://doi.org/10.1021/ar00072a001
Tomasi J, Persico M (1994) Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem Rev 94(7). https://doi.org/10.1021/cr00031a013
Parr RG, Szentpály LV, Liu S (1999) Electrophilicity index. J Am Chem Soc 121(9). https://doi.org/10.1021/ja983494x
Parr RG, Pearson RG (1983) Absolute hardness: companion parameter to absolute electronegativity. J Am Chem Soc 105(26). https://doi.org/10.1021/ja00364a005
Chermette H (1999) Chemical reactivity indexes in density functional theory. J Comput Chem 20:129–154. https://doi.org/10.1002/(SICI)1096-987X(19990115)20:1%3c129::AID-JCC13%3e3.0.CO;2-A
Parr G, Yang W (1989) Density-functional theory of atoms and molecules. R Oxford University Press, New York, Oxford
Jaramillo P, Domingo LR, Chamorro E, Pérez P (2008) A further exploration of a nucleophilicity index based on the gas-phase ionization potentials. J Mol Struct Theochem 865(1–3). https://doi.org/10.1016/j.theochem.2008.06.022
Domingo LR, Aurell MJ, Pérez P, Contreras R (2002) Quantitative characterization of the global electrophilicity power of common diene/dienophile pairs in Diels-Alder reactions. Tetrahedron 58(22). https://doi.org/10.1016/S0040-4020(02)00410-6
Reed AE, Weinstock RB, Weinhold F (1985) Natural population analysis. J Chem Phys 83(2). https://doi.org/10.1063/1.449486
Noury S, Krokidis X, Fuster F, Silvi B (1999) Computational tools for the electron localization function topological analysis. Comput Chem 23(6):597–604. https://doi.org/10.1016/S0097-8485(99)00039-X
Dennington R, Keith TA, Millam JM (2016) GaussView, version 6.0. 16. GaussView, Version 6 Semichem Inc Shawnee Mission KS
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1). https://doi.org/10.1016/0263-7855(96)00018-5
Borkotoky S (2012) Docking studies on HIV integrase inhibitors based on potential ligand binding sites. Int J Bioinforma Biosci 2(3):21–29. https://doi.org/10.5121/ijbb.2012.2303
Morris GM, Ruth H, Lindstrom W et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791. https://doi.org/10.1002/JCC.21256
Morris GM, Goodsell DS, Halliday RS et al (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14). https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
Delano WL (2002) The PyMOL molecular graphics system. CCP4 Newsl Protein Crystallogr 40(1)
Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7. https://doi.org/10.1038/srep42717
Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1(4):337–341. https://doi.org/10.1016/J.DDTEC.2004.11.007
Guan L, Yang H, Cai Y et al (2019) ADMET-score – a comprehensive scoring function for evaluation of chemical drug-likeness. Medchemcomm 10(1):148–157. https://doi.org/10.1039/C8MD00472B
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The authors extend their appreciation to the Researchers Supporting Project (number RSP2023R15), King Saud University, Riyadh, Saudi Arabia and we would like to thank Ling Shing Wong for supporting this research.
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The authors extend their appreciation to the Researchers Supporting Project (number RSP2023R15), King Saud University, Riyadh, Saudi Arabia.
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Anas Ouled Aitouna, Abdellah Zeroual: article writing. Abdellah Zeroual and Noureddine Mazoir: numerical calculations; Abdallah M. Elgorban, Ali H. Bahkali, and Asad Syed: acquisition of data; Meenakshi Verma, Radomir Jasiński, and Mohammed El idrissi: final review and editing. All authors: analysis and interpretation of data and drafting the article.
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Aitouna, A.O., Mazoir, N., Zeroual, A. et al. Molecular docking, expounding the regiospecificity, stereoselectivity, and the mechanism of [5+2] cycloaddition reaction between ethereal ether and oxidopyrylium. Struct Chem 35, 841–852 (2024). https://doi.org/10.1007/s11224-023-02239-4
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DOI: https://doi.org/10.1007/s11224-023-02239-4