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Baroudi A, Jaradat K, Karton A. 6-Endo-dig versus 5-exo-dig: Exploring Radical Cyclization Preference with First-, Second-, and Third-row Linkers using High-level Quantum Chemical Methods. Chemphyschem 2023; 24:e202300426. [PMID: 37392178 DOI: 10.1002/cphc.202300426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
As an expansion upon Baldwin rules, the cyclization reactions of hex-5-yn-1-yl radical systems with different first-, second-, and third-row linkers are explored at the CCSD(T) level via means of the SMD(benzene)-G4(MP2) thermochemical protocol. Unlike C, O, and N linkers, systems with B, Si, P, S, Ge, As, and Se linkers are shown to favor 6-endo-dig cyclization. This offers fundamental insights into the rational synthetic design of cyclic compounds. A thorough analysis of stereoelectronic effects, cyclization barriers, and intrinsic barriers illustrates that structural changes alter the cyclization preference by mainly impacting 5-exo-dig reaction barriers. Based on the high-level computational modeling, we proceed to develop a new tool for cyclization preference prediction from the correlation between cyclization barriers and radical structural parameters (e. g., linker bond length and bond angle). A strong correlation is found between the radical attack trajectory angle and the reaction barrier heights, i. e., cyclization preference. Finally, the influence of stereoelectronic effects on the two radical cyclization pathways is further investigated in stereoisomers of hypervalent silicon system, which provides novel insight into cyclization control.
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Affiliation(s)
- Abdulkader Baroudi
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Khaled Jaradat
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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2
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Van Den Broeck E, Verbraeken B, Dedecker K, Cnudde P, Vanduyfhuys L, Verstraelen T, Van Hecke K, Jerca VV, Catak S, Hoogenboom R, Van Speybroeck V. Cation−π Interactions Accelerate the Living Cationic Ring-Opening Polymerization of Unsaturated 2-Alkyl-2-oxazolines. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Elias Van Den Broeck
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Bart Verbraeken
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
| | - Karen Dedecker
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Pieter Cnudde
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Louis Vanduyfhuys
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-S3, B-9000 Ghent, Belgium
| | - Valentin Victor Jerca
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
- Centre for Organic Chemistry “Costin D. Nenitzescu”, Romanian Academy, 202B Spl. Independentei CP 35-108, Bucharest 060023, Romania
| | - Saron Catak
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
- Department of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
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Bolshchikov BD, Tsvetkov VB, Serbin AV. Practical procedure for a theoretical investigation of thermodynamics and kinetics aspects of different-scale radical reactions from addition and cyclization to cyclocopolymerization involving maleic anhydride and divinyl ether. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Steffen J, Hartke B. Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields. J Chem Phys 2017; 147:161701. [DOI: 10.1063/1.4979712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hancock AN, Kyne SH, Aitken HM, Schiesser CH. Intramolecular homolytic substitution in selenoxides and selenones. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.08.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment.
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Affiliation(s)
- Junming Ho
- Agency for Science, Technology and Research, Institute of High Performance Computing , 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632.,Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mehmed Z Ertem
- Chemistry Department, Brookhaven National Laboratory , Upton, New York 11973, United States
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Wallace CM, Schiesser CH, Hancock AN. Slow homolytic substitution reactions at selenium: 2-Selenabicyclo[1.1.1]pentane. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.06.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 752] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Hancock AN, Lobachevsky S, Haworth NL, Coote ML, Schiesser CH. The effect of leaving radical on the formation of tetrahydroselenophene by SHi ring closure: an experimental and computational study. Org Biomol Chem 2015; 13:2310-6. [DOI: 10.1039/c4ob02434f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Competition kinetic studies augmented with laser-flash photolysis and high-level computational techniques [G3(MP2)-RAD], with [COSMO-RS, SMD] and without solvent correction, provide kinetic parameters for the ring closures of a series of 4-(alkylseleno)butyl radicals.
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Affiliation(s)
- Amber N. Hancock
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
| | - Sofia Lobachevsky
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
| | - Naomi L. Haworth
- ARC Centre of Excellence for Electromaterials Science
- Australia
- Research School of Chemistry
- The Australian National University
- Canberra
| | - Michelle L. Coote
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- ARC Centre of Excellence for Electromaterials Science
- Australia
- Research School of Chemistry
| | - Carl H. Schiesser
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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Abstract
Kinetic data for intramolecular homolytic substitution reactions of a series of acyl and oxyacyl radicals are reported.
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Affiliation(s)
- Amber N. Hancock
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- , Australia
| | - Carl H. Schiesser
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- , Australia
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Gansäuer A, Seddiqzai M, Dahmen T, Sure R, Grimme S. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines. Beilstein J Org Chem 2013; 9:1620-9. [PMID: 24062821 PMCID: PMC3778327 DOI: 10.3762/bjoc.9.185] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/17/2013] [Indexed: 12/02/2022] Open
Abstract
The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol−1 and was therefore employed in further calculations. Corrections for intramolecular London dispersion and solvation effects in the quantum chemical treatment are essential to obtain consistent and accurate theoretical data. For the investigated radical addition reaction it turned out that the polarity of the molecules is important and that a combination of electrophilic radicals with preferably nucleophilic arenes results in the highest rate constants. This is opposite to the Minisci reaction where the radical acts as nucleophile and the arene as electrophile. The substitution at the N-atom of the aniline is crucial. Methyl substitution leads to slower addition than phenyl substitution. Carbamates as substituents are suitable only when the radical center is not too electrophilic. No correlations between free reaction barriers and energies (ΔG‡ and ΔGR) are found. Addition reactions leading to indanes or dihydrobenzofurans are too slow to be useful synthetically.
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Affiliation(s)
- Andreas Gansäuer
- Kekulé-Institut für Organische Chemie und Biochemie der Rheinischen-Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, D-53121 Bonn, Germany
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Aitken HM, Horvat SM, Coote ML, Lin CY, Schiesser CH. Rate Coefficients for Intramolecular Homolytic Substitution of Oxyacyl Radicals at Sulfur. Aust J Chem 2013. [DOI: 10.1071/ch12477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
It is predicted on the basis of ab initio and density functional calculations that intramolecular homolytic substitution of oxyacyl radicals at the sulfur atom in ω-alkylthio-substituted radicals do not involve hypervalent intermediates. With tert-butyl as the leaving radical, free energy barriers ΔG‡ (G3(MP2)-RAD) for these reactions range from 45.8 kJ mol–1 for the formation of the five-membered cyclic thiocarbonate (8) to 56.7 kJ mol–1 for the formation of the six-membered thiocarbonate (9). Rate coefficients in the order of 104–106 s–1 and 101–104 s–1 for the formation of 8 and 9, respectively, at 353.15 K in the gas phase are predicted at the G3(MP2)-RAD level of theory.
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Macdougall PE, Aitken HM, Scammells PJ, Kavanagh Y, Kyne SH, Schiesser CH. 7-Selenabicyclo[2.2.1]heptane. Chem Commun (Camb) 2012; 48:9126-8. [DOI: 10.1039/c2cc34984a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Aitken HM, Hancock AN, Schiesser CH. Understanding (the lack of) homolytic substitution chemistry of sulfones. Chem Commun (Camb) 2012; 48:8326-8. [DOI: 10.1039/c2cc33856d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Aitken HM, Horvat SM, Schiesser CH, Lin CY, Coote ML. Rate coefficients for intramolecular homolytic substitution of oxyacyl radicals at selenium. INT J CHEM KINET 2011. [DOI: 10.1002/kin.20604] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kyne SH, Lin CY, Ryu I, Coote ML, Schiesser CH. First determination of the rate constant for ring-closure of an azahexenoyl radical: 6-aza-7-ethyl-5-hexenoyl. Chem Commun (Camb) 2010; 46:6521-3. [DOI: 10.1039/c0cc01262a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Horvat SM, Schiesser CH. An ab initio and DFT study of homolytic substitution reactions of acyl radicals at sulfur, selenium, and tellurium. NEW J CHEM 2010. [DOI: 10.1039/c0nj00125b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lin CY, Izgorodina EI, Coote ML. First Principles Prediction of The Propagation Rate Coefficients of Acrylic and Vinyl Esters: Are We There Yet? Macromolecules 2009. [DOI: 10.1021/ma902049g] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ching Yeh Lin
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ekaterina I. Izgorodina
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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Coulomb J, Certal V, Larraufie MH, Ollivier C, Corbet JP, Mignani G, Fensterbank L, Lacôte E, Malacria M. Intramolecular Homolytic Substitution of Sulfinates and Sulfinamides. Chemistry 2009; 15:10225-32. [DOI: 10.1002/chem.200900942] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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