1
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Tiekink EH, Vermeeren P, Hamlin TA. Correction: Not antiaromaticity gain, but increased asynchronicity enhances the Diels-Alder reactivity of tropone. Chem Commun (Camb) 2024; 60:4858-4859. [PMID: 38605667 DOI: 10.1039/d4cc90104e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Correction for 'Not antiaromaticity gain, but increased asynchronicity enhances the Diels-Alder reactivity of tropone' by Eveline H. Tiekink et al., Chem. Commun., 2023, 59, 3703-3706, https://doi.org/10.1039/D3CC00512G.
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Affiliation(s)
- Eveline H Tiekink
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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2
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Staronova L, Yamazaki K, Xu X, Shi H, Bickelhaupt FM, Hamlin TA, Dixon DJ. Cobalt-Catalyzed Enantio- and Regioselective C(sp 3 )-H Alkenylation of Thioamides. Angew Chem Int Ed Engl 2024; 63:e202316021. [PMID: 38143241 DOI: 10.1002/anie.202316021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
An enantioselective cobalt-catalyzed C(sp3 )-H alkenylation of thioamides with but-2-ynoate ester coupling partners employing thioamide directing groups is presented. The method is operationally simple and requires only mild reaction conditions, while providing alkenylated products as single regioisomers in excellent yields (up to 85 %) and high enantiomeric excess [up to 91 : 9 enantiomeric ratio (er), or up to >99 : 1 er after a single recrystallization]. Diverse downstream derivatizations of the products are demonstrated, delivering a range of enantioenriched constructs. Extensive computational studies using density functional theory provide insight into the detailed reaction mechanism, origin of enantiocontrol, and the unusual regioselectivity of the alkenylation reaction.
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Affiliation(s)
- Lucia Staronova
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ken Yamazaki
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Xing Xu
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Heyao Shi
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Institute of Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Trevor A Hamlin
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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3
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Vermeeren P, Dalla Tiezza M, Wolf ME, Lahm ME, Allen WD, Schaefer HF, Hamlin TA, Bickelhaupt FM. Correction: Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance. Phys Chem Chem Phys 2024; 26:9073. [PMID: 38436412 PMCID: PMC10936691 DOI: 10.1039/d4cp90047b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Correction for 'Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance' by Pascal Vermeeren et al., Phys. Chem. Chem. Phys., 2022, 24, 18028-18042, https://doi.org/10.1039/D2CP02234F.
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Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Marco Dalla Tiezza
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Mark E Wolf
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Mitchell E Lahm
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Wesley D Allen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
- Allen Heritage Foundation, Dickson, TN 37055, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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4
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Rodrigues Silva D, Blokker E, van der Schuur JM, Hamlin TA, Bickelhaupt FM. Nature and strength of group-14 A-A' bonds. Chem Sci 2024; 15:1648-1656. [PMID: 38303946 PMCID: PMC10829027 DOI: 10.1039/d3sc06215e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/07/2024] [Indexed: 02/03/2024] Open
Abstract
We have quantum chemically investigated the nature and stability of C-C and Si-Si bonds in R3A-AR3 (A = C, Si; R3 = H3, Me3, Me2Ph, MePh2, Ph3, t-Bu3) using density functional theory (DFT). Systematic increase of steric bulk of the substituents R has opposite effects on C-C and Si-Si bonds: the former becomes weaker whereas the latter becomes stronger. Only upon going further, from R = Ph to the bulkiest R = t-Bu, the R3Si-SiR3 bond begins to weaken. Our bonding analyses show how different behavior upon increasing the steric bulk of the substituents stems from the interplay of (Pauli) repulsive and (dispersion) attractive steric mechanisms. Extension of our analyses to other model systems shows that C-Si bonds display behavior that is in between that of C-C and Si-Si bonds. Further increasing the size of the group-14 atoms from C-C and Si-Si to Ge-Ge, Sn-Sn and Pb-Pb leads to a further decrease in the sensitivity of the bond strength with respect to the substituents' bulkiness. Our findings can be used as design principles for tuning A-A and A-A' bond strengths.
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Affiliation(s)
- Daniela Rodrigues Silva
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam 1081 HZ The Netherlands https://www.theochem.nl
| | - Eva Blokker
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam 1081 HZ The Netherlands https://www.theochem.nl
| | | | - Trevor A Hamlin
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam 1081 HZ The Netherlands https://www.theochem.nl
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam 1081 HZ The Netherlands https://www.theochem.nl
- Institute of Molecules and Materials, Radboud University Heyendaalseweg 135 Nijmegen 6525 AJ The Netherlands
- Department of Chemical Sciences, University of Johannesburg Auckland Park Johannesburg 2006 South Africa
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5
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Hansen T, Vermeeren P, Zijderveld KWJ, Bickelhaupt FM, Hamlin TA. S N 2 versus E2 Competition of Cyclic Ethers. Chemistry 2023; 29:e202301308. [PMID: 37338310 DOI: 10.1002/chem.202301308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
We have quantum chemically studied the influence of ring strain on the competition between the two mechanistically different SN 2 and E2 pathways using a series of archetypal ethers as substrate in combination with a diverse set of Lewis bases (F- , Cl- , Br- , HO- , H3 CO- , HS- , H3 CS- ), using relativistic density functional theory at ZORA-OLYP/QZ4P. The ring strain in the substrate is systematically increased on going from a model acyclic ether to a 6- to 5- to 4- to 3-membered ether ring. We have found that the activation energy of the SN 2 pathway sharply decreases when the ring strain of the system is increased, thus on going from large to small cyclic ethers, the SN 2 reactivity increases. In contrast, the activation energy of the E2 pathway generally rises along this same series, that is, from large to small cyclic ethers. The opposing reactivity trends induce a mechanistic switch in the preferred reaction pathway for strong Lewis bases from E2, for large cyclic substrates, to SN 2, for small cyclic substrates. Weak Lewis bases are unable to overcome the higher intrinsic distortivity of the E2 pathway and, therefore, always favor the less distortive SN 2 reaction.
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Affiliation(s)
- Thomas Hansen
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Pascal Vermeeren
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Kim W J Zijderveld
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen (The, Netherlands
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Trevor A Hamlin
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
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6
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Poater J, Vermeeren P, Hamlin TA, Bickelhaupt FM, Solà M. On the existence of collective interactions reinforcing the metal-ligand bond in organometallic compounds. Nat Commun 2023; 14:3872. [PMID: 37400461 DOI: 10.1038/s41467-023-39498-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Affiliation(s)
- Jordi Poater
- Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Pascal Vermeeren
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.
- Institute of Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa.
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany, 69, 17003, Girona, Catalonia, Spain.
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7
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Su G, Formica M, Yamazaki K, Hamlin TA, Dixon DJ. Catalytic Enantioselective Intramolecular Oxa-Michael Reaction to α,β-Unsaturated Esters and Amides. J Am Chem Soc 2023. [PMID: 37253087 DOI: 10.1021/jacs.3c03182] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A bifunctional iminophosphorane (BIMP)-catalyzed, enantioselective intramolecular oxa-Michael reaction of alcohols to tethered, low electrophilicity Michael acceptors is described. Improved reactivity over previous reports (1 day vs 7 days), excellent yields (up to 99%), and enantiomeric ratios (up to 99.5:0.5 er) are demonstrated. The broad reaction scope, enabled by catalyst modularity and tunability, includes substituted tetrahydrofurans (THFs) and tetrahydropyrans (THPs), oxaspirocycles, sugar and natural product derivatives, dihydro-(iso)-benzofurans, and iso-chromans. A state-of-the-art computational study revealed that the enantioselectivity originates from the presence of several favorable intermolecular hydrogen bonds between the BIMP catalyst and the substrate that induce stabilizing electrostatic and orbital interactions. The newly developed catalytic enantioselective approach was carried out on multigram scale, and multiple Michael adducts were further derivatized to an array of useful building blocks, providing access to enantioenriched biologically active molecules and natural products.
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Affiliation(s)
- Guanglong Su
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K
| | - Michele Formica
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K
| | - Ken Yamazaki
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, U.K
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8
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Tiekink EH, Vermeeren P, Hamlin TA. The Origin of Catalysis and Regioselectivity of Lewis Acid-Catalyzed Diels-Alder Reactions with Tropone. Chemistry 2023:e202301223. [PMID: 37078400 DOI: 10.1002/chem.202301223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/21/2023]
Abstract
We have studied the uncatalyzed and Lewis acid (LA)-catalyzed cycloaddition reaction between tropone and 1,1-dimethoxyethene using dispersion-corrected relativistic density functional theory (DFT). The LA catalysts BF3, B(C6H5)3, and B(C6F5)3 efficiently accelerate both the competing [4+2] and [8+2] cycloaddition reactions by lowering the activation barrier up to 12 kcal mol-1 compared to the uncatalyzed reaction. Our study reveals that the LA catalyst promotes both cycloaddition reaction pathways by LUMO-lowering catalysis and demonstrates that Pauli-lowering catalysis is not always the operative catalytic mechanism in cycloaddition reactions. Judicious choice of the LA catalyst can effectively impart regiocontrol of the cycloaddition: B(C6H5)3 furnishes the [8+2] adduct while B(C6F5)3 yields the [4+2] adduct. We discovered that the regioselectivity shift finds its origin in the ability of the LA to absorb distortion by adopting a trigonal pyramidal geometry around the boron atom.
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Affiliation(s)
| | - Pascal Vermeeren
- Vrije Universiteit Amsterdam, Theoretical Chemistry, NETHERLANDS
| | - Trevor A Hamlin
- Vrije Universiteit Amsterdam, Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, De Boelelaan 1083, 1081 HV, Amsterdam, NETHERLANDS
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9
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Tiekink EH, Vermeeren P, Hamlin TA. Not antiaromaticity gain, but increased asynchronicity enhances the Diels-Alder reactivity of tropone. Chem Commun (Camb) 2023; 59:3703-3706. [PMID: 36880301 DOI: 10.1039/d3cc00512g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Tropone is an unreactive diene in normal electron demand Diels-Alder reactions, but it can be activated via carbonyl umpolung by using hydrazone ion analogs. Recently, the higher reactivity of hydrazone ion analogs was ascribed to a raised HOMO energy induced by antiaromaticity (L. J. Karas, A. T. Campbell, I. V. Alabugin and J. I. Wu, Org. Lett., 2020, 22, 7083). We show that this is incorrect, and that the activation barrier is lowered by increased asynchronicity.
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Affiliation(s)
- Eveline H Tiekink
- Department of Theoretical Chemistry, Amsterdam Institute of Molecfular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands.
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecfular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecfular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands.
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10
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Kučera R, Ellis SR, Yamazaki K, Hayward Cooke J, Chekshin N, Christensen KE, Hamlin TA, Dixon DJ. Enantioselective Total Synthesis of (-)-Himalensine A via a Palladium and 4-Hydroxyproline Co-catalyzed Desymmetrization of Vinyl-bromide-tethered Cyclohexanones. J Am Chem Soc 2023; 145:5422-5430. [PMID: 36820616 PMCID: PMC9999414 DOI: 10.1021/jacs.2c13710] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Herein, we describe the convergent enantioselective total synthesis of himalensine A in 18 steps, enabled by a highly enantio- and diastereoselective construction of the morphan core via a palladium/hydroxy proline co-catalyzed desymmetrization of vinyl-bromide-tethered cyclohexanones. The reaction pathway was illuminated by density functional theory calculations, which support an intramolecular Heck reaction of an in situ-generated enamine intermediate, where exquisite enantioselectivity arises from intramolecular carboxylate coordination to the vinyl palladium species in the rate- and enantio-determining carbopalladation steps. The reaction tolerates diverse N-derivatives, all-carbon quaternary centers, and trisubstituted olefins, providing access to molecular scaffolds found in a range of complex natural products. Following large-scale preparation of a key substrate and installation of a β-substituted enone moiety, the rapid construction of himalensine A was achieved using a highly convergent strategy based on an amide coupling/Michael addition/allylation/ring-closing metathesis sequence which allowed the introduction of three of the five rings in only three synthetic steps (after telescoping). Moreover, our strategy provides a new enantioselective access to a known tetracyclic late-stage intermediate that has been used previously in the synthesis of many Daphniphyllum alkaloids.
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Affiliation(s)
- Roman Kučera
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Sam R Ellis
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Ken Yamazaki
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - Jack Hayward Cooke
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Nikita Chekshin
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, Amsterdam 1081 HV, The Netherlands
| | - Darren J Dixon
- Department of Chemistry, Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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11
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Intermolecular Covalent Interactions: Nature and Directionality. Chemistry 2023; 29:e202203791. [PMID: 36478415 DOI: 10.1002/chem.202203791] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Quantum chemical methods were employed to analyze the nature and the origin of the directionality of pnictogen (PnB), chalcogen (ChB), and halogen bonds (XB) in archetypal Fm Z⋅⋅⋅F- complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA-M06/QZ4P. Quantitative Kohn-Sham MO and energy decomposition analyses (EDA) show that all these intermolecular interactions have in common that covalence, that is, HOMO-LUMO interactions, provide a crucial contribution to the bond energy, besides electrostatic attraction. Strikingly, all these bonds are directional (i.e., F-Z⋅⋅⋅F- is approximately linear) despite, and not because of, the electrostatic interactions which, in fact, favor bending. This constitutes a breakdown of the σ-hole model. It was shown how the σ-hole model fails by neglecting both, the essential physics behind the electrostatic interaction and that behind the directionality of electron-rich intermolecular interactions. Our findings are general and extend to the neutral, weaker ClI⋅⋅⋅NH3 , HClTe⋅⋅⋅NH3 , and H2 ClSb⋅⋅⋅NH3 complexes.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Teodorico C Ramalho
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras CEP, 37200-900, Lavras, MG, Brazil.,Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute for Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Chemical Sciences, University of Johannesburg Auckland Park, Johannesburg, 2006, South Africa
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12
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Remmerswaal WA, Hansen T, Hamlin TA, Codée JDC. Origin of Stereoselectivity in S E 2' Reactions of Six-membered Ring Oxocarbenium Ions. Chemistry 2023; 29:e202203490. [PMID: 36511875 DOI: 10.1002/chem.202203490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Oxocarbenium ions are key reactive intermediates in organic chemistry. To generate a series of structure-reactivity-stereoselectivity principles for these species, we herein investigated the bimolecular electrophilic substitution reactions (SE 2') between allyltrimethylsilane and a series of archetypal six-membered ring oxocarbenium ions using a combined density functional theory (DFT) and coupled-cluster theory approach. These reactions preferentially proceed following a reaction path where the oxocarbenium ion transforms from a half chair (3 H4 or 4 H3 ) to a chair conformation. The introduction of alkoxy substituents on six-membered ring oxocarbenium ions, dramatically influences the conformational preference of the canonical 3 H4 and 4 H3 conformers, and thereby the stereochemical outcome of the SE 2' reaction. In general, we find that the stereoselectivity in the reactions correlates to the "intrinsic preference" of the cations, as dictated by their shape. However, for the C5-CH2 OMe substituent, steric factors override the "intrinsic preference", showing a more selective reaction than expected based on the shape of the ion. Our SE 2' energetics correlate well with experimentally observed stereoselectivity, and the use of the activation strain model has enabled us to quantify important interactions and structural features that occur in the transition state of the reactions to precisely understand the relative energy barriers of the diastereotopic addition reactions. The fundamental mechanistic insight provided in this study will aid in understanding the reactivity of more complex glycosyl cations featuring multiple substituents and will facilitate our general understanding of glycosylation reactions.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands.,Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
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13
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Roose TR, Preschel HD, Mayo Tejedor H, Roozee JC, Hamlin TA, Maes BUW, Ruijter E, Orru RVA. Iron-Catalysed Carbene Transfer to Isocyanides as a Platform for Heterocycle Synthesis. Chemistry 2023; 29:e202203074. [PMID: 36305372 PMCID: PMC10108253 DOI: 10.1002/chem.202203074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
An iron-catalysed carbene transfer reaction of diazo compounds to isocyanides has been developed. The resulting ketenimines are trapped in situ with various bisnucleophiles to access a range of densely functionalized heterocycles (pyrimidinones, dihydropyrazolones, 1H-tetrazoles) in a one-pot process. The electron-rich Hieber anion ([Fe(CO)3 NO]- ) facilitates efficient catalytic carbene transfer from acceptor-type α-diazo carbonyl compounds to isocyanides, providing a cost-efficient and benign alternative to similar noble metal-catalysed processes. Based on DFT calculations a plausible reaction mechanism for activation of the α-diazo carbonyl carbene precursor and ketenimine formation is provided.
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Affiliation(s)
- Thomas R Roose
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - H Daniel Preschel
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Helena Mayo Tejedor
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Jasper C Roozee
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Bert U W Maes
- Organic Synthesis Division Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerp, Belgium
| | - Eelco Ruijter
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Romano V A Orru
- Department of Chemistry & Pharmaceutical Sciences Amsterdam Institute for Molecular & Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.,Department of Organic Chemistry Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Urmonderbaan 22, 6167 KD, Geleen, The Netherlands
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14
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Sun X, Hansen T, Poater J, Hamlin TA, Bickelhaupt FM. Rational design of iron catalysts for C-X bond activation. J Comput Chem 2023; 44:495-505. [PMID: 35137432 PMCID: PMC10078697 DOI: 10.1002/jcc.26818] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/16/2022] [Accepted: 01/20/2022] [Indexed: 01/10/2023]
Abstract
We have quantum chemically studied the iron-mediated CX bond activation (X = H, Cl, CH3 ) by d8 -FeL4 complexes using relativistic density functional theory at ZORA-OPBE/TZ2P. We find that by either modulating the electronic effects of a generic iron-catalyst by a set of ligands, that is, CO, BF, PH3 , BN(CH3 )2 , or by manipulating structural effects through the introduction of bidentate ligands, that is, PH2 (CH2 )n PH2 with n = 6-1, one can significantly decrease the reaction barrier for the CX bond activation. The combination of both tuning handles causes a decrease of the CH activation barrier from 10.4 to 4.6 kcal mol-1 . Our activation strain and Kohn-Sham molecular orbital analyses reveal that the electronic tuning works via optimizing the catalyst-substrate interaction by introducing a strong second backdonation interaction (i.e., "ligand-assisted" interaction), while the mechanism for structural tuning is mainly caused by the reduction of the required activation strain because of the pre-distortion of the catalyst. In all, we present design principles for iron-based catalysts that mimic the favorable behavior of their well-known palladium analogs in the bond-activation step of cross-coupling reactions.
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Affiliation(s)
- Xiaobo Sun
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Barcelona, Spain
| | - Thomas Hansen
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Barcelona, Spain.,Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Friedrich Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
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15
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Moloto BP, Vermeeren P, Tiezza MD, Bouwens T, Esterhuysen C, Hamlin TA, Bickelhaupt FM. Palladium-catalyzed activation of H nA–AH n bonds (AH n = CH 3, NH 2, OH, F). PURE APPL CHEM 2023. [DOI: 10.1515/pac-2022-1004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
We have quantum chemically studied activation of HnA–AHn bonds (AHn = CH3, NH2, OH, F) by PdLn catalysts with Ln = no ligand, PH3, (PH3)2, using relativistic density functional theory at ZORA-BLYP/TZ2P. The activation energy associated with the oxidative addition step decreases from H3C–CH3 to H2N–NH2 to HO–OH to F–F, where the activation of the F–F bond is barrierless. Activation strain and Kohn–Sham molecular orbital analyses reveal that the enhanced reactivity along this series of substrates originates from a combination of (i) reduced activation strain due to a weaker HnA–AHn bond; (ii) decreased Pauli repulsion as a result of a difference in steric shielding of the HnA–AHn bond; and (iii) enhanced backbonding interaction between the occupied 4d atomic orbitals of the palladium catalyst and σ* acceptor orbital of the substrate.
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Affiliation(s)
- Bryan Phuti Moloto
- Department of Theoretical Chemistry , Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam , The Netherlands , URL:
- Department of Chemistry and Polymer Science , Stellenbosch University , Private Bag X1 , Matieland , Stellenbosch , 7602 , South Africa
| | - Pascal Vermeeren
- Department of Theoretical Chemistry , Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam , The Netherlands , URL:
| | - Marco Dalla Tiezza
- Department of Theoretical Chemistry , Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam , The Netherlands , URL:
| | - Tessel Bouwens
- Department of Theoretical Chemistry , Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam , The Netherlands , URL:
| | - Catharine Esterhuysen
- Department of Chemistry and Polymer Science , Stellenbosch University , Private Bag X1 , Matieland , Stellenbosch , 7602 , South Africa
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry , Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam , The Netherlands , URL:
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry , Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam , The Netherlands , URL:
- Institute for Molecules and Materials (IMM), Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen , The Netherlands
- Department of Chemical Sciences , University of Johannesburg , Auckland Park , Johannesburg 2006 , South Africa
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16
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Yu S, Tiekink EH, Vermeeren P, Bickelhaupt FM, Hamlin TA. How Bases Catalyze Diels-Alder Reactions. Chemistry 2023; 29:e202203121. [PMID: 36330879 PMCID: PMC10108159 DOI: 10.1002/chem.202203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/06/2022]
Abstract
We have quantum chemically studied the base-catalyzed Diels-Alder (DA) reaction between 3-hydroxy-2-pyrone and N-methylmaleimide using dispersion-corrected density functional theory. The uncatalyzed reaction is slow and is preceded by the extrusion of CO2 via a retro-DA reaction. Base catalysis, for example, by triethylamine, lowers the reaction barrier up to 10 kcal mol-1 , causing the reaction to proceed smoothly at low temperature, which quenches the expulsion of CO2 , yielding efficient access to polyoxygenated natural compounds. Our activation strain analyses reveal that the base accelerates the DA reaction via two distinct electronic mechanisms: i) by the HOMO-raising effect, which enhances the normal electron demand orbital interaction; and ii) by donating charge into 3-hydroxy-2-pyrone which accumulates in its reactive region and promotes strongly stabilizing secondary electrostatic interactions with N-methylmaleimide.
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Affiliation(s)
- Song Yu
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, (TheNetherlands
| | - Eveline H Tiekink
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, (TheNetherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, (TheNetherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, (TheNetherlands.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen (The, Netherlands.,Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, (TheNetherlands
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17
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Trujillo-González DE, González-García G, Hamlin TA, Bickelhaupt FM, Braunschweig H, Jiménez-Halla JOC, Solà M. The Search for Enhanced σ‐Donor Ligands to Stabilize Boron‐Boron Multiple Bonds. Eur J Inorg Chem 2023. [DOI: 10.1002/ejic.202200767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | | | - Trevor A. Hamlin
- Vrije Universiteit Amsterdam Amsterdam Center for Multiscale Modeling 1081 HV Amsterdam NETHERLANDS
| | - F. Matthias Bickelhaupt
- Vrije Universiteit Amsterdam Amsterdam Center for Multiscale Modeling De Boelelaan 1083 1081 HV Amsterdam NETHERLANDS
| | - Holger Braunschweig
- Julius-Maximilians-Universität Würzburg: Julius-Maximilians-Universitat Wurzburg Chemical Sciences 97074 Würzburg GERMANY
| | | | - Miquel Solà
- Universitat de Girona Institute of Computational Chemistry and Department of Chemistry C/ Maria Aurèlia Capmany, 69 17003 Girona SPAIN
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18
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Bołt M, Tiekink EH, Hansen T, Bickelhaupt FM, Hamlin TA. C(spn)–X (n = 1–3) Bond Activation by Iron. European J Org Chem 2022. [DOI: 10.1002/ejoc.202201144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Małgorzata Bołt
- VU Amsterdam: Vrije Universiteit Amsterdam Theoretical Chemistry NETHERLANDS
| | - Eveline H. Tiekink
- VU Amsterdam: Vrije Universiteit Amsterdam Theoretical Chemistry NETHERLANDS
| | - Thomas Hansen
- VU Amsterdam: Vrije Universiteit Amsterdam Theoretical Chemistry NETHERLANDS
| | | | - Trevor A. Hamlin
- Vrije Universiteit Amsterdam Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling De Boelelaan 1083 1081 HV Amsterdam NETHERLANDS
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19
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Hansen T, Nin-Hill A, Codée JDC, Hamlin TA, Rovira C. Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via S N 2 Reactions. Chemistry 2022; 28:e202201649. [PMID: 35896443 DOI: 10.1002/chem.202201649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Indexed: 01/07/2023]
Abstract
The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the "electrophilic trap" that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C6 H10 Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C-Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMONu -LUMOSubstrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.
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Affiliation(s)
- Thomas Hansen
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain.,Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020, Barcelona, Spain
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20
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Blokker E, van Zeist W, Sun X, Poater J, van der Schuur JM, Hamlin TA, Bickelhaupt FM. Methyl Substitution Destabilizes Alkyl Radicals. Angew Chem Int Ed Engl 2022; 61:e202207477. [PMID: 35819818 PMCID: PMC9545886 DOI: 10.1002/anie.202207477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 12/02/2022]
Abstract
We have quantum chemically investigated how methyl substituents affect the stability of alkyl radicals MemH3−mC⋅ and the corresponding MemH3−mC−X bonds (X = H, CH3, OH; m = 0 – 3) using density functional theory at M06‐2X/TZ2P. The state‐of‐the‐art in physical organic chemistry is that alkyl radicals are stabilized upon an increase in their degree of substitution from methyl<primary<secondary<tertiary, and that this is the underlying cause for the decrease in C−H bond strength along this series. Here, we provide evidence that falsifies this model and show that, on the contrary, the MemH3−mC⋅ radical is destabilized with increasing substitution. The reason that the corresponding C−H bond nevertheless becomes weaker is that substitution destabilizes the sterically more congested MemH3−mC−H molecule even more.
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Affiliation(s)
- Eva Blokker
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Willem‐Jan van Zeist
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Xiaobo Sun
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Departament de Química Inorgànica i Orgànica & IQTCUB Universitat de Barcelona Martí i Franquès 1–11 08028 Barcelona Spain
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB Universitat de Barcelona Martí i Franquès 1–11 08028 Barcelona Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
| | | | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute of Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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21
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Hansen T, Sun X, Dalla Tiezza M, van Zeist W, van Stralen JNP, Geerke DP, Wolters LP, Poater J, Hamlin TA, Bickelhaupt FM. C−X Bond Activation by Palladium: Steric Shielding versus Steric Attraction. Chemistry 2022; 28:e202201093. [PMID: 35420229 PMCID: PMC9401605 DOI: 10.1002/chem.202201093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Indexed: 11/07/2022]
Abstract
The C−X bond activation (X = H, C) of a series of substituted C(n°)−H and C(n°)−C(m°) bonds with C(n°) and C(m°) = H3C− (methyl, 0°), CH3H2C− (primary, 1°), (CH3)2HC− (secondary, 2°), (CH3)3C− (tertiary, 3°) by palladium were investigated using relativistic dispersion‐corrected density functional theory at ZORA‐BLYP‐D3(BJ)/TZ2P. The effect of the stepwise introduction of substituents was pinpointed at the C−X bond on the bond activation process. The C(n°)−X bonds become substantially weaker going from C(0°)−X, to C(1°)−X, to C(2°)−X, to C(3°)−X because of the increasing steric repulsion between the C(n°)‐ and X‐group. Interestingly, this often does not lead to a lower barrier for the C(n°)−X bond activation. The C−H activation barrier, for example, decreases from C(0°)−X, to C(1°)−X, to C(2°)−X and then increases again for the very crowded C(3°)−X bond. For the more congested C−C bond, in contrast, the activation barrier always increases as the degree of substitution is increased. Our activation strain and matching energy decomposition analyses reveal that these differences in C−H and C−C bond activation can be traced back to the opposing interplay between steric repulsion across the C−X bond versus that between the catalyst and substrate.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
- Departament de Química Inorgànicai i Orgànica & IQTCUB Universitat de Barcelona Martí i Franquès 1-11 08028 Barcelona Spain
| | - Xiaobo Sun
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Departament de Química Inorgànicai i Orgànica & IQTCUB Universitat de Barcelona Martí i Franquès 1-11 08028 Barcelona Spain
| | - Marco Dalla Tiezza
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Willem‐Jan van Zeist
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Joost N. P. van Stralen
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Daan P. Geerke
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Lando P. Wolters
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Jordi Poater
- Departament de Química Inorgànicai i Orgànica & IQTCUB Universitat de Barcelona Martí i Franquès 1-11 08028 Barcelona Spain
- ICREA Passeig Lluís Companys 23 08010 Barcelona Spain
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM) Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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22
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Vermeeren P, Dalla Tiezza M, Wolf ME, Lahm ME, Allen WD, Schaefer HF, Hamlin TA, Bickelhaupt FM. Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance. Phys Chem Chem Phys 2022; 24:18028-18042. [PMID: 35861164 PMCID: PMC9348522 DOI: 10.1039/d2cp02234f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022]
Abstract
Hierarchical, convergent ab initio benchmark computations were performed followed by a systematic analysis of DFT performance for five pericyclic reactions comprising Diels-Alder, 1,3-dipolar cycloaddition, electrocyclic rearrangement, sigmatropic rearrangement, and double group transfer prototypes. Focal point analyses (FPA) extrapolating to the ab initio limit were executed via explicit quantum chemical computations with electron correlation treatments through CCSDT(Q) and correlation-consistent Gaussian basis sets up to aug'-cc-pV5Z. Optimized geometric structures and vibrational frequencies of all stationary points were obtained at the CCSD(T)/cc-pVTZ level of theory. The FPA reaction barriers and energies exhibit convergence to within a few tenths of a kcal mol-1. The FPA benchmarks were used to evaluate the performance of 60 density functionals (eight dispersion-corrected), covering the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. The meta-hybrid M06-2X functional provided the best overall performance [mean absolute error (MAE) of 1.1 kcal mol-1] followed closely by the double-hybrids B2K-PLYP, mPW2K-PLYP, and revDSD-PBEP86 [MAE of 1.4-1.5 kcal mol-1]. The regularly used GGA functional BP86 gave a higher MAE of 5.8 kcal mol-1, but it qualitatively described the trends in reaction barriers and energies. Importantly, we established that accurate yet efficient meta-hybrid or double-hybrid DFT potential energy surfaces can be acquired based on geometries from the computationally efficient and robust BP86/DZP level.
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Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Marco Dalla Tiezza
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Mark E Wolf
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Mitchell E Lahm
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Wesley D Allen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
- Allen Heritage Foundation, Dickson, TN 37055, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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23
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Vermeeren P, Hamlin TA, Bickelhaupt FM. Front Cover: How Ionization Catalyzes Diels‐Alder Reactions (Chem. Eur. J. 40/2022). Chemistry 2022. [DOI: 10.1002/chem.202201619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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24
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Vermeeren P, Hamlin TA, Bickelhaupt FM. How Ionization Catalyzes Diels–Alder Reactions. Chemistry 2022; 28:e202201620. [DOI: 10.1002/chem.202201620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV Amsterdam The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV Amsterdam The Netherlands
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525AJ Nijmegen The Netherlands
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25
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Abstract
The catalytic effect of ionization on the Diels‐Alder reaction between 1,3‐butadiene and acrylaldehyde has been studied using relativistic density functional theory (DFT). Removal of an electron from the dienophile, acrylaldehyde, significantly accelerates the Diels‐Alder reaction and shifts the reaction mechanism from concerted asynchronous for the neutral Diels‐Alder reaction to stepwise for the radical‐cation Diels‐Alder reaction. Our detailed activation strain and Kohn‐Sham molecular orbital analyses reveal how ionization of the dienophile enhances the Diels‐Alder reactivity via two mechanisms: (i) by amplifying the asymmetry in the dienophile's occupied π‐orbitals to such an extent that the reaction goes from concerted asynchronous to stepwise and thus with substantially less steric (Pauli) repulsion per reaction step; (ii) by enhancing the stabilizing orbital interactions that result from the ability of the singly occupied molecular orbital of the radical‐cation dienophile to engage in an additional three‐electron bonding interaction with the highest occupied molecular orbital of the diene.
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Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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26
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Beutick SE, Vermeeren P, Hamlin TA. The 1,3-Dipolar Cycloaddition From Conception to Quantum Chemical Design. Chem Asian J 2022; 17:e202200553. [PMID: 35822651 PMCID: PMC9539489 DOI: 10.1002/asia.202200553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/08/2022] [Indexed: 11/12/2022]
Abstract
The 1,3‐dipolar cycloaddition (1,3‐DCA) reaction, conceptualized by Rolf Huisgen in 1960, has proven immensely useful in organic, material, and biological chemistry. The uncatalyzed, thermal transformation is generally sluggish and unselective, but the reactivity can be enhanced by means of metal catalysis or by the introduction of either predistortion or electronic tuning of the dipolarophile. These promoted reactions generally go with a much higher reactivity, selectivity, and yields, often at ambient temperatures. The rapid orthogonal reactivity and compatibility with aqueous and physiological conditions positions the 1,3‐DCA as an excellent bioorthogonal reaction. Quantum chemical calculations have been critical for providing an understanding of the physical factors that control the reactivity and selectivity of 1,3‐DCAs. In silico derived design principles have proven invaluable for the design of new dipolarophiles with tailored reactivity. This review discusses everything from the conception of the 1,3‐DCA all the way to the state‐of‐the‐art methods and models used for the quantum chemical design of novel (bioorthogonal) reagents.
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Affiliation(s)
- Steven E Beutick
- Vrije Universiteit Amsterdam, theoretical chemistry, NETHERLANDS
| | - Pascal Vermeeren
- Vrije Universiteit Amsterdam, theoretical chemistry, NETHERLANDS
| | - Trevor A Hamlin
- Vrije Universiteit Amsterdam, Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, De Boelelaan 1083, 1081 HV, Amsterdam, NETHERLANDS
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27
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Blokker E, van Zeist WJ, Sun X, Poater J, van der Schuur JM, Hamlin TA, Bickelhaupt FM. Methyl Substitution Destabilizes Alkyl Radicals. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eva Blokker
- Vrije Universiteit Amsterdam Department of Theoretical Chemistry NETHERLANDS
| | | | - Xiaobo Sun
- Universitat de Barcelona CRAI: Universitat de Barcelona Departament de Química Inorgànica i Orgànica SPAIN
| | - Jordi Poater
- Universitat de Barcelona Departament de Química Inorgànica i Orgànica SPAIN
| | | | - Trevor A. Hamlin
- Vrije Universiteit Amsterdam Department of Theoretical Chemistry NETHERLANDS
| | - F. Matthias Bickelhaupt
- VU University Amsterdam Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam NETHERLANDS
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28
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Abstract
We have quantum chemically explored the competition between the SN2 and SN2' pathways for X- + H2C═CHCH2Y (X, Y = F, Cl, Br, I) using a combined relativistic density functional theory and coupled-cluster theory approach. Bimolecular nucleophilic substitution reactions at allylic systems, i.e., Cγ═Cβ-Cα-Y, bearing a leaving-group at the α-position, proceed either via a direct attack at the α-carbon (SN2) or via an attack at the γ-carbon, involving a concerted allylic rearrangement (SN2'), in both cases leading to the expulsion of the leaving-group. Herein, we provide a physically sound model to rationalize under which circumstances a nucleophile will follow either the aliphatic SN2 or allylic SN2' pathway. Our activation strain analyses expose the underlying physical factors that steer the SN2/SN2' competition and, again, demonstrate that the concepts of a reaction's "characteristic distortivity" and "transition state acidity" provide explanations and design tools for understanding and predicting reactivity trends in organic synthesis.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lea de Jong
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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29
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Moloto BP, Vermeeren P, Dalla Tiezza M, Esterhuysen C, Bickelhaupt FM, Hamlin TA. Palladium‐Catalyzed Activation of Carbon–Halogen Bonds: Electrostatics‐Controlled Reactivity. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | | | | | | | - Trevor A. Hamlin
- Vrije Universiteit Amsterdam Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling De Boelelaan 1083 1081 HV Amsterdam NETHERLANDS
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30
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Svatunek D, Houszka N, Hamlin TA, Bickelhaupt FM, Mikula H. Corrigendum: Chemoselectivity of Tertiary Azides in Strain‐Promoted Alkyne–Azide Cycloadditions. Chemistry 2022; 28:e202200414. [DOI: 10.1002/chem.202200414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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31
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Nieuwland C, Hamlin TA, Fonseca Guerra C, Barone G, Bickelhaupt FM. B-DNA Structure and Stability: The Role of Nucleotide Composition and Order. Chemistry 2022; 11:e202200013. [PMID: 35103418 DOI: 10.1002/open.202200013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Invited for this month's cover are the groups of Célia Fonseca Guerra at the Vrije Universiteit Amsterdam and Leiden University, Giampaolo Barone from the Università degli Studi di Palermo, and F. Matthias Bickelhaupt at Vrije Universiteit Amsterdam and Radboud University Nijmegen. The cover picture shows the four primary interaction components (hydrogen bonding, cross-terms, base stacking, and solvation) that determine the stability of B-DNA duplexes. Quantum chemical analyses identify an interplay between the stabilizing hydrogen bonds between nucleotides that drive the formation of the DNA double-strand, and the destabilizing loss of stacking interactions within individual strands combined with partial desolvation. The sequence-dependence in the duplex stability originates mainly from the cross-terms, which can be attractive or repulsive. Read the full text of their Research Article at 10.1002/open.202100231.
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Affiliation(s)
- Celine Nieuwland
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 CC, Leiden (The, Netherlands
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, Edificio 17, 90128, Palermo, Italy
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands.,Institute of Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen (The, Netherlands
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32
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Nieuwland C, Hamlin TA, Fonseca Guerra C, Barone G, Bickelhaupt FM. B-DNA Structure and Stability: The Role of Nucleotide Composition and Order. ChemistryOpen 2022; 11:e202100231. [PMID: 35083880 PMCID: PMC8805170 DOI: 10.1002/open.202100231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/10/2021] [Indexed: 11/08/2022] Open
Abstract
We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.
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Affiliation(s)
- Celine Nieuwland
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
| | - Célia Fonseca Guerra
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Leiden Institute of ChemistryGorlaeus LaboratoriesLeiden UniversityEinsteinweg 552300 CCLeiden (TheNetherlands
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e FarmaceuticheUniversità degli Studi di PalermoViale delle Scienze, Edificio 1790128PalermoItaly
| | - F. Matthias Bickelhaupt
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Institute of Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
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33
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Nieuwland C, Hamlin TA, Fonseca Guerra C, Barone G, Bickelhaupt FM. Front Cover: B‐DNA Structure and Stability: The Role of Nucleotide Composition and Order (ChemistryOpen 2/2022). Chemistry 2022. [DOI: 10.1002/open.202200014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Celine Nieuwland
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam (The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam (The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam (The Netherlands
- Leiden Institute of Chemistry Gorlaeus Laboratories Leiden University Einsteinweg 55 2300 CC Leiden (The Netherlands
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche Università degli Studi di Palermo Viale delle Scienze, Edificio 17 90128 Palermo Italy
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam (The Netherlands
- Institute of Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen (The Netherlands
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34
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Rozsar D, Formica M, Yamazaki K, Hamlin TA, Dixon DJ. Bifunctional Iminophosphorane-Catalyzed Enantioselective Sulfa-Michael Addition to Unactivated α,β-Unsaturated Amides. J Am Chem Soc 2022; 144:1006-1015. [PMID: 34990142 PMCID: PMC8793149 DOI: 10.1021/jacs.1c11898] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The
first metal-free catalytic intermolecular enantioselective
Michael addition to unactivated α,β-unsaturated amides
is described. Consistently high enantiomeric excesses and yields were
obtained over a wide range of alkyl thiol pronucleophiles and electrophiles
under mild reaction conditions, enabled by a novel squaramide-based
bifunctional iminophosphorane catalyst. Low catalyst loadings (2.0
mol %) were achieved on a decagram scale, demonstrating the scalability
of the reaction. Computational analysis revealed the origin of the
high enantiofacial selectivity via analysis of relevant transition
structures and provided substantial support for specific noncovalent
activation of the carbonyl group of the α,β-unsaturated
amide by the catalyst.
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Affiliation(s)
- Daniel Rozsar
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Michele Formica
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Ken Yamazaki
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.,Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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35
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Shiomi S, Shennan BDA, Yamazaki K, Fuentes de Arriba ÁL, Vasu D, Hamlin TA, Dixon DJ. A New Organocatalytic Desymmetrization Reaction Enables the Enantioselective Total Synthesis of Madangamine E. J Am Chem Soc 2022; 144:1407-1415. [PMID: 35037758 PMCID: PMC8796237 DOI: 10.1021/jacs.1c12040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The
enantioselective total synthesis of madangamine E has been
completed in 30 steps, enabled by a new catalytic and highly enantioselective
desymmetrizing intramolecular Michael addition reaction of a prochiral
ketone to a tethered β,β′-disubstituted
nitroolefin. This key carbon–carbon bond forming reaction efficiently
constructed a chiral bicyclic core in near-perfect enantio- and diastereo-selectivity,
concurrently established three stereogenic centers, including a quaternary
carbon, and proved highly scalable. Furthermore, the pathway and origins
of enantioselectivity in this catalytic cyclization were probed using
density functional theory (DFT) calculations, which revealed the crucial
substrate/catalyst interactions in the enantio-determining step. Following
construction of the bicyclic core, the total synthesis of madangamine
E could be completed, with key steps including a mild one-pot oxidative
lactamization of an amino alcohol, a two-step Z-selective
olefination of a sterically hindered ketone, and ring-closing metatheses
to install the two macrocyclic rings.
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Affiliation(s)
- Shinya Shiomi
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Benjamin D A Shennan
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ken Yamazaki
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K.,Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ángel L Fuentes de Arriba
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Dhananjayan Vasu
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
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36
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Hansen T, Vermeeren P, Bickelhaupt FM, Hamlin TA. Stability of alkyl carbocations. Chem Commun (Camb) 2022; 58:12050-12053. [DOI: 10.1039/d2cc04034d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The traditional and widespread rationale behind the stability trend of alkyl-substituted carbocations is incomplete.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Mul-tiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Mul-tiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Mul-tiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Mul-tiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Hansen T, Sun X, Dalla Tiezza M, van Zeist WJ, Poater J, Hamlin TA, Bickelhaupt FM. C(spn)-X (n = 1-3) Bond Activation by Palladium. Chemistry 2021; 28:e202103953. [PMID: 34958486 PMCID: PMC9306469 DOI: 10.1002/chem.202103953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 11/09/2022]
Abstract
We have studied the palladium-mediated activation of C( sp n )-X bonds (n = 1-3 and X = H, CH 3 , Cl) in archetypal model substrates H 3 C-CH 2 -X, H 2 C=CH-X and HC≡C-X by catalysts PdL n with L n = no ligand, Cl - , and (PH 3 ) 2 , using relativistic density functional theory at ZORA-BLYP/TZ2P. The oxidative addition barrier decreases along this series, even though the strength of the bonds increases going from C( sp 3 )-X, to C( sp 2 )-X, to C( sp )-X. Activation strain and matching energy decomposition analyses reveal that the decreased oxidative addition barrier going from sp 3 to sp 2 to sp , originates from a reduction in the destabilizing steric (Pauli) repulsion between catalyst and substrate. This is the direct consequence of the decreasing coordination number of the carbon atom in C( sp n )-X, which goes from four, to three, to two along this series. The associated net stabilization of the catalyst-substrate interaction dominates the trend in strain energy which indeed becomes more destabilizing along this same series as the bond becomes stronger from C( sp 3 )-X to C( sp )-X.
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Affiliation(s)
- Thomas Hansen
- Vrije Universiteit Amsterdam, Theoretical Chemistry, NETHERLANDS
| | - Xiaobo Sun
- Vrije Universiteit Amsterdam, Theoretical Chemistry, NETHERLANDS
| | | | | | - Jordi Poater
- University of Barcelona: Universitat de Barcelona, Inorganic and organic chemistry, SPAIN
| | - Trevor A Hamlin
- Vrije Universiteit Amsterdam, Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, De Boelelaan 1083, 1081 HV, Amsterdam, NETHERLANDS
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Abstract
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We have quantum chemically
investigated how solvation influences
the competition between the SN2 and E2 pathways of the
model F– + C2H5Cl reaction.
The system is solvated in a stepwise manner by going from the gas
phase, then via microsolvation of one to three explicit solvent molecules,
then last to bulk solvation using relativistic density functional
theory at (COSMO)-ZORA-OLYP/QZ4P. We explain how and why the mechanistic
pathway of the system shifts from E2 in the gas phase to SN2 upon strong solvation of the Lewis base (i.e., nucleophile/protophile).
The E2 pathway is preferred under weak solvation of the system by
dichloromethane, whereas a switch in reactivity from E2 to SN2 is observed under strong solvation by water. Our activation strain
and Kohn–Sham molecular orbital analyses reveal that solvation
of the Lewis base has a significant impact on the strength of the
Lewis base. We show how strong solvation furnishes a weaker Lewis
base that is unable to overcome the high characteristic distortivity
associated with the E2 pathway, and thus the SN2 pathway
becomes viable.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Jasper C Roozee
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2265-2266. [PMID: 34791760 DOI: 10.1002/cphc.202100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The front cover artwork is provided by the TheoCheM group of the Vrije Universiteit Amsterdam. The image shows that guanine quadruplexes have a stronger binding affinity for divalent cations than monovalent cations. Read the full text of the Article at 10.1002/cphc.202100529.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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Blokker E, Sun X, Poater J, van der Schuur JM, Hamlin TA, Bickelhaupt FM. The Chemical Bond: When Atom Size Instead of Electronegativity Difference Determines Trend in Bond Strength. Chemistry 2021; 27:15616-15622. [PMID: 34609774 PMCID: PMC9298008 DOI: 10.1002/chem.202103544] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 11/28/2022]
Abstract
We have quantum chemically analyzed element−element bonds of archetypal HnX−YHn molecules (X, Y=C, N, O, F, Si, P, S, Cl, Br, I), using density functional theory. One purpose is to obtain a set of consistent homolytic bond dissociation energies (BDE) for establishing accurate trends across the periodic table. The main objective is to elucidate the underlying physical factors behind these chemical bonding trends. On one hand, we confirm that, along a period (e. g., from C−C to C−F), bonds strengthen because the electronegativity difference across the bond increases. But, down a period, our findings constitute a paradigm shift. From C−F to C−I, for example, bonds do become weaker, however, not because of the decreasing electronegativity difference. Instead, we show that the effective atom size (via steric Pauli repulsion) is the causal factor behind bond weakening in this series, and behind the weakening in orbital interactions at the equilibrium distance. We discuss the actual bonding mechanism and the importance of analyzing this mechanism as a function of the bond distance.
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Affiliation(s)
- Eva Blokker
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Xiaobo Sun
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Jordi Poater
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | | | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute of Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Maitland JAP, Leitch JA, Yamazaki K, Christensen KE, Cassar DJ, Hamlin TA, Dixon DJ. Switchable, Reagent‐Controlled Diastereodivergent Photocatalytic Carbocyclisation of Imine‐Derived α‐Amino Radicals. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J. Andrew P. Maitland
- Department of Chemistry Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Jamie A. Leitch
- Department of Chemistry Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
- Current address: Department of Pharmaceutical and Biological Chemistry UCL (University College London) School of Pharmacy 29–39 Brunswick Square London WC1N 1AX UK
| | - Ken Yamazaki
- Department of Chemistry Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Kirsten E. Christensen
- Department of Chemistry Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | | | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Darren J. Dixon
- Department of Chemistry Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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Maitland JAP, Leitch JA, Yamazaki K, Christensen KE, Cassar DJ, Hamlin TA, Dixon DJ. Switchable, Reagent-Controlled Diastereodivergent Photocatalytic Carbocyclisation of Imine-Derived α-Amino Radicals. Angew Chem Int Ed Engl 2021; 60:24116-24123. [PMID: 34449968 PMCID: PMC8597041 DOI: 10.1002/anie.202107253] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/13/2021] [Indexed: 12/15/2022]
Abstract
A reagent‐controlled stereodivergent carbocyclisation of aryl aldimine‐derived, photocatalytically generated, α‐amino radicals possessing adjacent conjugated alkenes, affording either bicyclic or tetracyclic products, is described. Under net reductive conditions using commercial Hantzsch ester, the α‐amino radical species underwent a single stereoselective cyclisation to give trans‐configured amino‐indane structures in good yield, whereas using a substituted Hantzsch ester as a milder reductant afforded cis‐fused tetracyclic tetrahydroquinoline frameworks, resulting from two consecutive radical cyclisations. Judicious choice of the reaction conditions allowed libraries of both single and dual cyclisation products to be synthesised with high selectivity, notable predictability, and good‐to‐excellent yields. Computational analysis employing DFT revealed the reaction pathway and mechanistic rationale behind this finely balanced yet readily controlled photocatalytic system.
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Affiliation(s)
- J Andrew P Maitland
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jamie A Leitch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Current address: Department of Pharmaceutical and Biological Chemistry, UCL (University College London), School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Ken Yamazaki
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Kirsten E Christensen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Affiliation(s)
- Eveline H. Tiekink
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam, The Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam, The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and Materials Radboud University Nijmegen Heyendaalseweg 135 6525 AJ Nijmegen, The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam, The Netherlands
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Rodrigues Silva D, de Azevedo Santos L, Hamlin TA, Bickelhaupt FM, P Freitas M, Fonseca Guerra C. Dipolar repulsion in α-halocarbonyl compounds revisited. Phys Chem Chem Phys 2021; 23:20883-20891. [PMID: 34528039 PMCID: PMC8479779 DOI: 10.1039/d1cp02502c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The concept of dipolar repulsion has been widely used to explain several phenomena in organic chemistry, including the conformational preferences of carbonyl compounds. This model, in which atoms and bonds are viewed as point charges and dipole moment vectors, respectively, is however oversimplified. To provide a causal model rooted in quantitative molecular orbital theory, we have analyzed the rotational isomerism of haloacetaldehydes OHC–CH2X (X = F, Cl, Br, I), using relativistic density functional theory. We have found that the overall trend in the rotational energy profiles is set by the combined effects of Pauli repulsion (introducing a barrier around gauche that separates minima at syn and anti), orbital interactions (which can pull the anti minimum towards anticlinal to maximize hyperconjugation), and electrostatic interactions. Only for X = F, not for X = Cl–I, electrostatic interactions push the preference from syn to anti. Our bonding analyses show how this trend is related to the compact nature of F versus the more diffuse nature of the heavier halogens. Beyond point charges! The point charge concept within dipolar repulsion model is valid for compact atoms like fluorine. This model breaks down for larger halogens, for which the electrostatic attraction between nuclei and charge densities dominates.![]()
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Affiliation(s)
- Daniela Rodrigues Silva
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. .,Departamento de Química, Instituto de Ciências Naturais, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil.
| | - Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. .,Departamento de Química, Instituto de Ciências Naturais, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. .,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Matheus P Freitas
- Departamento de Química, Instituto de Ciências Naturais, Universidade Federal de Lavras, 37200-900, Lavras, MG, Brazil.
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. .,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Vermeeren P, Hamlin TA, Bickelhaupt FM. Origin of asynchronicity in Diels-Alder reactions. Phys Chem Chem Phys 2021; 23:20095-20106. [PMID: 34499069 PMCID: PMC8457343 DOI: 10.1039/d1cp02456f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/02/2021] [Indexed: 02/02/2023]
Abstract
Asynchronicity in Diels-Alder reactions plays a crucial role in determining the height of the reaction barrier. Currently, the origin of asynchronicity is ascribed to the stronger orbital interaction between the diene and the terminal carbon of an asymmetric dienophile, which shortens the corresponding newly formed C-C bond and hence induces asynchronicity in the reaction. Here, we show, using the activation strain model and Kohn-Sham molecular orbital theory at ZORA-BP86/TZ2P, that this rationale behind asynchronicity is incorrect. We, in fact, found that following a more asynchronous reaction mode costs favorable HOMO-LUMO orbital overlap and, therefore, weakens (not strengthens) these orbital interactions. Instead, it is the Pauli repulsion that induces asynchronicity in Diels-Alder reactions. An asynchronous reaction pathway also lowers repulsive occupied-occupied orbital overlap which, therefore, reduces the unfavorable Pauli repulsion. As soon as this mechanism of reducing Pauli repulsion dominates, the reaction begins to deviate from synchronicity and adopts an asynchronous mode. The eventual degree of asynchronicity, as observed in the transition state of a Diels-Alder reaction, is ultimately achieved when the gain in stability, as a response to the reduced Pauli repulsion, balances with the loss of favorable orbital interactions.
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Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Dalla Tiezza M, Hamlin TA, Bickelhaupt FM, Orian L. Radical Scavenging Potential of the Phenothiazine Scaffold: A Computational Analysis. ChemMedChem 2021; 16:3763-3771. [PMID: 34536069 PMCID: PMC9292796 DOI: 10.1002/cmdc.202100546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Indexed: 01/05/2023]
Abstract
The reactivity of phenothiazine (PS), phenoselenazine (PSE), and phenotellurazine (PTE) with different reactive oxygen species (ROS) has been studied using density functional theory (DFT) in combination with the QM‐ORSA (Quantum Mechanics‐based Test for Overall Free Radical Scavenging Activity) protocol for an accurate kinetic rate calculation. Four radical scavenging mechanisms have been screened, namely hydrogen atom transfer (HAT), radical adduct formation (RAF), single electron transfer (SET), and the direct oxidation of the chalcogen atom. The chosen ROS are HO., HOO., and CH3OO.. PS, PSE, and PTE exhibit an excellent antioxidant activity in water regardless of the ROS due to their characteristic diffusion‐controlled regime processes. For the HO. radical, the primary active reaction mechanism is, for all antioxidants, RAF. But, for HOO. and CH3OO., the dominant mechanism strongly depends on the antioxidant: HAT for PS and PSE, and SET for PTE. The scavenging efficiency decreases dramatically in lipid environment and remains only significant (via RAF) for the most reactive radical (HO.). Therefore, PS, PSE, and PTE are excellent antioxidant molecules, especially in aqueous, physiological environments where they are active against a broad spectrum of harmful radicals. There is no advantage or significant difference in the scavenging efficiency when changing the chalcogen since the reactivity mainly derives from the amino hydrogen and the aromatic sites.
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Affiliation(s)
- Marco Dalla Tiezza
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
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47
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Hansen T, Vermeeren P, Bickelhaupt FM, Hamlin TA. Innenrücktitelbild: Origin of the α‐Effect in S
N
2 Reactions (Angew. Chem. 38/2021). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
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48
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
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Abstract
The α-effect is a term used to explain the dramatically enhanced reactivity of α-nucleophiles (R-Y-X:- ) compared to their parent normal nucleophile (R-X:- ) by deviating from the classical Brønsted-type reactivity-basicity relationship. The exact origin of this effect is, however, still heavily under debate. In this work, we have quantum chemically analyzed the α-effect of a set of anionic nucleophiles, including O-, N- and S-based normal and α-nucleophiles, participating in an SN 2 reaction with ethyl chloride using relativistic density functional theory at ZORA-OLYP/QZ4P. Our activation strain and Kohn-Sham molecular orbital analyses identified two criteria an α-nucleophile needs to fulfill in order to show α-effect: (i) a small HOMO lobe on the nucleophilic center, pointing towards the substrate, to reduce the repulsive occupied-occupied orbital overlap and hence (steric) Pauli repulsion with the substrate; and (ii) a sufficiently high energy HOMO to overcome the loss of favorable HOMO-LUMO orbital overlap with the substrate, as a consequence of the first criterion, by reducing the HOMO-LUMO orbital energy gap. If one of these two criteria is not fulfilled, one can expect no α-effect or inverse α-effect.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Pascal Vermeeren
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2286-2296. [PMID: 34435425 PMCID: PMC9293024 DOI: 10.1002/cphc.202100529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/24/2021] [Indexed: 11/06/2022]
Abstract
The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post‐)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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