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Li H, Mansoori Kermani M, Ottochian A, Crescenzi O, Janesko BG, Truhlar DG, Scalmani G, Frisch MJ, Ciofini I, Adamo C. Modeling Multi-Step Organic Reactions: Can Density Functional Theory Deliver Misleading Chemistry? J Am Chem Soc 2024; 146:6721-6732. [PMID: 38413362 DOI: 10.1021/jacs.3c12713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree-Fock exchange. These results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
| | - Maryam Mansoori Kermani
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Alistar Ottochian
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
| | - Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, Napoli 80126, Italy
| | - Benjamin G Janesko
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | | | | | - Ilaria Ciofini
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, Paris F-75005, France
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Ji K, Johnson RP, McNeely J, Al Faruk M, Porco JA. Asymmetric Synthesis of Nidulalin A and Nidulaxanthone A: Selective Carbonyl Desaturation Using an Oxoammonium Salt. J Am Chem Soc 2024; 146:4892-4902. [PMID: 38319883 PMCID: PMC10922861 DOI: 10.1021/jacs.3c13864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Nidulaxanthone A is a dimeric, dihydroxanthone natural product that was isolated in 2020 from Aspergillus sp. Structurally, the compound features an unprecedented heptacyclic 6/6/6/6/6/6/6 ring system which is unusual for natural xanthone dimers. Biosynthetically, nidulaxanthone A originates from the monomer nidulalin A via stereoselective Diels-Alder dimerization. To expedite the synthesis of nidulalin A and study the proposed dimerization, we developed methodology involving the use of allyl triflate for chromone ester activation, followed by vinylogous addition, to rapidly forge the nidulalin A scaffold in a four-step sequence which also features ketone desaturation using Bobbitt's oxoammonium salt. An asymmetric synthesis of nidulalin A was achieved using acylative kinetic resolution (AKR) of chiral, racemic 2H-nidulalin A. Dimerization of enantioenriched nidulalin A to nidulaxanthone A was achieved using solvent-free, thermolytic conditions. Computational studies have been conducted to probe both the oxoammonium-mediated desaturation and (4 + 2) dimerization events.
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Affiliation(s)
- Kaijie Ji
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Richard P. Johnson
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - James McNeely
- Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Md Al Faruk
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - John A. Porco
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
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The dynamical significance of valley-ridge inflection points. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wollenhaupt M, Schran C, Krupička M, Marx D. Force‐Induced Catastrophes on Energy Landscapes: Mechanochemical Manipulation of Downhill and Uphill Bifurcations Explains the Ring‐Opening Selectivity of Cyclopropanes. Chemphyschem 2018; 19:837-847. [DOI: 10.1002/cphc.201701209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Miriam Wollenhaupt
- Lehrstuhl für Theoretische ChemieRuhr-Universität Bochum 44780 Bochum Germany
| | - Christoph Schran
- Lehrstuhl für Theoretische ChemieRuhr-Universität Bochum 44780 Bochum Germany
| | - Martin Krupička
- Lehrstuhl für Theoretische ChemieRuhr-Universität Bochum 44780 Bochum Germany
- Present Address: Department of Organic ChemistryUniversity of Chemistry and Technology Technicka 5 16628 Prague Czech Republic
| | - Dominik Marx
- Lehrstuhl für Theoretische ChemieRuhr-Universität Bochum 44780 Bochum Germany
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Kramer ZC, Carpenter BK, Ezra GS, Wiggins S. Reaction Path Bifurcation in an Electrocyclic Reaction: Ring-Opening of the Cyclopropyl Radical. J Phys Chem A 2015; 119:6611-30. [DOI: 10.1021/acs.jpca.5b02834] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zeb C. Kramer
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14853 United States
| | - Barry K. Carpenter
- School
of Chemistry, University of Cardiff, Cardiff CF10 3AT, United Kingdom
| | - Gregory S. Ezra
- Department
of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, New York 14853 United States
| | - Stephen Wiggins
- School
of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
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Collins P, Carpenter BK, Ezra GS, Wiggins S. Nonstatistical dynamics on potentials exhibiting reaction path bifurcations and valley-ridge inflection points. J Chem Phys 2013; 139:154108. [DOI: 10.1063/1.4825155] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Affiliation(s)
- Barry K. Carpenter
- Physical
Organic Chemistry Centre, Cardiff University, Cardiff CF10 3AT, United Kingdom
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Laser control in open quantum systems: preliminary analysis toward the Cope rearrangement control in methyl-cyclopentadienylcarboxylate dimer. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1236-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Rehbein J, Carpenter BK. Do we fully understand what controls chemical selectivity? Phys Chem Chem Phys 2011; 13:20906-22. [DOI: 10.1039/c1cp22565k] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Kelly KK, Hirschi JS, Singleton DA. Newtonian kinetic isotope effects. Observation, prediction, and origin of heavy-atom dynamic isotope effects. J Am Chem Soc 2009; 131:8382-3. [PMID: 19485324 DOI: 10.1021/ja9031083] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intramolecular (13)C kinetic isotope effects were determined for the dimerization of cyclopentadiene. Substantial isotope effects were observed in three positions, despite the C(2) symmetry of the cycloaddition transition state and the absence of dynamical bottlenecks after this transition state. The observed isotope effects were predicted well from trajectory studies by extrapolating the outcomes of trajectories incorporating superheavy isotopes of carbon, ranging from (20)C to (140)C. Trajectory studies suggest that the isotope effects are unrelated to zero-point energy or the geometrical and momentum properties of the transition state. However, steepest-descent paths in mass-weighted coordinates correctly predict the direction of the isotope effects, supporting a novel origin in Newton's second law of motion.
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Affiliation(s)
- Kelmara K Kelly
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, USA
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Ess D, Wheeler S, Iafe R, Xu L, Çelebi-Ölçüm N, Houk K. Bifurkationen auf den Potentialenergiehyperflächen organischer Reaktionen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800918] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ess DH, Hayden AE, Klärner FG, Houk KN. Transition states for the dimerization of 1,3-cyclohexadiene: a DFT, CASPT2, and CBS-QB3 quantum mechanical investigation. J Org Chem 2008; 73:7586-92. [PMID: 18763823 DOI: 10.1021/jo8011804] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum mechanical calculations using restricted and unrestricted B3LYP density functional theory, CASPT2, and CBS-QB3 methods for the dimerization of 1,3-cyclohexadiene (1) reveal several highly competitive concerted and stepwise reaction pathways leading to [4 + 2] and [2 + 2] cycloadducts, as well as a novel [6 + 4] ene product. The transition state for endo-[4 + 2] cycloaddition (endo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 28.7 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 19.0 kcal/mol) is not bis-pericyclic, leading to nondegenerate primary and secondary orbital interactions. However, the C(s) symmetric second-order saddle point on the B3LYP energy surface is only 0.3 kcal/mol above endo-2TS. The activation enthalpy for the concerted exo-[4 + 2] cycloaddition (exo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 30.1 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 21.1 kcal/mol) is 1.4 kcal/mol higher than that of the endo transition state. Stepwise pathways involving diallyl radicals are formed via two different C-C forming transition states (rac-5TS and meso-5TS) and are predicted to be competitive with the concerted cycloaddition. Transition states were located for cyclization from intermediate rac-5 leading to the endo-[4 + 2] (endo-2) and exo-[2 + 2] (anti-3) cycloadducts. Only the endo-[2 + 2] (syn-3) transition state was located for cyclization of intermediate meso-5. The novel [6 + 4] "concerted" ene transition state (threo-4TS, DeltaH(double dagger)(UB3LYP(0K)) = 28.3 kcal/mol) is found to be unstable with respect to an unrestricted calculation. This diradicaloid transition state closely resembles the cyclohexadiallyl radical rather than the linked cyclohexadienyl radical. Several [3,3] sigmatropic rearrangement transition states were also located and have activation enthalpies between 27 and 31 kcal/mol.
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Affiliation(s)
- Daniel H Ess
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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Ess DH, Wheeler SE, Iafe RG, Xu L, Çelebi-Ölçüm N, Houk KN. Bifurcations on potential energy surfaces of organic reactions. Angew Chem Int Ed Engl 2008; 47:7592-601. [PMID: 18767086 PMCID: PMC2790825 DOI: 10.1002/anie.200800918] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A single transition state may lead to multiple intermediates or products if there is a post-transition-state reaction pathway bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects, rather than transition-state energetics, control selectivity. This Minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions.
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Affiliation(s)
| | | | | | | | | | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, (USA), (+ 1) 310-206-1843, E-mail:
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Lauvergnat D, Baloïtcha E, Dive G, Desouter-Lecomte M. Dynamics of complex molecular systems with numerical kinetic energy operators in generalized coordinates. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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