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Gallegos M, Vassilev-Galindo V, Poltavsky I, Martín Pendás Á, Tkatchenko A. Explainable chemical artificial intelligence from accurate machine learning of real-space chemical descriptors. Nat Commun 2024; 15:4345. [PMID: 38773090 DOI: 10.1038/s41467-024-48567-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/24/2024] [Indexed: 05/23/2024] Open
Abstract
Machine-learned computational chemistry has led to a paradoxical situation in which molecular properties can be accurately predicted, but they are difficult to interpret. Explainable AI (XAI) tools can be used to analyze complex models, but they are highly dependent on the AI technique and the origin of the reference data. Alternatively, interpretable real-space tools can be employed directly, but they are often expensive to compute. To address this dilemma between explainability and accuracy, we developed SchNet4AIM, a SchNet-based architecture capable of dealing with local one-body (atomic) and two-body (interatomic) descriptors. The performance of SchNet4AIM is tested by predicting a wide collection of real-space quantities ranging from atomic charges and delocalization indices to pairwise interaction energies. The accuracy and speed of SchNet4AIM breaks the bottleneck that has prevented the use of real-space chemical descriptors in complex systems. We show that the group delocalization indices, arising from our physically rigorous atomistic predictions, provide reliable indicators of supramolecular binding events, thus contributing to the development of Explainable Chemical Artificial Intelligence (XCAI) models.
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Affiliation(s)
- Miguel Gallegos
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
| | | | - Igor Poltavsky
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain.
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
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2
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Frenklach A, Amlani H, Kozuch S. Quantum Tunneling Instability in Pericyclic Reactions. J Am Chem Soc 2024; 146:11823-11834. [PMID: 38634836 DOI: 10.1021/jacs.4c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Several cycloreversion reactions of the retro-Diels-Alder type were computationally assessed to understand their quantum tunneling (QT) reactivity. N2, CO, and other leaving groups were considered based on their strong exothermicity, as it reduces their thermodynamic and kinetic stabilities. Our results indicate that for many of these reactions, it is essential to take into account their QT decomposition rate, which can massively weaken their molecular stability and shorten their half-lives even at deep cryogenic temperatures. In practical terms, this indicates that many supposedly stable molecules will actually be unsynthesizable or unisolable, and therefore trying to prepare or detect them would be a futile attempt. In addition, we discuss the importance of tunneling to correctly understand the enthalpy of activation and the collective atomic effect on the tunneling kinetic isotope effects to test if third-row atoms can tunnel in a chemical reaction. This project raises the question of the importance of in silico chemistry to guide in vitro chemistry, especially in cases where the latter cannot solve its own uncertainties.
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Affiliation(s)
- Alexander Frenklach
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
| | - Hila Amlani
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
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3
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Powderly M, Roseau M, Frison G, Hammami R, Chausset-Boissarie L, Harrowven D, Legros J, Chataigner I. Controlling Diastereoselectivity in Dearomatizing Diels-Alder Reactions of Nitroarenes with 2-Trimethylsilyloxycyclohexadiene. Chemistry 2024:e202303697. [PMID: 38619531 DOI: 10.1002/chem.202303697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/29/2024] [Accepted: 04/15/2024] [Indexed: 04/16/2024]
Abstract
Dearomative Diels-Alder cycloadditions between nitroarenes and 2-trimethylsilyloxycyclohexadiene are carried out under high pressure at room temperature in the absence of any chemical promoter. Reactions are performed with different arenes, including the highly aromatic naphthalenes and quinolines. They lead to 3D-scaffolds with exquisite exo-diastereoselectivity. The exo approach is characterized by lower distortion of the substrates in a late TS and by more favorable orbital interactions presumably between the nitro group and the dienic part, explaining the stereoselectivity.
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Affiliation(s)
- Marian Powderly
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3 M FR 3038, 76000, Rouen, France
- Chemistry, University of Southampton, Highfield, Southampton, UK
| | - Mélanie Roseau
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3 M FR 3038, 76000, Rouen, France
| | - Gilles Frison
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, F-75005, Paris, France
| | - Rayhane Hammami
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3 M FR 3038, 76000, Rouen, France
| | - Laetitia Chausset-Boissarie
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3 M FR 3038, 76000, Rouen, France
| | - David Harrowven
- Chemistry, University of Southampton, Highfield, Southampton, UK
| | - Julien Legros
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3 M FR 3038, 76000, Rouen, France
| | - Isabelle Chataigner
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3 M FR 3038, 76000, Rouen, France
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, F-75005, Paris, France
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4
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Liao Q, Xie P, Wang Z. Enantiodetermining processes in the synthesis of alanine, serine, and isovaline. Phys Chem Chem Phys 2023; 25:28829-28834. [PMID: 37853775 DOI: 10.1039/d3cp03212d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
In this study, quantum chemical calculations were used to explore the synthesis of three chiral α-amino acids, specifically alanine, serine, and isovaline, from reactants found in interstellar space. Our focus is on the crucial step in the synthesis pathway that determines the chirality of the amino acids. The results indicate that in the case of alanine, the determination of enantiomer is primarily influenced by the direction of the collision of molecules or functional groups, which leads to the formation of a chirality center in a crucial intermediate. However, contrary to chemical expectations, the enantiodetermining/enantioselection step for serine and isovaline synthesis occurs prior to the creation of a chirality center.
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Affiliation(s)
- Qingli Liao
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
| | - Peng Xie
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Zhao Wang
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
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5
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Mlostoń G, Urbaniak K, Palusiak M, Witczak ZJ, Würthwein EU. (3+2)-Cycloadditions of Levoglucosenone (LGO) with Fluorinated Nitrile Imines Derived from Trifluoroacetonitrile: An Experimental and Computational Study. Molecules 2023; 28:7348. [PMID: 37959767 PMCID: PMC10647924 DOI: 10.3390/molecules28217348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The in situ-generated N-aryl nitrile imines derived from trifluoroacetonitrile smoothly undergo (3+2)-cycloadditions onto the enone fragment of the levoglucosenone molecule, yielding the corresponding, five-membered cycloadducts. In contrast to the 'classic' C(Ph),N(Ph) nitrile imine, reactions with fluorinated C(CF3),N(Ar) analogues lead to stable pyrazolines in a chemo- and stereoselective manner. Based on the result of X-ray single crystal diffraction analysis, their structures were established as exo-cycloadducts with the location of the N-Ar terminus of the 1,3-dipole at the α-position of the enone moiety. The DFT computation demonstrated that the observed reaction pathway results from the strong dominance of kinetic control over thermodynamic control.
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Affiliation(s)
- Grzegorz Mlostoń
- Department of Organic & Applied Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, PL-91-403 Lodz, Poland;
| | - Katarzyna Urbaniak
- Department of Organic & Applied Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, PL-91-403 Lodz, Poland;
| | - Marcin Palusiak
- Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, PL-90-236 Lodz, Poland;
| | - Zbigniew J. Witczak
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA;
| | - Ernst-Ulrich Würthwein
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation (CMTC), Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany
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6
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Angles SN, Guo W, Darko K, Erzuah M, Pauley KG, Promise IE, Goodell JR, Tantillo DJ, Mitchell TA. Net Intermolecular Silyloxypyrone-Based (5+2) Cycloadditions Utilizing Amides as Enabling and Cleavable Tethers. Org Lett 2023; 25:7137-7141. [PMID: 37750489 DOI: 10.1021/acs.orglett.3c02635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Silyloxypyrone-based (5+2) cycloadditions were facilitated by amides that allowed for increased reactivity and a pathway for cleaving the tether to afford net intermolecular cycloadducts. Various amides underwent facile cycloaddition, and several experiments revealed steric and electronic factors that accelerate the reaction. tert-Butyl amides reacted faster than less hindered variants in multiple cases. In the case of dearomative oxidopyrylium-indole (5+2) cycloadditions, an amine-based tether was ineffective, whereas amides enabled this powerful transformation. Theoretical calculations evidenced a concerted asynchronous reaction in which the amide facilitates a conformational driving force enabling cycloaddition. Finally, a one-pot acylation/(5+2) cycloaddition/nucleophilic lactam opening and other examples of tosyl lactam opening of a modified cycloadduct were demonstrated.
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Affiliation(s)
- Susanna N Angles
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
| | - Wentao Guo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Kwabena Darko
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
| | - Marymoud Erzuah
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
| | - Kenneth G Pauley
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
| | - Ifeanyichukwu E Promise
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
| | - John R Goodell
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - T Andrew Mitchell
- Department of Chemistry, Illinois State University, Campus Box 4160, Normal, Illinois 61790-4160, United States
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7
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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] [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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8
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Kee CW. Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities. Molecules 2023; 28:molecules28041715. [PMID: 36838703 PMCID: PMC9966076 DOI: 10.3390/molecules28041715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/25/2023] Open
Abstract
Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.
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Affiliation(s)
- Choon Wee Kee
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
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9
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Stuyver T, Jorner K, Coley CW. Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions. Sci Data 2023; 10:66. [PMID: 36725850 PMCID: PMC9892576 DOI: 10.1038/s41597-023-01977-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Bio-orthogonal click chemistry based on [3 + 2] dipolar cycloadditions has had a profound impact on the field of biochemistry and significant effort has been devoted to identify promising new candidate reactions for this purpose. To gauge whether a prospective reaction could be a suitable bio-orthogonal click reaction, information about both on- and off-target activation and reaction energies is highly valuable. Here, we use an automated workflow, based on the autodE program, to compute over 5000 reaction profiles for [3 + 2] cycloadditions involving both synthetic dipolarophiles and a set of biologically-inspired structural motifs. Based on a succinct benchmarking study, the B3LYP-D3(BJ)/def2-TZVP//B3LYP-D3(BJ)/def2-SVP level of theory was selected for the DFT calculations, and standard conditions and an (aqueous) SMD model were imposed to mimic physiological conditions. We believe that this data, as well as the presented workflow for high-throughput reaction profile computation, will be useful to screen for new bio-orthogonal reactions, as well as for the development of novel machine learning models for the prediction of chemical reactivity more broadly.
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Affiliation(s)
- Thijs Stuyver
- grid.116068.80000 0001 2341 2786Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 USA
| | - Kjell Jorner
- grid.17063.330000 0001 2157 2938Department of Computer Science, University of Toronto, 40 St George St, Toronto, Ontario M5S 2E4 Canada ,grid.17063.330000 0001 2157 2938Department of Chemistry, Chemical Physics Theory Group, 80 St. George St., University of Toronto, Ontario, M5S 3H6 Canada ,grid.5371.00000 0001 0775 6028Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, SE-41258 Gothenburg, Sweden
| | - Connor W. Coley
- grid.116068.80000 0001 2341 2786Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 USA ,grid.116068.80000 0001 2341 2786Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 USA
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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] [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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11
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Puzzarini C, Stanton JF. Connections between the accuracy of rotational constants and equilibrium molecular structures. Phys Chem Chem Phys 2023; 25:1421-1429. [PMID: 36562443 DOI: 10.1039/d2cp04706c] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126, Bologna, Italy.
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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12
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Hanaway D, Kennedy CR. Automated Variable Electric-Field DFT Application for Evaluation of Optimally Oriented Electric Fields on Chemical Reactivity. J Org Chem 2023; 88:106-115. [PMID: 36507909 PMCID: PMC9830642 DOI: 10.1021/acs.joc.2c01893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent theoretical work and experiments at molecular junctions have provided a strong conceptualization for the effects of oriented electric fields (OEFs) on organic reactions. Depending on the axis of application, OEFs can increase (or decrease) the reaction rate or distinguish between isomeric pathways. Despite the conceptual elegance of OEFs, which may be applied externally or induced locally, as tools for catalyzing organic reactions, implementation in synthetically relevant systems has been hampered by inefficiencies in evaluating reaction sensitivity to field effects. Herein, we describe the development of the Automated Variable Electric-Field DFT Application (A.V.E.D.A.) for streamlined evaluation of a reaction's susceptibility to OEFs. This open-source software was designed to be accessible for nonexpert users of computational and programming tools. Following initiation by a single command (and with no subsequent intervention) the Linux workflow manages a series of density functional theory calculations and mathematical manipulations to optimize local-minimum and transition-state structures in oriented electric fields of increasing magnitude. The resulting molecular and reaction dipole moments, field-perturbed geometries, and net effective activation energies are compiled for user interpretation. Ten representative pericyclic reactions that showcase the development and evaluation of A.V.E.D.A. are described.
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13
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Hashimoto Y, Tantillo DJ. Mechanism and the Origins of Periselectivity in Cycloaddition Reactions of Benzyne with Dienes. J Org Chem 2022; 87:12954-12962. [PMID: 36121919 DOI: 10.1021/acs.joc.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory calculations have been used to explore the reaction mechanism of (4 + 2) and (2 + 2) cycloadditions of benzyne with classical dienes. The results indicate the following: (1) (4 + 2) products arise via concerted pathways, (2) (2 + 2) products arise via stepwise pathways with diradical intermediates, and (3) these diradical intermediates are formed via isomerization of carbene intermediates. The origins of periselectivity in these reactions are analyzed using distortion/interaction analysis for the key steps, and they indicate that the tiny distortion in the very early [4 + 2] transition structure, coupled with an entropic favorability, controls selective (4 + 2) cycloaddition.
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Affiliation(s)
- Yoshimitsu Hashimoto
- Department of Chemistry, University of California-Davis, Davis, California95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California95616, United States
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