1
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Zhou Q, Kukier G, Gordiy I, Hoffmann R, Seeman JI, Houk KN. A 21st Century View of Allowed and Forbidden Electrocyclic Reactions. J Org Chem 2024; 89:1018-1034. [PMID: 38153322 PMCID: PMC10804416 DOI: 10.1021/acs.joc.3c02103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
In 1965, Woodward and Hoffmann proposed a theory to predict the stereochemistry of electrocyclic reactions, which, after expansion and generalization, became known as the Woodward-Hoffmann Rules. Subsequently, Longuet-Higgins and Abrahamson used correlation diagrams to propose that the stereoselectivity of electrocyclizations could be explained by the correlation of reactant and product orbitals with the same symmetry. Immediately thereafter, Hoffmann and Woodward applied correlation diagrams to explain the mechanism of cycloadditions. We describe these discoveries and their evolution. We now report an investigation of various electrocyclic reactions using DFT and CASSCF. We track the frontier molecular orbitals along the intrinsic reaction coordinate and modeled trajectories and examine the correlation between HOMO and LUMO for thermally forbidden systems. We also investigate the electrocyclizations of several highly polarized systems for which the Houk group had predicted that donor-acceptor substitution can induce zwitterionic character, thereby providing low-energy pathways for formally forbidden reactions. We conclude with perspectives on the field of pericyclic reactions, including a refinement as the meaning of Woodward and Hoffmann's "Violations. There are none!" Lastly, we comment on the burgeoning influence of computations on all fields of chemistry.
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Affiliation(s)
- Qingyang Zhou
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Garrett Kukier
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Igor Gordiy
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Roald Hoffmann
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14850, United States
| | - Jeffrey I. Seeman
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095-1569. United States
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2
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Shin W, Ran X, Yang ZJ. Accelerated Entropic Path Sampling with a Bidirectional Generative Adversarial Network. J Phys Chem B 2023; 127:4254-4260. [PMID: 37133810 DOI: 10.1021/acs.jpcb.3c01202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The role of entropy in mediating the dynamic outcomes of chemical reactions remains largely unknown. To evaluate the change of entropy along post-transition state paths, we have previously developed entropic path sampling that computes configurational entropy from an ensemble of reaction trajectories. However, one major caveat of this approach lies in its high computational demand: about 2000 trajectories are needed to converge the computation of an entropic profile. Here, by leveraging a deep generative model, we developed an accelerated entropic path sampling approach that evaluates entropic profiles using merely a few hundred reaction dynamic trajectories. The new method, called bidirectional generative adversarial network-entropic path sampling, can enhance the estimation of probability density functions of molecular configurations by generating pseudo-molecular configurations that are statistically indistinguishable from the true data. The method was established using cyclopentadiene dimerization, in which we reproduced the reference entropic profiles (derived from 2480 trajectories) using merely 124 trajectories. The method was further benchmarked using three reactions with symmetric post-transition-state bifurcation, including endo-butadiene dimerization, 5-fluoro-1,3-cyclopentadiene dimerization, and 5-methyl-1,3-cyclopentadiene dimerization. The results indicate the existence of a "hidden entropic intermediate", which is a dynamic species that binds to a local entropic maximum where no free energy minimum is formed.
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Affiliation(s)
- Wook Shin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Xinchun Ran
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
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3
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Liu GX, Jie XT, Li XL, Yang LS, Qiu H, Hu WH. Carbon-Centered Radical with Leaving Group-Mediated Ring Opening of Cyclopropenes via the Rearrangement of Cyclopropyl to the Allyl Radical: A General Access to Multisubstituted 1,3-Dienes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Affiliation(s)
- Geng-Xin Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong Province, China
| | - Xiao-Ting Jie
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong Province, China
| | - Xing-lin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong Province, China
| | - Li-Sheng Yang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong Province, China
| | - Huang Qiu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong Province, China
| | - Wen-Hao Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong Province, China
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4
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Seeman JI, Tantillo DJ. Understanding chemistry: from "heuristic (soft) explanations and reasoning by analogy" to "quantum chemistry". Chem Sci 2022; 13:11461-11486. [PMID: 36320403 PMCID: PMC9575397 DOI: 10.1039/d2sc02535c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
"Soft theories," i.e., "heuristic models based on reasoning by analogy" largely drove chemistry understanding for 150 years or more. But soft theories have their limitations and with the expansion of chemistry in the mid-20th century, more and more inexplicable (by soft theory) experimental results were being obtained. In the past 50 years, quantum chemistry, most often in the guise of applied theoretical chemistry including computational chemistry, has provided (a) the underlying "hard evidence" for many soft theories and (b) the explanations for chemical phenomena that were unavailable by soft theories. In this publication, we define "hard theories" as "theories derived from quantum chemistry." Both soft and hard theories can be qualitative and quantitative, and the "Houk quadrant" is proposed as a helpful categorization tool. Furthermore, the language of soft theories is often used appropriately to describe quantum chemical results. A valid and useful way of doing science is the appropriate use and application of both soft and hard theories along with the best nomenclature available for successful communication of results and ideas.
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Affiliation(s)
- Jeffrey I Seeman
- Department of Chemistry, University of Richmond Richmond VA 23173 USA
| | - Dean J Tantillo
- Department of Chemistry, University of California - Davis Davis CA 95616 USA
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5
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Pandey P, Keshavamurthy S. Dynamic matching ‐ revisiting the Carpenter model. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Priyanka Pandey
- Department of Chemistry Indian Institute of Technology Kanpur Uttar Pradesh India
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6
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Seeman JI. My First and My Latest Publication
†. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Tremblay MT, Yang ZJ. The effect of zero‐point energy in simulating organic reactions with post‐transition state bifurcation. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Zhongyue J. Yang
- Department of Chemistry Vanderbilt University Nashville Tennessee USA
- Center for Structural Biology Vanderbilt University Nashville Tennessee USA
- Vanderbilt Institute of Chemical Biology Vanderbilt University Nashville Tennessee USA
- Data Science Institute Vanderbilt University Nashville Tennessee USA
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8
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Milrod ML, Northrop BH. Computational investigation of cycloadditions between cyclopentadiene and tropone-3,4-dimethylester. Org Biomol Chem 2022; 20:8443-8453. [DOI: 10.1039/d2ob01623k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Thermally promoted cycloaddition reactions of tropone-3,4-dimethylester and cyclopentadiene have been investigated using density functional theory calculations at the M06-2X level and the CBS-QB3 method.
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Affiliation(s)
- Maya L. Milrod
- Wesleyan University, Department of Chemistry, 52 Lawn Ave., Middletown, CT 06459, USA
| | - Brian H. Northrop
- Wesleyan University, Department of Chemistry, 52 Lawn Ave., Middletown, CT 06459, USA
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9
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Wang X, Zhang C, Jiang Y, Wang W, Zhou Y, Chen Y, Zhang B, Tan RX, Ge HM, Yang ZJ, Liang Y. Influence of Water and Enzyme on the Post-Transition State Bifurcation of NgnD-Catalyzed Ambimodal [6+4]/[4+2] Cycloaddition. J Am Chem Soc 2021; 143:21003-21009. [PMID: 34851644 DOI: 10.1021/jacs.1c10760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme NgnD catalyzes an ambimodal cycloaddition that bifurcates to [6+4]- and [4+2]-adducts. Both products have been isolated in experiments, but it remains unknown how enzyme and water influence the bifurcation selectivity at the femtosecond time scale. Here, we study the impact of water and enzyme on the post-transition state bifurcation of NgnD-catalyzed [6+4]/[4+2] cycloaddition by integrating quantum mechanics/molecular mechanics quasiclassical dynamics simulations and biochemical assays. The ratio of [6+4]/[4+2] products significantly differs in the gas phase, water, and enzyme. Biochemical assays were employed to validate computational predictions. The study informs how water and enzyme affect the bifurcation selectivity through perturbation of the reaction dynamics in the femtosecond time scale, revealing the fundamental roles of condensed media in dynamically controlling the chemical selectivity for biosynthetic reactions.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Chun Zhang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Wen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuan Zhou
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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10
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Nagahata Y, Hernandez R, Komatsuzaki T. Phase space geometry of isolated to condensed chemical reactions. J Chem Phys 2021; 155:210901. [PMID: 34879678 DOI: 10.1063/5.0059618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The complexity of gas and condensed phase chemical reactions has generally been uncovered either approximately through transition state theories or exactly through (analytic or computational) integration of trajectories. These approaches can be improved by recognizing that the dynamics and associated geometric structures exist in phase space, ensuring that the propagator is symplectic as in velocity-Verlet integrators and by extending the space of dividing surfaces to optimize the rate variationally, respectively. The dividing surface can be analytically or variationally optimized in phase space, not just over configuration space, to obtain more accurate rates. Thus, a phase space perspective is of primary importance in creating a deeper understanding of the geometric structure of chemical reactions. A key contribution from dynamical systems theory is the generalization of the transition state (TS) in terms of the normally hyperbolic invariant manifold (NHIM) whose geometric phase-space structure persists under perturbation. The NHIM can be regarded as an anchor of a dividing surface in phase space and it gives rise to an exact non-recrossing TS theory rate in reactions that are dominated by a single bottleneck. Here, we review recent advances of phase space geometrical structures of particular relevance to chemical reactions in the condensed phase. We also provide conjectures on the promise of these techniques toward the design and control of chemical reactions.
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Affiliation(s)
- Yutaka Nagahata
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Tamiki Komatsuzaki
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0 020, Japan
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11
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Maley SM, Melville J, Yu S, Teynor MS, Carlsen R, Hargis C, Hamilton RS, Grant BO, Ess DH. Machine learning classification of disrotatory IRC and conrotatory non-IRC trajectory motion for cyclopropyl radical ring opening. Phys Chem Chem Phys 2021; 23:12309-12320. [PMID: 34018524 DOI: 10.1039/d1cp00612f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quasiclassical trajectory analysis is now a standard tool to analyze non-minimum energy pathway motion of organic reactions. However, due to the large amount of information associated with trajectories, quantitative analysis of the dynamic origin of reaction selectivity is complex. For the electrocyclic ring opening of cyclopropyl radical, more than 4000 trajectories were run showing that allyl radicals are formed through a mixture of disrotatory intrinsic reaction coordinate (IRC) motion as well as conrotatory non-IRC motion. Geometric, vibrational mode, and atomic velocity transition-state features from these trajectories were used for supervised machine learning analysis with classification algorithms. Accuracy >80% with a random forest model enabled quantitative and qualitative assessment of transition-state trajectory features controlling disrotatory IRC versus conrotatory non-IRC motion. This analysis revealed that there are two key vibrational modes where their directional combination provides prediction of IRC versus non-IRC motion.
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Affiliation(s)
- Steven M Maley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Jesse Melville
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Spencer Yu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Matthew S Teynor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Ryan Carlsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Cal Hargis
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - R Spencer Hamilton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Benjamin O Grant
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
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12
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Reiff J, Feldmaier M, Main J, Hernandez R. Dynamics and decay rates of a time-dependent two-saddle system. Phys Rev E 2021; 103:022121. [PMID: 33736042 DOI: 10.1103/physreve.103.022121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/20/2021] [Indexed: 11/07/2022]
Abstract
The framework of transition state theory (TST) provides a powerful way for analyzing the dynamics of physical and chemical reactions. While TST has already been successfully used to obtain reaction rates for systems with a single time-dependent saddle point, multiple driven saddles have proven challenging because of their fractal-like phase space structure. This paper presents the construction of an approximately recrossing-free dividing surface based on the normally hyperbolic invariant manifold in a time-dependent two-saddle model system. Based on this, multiple methods for obtaining instantaneous (time-resolved) decay rates of the underlying activated complex are presented and their results discussed.
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Affiliation(s)
- Johannes Reiff
- Institut für Theoretische Physik I, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Matthias Feldmaier
- Institut für Theoretische Physik I, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Jörg Main
- Institut für Theoretische Physik I, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Departments of Chemical & Biomolecular Engineering, and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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13
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Palazzetti F, Tsai PY. Photodissociation Dynamics of CO-Forming Channels on the Ground-State Surface of Methyl Formate at 248 nm: Direct Dynamics Study and Assessment of Generalized Multicenter Impulsive Models. J Phys Chem A 2021; 125:1198-1220. [PMID: 33507759 DOI: 10.1021/acs.jpca.0c10464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The photodissociation dynamics of methyl formate in the electronic ground state S0, initiated by a 248 nm-wavelength laser, is studied by direct dynamics simulations. We analyze five channels, where four of them have as products CH3OH + CO, one leading to the formation of three fragments, H2CO + H2 + CO, and a channel characterized by a roaming transition state. The analysis of energy distribution among the degrees of freedom of the product and the comparison with experimental results previously published by other groups provide the ingredients to distinguish the examined dissociation pathways. The interpretation of the results proves that the characterization of dissociation mechanisms must rely on a dynamics approach involving multiple electronic states, including considerations on the features of the S1/S0 conical intersection. Here, we also assess the generalized multicenter impulsive model, GMCIM, that has been designed for dissociation processes with exit barriers, and the energy distribution in the products is predicted on the basis of information from the saddle points and the intrinsic reaction coordinates. Main features, advantages, limits, and future perspectives of the method are reported and discussed.
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Affiliation(s)
- Federico Palazzetti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia 06123, Italy
| | - Po-Yu Tsai
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan
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14
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Abstract
Nonstatistical dynamics is important for many chemical reactions. The Rice-Ramsperger-Kassel-Marcus (RRKM) theory of unimolecular kinetics assumes a reactant molecule maintains a statistical microcanonical ensemble of vibrational states during its dissociation so that its unimolecular dynamics are time independent. Such dynamics results when the reactant's atomic motion is chaotic or irregular. Intrinsic non-RRKM dynamics occurs when part of the reactant's phase space consists of quasiperiodic/regular motion and a bottleneck exists, so that the unimolecular rate constant is time dependent. Nonrandom excitation of a molecule may result in short-time apparent non-RRKM dynamics. For rotational activation, the 2J + 1 K levels for a particular J may be highly mixed, making K an active degree of freedom, or K may be a good quantum number and an adiabatic degree of freedom. Nonstatistical dynamics is often important for bimolecular reactions and their intermediates and for product-energy partitioning of bimolecular and unimolecular reactions. Post–transition state dynamics is often highly complex and nonstatistical.
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Affiliation(s)
- Bhumika Jayee
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
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15
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Maldonado-Domínguez M, Srnec M. Understanding and Predicting Post H-Atom Abstraction Selectivity through Reactive Mode Composition Factor Analysis. J Am Chem Soc 2020; 142:3947-3958. [PMID: 32000494 DOI: 10.1021/jacs.9b12800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The selective functionalization of C-H bonds is one of the Grails of synthetic chemistry. In this work, we demonstrate that the selectivity toward fast hydroxylation or radical diffusion (known as the OH-rebound and dissociation mechanisms) following H-atom abstraction (HAA) from a substrate C-H bond by high-valent iron-oxo oxidants is already encoded in the HAA step when the post-HAA barriers are much lower than the preceding one. By applying the reactive mode composition factor (RMCF) analysis, which quantifies the kinetic energy distribution (KED) at the reactive mode (RM) of transition states, we show that reactions following the OH-rebound coordinate concentrate the RM kinetic energy on the motion of the reacting oxygen atom and the nascent substrate radical, whereas reactions following the dissociation channel localize most of their kinetic energy in H-atom motion. These motion signatures serve to predict the post-HAA selectivity, and since KED is affected by the free energy of reaction and asynchronicity (factor η) of HAA, we show that bimolecular HAA reactions in solution that are electron transfer-driven and highly exergonic have the lowest fraction of KED on the transferred H-atom and the highest chance to follow rebound hydroxylation. Finally, the RMCF analysis predicts that the H/D primary kinetic isotope effect can serve as a probe for these mechanisms, as confirmed in virtually all reported examples in the literature.
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Affiliation(s)
- Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
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16
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Karmakar S, Keshavamurthy S. Intramolecular vibrational energy redistribution and the quantum ergodicity transition: a phase space perspective. Phys Chem Chem Phys 2020; 22:11139-11173. [DOI: 10.1039/d0cp01413c] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The onset of facile intramolecular vibrational energy flow can be related to features in the connected network of anharmonic resonances in the classical phase space.
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Affiliation(s)
- Sourav Karmakar
- Department of Chemistry
- Indian Institute of Technology
- Kanpur
- India
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17
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Nikitin K, O'Gara R. Mechanisms and Beyond: Elucidation of Fluxional Dynamics by Exchange NMR Spectroscopy. Chemistry 2019; 25:4551-4589. [PMID: 30421834 DOI: 10.1002/chem.201804123] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 12/31/2022]
Abstract
Detailed mechanistic information is crucial to our understanding of reaction pathways and selectivity. Dynamic exchange NMR techniques, in particular 2D exchange spectroscopy (EXSY) and its modifications, provide indispensable intricate information on the mechanisms of organic and inorganic reactions and other phenomena, for example, the dynamics of interfacial processes. In this Review, key results from exchange NMR studies of small molecules over the last few decades are systemised and discussed. After a brief introduction to the theory, the key types of dynamic processes are identified and fundamental examples given of intra- and intermolecular reactions, which, in turn, could involve, or not, bond-making and bond-breaking events. Following that logic, internal molecular rotation, intramolecular stereomutation and molecular recognition will first be considered because they do not typically involve bond breaking. Then, rearrangements, substitution-type reactions, cyclisations, additions and other processes affecting chemical bonds will be discussed. Finally, interfacial molecular dynamics and unexpected combinations of different types of fluxional processes will also be highlighted. How exchange NMR spectroscopy helps to identify conformational changes, coordination and molecular recognition processes as well as quantify reaction energy barriers and extract detailed mechanistic information by using reaction rate theory in conjunction with computational techniques will be shown.
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Affiliation(s)
- Kirill Nikitin
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Ryan O'Gara
- School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
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18
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Chen S, Yu P, Houk KN. Ambimodal Dipolar/Diels–Alder Cycloaddition Transition States Involving Proton Transfers. J Am Chem Soc 2018; 140:18124-18131. [DOI: 10.1021/jacs.8b11080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Shuming Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Peiyuan Yu
- Energy Storage and Distributed Resources Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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19
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Yang Z, Dong X, Yu Y, Yu P, Li Y, Jamieson C, Houk KN. Relationships between Product Ratios in Ambimodal Pericyclic Reactions and Bond Lengths in Transition Structures. J Am Chem Soc 2018; 140:3061-3067. [DOI: 10.1021/jacs.7b13562] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zhongyue Yang
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Xiaofei Dong
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yanmin Yu
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Beijing
Key Laboratory for Green Catalysis and Separation, Department of Chemistry
and Chemical Engineering, Beijing University of Technology, Beijing 100124, China
| | - Peiyuan Yu
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Energy
Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yingzi Li
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Cooper Jamieson
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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20
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Ansari AJ, Pathare RS, Maurya AK, Agnihotri VK, Khan S, Roy TK, Sawant DM, Pardasani RT. Synthesis of Diverse Nitrogen Heterocycles via
Palladium-Catalyzed Tandem Azide-Isocyanide Cross-Coupling/Cyclization: Mechanistic Insight using Experimental and Theoretical Studies. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700928] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Arshad J. Ansari
- Department of Pharmacy; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| | - Ramdas S. Pathare
- Department of Chemistry; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| | - Antim K. Maurya
- Natural Product Chemistry and Process Development division; CSIR - Institute of Himalayan Bioresource Technology, Palmpur; Himachal Pradesh 176061 India
| | - Vijai K. Agnihotri
- Natural Product Chemistry and Process Development division; CSIR - Institute of Himalayan Bioresource Technology, Palmpur; Himachal Pradesh 176061 India
| | - Shahnawaz Khan
- Department of Chemistry; Bhupal Nobles' University; Udaipur 313001 India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences; Central University of Jammu; Jammu 180011 India
| | - Devesh M. Sawant
- Department of Pharmacy; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
| | - Ram T. Pardasani
- Department of Chemistry; Central University of Rajasthan; NH8 (Jaipur-Ajmer Highway), Bandarsindri Ajmer 305817 India
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21
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Craven GT, Junginger A, Hernandez R. Lagrangian descriptors of driven chemical reaction manifolds. Phys Rev E 2017; 96:022222. [PMID: 28950601 DOI: 10.1103/physreve.96.022222] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Indexed: 06/07/2023]
Abstract
The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven and R. Hernandez, Phys. Rev. Lett. 115, 148301 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.148301], we obtain this so-called distinguished trajectory and the associated moving reaction manifolds on model energy surfaces subject to various driving and dissipative conditions. In particular, we demonstrate that this is exact for harmonic barriers in one dimension and this verification gives impetus to the application of Lagrangian descriptor-based methods in diverse classes of chemical reactions. The development of these objects is paramount in the theory of reaction dynamics as the transition state structure and its underlying network of manifolds directly dictate reactivity and selectivity.
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Affiliation(s)
- Galen T Craven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrej Junginger
- Institut für Theoretische Physik 1, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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22
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Hare SR, Tantillo DJ. Post-transition state bifurcations gain momentum – current state of the field. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0104] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurcations have been occurring at a much higher rate. Beyond simply discovering bifurcations, computational chemists are developing techniques to understand what aspects of molecular structure and vibrations control the product selectivity in systems containing bifurcations. For example, the distribution of products seen in simulations has been found to be extremely sensitive to the local environment of the reacting system (i.e. the presence of a catalyst, enzyme, or explicit solvent molecules). The outlook for the future of this field is discussed, with an eye towards the application of the principles discussed here by experimental chemists to design a reaction setup to efficiently generate desired products.
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Affiliation(s)
- Stephanie R. Hare
- University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Dean J. Tantillo
- University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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23
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Ma X, Hase WL. Perspective: chemical dynamics simulations of non-statistical reaction dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0204. [PMID: 28320906 PMCID: PMC5360902 DOI: 10.1098/rsta.2016.0204] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Xinyou Ma
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - William L Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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24
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Griesbeck AG, Goldfuss B, Jäger C, Brüllingen E, Lippold T, Kleczka M. Strong Asymmetry in the Perepoxide Bifurcation Mechanism: The Large-Group Effect in the Singlet Oxygen Ene Reaction with Allylic Alcohols. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201600041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Axel G. Griesbeck
- Department of Chemistry; University of Cologne; Greinstraße 4 50939 Köln Germany), Fax: (+49) 221-4701166
| | - Bernd Goldfuss
- Department of Chemistry; University of Cologne; Greinstraße 4 50939 Köln Germany), Fax: (+49) 221-4701166
| | - Christina Jäger
- Department of Chemistry; University of Cologne; Greinstraße 4 50939 Köln Germany), Fax: (+49) 221-4701166
| | - Eric Brüllingen
- Department of Chemistry; University of Cologne; Greinstraße 4 50939 Köln Germany), Fax: (+49) 221-4701166
| | - Tim Lippold
- Department of Chemistry; University of Cologne; Greinstraße 4 50939 Köln Germany), Fax: (+49) 221-4701166
| | - Margarethe Kleczka
- Department of Chemistry; University of Cologne; Greinstraße 4 50939 Köln Germany), Fax: (+49) 221-4701166
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25
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Pratihar S, Ma X, Homayoon Z, Barnes GL, Hase WL. Direct Chemical Dynamics Simulations. J Am Chem Soc 2017; 139:3570-3590. [DOI: 10.1021/jacs.6b12017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Xinyou Ma
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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26
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Gillick-Healy MW, Jennings EV, Müller-Bunz H, Ortin Y, Nikitin K, Gilheany DG. Two Independent Orthogonal Stereomutations at a Single Asymmetric Center: A Narcissistic Couple. Chemistry 2016; 23:2332-2339. [DOI: 10.1002/chem.201604080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Indexed: 01/31/2023]
Affiliation(s)
| | | | | | - Yannick Ortin
- School of Chemistry; University College Dublin; Ireland
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27
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Hare SR, Tantillo DJ. Cryptic post-transition state bifurcations that reduce the efficiency of lactone-forming Rh-carbenoid C-H insertions. Chem Sci 2016; 8:1442-1449. [PMID: 28451284 PMCID: PMC5390789 DOI: 10.1039/c6sc03745c] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/18/2016] [Indexed: 11/21/2022] Open
Abstract
Post-transition state bifurcations are described that lead to unexpected byproducts in Rh-promoted C–H insertion reactions.
Byproducts of chemical reactions are generally thought to result from the competition between two reaction pathways, each with its own rate-determining transition state structure. We show here, however, that pathways with a single transition state structure followed by a post-transition state bifurcation may also be a source of undesired products, especially those whose appearance is unexpected. The viability of this scenario for intramolecular C–H insertion reactions affording β-lactones via Rh-carbenoid intermediates is assessed through quantum chemical calculations on potential energy surfaces and quasi-classical molecular dynamics simulations. It appears that, in these cases, the rhodium catalyst is to blame for the accessibility of a second, unintended, pathway following the transition state structure for β-lactone formation that leads to fragmentation to a ketene and carbonyl compound. If an unexpected product is formed via a post-transition state bifurcation, conventional strategies for suppressing its formation are unlikely to succeed. Guidelines for recognizing the presence of a post-transition state bifurcation are described here, along with hints at means for controlling product distributions.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry , University of California - Davis , One Shields Ave Davis , CA 95616 , USA .
| | - Dean J Tantillo
- Department of Chemistry , University of California - Davis , One Shields Ave Davis , CA 95616 , USA .
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28
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Pandit S, Preston TJ, King SJ, Vallance C, Orr-Ewing AJ. Evidence for concerted ring opening and C–Br bond breaking in UV-excited bromocyclopropane. J Chem Phys 2016; 144:244312. [DOI: 10.1063/1.4954373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Shubhrangshu Pandit
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Thomas J. Preston
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Simon J. King
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Claire Vallance
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Andrew J. Orr-Ewing
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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29
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Carpenter BK, Harvey JN, Orr-Ewing AJ. The Study of Reactive Intermediates in Condensed Phases. J Am Chem Soc 2016; 138:4695-705. [DOI: 10.1021/jacs.6b01761] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Barry K. Carpenter
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - Jeremy N. Harvey
- Department
of Chemistry, KU Leuven, Celestijnen Laan 200F, B-3001 Heverlee, Belgium
| | - Andrew J. Orr-Ewing
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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30
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Craven GT, Hernandez R. Deconstructing field-induced ketene isomerization through Lagrangian descriptors. Phys Chem Chem Phys 2016; 18:4008-18. [DOI: 10.1039/c5cp06624g] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phase space contours (shown in color) constructed using the method of Lagrangian descriptors resolve the separatrices governing state transitions on the reaction-path potential energy surface (shown in white) for field-induced ketene isomerization.
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Affiliation(s)
- Galen T. Craven
- Center for Computational Molecular Science and Technology
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
| | - Rigoberto Hernandez
- Center for Computational Molecular Science and Technology
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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